1
|
Stiller J, Feng S, Chowdhury AA, Rivas-González I, Duchêne DA, Fang Q, Deng Y, Kozlov A, Stamatakis A, Claramunt S, Nguyen JMT, Ho SYW, Faircloth BC, Haag J, Houde P, Cracraft J, Balaban M, Mai U, Chen G, Gao R, Zhou C, Xie Y, Huang Z, Cao Z, Yan Z, Ogilvie HA, Nakhleh L, Lindow B, Morel B, Fjeldså J, Hosner PA, da Fonseca RR, Petersen B, Tobias JA, Székely T, Kennedy JD, Reeve AH, Liker A, Stervander M, Antunes A, Tietze DT, Bertelsen M, Lei F, Rahbek C, Graves GR, Schierup MH, Warnow T, Braun EL, Gilbert MTP, Jarvis ED, Mirarab S, Zhang G. Complexity of avian evolution revealed by family-level genomes. Nature 2024:10.1038/s41586-024-07323-1. [PMID: 38560995 DOI: 10.1038/s41586-024-07323-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method, and the choice of genomic regions 1-3. Here, we address these issues by analyzing genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Paleogene (K-Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K-Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
Collapse
Affiliation(s)
- Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | - David A Duchêne
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Yuan Deng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Alexey Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Santiago Claramunt
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Jacqueline M T Nguyen
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Julia Haag
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Uyen Mai
- Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongsheng Gao
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chengran Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Yulong Xie
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zijian Huang
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhen Cao
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Zhi Yan
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bent Lindow
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Jon Fjeldså
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rute R da Fonseca
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bent Petersen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, UK
| | - Tamás Székely
- Milner Centre for Evolution, University of Bath, Bath, UK
- ELKH-DE Reproductive Strategies Research Group, University of Debrecen, Debrecen, Hungary
| | - Jonathan David Kennedy
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Hart Reeve
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andras Liker
- HUN-REN-PE Evolutionary Ecology Research Group, University of Pannonia, Veszprém, Hungary
- Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém, Hungary
| | - Martin Stervander
- Bird Group, Natural History Museum, Akeman St, Tring, Hertfordshire, United Kingdom
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Mads Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Carsten Rahbek
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Ecology, Peking University, Beijing, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Tandy Warnow
- University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Durham, NC, USA
| | | | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- Villum Center for Biodiversity Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
2
|
Laine J, Mak SST, Martins NFG, Chen X, Gilbert MTP, Jones FC, Pedersen MW, Romundset A, Foote AD. Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Curr Biol 2024; 34:1142-1147.e6. [PMID: 38350445 DOI: 10.1016/j.cub.2024.01.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.
Collapse
Affiliation(s)
- Jan Laine
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Nuno F G Martins
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Xihan Chen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
| |
Collapse
|
3
|
Brealey JC, Kodama M, Rasmussen JA, Hansen SB, Santos-Bay L, Lecaudey LA, Hansen M, Fjære E, Myrmel LS, Madsen L, Bernhard A, Sveier H, Kristiansen K, Gilbert MTP, Martin MD, Limborg MT. Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. mSystems 2024; 9:e0104323. [PMID: 38294254 PMCID: PMC10886447 DOI: 10.1128/msystems.01043-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.
Collapse
Affiliation(s)
- Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Laurène A Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Aquaculture Department, SINTEF Ocean, Trondheim, Norway
| | - Martin Hansen
- Department of Environmental Science, Environmental Metabolomics Lab, Aarhus University, Roskilde, Denmark
| | - Even Fjære
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Norway, Bergen, Norway
| | | | | | - Karsten Kristiansen
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
4
|
Kothe CI, Rasmussen JA, Mak SST, Gilbert MTP, Evans J. Exploring the microbial diversity of novel misos with metagenomics. Food Microbiol 2024; 117:104372. [PMID: 37919016 DOI: 10.1016/j.fm.2023.104372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 11/04/2023]
Abstract
Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of kōji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.
Collapse
Affiliation(s)
- Caroline Isabel Kothe
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| | - Jacob Agerbo Rasmussen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Denmark
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Denmark; University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Joshua Evans
- Sustainable Food Innovation Group, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| |
Collapse
|
5
|
Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
Collapse
Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
6
|
Rice ES, Alberdi A, Alfieri J, Athrey G, Balacco JR, Bardou P, Blackmon H, Charles M, Cheng HH, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Gilbert MTP, Hearn CJ, Jarvis ED, Klopp C, Marcos S, Mason AS, Velez-Irizarry D, Xu L, Warren WC. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol 2023; 21:267. [PMID: 37993882 PMCID: PMC10664547 DOI: 10.1186/s12915-023-01758-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. METHODS We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. RESULTS We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. CONCLUSIONS We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.
Collapse
Affiliation(s)
- Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - James Alfieri
- Department of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Giridhar Athrey
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Philippe Bardou
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, 31326, France
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Mathieu Charles
- University Paris-Saclay, INRAE, AgroParisTech, GABI, Sigenae, Jouy-en-Josas, France
| | - Hans H Cheng
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Laurent A F Frantz
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4DQ, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Cari J Hearn
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Christophe Klopp
- Sigenae, Genotoul Bioinfo, MIAT UR875, INRAE, Castanet Tolosan, France
| | - Sofia Marcos
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | | | | | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
7
|
Hernández-Alonso G, Ramos-Madrigal J, van Grouw H, Ciucani MM, Cavill EL, Sinding MHS, Gopalakrishnan S, Pacheco G, Gilbert MTP. Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences. Mol Biol Evol 2023; 40:msad243. [PMID: 37950889 PMCID: PMC10667084 DOI: 10.1093/molbev/msad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 11/13/2023] Open
Abstract
The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.
Collapse
Affiliation(s)
- Germán Hernández-Alonso
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hein van Grouw
- Bird Group, Department of Life Sciences, Natural History Museum, Tring, United Kingdom
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily Louisa Cavill
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - George Pacheco
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
8
|
Alfaro-Núñez A, Gilbert MTP. Corrigendum to "Validation of a sensitive PCR assay for the detection of Chelonid fibropapilloma-associated herpesvirus in latent turtle infections" J. Virol. Methods 206 (2014) 38-41. J Virol Methods 2023; 321:114803. [PMID: 37634273 PMCID: PMC11042464 DOI: 10.1016/j.jviromet.2023.114803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Affiliation(s)
- Alonzo Alfaro-Núñez
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| |
Collapse
|
9
|
Sun X, Liu YC, Tiunov MP, Gimranov DO, Zhuang Y, Han Y, Driscoll CA, Pang Y, Li C, Pan Y, Velasco MS, Gopalakrishnan S, Yang RZ, Li BG, Jin K, Xu X, Uphyrkina O, Huang Y, Wu XH, Gilbert MTP, O'Brien SJ, Yamaguchi N, Luo SJ. Ancient DNA reveals genetic admixture in China during tiger evolution. Nat Ecol Evol 2023; 7:1914-1929. [PMID: 37652999 DOI: 10.1038/s41559-023-02185-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.
Collapse
Affiliation(s)
- Xin Sun
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yue-Chen Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Dmitry O Gimranov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Ural Federal University, Yekaterinburg, Russia
| | - Yan Zhuang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Han
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Carlos A Driscoll
- Section of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, MD, USA
| | - Yuhong Pang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Chunmei Li
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Yan Pan
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Marcela Sandoval Velasco
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui-Zheng Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kun Jin
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Guangdong, China
| | - Xiao-Hong Wu
- School of Archaeology and Museology, Peking University, Beijing, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University of Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia.
