1
|
Andrews AJ, Eriksen EF, Star B, Præbel K, Di Natale A, Malca E, Onar V, Aniceti V, Carenti G, Piquès G, Nielsen SV, Persson P, Piattoni F, Fontani F, Atmore LM, Kersten O, Tinti F, Cilli E, Cariani A. Ancient DNA suggests a historical demographic decline and genetic erosion in the Atlantic bluefin tuna. Proc Natl Acad Sci U S A 2025; 122:e2409302122. [PMID: 40392844 DOI: 10.1073/pnas.2409302122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 04/08/2025] [Indexed: 05/22/2025] Open
Abstract
Overexploitation has depleted fish stocks during the past century; nonetheless, its genomic consequences remain poorly understood for most species. Characterizing the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna (Thunnus thynnus), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n = 49) and ancient (n = 41) specimens dating up to 5,000 y ago, uncovering several findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity were significantly lower in modern (2013 to 2020) than ancient (pre-1941) Mediterranean bluefin tuna, suggesting that bluefin tuna underwent a genetic bottleneck. With this work, we show how ancient DNA provides unique perspectives on ecological complexity with the potential to inform the management and conservation of fishes.
Collapse
Affiliation(s)
- Adam Jon Andrews
- Section for Marine Biology, Norwegian Institute of Water Research, Oslo 0579, Norway
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna 48123, Italy
| | - Emma Falkeid Eriksen
- Centre for Ecology and Evolutionary Synthesis, University of Oslo, Oslo 0371, Norway
| | - Bastiaan Star
- Centre for Ecology and Evolutionary Synthesis, University of Oslo, Oslo 0371, Norway
| | - Kim Præbel
- Norges fiskerihøgskole, University of Tromsø Arctic University of Norway, Tromsø 9037, Norway
| | | | - Estrella Malca
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL 33146
- National Oceanic and Atmospheric Administration Fisheries, Populations and Ecosystems Monitoring Division, Miami, FL 33149
| | - Vedat Onar
- Faculty of Veterinary Medicine, Muğla Sıtkı Kocman University, Milas 48100, Türkiye
| | - Veronica Aniceti
- Consejo Superior de Investigaciones Científicas, Institució Milà, Barcelona 08001, Spain
| | | | - Gäel Piquès
- Archéologie des Sociétés Méditerranéennes, CNRS, Université Paul Valéry, Montpellier 34199, France
| | | | - Per Persson
- Museum of Cultural History, University of Oslo, Oslo 0164, Norway
| | - Federica Piattoni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna 48123, Italy
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Ravenna 48121, Italy
| | - Lane M Atmore
- Centre for Ecology and Evolutionary Synthesis, University of Oslo, Oslo 0371, Norway
- Department of Anthropology, University of British Columbia, Vancouver 6303, Canada
| | - Oliver Kersten
- Centre for Ecology and Evolutionary Synthesis, University of Oslo, Oslo 0371, Norway
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna 48123, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna 48121, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna 48123, Italy
| |
Collapse
|
2
|
Miga M, Awg Abdul Rahman A, Parimannan S, Rajandas H, Sitam FT, Tokiman L, Kemalok J, Shamsir MS, Mohd Salleh F. Complete mitochondrial genome data and phylogenetic analysis of the Plain Banded Awl, Hasora vitta (Lepidoptera: Hesperiidae: Coeliadinae) from Malaysia. Mitochondrial DNA B Resour 2025; 10:528-531. [PMID: 40433468 PMCID: PMC12107662 DOI: 10.1080/23802359.2025.2509807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 05/19/2025] [Indexed: 05/29/2025] Open
Abstract
We report the complete mitogenome of Hasora vitta (Plain Banded Awl) sampled from Malaysia. The mitogenome is 15,289 bp long, comprising of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region. All PCGs were initiated by the typical ATN codon, except for COX1 with a CGA start codon. Two PCGs (COX1 and COX2) were terminated with an incomplete stop codon T. Phylogenetic analysis highly supported the placement of Hasora vitta from Malaysia within Coeliadinae and is clustered with two Hasora vitta samples from China.
Collapse
Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Aqilah Awg Abdul Rahman
- Department of Technology and Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Malaysia
- Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Sivachandran Parimannan
- Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia
| | - Heera Rajandas
- Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia
| | - Frankie Thomas Sitam
- Department of Wildlife and National Parks (PERHILITAN), National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Kuala Lumpur, Malaysia
| | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, Iskandar Puteri, Malaysia
| | - Jai Kemalok
- Department of Technology and Natural Resources, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Muar, Malaysia
- Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
- Investigative and Forensic Sciences Research Group, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| |
Collapse
|
3
|
Grasso G, Debruyne R, Adamo M, Rué O, Lejzerowicz F, Bittner L, Bianciotto V, Marmeisse R. Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil. Mol Ecol Resour 2025:e14122. [PMID: 40411280 DOI: 10.1111/1755-0998.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 02/27/2025] [Accepted: 04/30/2025] [Indexed: 05/26/2025]
Abstract
Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century-old soils occasionally found on the roots of herbarium plants to assess the diversity of ancient soil microbial communities originally associated with these plants. We extracted total DNA and sequenced libraries produced from rhizospheric soils and roots of four plants preserved in herbaria for more than 120 years in order to characterise the preservation and taxonomic diversity that can be recovered in such contexts. Extracted DNA displayed typical features of ancient DNA, with cytosine deamination at the ends of fragments predominantly shorter than 50 bp. When compared to extant microbiomes, herbarium microbial communities clustered with soil communities and were distinct from communities from other environments. Herbarium communities also displayed biodiversity features and assembly rules typical of soil and plant-associated ones. Soil communities were richer than root-associated ones with which they shared most taxa. Regarding community turnover, we detected collection site, soil versus root and plant species effects. Eukaryotic taxa that displayed a higher abundance in roots were mostly plant pathogens that were not identified among soil-enriched ones. Conservation of these biodiversity features and assembly rules in herbarium-associated microbial communities indicates that herbarium-extracted DNA might reflect the composition of the original plant-associated microbial communities and that preservation in herbaria seemingly did not dramatically alter these characteristics. Using this approach, it should be possible to investigate historical soils and herbarium plant roots to explore the diversity and temporal dynamics of soil microbial communities.