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
10
|
Sandoval-Velasco M, Jagadeesan A, Ramos-Madrigal J, Ávila-Arcos MC, Fortes-Lima CA, Watson J, Johannesdóttir E, Cruz-Dávalos DI, Gopalakrishnan S, Moreno-Mayar JV, Niemann J, Renaud G, Robson Brown KA, Bennett H, Pearson A, Helgason A, Gilbert MTP, Schroeder H. The ancestry and geographical origins of St Helena's liberated Africans. Am J Hum Genet 2023; 110:1825. [PMID: 37802045 PMCID: PMC10577070 DOI: 10.1016/j.ajhg.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023] Open
|
11
|
Aizpurua O, Blijleven K, Trivedi U, Gilbert MTP, Alberdi A. Unravelling animal-microbiota evolution on a chip. Trends Microbiol 2023; 31:995-1002. [PMID: 37217368 DOI: 10.1016/j.tim.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023]
Abstract
Whether and how microorganisms have shaped the evolution of their animal hosts is a major question in biology. Although many animal evolutionary processes appear to correlate with changes in their associated microbial communities, the mechanistic processes leading to these patterns and their causal relationships are still far from being resolved. Gut-on-a-chip models provide an innovative approach that expands beyond the potential of conventional microbiome profiling to study how different animals sense and react to microbes by comparing responses of animal intestinal tissue models to different microbial stimuli. This complementary knowledge can contribute to our understanding of how host genetic features facilitate or prevent different microbiomes from being assembled, and in doing so elucidate the role of host-microbiota interactions in animal evolution.
Collapse
Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Kees Blijleven
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Urvish Trivedi
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
12
|
Rasmussen L, Fontsere C, Soto-Calderón ID, Guillen R, Savage A, Hansen AJ, Hvilsom C, Gilbert MTP. Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact. Mol Ecol 2023; 32:5514-5527. [PMID: 37702122 DOI: 10.1111/mec.17130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
During the last century, the critically endangered cotton-top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling to determine the genetic makeup before detrimental anthropogenic impact. Genomes were resequenced from a combination of historical museum samples and modern wild samples at low-medium coverage, to unravel how the cotton-top tamarin population structure and genomic diversity may have changed during this period. Our data suggest two populations can be differentiated, probably separated historically by the mountain ranges of the Paramillo Massif in Colombia. Although this population structure persists in the current populations, modern samples exhibit genomic signals consistent with recent inbreeding, such as long runs of homozygosity and a reduction in genome-wide heterozygosity especially in the greater northeast population. This loss is likely the consequence of the population reduction following the mass exportation of cotton-top tamarins for biomedical research in the 1960s, coupled with the habitat loss this species continues to experience. However, current populations have not experienced an increase in genetic load. We propose that the historical genetic baseline established in this study can be used to provide insight into alteration in the modern population influenced by a drastic reduction in population size as well as providing background information to be used for future conservation decision-making for the species.
Collapse
Affiliation(s)
- Linett Rasmussen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Research and Conservation, Copenhagen Zoo, Frederiksberg, Denmark
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Iván D Soto-Calderón
- Laboratorio de Genética Animal. Grupo Agrociencias, Biodiversidad y Territorio, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Medellín, Colombia
| | | | | | - Anders Johannes Hansen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| |
Collapse
|
13
|
Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2023:1-19. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
Collapse
Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
14
|
Sandoval-Velasco M, Jagadeesan A, Ramos-Madrigal J, Ávila-Arcos MC, Fortes-Lima CA, Watson J, Johannesdóttir E, Cruz-Dávalos DI, Gopalakrishnan S, Moreno-Mayar JV, Niemann J, Renaud G, Robson Brown KA, Bennett H, Pearson A, Helgason A, Gilbert MTP, Schroeder H. The ancestry and geographical origins of St Helena's liberated Africans. Am J Hum Genet 2023; 110:1590-1599. [PMID: 37683613 PMCID: PMC10502851 DOI: 10.1016/j.ajhg.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/10/2023] Open
Abstract
The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.
Collapse
Affiliation(s)
- Marcela Sandoval-Velasco
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Anuradha Jagadeesan
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - Jazmín Ramos-Madrigal
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Juriquilla, 76230 Santiago de Querétaro, México
| | - Cesar A Fortes-Lima
- Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Judy Watson
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Erna Johannesdóttir
- Department of Anthropology and Archaeology, University of Bristol, BS8 1UU Bristol, UK
| | - Diana I Cruz-Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Shyam Gopalakrishnan
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Jonas Niemann
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology Bioinformatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | - Helena Bennett
- St Helena National Trust, Broadway House, Mainstreet, Jamestown, St Helena
| | - Andrew Pearson
- Environmental Dimension Partnership, Atlantic Wharf, CF10 4HF Cardiff, UK
| | - Agnar Helgason
- deCODE Genetics/Amgen, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 101 Reykjavik, Iceland
| | - M Thomas P Gilbert
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| |
Collapse
|
15
|
Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IRM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros. Mol Biol Evol 2023; 40:msad180. [PMID: 37561011 PMCID: PMC10500089 DOI: 10.1093/molbev/msad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
Collapse
Affiliation(s)
| | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Xin Sun
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Fontsere
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | | | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Department of Zoology, Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People's Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China
- BGI Research, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Life & Medical Sciences, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Republic of South Africa
| |
Collapse
|
16
|
Ciucani MM, Ramos-Madrigal J, Hernández-Alonso G, Carmagnini A, Aninta SG, Sun X, Scharff-Olsen CH, Lanigan LT, Fracasso I, Clausen CG, Aspi J, Kojola I, Baltrūnaitė L, Balčiauskas L, Moore J, Åkesson M, Saarma U, Hindrikson M, Hulva P, Bolfíková BČ, Nowak C, Godinho R, Smith S, Paule L, Nowak S, Mysłajek RW, Lo Brutto S, Ciucci P, Boitani L, Vernesi C, Stenøien HK, Smith O, Frantz L, Rossi L, Angelici FM, Cilli E, Sinding MHS, Gilbert MTP, Gopalakrishnan S. The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs. iScience 2023; 26:107307. [PMID: 37559898 PMCID: PMC10407145 DOI: 10.1016/j.isci.2023.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 07/04/2023] [Indexed: 08/11/2023] Open
Abstract
The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.
Collapse
Affiliation(s)
- Marta Maria Ciucani
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Germán Hernández-Alonso
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sabhrina Gita Aninta
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Xin Sun
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Liam Thomas Lanigan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ilaria Fracasso
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Cecilie G. Clausen
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland, Rovaniemi, Finland
| | | | | | - Jane Moore
- Società Amatori Cirneco dell’Etna, Modica (RG), Italy
| | - Mikael Åkesson
- Swedish University of Agricultural Sciences, Grimsö Wildlife Research Station, Department of Ecology, Riddarhyttan, Sweden
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pavel Hulva
- Charles University, Department of Zoology, Faculty of Science, Prague 2, Czech Republic
| | | | - Carsten Nowak
- Center for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Raquel Godinho
- CIBIO/InBIO, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Steve Smith
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Ladislav Paule
- Faculty of Forestry, Technical University, Zvolen, Slovakia
| | - Sabina Nowak
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Robert W. Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Biological and Chemical Research Centre, Warszawa, Poland
| | - Sabrina Lo Brutto
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technology (STEBICEF), University of Palermo, Palermo, Italy
- Museum of Zoology "P. Doderlein", SIMUA, University of Palermo, Palermo, Italy
| | - Paolo Ciucci
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Luigi Boitani
- Università di Roma La Sapienza, Department Biology and Biotechnologies "Charles Darwin", Roma, Italy
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN), Italy
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oliver Smith
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Francesco Maria Angelici
- FIZV, Via Marco Aurelio 2, Roma, Italy
- National Center for Wildlife, Al Imam Faisal Ibn Turki Ibn Abdullah, Ulaishah, Saudi Arabia
| | - Elisabetta Cilli
- Laboratory of Ancient DNA, Department of Cultural Heritage (DBC), University of Bologna, Bologna, Italy
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
17
|
Hernández‐Alonso G, Ramos‐Madrigal J, Sun X, Scharff‐Olsen CH, Sinding MS, Martins NF, Ciucani MM, Mak SST, Lanigan LT, Clausen CG, Bhak J, Jeon S, Kim C, Eo KY, Cho S, Boldgiv B, Gantulga G, Unudbayasgalan Z, Kosintsev PA, Stenøien HK, Gilbert MTP, Gopalakrishnan S. Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing. Ecol Evol 2023; 13:e10404. [PMID: 37546572 PMCID: PMC10401669 DOI: 10.1002/ece3.10404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.
Collapse
Affiliation(s)
- Germán Hernández‐Alonso
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jazmín Ramos‐Madrigal
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Xin Sun
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Nuno F. Martins
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Marta Maria Ciucani
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Sarah S. T. Mak
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Liam Thomas Lanigan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Cecilie G. Clausen
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Jong Bhak
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
- Department of Biomedical Engineering, College of Information‐Bio Convergence EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
- Personal Genomics InstituteGenome Research FoundationOsongKorea
| | - Sungwon Jeon
- Clinomics Inc.UlsanKorea
- Korean Genomics CenterUlsan National Institute of Science and TechnologyUlsanKorea
| | | | - Kyung Yeon Eo
- Department of Animal Health & WelfareSemyung UniversityJecheonKorea
| | - Seong‐Ho Cho
- Natural History MuseumKyungpook National UniversityGunwiKorea
| | - Bazartseren Boldgiv
- Laboratory of Ecological and Evolutionary SynthesisNational University of MongoliaUlaanbaatarMongolia
| | | | | | - Pavel A. Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of SciencesYekaterinburgRussia
- Ural Federal UniversityEkaterinburgRussia
| | - Hans K. Stenøien
- NTNU University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - M. Thomas P. Gilbert
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- University MuseumNorwegian University of Science and TechnologyTrondheimNorway
| | - Shyam Gopalakrishnan
- Section for Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Center for Evolutionary Hologenomics, The Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Bioinformatics, Department of Health TechnologyTechnical University of DenmarkLyngbyDenmark
| |
Collapse
|
18
|
Díez-Del-Molino D, Dehasque M, Chacón-Duque JC, Pečnerová P, Tikhonov A, Protopopov A, Plotnikov V, Kanellidou F, Nikolskiy P, Mortensen P, Danilov GK, Vartanyan S, Gilbert MTP, Lister AM, Heintzman PD, van der Valk T, Dalén L. Genomics of adaptive evolution in the woolly mammoth. Curr Biol 2023; 33:1753-1764.e4. [PMID: 37030294 DOI: 10.1016/j.cub.2023.03.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/24/2023] [Accepted: 03/29/2023] [Indexed: 04/10/2023]
Abstract
Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
Collapse
Affiliation(s)
- David Díez-Del-Molino
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
| | - Marianne Dehasque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alexei Tikhonov
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | | | - Foteini Kanellidou
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Peter Mortensen
- Department of Zoology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), 685000 Magadan, Russia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway
| | | | - Peter D Heintzman
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
| |
Collapse
|
19
|
Germain RR, Feng S, Chen G, Graves GR, Tobias JA, Rahbek C, Lei F, Fjeldså J, Hosner PA, Gilbert MTP, Zhang G, Nogués-Bravo D. Species-specific traits mediate avian demographic responses under past climate change. Nat Ecol Evol 2023:10.1038/s41559-023-02055-3. [PMID: 37106156 DOI: 10.1038/s41559-023-02055-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking, and the traits that mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to ongoing climate warming.
Collapse
Affiliation(s)
- Ryan R Germain
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Shaohong Feng
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China
| | - Guangji Chen
- BGI Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gary R Graves
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Life Sciences, Imperial College London, Ascot, UK
- Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jon Fjeldså
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| | - David Nogués-Bravo
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
20
|
Cohen P, Bacilieri R, Ramos-Madrigal J, Privman E, Boaretto E, Weber A, Fuks D, Weiss E, Erickson-Gini T, Bucking S, Tepper Y, Cvikel D, Schmidt J, Gilbert MTP, Wales N, Bar-Oz G, Meiri M. Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage. Proc Natl Acad Sci U S A 2023; 120:e2213563120. [PMID: 37068234 PMCID: PMC10151551 DOI: 10.1073/pnas.2213563120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.
Collapse
Affiliation(s)
- Pnina Cohen
- The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roberto Bacilieri
- UMR Amélioration génétique et adaptation de plantes Institut, Univ Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Institut Agro, F-34398 Montpellier, France
| | - Jazmín Ramos-Madrigal
- Faculty of Health and Medical Sciences, Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Elisabetta Boaretto
- Max Planck-Weizmann Center for Integrative Archaeology and Anthropology, Dangoor Research Accelerator Mass Spectrometry Laboratory, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Audrey Weber
- UMR Amélioration génétique et adaptation de plantes Institut, Univ Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Institut Agro, F-34398 Montpellier, France
| | - Daniel Fuks
- Department of Archaeology, McDonald Institute for Archaeological Research, Cambridge CB2 3ER, UK
| | - Ehud Weiss
- The Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, 52900 Ramat Gan, Israel
| | - Tali Erickson-Gini
- Archaeological Division, Israel Antiquities Authority, 61012 Tel Aviv, Israel
| | - Scott Bucking
- Department of History, DePaul University, Chicago, IL 60614
| | - Yotam Tepper
- Department of Archaeology, Zinman Institute of Archaeology, University of Haifa, Haifa 3498837, Israel
| | - Deborah Cvikel
- Department of Maritime Civilizations, University of Haifa, Mount Carmel, Haifa 3498838, Israel
- The Leon Recanati Institute for Maritime Studies, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Joshua Schmidt
- Department of Archaeology, Zinman Institute of Archaeology, University of Haifa, Haifa 3498837, Israel
| | - M Thomas P Gilbert
- Faculty of Health and Medical Sciences, Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1353 Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, 7012 Trondheim, Norway
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom
| | - Guy Bar-Oz
- School of Archaeology and Maritime Cultures, University of Haifa, Mount Carmel, Haifa 3498837, Israel
| | - Meirav Meiri
- The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel
| |
Collapse
|
21
|
Hansen SB, Bozzi D, Mak SST, Clausen CG, Nielsen TK, Kodama M, Hansen LH, Gilbert MTP, Limborg MT. Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Genomics 2023; 115:110629. [PMID: 37100093 DOI: 10.1016/j.ygeno.2023.110629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/05/2023] [Accepted: 04/22/2023] [Indexed: 04/28/2023]
Abstract
It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value off considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.
Collapse
Affiliation(s)
- Søren B Hansen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Davide Bozzi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie G Clausen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Denmark
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; University Museum NTNU, Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
22
|
Bergeron LA, Besenbacher S, Zheng J, Li P, Bertelsen MF, Quintard B, Hoffman JI, Li Z, St Leger J, Shao C, Stiller J, Gilbert MTP, Schierup MH, Zhang G. Evolution of the germline mutation rate across vertebrates. Nature 2023; 615:285-291. [PMID: 36859541 PMCID: PMC9995274 DOI: 10.1038/s41586-023-05752-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/23/2023] [Indexed: 03/03/2023]
Abstract
The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies2. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis3. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.
Collapse
Affiliation(s)
- Lucie A Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Besenbacher
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Jiao Zheng
- BGI-Shenzhen, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | | | | | | | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- British Antarctic Survey, High Cross, Cambridge, UK
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Judy St Leger
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Josefin Stiller
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | | | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Centre for Evolutionary & Organismal Biology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
| |
Collapse
|
23
|
Zhang P, Zhu Y, Guo Q, Li J, Zhan X, Yu H, Xie N, Tan H, Lundholm N, Garcia-Cuetos L, Martin MD, Subirats MA, Su YH, Ruiz-Trillo I, Martindale MQ, Yu JK, Gilbert MTP, Zhang G, Li Q. On the origin and evolution of RNA editing in metazoans. Cell Rep 2023; 42:112112. [PMID: 36795564 PMCID: PMC9989829 DOI: 10.1016/j.celrep.2023.112112] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
Collapse
Affiliation(s)
- Pei Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Li
- BGI Research-Wuhan, BGI, Wuhan 430074, China
| | | | - Hao Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Nianxia Xie
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Lydia Garcia-Cuetos
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology, UPF-CSIC Barcelona, 08003 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Bilogia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan 26242, Taiwan
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guojie Zhang
- Center of Evolutionary and Organismal Biology, & Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
24
|
Rasmussen JA, Kiilerich P, Madhun AS, Waagbø R, Lock EJR, Madsen L, Gilbert MTP, Kristiansen K, Limborg MT. Co-diversification of an intestinal Mycoplasma and its salmonid host. ISME J 2023; 17:682-692. [PMID: 36807409 PMCID: PMC10119124 DOI: 10.1038/s41396-023-01379-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/19/2023]
Abstract
Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.
Collapse
Affiliation(s)
- Jacob A Rasmussen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Pia Kiilerich
- Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, 2300, Copenhagen, Denmark
| | | | - Rune Waagbø
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
25
|
Hansen CCR, Láruson ÁJ, Rasmussen JA, Ballesteros JAC, Sinding MHS, Hallgrimsson GT, von Schmalensee M, Stefansson RA, Skarphédinsson KH, Labansen AL, Leivits M, Sonne C, Dietz R, Skelmose K, Boertmann D, Eulaers I, Martin MD, Helgason AS, Gilbert MTP, Pálsson S. Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla). Mol Ecol 2023; 32:1925-1942. [PMID: 36680370 DOI: 10.1111/mec.16858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: (1) Isolation of refugia during the last glacial period 110-115,000 years ago, (2) population divergence following the colonization of the deglaciated areas ~10,000 years ago, (3) human population expansion, which led to the settlement in Iceland ~1100 years ago, and (4) human persecution and exposure to toxic pollutants during the last two centuries.
Collapse
Affiliation(s)
| | - Áki Jarl Láruson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Jacob Agerbo Rasmussen
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesus Adrian Chimal Ballesteros
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Mikkel-Holger S Sinding
- Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar T Hallgrimsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | - Madis Leivits
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Christian Sonne
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Rune Dietz
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Kim Skelmose
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David Boertmann
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Igor Eulaers
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Agnar S Helgason
- Department of Anthropology, University of Iceland, Reykjavik, Iceland.,deCODE Genetics, Reykjavik, Iceland
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Snaebjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| |
Collapse
|
26
|
Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
Collapse
Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| |
Collapse
|
27
|
Bolt Botnen A, Bjørnsen MB, Alberdi A, Gilbert MTP, Aizpurua O. A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. Heliyon 2023; 9:e12861. [PMID: 36699263 PMCID: PMC9868478 DOI: 10.1016/j.heliyon.2023.e12861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
Collapse
Affiliation(s)
- Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Mads Bjørn Bjørnsen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| |
Collapse
|
28
|
Neves RC, Møbjerg A, Kodama M, Ramos-Madrigal J, Gilbert MTP, Møbjerg N. Corrigendum to "Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome" [Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 267 (2022), 111169]. Comp Biochem Physiol A Mol Integr Physiol 2022; 274:111316. [PMID: 36115214 DOI: 10.1016/j.cbpa.2022.111316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Ask Møbjerg
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Nadja Møbjerg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
29
|
Møbjerg A, Kodama M, Ramos-Madrigal J, Neves RC, Jørgensen A, Schiøtt M, Gilbert MTP, Møbjerg N. Corrigendum to "Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription" [Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 271 (2022), 111245]. Comp Biochem Physiol A Mol Integr Physiol 2022; 274:111317. [PMID: 36115215 DOI: 10.1016/j.cbpa.2022.111317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ask Møbjerg
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Aslak Jørgensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Schiøtt
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Nadja Møbjerg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
30
|
Koziol A, Odriozola I, Nyholm L, Leonard A, San José C, Pauperio J, Ferreira C, Hansen AJ, Aizpurua O, Gilbert MTP, Alberdi A. Enriching captivity conditions with natural elements does not prevent the loss of wild‐like gut microbiota but shapes its compositional variation in two small mammals. Microbiologyopen 2022; 11:e1318. [PMCID: PMC9517064 DOI: 10.1002/mbo3.1318] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Abstract
As continued growth in gut microbiota studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild‐like microbial community is becoming increasingly important to obtain representative results from captive animals. In this study, we assessed how the gut microbiota of two wild‐caught small mammals, namely Crocidura russula (Eulipotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula, immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a “natural” setup enriched with elements freshly collected from nature and a “laboratory” setup with sterile artificial elements. Through sequencing of the V3–V4 region of the 16S recombinant RNA gene, we found that the initial microbial diversity dropped during captivity in both species, regardless of treatment. Community composition underwent a change of similar magnitude in both species and under both treatments. However, we did observe that the temporal development of the gut microbiome took different trajectories (i.e., changed in different directions) under different treatments, particularly in C. russula, suggesting that C. russula may be more susceptible to environmental change. The results of this experiment do not support the use of microbially enriched environments to retain wild‐like microbial diversities and compositions, yet show that specific housing conditions can significantly affect the drift of microbial communities under captivity.
Collapse
Affiliation(s)
- Adam Koziol
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Lasse Nyholm
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Aoife Leonard
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Carlos San José
- Biodonostia Health Research Institute Donostia‐San Sebastian Spain
| | - Joana Pauperio
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Universidade do Porto Vila do Conde Campus de Vairão Portugal
| | - Clara Ferreira
- Animal Ecology, Institute for Biochemistry and Biology University of Potsdam Potsdam Germany
| | - Anders J. Hansen
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| | - M. Thomas P. Gilbert
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
- University Museum, Norwegian University of Science and Technology Trondheim Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute University of Copenhagen Copenhagen Denmark
| |
Collapse
|
31
|
Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P, Margaryan A, Martin MD, Ellegaard MR, Magnússon ÓÞ, Sigurðsson Á, Snorradóttir S, Magnúsdóttir DN, Laffoon JE, van Dorp L, Liu X, Moltke I, Ávila-Arcos MC, Schraiber JG, Rasmussen S, Juan D, Gelabert P, de-Dios T, Fotakis AK, Iraeta-Orbegozo M, Vågene ÅJ, Denham SD, Christophersen A, Stenøien HK, Vieira FG, Liu S, Günther T, Kivisild T, Moseng OG, Skar B, Cheung C, Sandoval-Velasco M, Wales N, Schroeder H, Campos PF, Guðmundsdóttir VB, Sicheritz-Ponten T, Petersen B, Halgunset J, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Willerslev E, Balloux F, Marques-Bonet T, Lalueza-Fox C, Nielsen R, Stefánsson K, Helgason A, Gilbert MTP. The population genomic legacy of the second plague pandemic. Curr Biol 2022; 32:4743-4751.e6. [PMID: 36182700 DOI: 10.1016/j.cub.2022.09.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/15/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.
Collapse
Affiliation(s)
- Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark.
| | - S Sunna Ebenesersdóttir
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - Inge K C Lundstrøm
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Gordon Turner-Walker
- National Yunlin University of Science & Technology, 123 University Road, Section 3, 64002 Douliu, Yun-Lin County, Taiwan; Department of Archaeology and Anthropology, National Museum of Natural Science, 1 Guanqian Road, North District Taichung City 404023, Taiwan
| | | | - Pierre Luisi
- Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba, Argentina; Microbial Paleogenomics Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Michael D Martin
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Martin Rene Ellegaard
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | | | | | | | | | - Jason E Laffoon
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), 3001 Boulevard Juriquilla, 76230 Querétaro, Mexico
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., San Diego, CA, USA
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Toni de-Dios
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anna K Fotakis
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Miren Iraeta-Orbegozo
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Åshild J Vågene
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany; Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | | | - Axel Christophersen
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Filipe G Vieira
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Shanlin Liu
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Torsten Günther
- Evolutionsbiologisk Centrum EBC, Norbyv. 18A, 752 36 Uppsala, Sweden
| | - Toomas Kivisild
- KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Institute of Genomics, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Ole Georg Moseng
- Department of Business, History and Social Sciences, University of South-Eastern Norway, Notodden, Norway
| | - Birgitte Skar
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Christina Cheung
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; EA - Eco-anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, Paris, France
| | - Marcela Sandoval-Velasco
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Nathan Wales
- Department of Archaeology, Kings Manor and Principals House, University of York, Exhibition Square, York YO1 7EP, UK
| | - Hannes Schroeder
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark
| | - Paula F Campos
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos, Portugal
| | - Valdís B Guðmundsdóttir
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | - Bent Petersen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | | | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark; The Globe Institute, Lundbeck Foundation Center for Geogenetics, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Eske Willerslev
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Francois Balloux
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain; Museu de Ciències Naturals de Barcelona, 08019 Barcelona, Spain
| | - Rasmus Nielsen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Bldg #3140, Berkeley, CA 94720-3140, USA
| | - Kári Stefánsson
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Agnar Helgason
- deCODE Genetics, AMGEN Inc., Sturlugata 8, 102 Reykjavík, Iceland; Department of Anthropology, School of Social Sciences, University of Iceland, Gimli, Sæmundargata, 102 Reykjavík, Iceland
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, 1353 Copenhagen, Denmark; NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| |
Collapse
|
32
|
Tous N, Marcos S, Goodarzi Boroojeni F, Pérez de Rozas A, Zentek J, Estonba A, Sandvang D, Gilbert MTP, Esteve-Garcia E, Finn R, Alberdi A, Tarradas J. Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics. Front Physiol 2022; 13:884925. [PMID: 36148301 PMCID: PMC9485813 DOI: 10.3389/fphys.2022.884925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.
Collapse
Affiliation(s)
- Núria Tous
- Animal Nutrition, Institute of Agrifood Research and Technology (IRTA), Constantí, Spain
| | - Sofia Marcos
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU, Bilbao, Spain
| | - Farshad Goodarzi Boroojeni
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin (FUB), Berlin, Germany
| | - Ana Pérez de Rozas
- Animal Health-CReSA, Institute of Agrifood Research and Technology (IRTA), Bellaterra, Spain
| | - Jürgen Zentek
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin (FUB), Berlin, Germany
| | - Andone Estonba
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU, Bilbao, Spain
| | - Dorthe Sandvang
- Chr. Hansen A/S, Animal Health Innovation, Hoersholm, Denmark
| | - M. Thomas P. Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Enric Esteve-Garcia
- Animal Nutrition, Institute of Agrifood Research and Technology (IRTA), Constantí, Spain
| | - Robert Finn
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Antton Alberdi,
| | - Joan Tarradas
- Animal Nutrition, Institute of Agrifood Research and Technology (IRTA), Constantí, Spain
| |
Collapse
|
33
|
Bieker VC, Battlay P, Petersen B, Sun X, Wilson J, Brealey JC, Bretagnolle F, Nurkowski K, Lee C, Barreiro FS, Owens GL, Lee JY, Kellner FL, van Boheeman L, Gopalakrishnan S, Gaudeul M, Mueller-Schaerer H, Lommen S, Karrer G, Chauvel B, Sun Y, Kostantinovic B, Dalén L, Poczai P, Rieseberg LH, Gilbert MTP, Hodgins KA, Martin MD. Uncovering the genomic basis of an extraordinary plant invasion. Sci Adv 2022; 8:eabo5115. [PMID: 36001672 PMCID: PMC9401624 DOI: 10.1126/sciadv.abo5115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/11/2022] [Indexed: 05/31/2023]
Abstract
Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.
Collapse
Affiliation(s)
- Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100 Kedah, Malaysia
| | - Xin Sun
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - François Bretagnolle
- UMR CNRS/uB 6282 Biogéosciences, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Kristin Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Chris Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fátima Sánchez Barreiro
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jacqueline Y. Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fabian L. Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Myriam Gaudeul
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA, National Herbarium (P), 57 rue Cuvier, CP39, 75005 Paris, France
| | | | - Suzanne Lommen
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA Leiden, Netherlands
- Koppert Biological Systems, Department R&D Macrobiology, Veilingweg 14, 2651 BE Berkel en Rodenrijs, Netherlands
| | - Gerhard Karrer
- Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bruno Chauvel
- UMR Agroécologie, Institut Agro, INRAE, Univ. Bourgogne, Univ. Bourgogne-Franche-Comté, F-21000 Dijon, France
| | - Yan Sun
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Bojan Kostantinovic
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), Kőszeg, Hungary
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - M. Thomas P. Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| |
Collapse
|
34
|
Paez S, Kraus RHS, Shapiro B, Gilbert MTP, Jarvis ED, Al-Ajli FO, Ceballos G, Crawford AJ, Fedrigo O, Johnson RN, Johnson WE, Marques-Bonet T, Morin PA, Mueller RC, Ryder OA, Teeling EC, Venkatesh B. Reference genomes for conservation. Science 2022; 377:364-366. [PMID: 35862547 DOI: 10.1126/science.abm8127] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
High-quality reference genomes for non-model species can benefit conservation.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Farooq Omar Al-Ajli
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.,Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia.,Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
| | - Gerardo Ceballos
- Instituto de Ecologia, Universidad Nacional Autónoma de Mexico, CU, Coyoacán, 04510 Ciudad de México, Mexico
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
| | - Rebecca N Johnson
- Smithsonian National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Warren E Johnson
- The Walter Reed Biosystematics Unit and Smithsonian Conservation Biology Institute, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Baldiri i Reixac 4 08028, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Spain
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Ralf C Mueller
- Department of Migration, Max Planck Institute of Animal Behavior, 78315 Radolfzell, Germany.,Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center, Escondido, CA 92027, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, University College, Dublin, Ireland
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| |
Collapse
|
35
|
Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
Collapse
Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| |
Collapse
|
36
|
de Ferran V, Figueiró HV, de Jesus Trindade F, Smith O, Sinding MHS, Trinca CS, Lazzari GZ, Veron G, Vianna JA, Barbanera F, Kliver S, Serdyukova N, Bulyonkova T, Ryder OA, Gilbert MTP, Koepfli KP, Eizirik E. Phylogenomics of the world's otters. Curr Biol 2022; 32:3650-3658.e4. [PMID: 35779528 DOI: 10.1016/j.cub.2022.06.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.
Collapse
Affiliation(s)
- Vera de Ferran
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Henrique Vieira Figueiró
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Fernanda de Jesus Trindade
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Oliver Smith
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Mikkel-Holger S Sinding
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Cristine S Trinca
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Gabriele Zenato Lazzari
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75231 Paris Cedex 5, France
| | - Juliana A Vianna
- Millennium Institute Center for Genome Regulation (CRG), Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuna Mackenna 4860, Santiago 782-0436, Chile
| | - Filippo Barbanera
- Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Natalia Serdyukova
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Tatiana Bulyonkova
- A. P. Ershov Institute of Informatics Systems SB RAS, 6 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA; Department of Evolution, Behavior, and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA.
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil; Instituto Pró-Carnívoros, Av. Horácio Netto, 1030 - Parque Edmundo Zanoni, Atibaia, São Paulo 12945-010, Brazil.
| |
Collapse
|
37
|
Cerca J, Petersen B, Lazaro-Guevara JM, Rivera-Colón A, Birkeland S, Vizueta J, Li S, Li Q, Loureiro J, Kosawang C, Díaz PJ, Rivas-Torres G, Fernández-Mazuecos M, Vargas P, McCauley RA, Petersen G, Santos-Bay L, Wales N, Catchen JM, Machado D, Nowak MD, Suh A, Sinha NR, Nielsen LR, Seberg O, Gilbert MTP, Leebens-Mack JH, Rieseberg LH, Martin MD. The genomic basis of the plant island syndrome in Darwin's giant daisies. Nat Commun 2022; 13:3729. [PMID: 35764640 PMCID: PMC9240058 DOI: 10.1038/s41467-022-31280-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/09/2022] [Indexed: 12/04/2022] Open
Abstract
The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies. Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin’s giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly.
Collapse
Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Bent Petersen
- Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - José Miguel Lazaro-Guevara
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Angel Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Siri Birkeland
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Joel Vizueta
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Siyu Li
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Qionghou Li
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-095, Coimbra, Portugal
| | - Chatchai Kosawang
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador.,Department of Botany and Plant Physiology, University of Malaga, Malaga, Spain
| | - Gonzalo Rivas-Torres
- Colegio de Ciencias Biológicas y Ambientales COCIBA & Extensión Galápagos, Universidad San Francisco de Quito USFQ, Quito, 170901, Ecuador.,Galapagos Science Center, USFQ, UNC Chapel Hill, San Cristobal, Galapagos, Ecuador.,Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Courtesy Faculty, Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
| | | | - Pablo Vargas
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Ross A McCauley
- Department of Biology, Fort Lewis College, Durango, CO, 81301, USA
| | - Gitte Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Luisa Santos-Bay
- Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - Nathan Wales
- Department of Archaeology, University of York, York, UK
| | - Julian M Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Daniel Machado
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, NR4 7TU, Norwich, UK.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, 75236, Uppsala, Sweden
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Lene R Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Ole Seberg
- The Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.,Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | | | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.
| |
Collapse
|
38
|
Iwanycki Ahlstrand N, Gopalakrishnan S, Vieira FG, Bieker VC, Meudt HM, Dunbar-Co S, Rothfels CJ, Martinez-Swatson KA, Maldonado C, Hassemer G, Shipunov A, Bowers MD, Gardner E, Xu M, Ghorbani A, Amano M, Grace OM, Pringle JS, Bishop M, Manzanilla V, Cotrim H, Blaney S, Zubov D, Choi HK, Yesil Y, Bennett B, Vimolmangkang S, El-Seedi HR, Staub PO, Li Z, Boldbaatar D, Hislop M, Caddy LJ, Muasya AM, Saslis-Lagoudakis CH, Gilbert MTP, Zerega NJC, Rønsted N. Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes. Front Plant Sci 2022; 13:838166. [PMID: 35755675 PMCID: PMC9218338 DOI: 10.3389/fpls.2022.838166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species' establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.
Collapse
Affiliation(s)
| | - Shyam Gopalakrishnan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Filipe G. Vieira
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | | | - Carl J. Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | | | - Carla Maldonado
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, La Paz, Bolivia
| | | | - Alexey Shipunov
- Department of Biology, Minot University, Minot, ND, United States
| | - M. Deane Bowers
- Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
| | - Elliot Gardner
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Maonian Xu
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Abdolbaset Ghorbani
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Makoto Amano
- Natural History Museum and Institute, Chiba, Japan
| | - Olwen M. Grace
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Madonna Bishop
- Memorial University Botanical Garden, St. John’s, NL, Canada
| | | | - Helena Cotrim
- Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Sean Blaney
- Atlantic Canada Conservation Data Centre, Sackville, NB, Canada
| | | | - Hong-Keun Choi
- Department of Life Sciences, Ajou University, Suweon, South Korea
| | - Yeter Yesil
- Department of Pharmaceutical Botany, Istanbul University, Istanbul, Turkey
| | - Bruce Bennett
- Yukon Conservation Data Centre, Yukon Territory, YT, Canada
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand
| | - Hesham R. El-Seedi
- Pharmacognosy Group, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Peter O. Staub
- Department of Biomedical Science, University of Cagliari, Cagliari, Italy
| | - Zhu Li
- Chinese Academy of Sciences, Beijing, China
| | - Delgerbat Boldbaatar
- Department of Liver Center, National University of Mongolia, Ulaanbaatar, Mongolia
| | | | - Laura J. Caddy
- Botanical Garden, The University of British Columbia, Vancouver, BC, Canada
| | - A. Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | | | | | - Nyree J. C. Zerega
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Chicago, IL, United States
- Plant Biology and Conservation, Northwestern University, Evanston, IL, United States
| | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- National Tropical Botanic Garden, Kaua‘i, HI, United States
| |
Collapse
|
39
|
Møbjerg A, Kodama M, Ramos-Madrigal J, Neves RC, Jørgensen A, Schiøtt M, Gilbert MTP, Møbjerg N. Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription. Comp Biochem Physiol A Mol Integr Physiol 2022; 271:111245. [PMID: 35640792 DOI: 10.1016/j.cbpa.2022.111245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/30/2022]
Abstract
Subzero temperatures are among the most significant factors defining the distribution of organisms, yet, certain taxa have evolved to overcome this barrier. The microscopic tardigrades are among the most freeze-tolerant animals, with selected species reported to survive milli-Kelvin temperatures. Here, we estimate survival of fully hydrated eutardigrades of the species Ramazzottius varieornatus following exposures to -20 °C and -80 °C as well as -196 °C with or without initial cooling to -80 °C. The tardigrades easily survive these temperatures, yet with a significant decrease in viability following rapid cooling by direct exposure to -196 °C. Hence, post-freeze recovery of R. varieornatus seems to rely on cooling rate and thus controlled ice formation. Cryophilic organisms are renowned for having cold-active enzymes that secure appropriate reaction rates at low temperatures. Hence, extreme freeze-tolerance in R. varieornatus could potentially involve syntheses of cryoprotectants and de novo transcription. We therefore generated a reference transcriptome for this cryophilic R. varieornatus population and explored for differential gene expression patterns following cooling to -80 °C as compared to active 5 °C controls. Specifically, we tested for fast transcription potentially occurring within 25 min of cooling from room temperature to a supercooling point of ca. -20 °C, at which the tardigrades presumably freeze and enter into the ametabolic state of cryobiosis. Our analyses revealed no evidence for differential gene expression. We, therefore, conclude that extreme freeze-tolerance in R. varieornatus relies on controlled extracellular freezing with any freeze-tolerance related genes being constitutively expressed.
Collapse
Affiliation(s)
- Ask Møbjerg
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark. https://twitter.com/askmobjerg
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Aslak Jørgensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Schiøtt
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Nadja Møbjerg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
40
|
Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
Collapse
Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| |
Collapse
|
41
|
Neves RC, Møbjerg A, Kodama M, Ramos-Madrigal J, Gilbert MTP, Møbjerg N. Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome. Comp Biochem Physiol A Mol Integr Physiol 2022; 267:111169. [PMID: 35182765 DOI: 10.1016/j.cbpa.2022.111169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 12/13/2022]
Abstract
Tardigrades are renowned for their extreme stress tolerance, which includes the ability to endure complete desiccation, high levels of radiation and very low sub-zero temperatures. Nevertheless, tardigrades appear to be vulnerable to high temperatures and thus the potential effects of global warming. Here, we provide the first analysis of transcriptome data obtained from heat stressed specimens of the eutardigrade Ramazzottius varieornatus, with the aim of providing new insights into the molecular processes affected by high temperatures. Specifically, we compare RNA-seq datasets obtained from active, heat-exposed (35 °C) tardigrades to that of active controls kept at 5 °C. Our data reveal a surprising shift in transcription, involving 9634 differentially expressed transcripts, corresponding to >35% of the transcriptome. The latter data are in striking contrast to the hitherto observed constitutive expression underlying tardigrade extreme stress tolerance and entrance into the latent state of life, known as cryptobiosis. Thus, when examining the molecular response, heat-stress appears to be more stressful for R. varieornatus than extreme conditions, such as desiccation or freezing. A gene ontology analysis reveals that the heat stress response involves a change in transcription and presumably translation, including an adjustment of metabolism, and, putatively, preparation for encystment and subsequent diapause. Among the differentially expressed transcripts we find heat-shock proteins as well as the eutardigrade specific proteins (CAHS, SAHS, MAHS, RvLEAM, and Dsup). The latter proteins thus seem to contribute to a general stress response, and may not be directly related to cryptobiosis.
Collapse
Affiliation(s)
| | - Ask Møbjerg
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jazmín Ramos-Madrigal
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Nadja Møbjerg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
42
|
Field MA, Yadav S, Dudchenko O, Esvaran M, Rosen BD, Skvortsova K, Edwards RJ, Keilwagen J, Cochran BJ, Manandhar B, Bustamante S, Rasmussen JA, Melvin RG, Chernoff B, Omer A, Colaric Z, Chan EKF, Minoche AE, Smith TPL, Gilbert MTP, Bogdanovic O, Zammit RA, Thomas T, Aiden EL, Ballard JWO. The Australian dingo is an early offshoot of modern breed dogs. Sci Adv 2022; 8:eabm5944. [PMID: 35452284 PMCID: PMC9032958 DOI: 10.1126/sciadv.abm5944] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/09/2022] [Indexed: 06/11/2023]
Abstract
Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.
Collapse
Affiliation(s)
- Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD 4878, Australia
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Sonu Yadav
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Meera Esvaran
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Blake J. Cochran
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bikash Manandhar
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Center for Evolutionary Hologenomics, Faculty of Health and Medical Sciences, The GLOBE Institute University of Copenhagen, Copenhagen, Denmark
| | - Richard G. Melvin
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, Duluth, MN 55812, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth and Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Arina Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eva K. F. Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle, NSW 2300, Australia
| | - Andre E. Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Timothy P. L. Smith
- U.S. Meat Animal Research Center, Agricultural Research Service, USDA, Rd 313, Clay Center, NE 68933, USA
| | - M. Thomas P. Gilbert
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Erez L. Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Pudong 201210, China
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J. William O. Ballard
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, VIC 3086, Australia
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC 3052, Australia
| |
Collapse
|
43
|
Rasmussen JA, Villumsen KR, Ernst M, Hansen M, Forberg T, Gopalakrishnan S, Gilbert MTP, Bojesen AM, Kristiansen K, Limborg MT. A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss). Microbiome 2022; 10:21. [PMID: 35094708 PMCID: PMC8802455 DOI: 10.1186/s40168-021-01221-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/27/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism. RESULTS Our findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related Candidatus Mycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence of Candidatus Mycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites. CONCLUSION Our results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments. Video Abstract.
Collapse
Affiliation(s)
- Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark.
| | - Kasper Rømer Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - Madeleine Ernst
- Section for Clinical Mass Spectrometry, Danish Center for Neonatal Screening, Department of Congenital Disorders, Statens Serum Institut, 2300, Copenhagen, Denmark
| | - Martin Hansen
- Department of Environmental Science, Aarhus University, Aarhus, Denmark
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
- University Museum NTNU, Trondheim, Norway
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Morten Tønsberg Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark.
| |
Collapse
|
44
|
Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A 2022; 119:e2115635118. [PMID: 35042800 PMCID: PMC8795548 DOI: 10.1073/pnas.2115635118] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616;
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
| | - Stephen Richards
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Erez Lieberman Aiden
- DNA Zoo and The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030
| | - Miguel L Allende
- Center for Genome Regulation, Universidad de Chile 3425 Santiago, Chile
- Facultad de Ciencias, Universidad de Chile 3425 Santiago, Chile
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Miklós Bálint
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus-Liebig University 35392 Giessen, Germany
| | - Katharine B Barker
- Global Genome Biodiversity Network Secretariat, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | | | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara 44121 Ferrara, Italy
| | - Mark L Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Nicolette D Caperello
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Keith Carlson
- The Novim Group, University of California, Santa Barbara, CA 93106
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica 11529 Taipei, Taiwan
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dalia A Conde
- Conservation Science, Species360 Conservation Science Alliance, Bloomington, MN 55425
- Department of Biology, University of Southern Denmark 5230 Odense M, Denmark
| | - Montserrat Corominas
- Department of Genetics, Microbiology, and Statistics, Universitat de Barcelona 08028 Barcelona, Spain
- Catalan Society for Biology, Institute for Catalan Studies 08001 Barcelona, Spain
| | - Keith A Crandall
- Department of Biostatistics & Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC 20052
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - ThankGod E Ebenezer
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Olivier Fedrigo
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Paul Flicek
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen 1350 Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology 7491 Trondheim, Norway
| | - Melissa M Goldstein
- Department of Health Policy and Management, George Washington University, Washington, DC 20052
| | - Jennifer Marshall Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Henry T Greely
- Stanford Law School, Stanford University, Stanford, CA 94305
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Kevin J Hackett
- Office of National Programs, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - David Haussler
- Genome Institute, University of California, Santa Cruz, CA 95060
- HHMI, Chevy Chase, MD 20815
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2000, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | | | - Axel Janke
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Warren E Johnson
- Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, MD 20746
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute 21990 Incheon, South Korea
| | - W John Kress
- Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics 411-8540 Shizuoka, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research 650-0047 Hyogo, Japan
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | | | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 752 36 Uppsala, Sweden
| | - Xin Liu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Pompeu Fabra University, Consejo Superior de Investigaciones Cientificas, Parc de Recerca Biomedica de Barcelona 08003 Barcelona, Spain
- Catalan Institute of Research and Advanced Studies 08010 Barcelona, Spain
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain
| | - Sophie Mazard
- Bioplatforms Australia, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonna A K Mazet
- One Health Institute, University of California Davis, CA 95616
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research 14195 Berlin, Germany
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research 10315 Berlin, Germany
| | - Eugene W Myers
- Max Planck Institute for Molecular Cell Biology and Genetics 01307 Dresden, Germany
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Sadye Paez
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Hyun Park
- Division of Biotechnology, Korea University 02841 Seoul, Korea
| | - Gene E Robinson
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants Associated Unit to Consejo Superior de Investigaciones Cientificas, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain
- Laboratoire d'Ecologie Alpine, University Grenoble Alpes, University Savoie Mont Blanc, CNRS 38000 Grenoble, France
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Division of Biology, Department of Evolution, Behavior, and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University 21589 Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University 21589 Jeddah, Saudi Arabia
| | - H Bradley Shaffer
- La Kretz Center for California Conservation Science, Institute of Environment and Sustainability, University of California, Los Angeles, CA 90024
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Timothy M Shank
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Jacob S Sherkow
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- College of Law, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University 224002 Yancheng, China
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu 50411 Tartu, Estonia
- College of Science, King Saud University 11451 Riyadh, Saudi Arabia
| | | | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Xiaofeng Wei
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007
- Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Julia L Wilson
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Xun Xu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Huanming Yang
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 2100 Copenhagen, Denmark
- China National Genebank, Beijing Genomics Institute 51803 Shenzhen, China
| |
Collapse
|
45
|
Jensen EL, Díez-del-Molino D, Gilbert MTP, Bertola LD, Borges F, Cubric-Curik V, de Navascués M, Frandsen P, Heuertz M, Hvilsom C, Jiménez-Mena B, Miettinen A, Moest M, Pečnerová P, Barnes I, Vernesi C. Ancient and historical DNA in conservation policy. Trends Ecol Evol 2022; 37:420-429. [DOI: 10.1016/j.tree.2021.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/15/2022]
|
46
|
Cavill EL, Liu S, Zhou X, Gilbert MTP. To bee, or not to bee? One leg is the question. Mol Ecol Resour 2021; 22:1868-1874. [PMID: 34957693 DOI: 10.1111/1755-0998.13578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/26/2021] [Accepted: 12/02/2021] [Indexed: 11/30/2022]
Abstract
Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, to name a few. However, given such analyses come at the cost of physical damage to museum specimens required for such work, there is a natural interest in the development and/or application of methods to minimise the damage incurred. We explored the efficacy of a recently published single stranded library construction protocol, on DNA extracted from single legs taken from eight dry-preserved historic bee specimens collected 150 years ago. Specifically, the DNA was extracted using a 'minimally destructive' method that leaves the samples' exterior intact. Our sequencing data revealed not only that the endogenous DNA recovered from some of the samples was at a relatively high level (up to 58%), but that the complexity of the libraries was sufficient in the best samples to theoretically allow deeper sequencing to a predicted level of 69x genome coverage. As such, these combined protocols offer the possibility to generate sequencing data at levels that are suitable for many common evolutionary genomic analyses, while simultaneously minimising the damage conferred to the valuable dried museum bee samples. Furthermore, we anticipate that these methods may have much wider application on many other invertebrate taxa stored in a similar way. We hope that the results from this research may be able to contribute to the increased willingness of museums to loan much needed dry-preserved insects for future genomic studies.
Collapse
Affiliation(s)
- Emily Louisa Cavill
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| |
Collapse
|
47
|
Puetz LC, Delmont TO, Aizpurua O, Guo C, Zhang G, Katajamaa R, Jensen P, Gilbert MTP. Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication. Adv Genet (Hoboken) 2021; 2:2100018. [PMID: 36619855 PMCID: PMC9744516 DOI: 10.1002/ggn2.202100018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/04/2021] [Indexed: 01/11/2023]
Abstract
Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.
Collapse
Affiliation(s)
- Lara C. Puetz
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| | - Tom O. Delmont
- Génomique MétaboliqueGenoscopeInstitut François JacobCEACNRSUniv EvryUniversité Paris‐SaclayEvry91057France
| | - Ostaizka Aizpurua
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| | - Chunxue Guo
- China National GeneBankBGI‐ShenzhenShenzhen518083China
| | - Guojie Zhang
- China National GeneBankBGI‐ShenzhenShenzhen518083China,Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagen2100Denmark,State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunming650223China,Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming650223China
| | - Rebecca Katajamaa
- IFM Biology, AVIAN Behaviour Genomics and Physiology GroupLinköping UniversityLinköping58330Sweden
| | - Per Jensen
- IFM Biology, AVIAN Behaviour Genomics and Physiology GroupLinköping UniversityLinköping58330Sweden
| | - M. Thomas P. Gilbert
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark,Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)Trondheim7491Norway
| |
Collapse
|
48
|
Sinding MHS, Ciucani MM, Ramos-Madrigal J, Carmagnini A, Rasmussen JA, Feng S, Chen G, Vieira FG, Mattiangeli V, Ganjoo RK, Larson G, Sicheritz-Pontén T, Petersen B, Frantz L, Gilbert MTP, Bradley DG. Kouprey ( Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience 2021; 24:103226. [PMID: 34712923 PMCID: PMC8531564 DOI: 10.1016/j.isci.2021.103226] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/11/2021] [Accepted: 10/01/2021] [Indexed: 12/30/2022] Open
Abstract
The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so. We generated two genomes from the likely extinct kouprey (Bos sauveli) Extensive mt and nuclear-genome-wide incomplete lineage sorting across wild Asian Bos Initial polytomic diversification of the wild Asian Bos—kouprey, banteng, and gaur
Collapse
Affiliation(s)
| | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jacob Agerbo Rasmussen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - M. Thomas P. Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
49
|
Aizpurua O, Nyholm L, Morris E, Chaverri G, Herrera Montalvo LG, Flores-Martinez JJ, Lin A, Razgour O, Gilbert MTP, Alberdi A. The role of the gut microbiota in the dietary niche expansion of fishing bats. Anim Microbiome 2021; 3:76. [PMID: 34711286 PMCID: PMC8555116 DOI: 10.1186/s42523-021-00137-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet. Results We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish. Conclusions Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00137-w.
Collapse
Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.
| | - Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
| | - Evie Morris
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - Gloriana Chaverri
- Sede del Sur, Universidad de Costa Rica, #4000 Alamedas, Golfito, 60701, Costa Rica.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, República de Panamá
| | - L Gerardo Herrera Montalvo
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 21, San Patricio, 48980, Jalisco, Mexico
| | - José Juan Flores-Martinez
- Laboratorio de Sistemas de Información Geográfica, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Orly Razgour
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
| |
Collapse
|
50
|
Pereira CL, Gilbert MTP, Araújo MB, Matias MG. Fine‐tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Cátia Lúcio Pereira
- Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
- Centre for Macroecology, Evolution and Climate Globe Institute University of Copenhagen Copenhagen Denmark
- Rui Nabeiro Biodiversity Chair MED – Mediterranean Institute for Agriculture Environment and Development University of Évora Évora Portugal
| | - M. Thomas P. Gilbert
- Centre for Evolutionary Hologenomics Globe Institute University of Copenhagen Copenhagen Denmark
- University MuseumNTNU Trondheim Norway
| | - Miguel Bastos Araújo
- Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
- Rui Nabeiro Biodiversity Chair MED – Mediterranean Institute for Agriculture Environment and Development University of Évora Évora Portugal
| | - Miguel Graça Matias
- Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
- Rui Nabeiro Biodiversity Chair MED – Mediterranean Institute for Agriculture Environment and Development University of Évora Évora Portugal
| |
Collapse
|