Collapse
Affiliation(s)
- Gianluca Grasso
- Department of Life Science and Systems Biology (DBIOS), Università Degli Studi di Torino, Torino, Italy
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National D'histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université Des Antilles, Paris, France
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Torino, Italy
| | - Régis Debruyne
- Bioarchéologie, Interactions Sociétés Environnements (BioArch: UMR 7209 CNRS-MNHN), Muséum National d'Histoire Naturelle, Paris, France
| | - Martino Adamo
- Department of Life Science and Systems Biology (DBIOS), Università Degli Studi di Torino, Torino, Italy
| | - Olivier Rué
- MaIAGE, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
- BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Franck Lejzerowicz
- Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National D'histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université Des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Torino, Italy
| | - Roland Marmeisse
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National D'histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université Des Antilles, Paris, France
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Torino, Italy
| |
Collapse
|
4
|
Bro‐Jørgensen MH, Ahlgren H, Glykou A, Ruiz‐Puerta EJ, Lõugas L, Gotfredsen AB, Olsen MT, Lidén K. The Evolutionary History of the Extinct Baltic Sea Harp Seal Population. Ecol Evol 2025; 15:e71322. [PMID: 40352621 PMCID: PMC12061552 DOI: 10.1002/ece3.71322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 04/01/2025] [Accepted: 04/07/2025] [Indexed: 05/14/2025] Open
Abstract
The now-extinct harp seal population that inhabited the Baltic Sea from the Mesolithic to the Iron Age is an enigma. It occurred outside the species' contemporary Arctic range, likely deviated from typical harp seal migratory behaviour, and experienced body size reductions and dramatic population fluctuations leading up to its extinction. Here we use ancient DNA analyses to shed more light on the evolutionary history of the Baltic Sea harp seal population, including its origin, timing of colonisation, diversity and factors contributing to its demise. We generated 49 ancient Baltic and eight ancient Arctic harp seal mitogenomes, which we analysed together with 53 contemporary Arctic harp seal mitogenomes. We detected limited phylogeographic resolution among ancient and contemporary populations, which we interpret as a late Pleistocene range expansion from a common refugial population with subsequent gene flow. Ancient Baltic harp seals were significantly genetically differentiated from contemporary harp seal populations and retained their own genetic composition throughout time. The genetic diversity of Baltic harp seals decreased over time, yet was comparable to that of contemporary populations. This suggests that Baltic harp seals formed a distinct breeding population, which may occasionally have received immigrants from the Arctic but was itself confined in the Baltic Sea until the end. We hypothesise that loss of genetic diversity and the ultimate extinction of the Baltic harp seal population was a consequence of population fluctuations caused by climatic change, reduced salinity and biological productivity, and periodic intense human harvest.
Collapse
Affiliation(s)
- Maiken Hemme Bro‐Jørgensen
- Archaeological Research Laboratory, Department of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
- Section for Molecular Ecology and Evolution, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Hans Ahlgren
- Archaeological Research Laboratory, Department of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Aikaterini Glykou
- Archaeological Research Laboratory, Department of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Emily J. Ruiz‐Puerta
- Section for Molecular Ecology and Evolution, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
- Arctic Centre/Groningen Institute of Archaeology, Faculty of ArtsUniversity of GroningenGroningenthe Netherlands
| | - Lembi Lõugas
- Archaeological Research CollectionTallinn UniversityTallinnEstonia
| | | | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Kerstin Lidén
- Archaeological Research Laboratory, Department of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| |
Collapse
|
5
|
Silver LW, Farquharson KA, Peel E, Gilbert MTP, Belov K, Morales HE, Hogg CJ. Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot. Mol Ecol 2025; 34:e17746. [PMID: 40130423 PMCID: PMC12010471 DOI: 10.1111/mec.17746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 02/14/2025] [Accepted: 03/13/2025] [Indexed: 03/26/2025]
Abstract
Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.
Collapse
Affiliation(s)
- Luke W. Silver
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - Katherine A. Farquharson
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - Emma Peel
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - M. Thomas P. Gilbert
- Centre for Evolutionary Hologenomics, The GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- University Museum, NTNUTrondheimNorway
| | - Katherine Belov
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| | - Hernán E. Morales
- Centre for Evolutionary Hologenomics, The GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
- Department of BiologyLund UniversityLundSweden
| | - Carolyn J. Hogg
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceSydneyNew South WalesAustralia
| |
Collapse
|
6
|
Garcia-Erill G, Liu S, Le MD, Hurley MM, Nguyen HD, Nguyen DQ, Nguyen DH, Santander CG, Sánchez Barreiro F, Gomes Martins NF, Hanghøj K, Salleh FM, Ramos-Madrigal J, Wang X, Sinding MHS, Morales HE, Stæger FF, Wilkinson N, Meng G, Pečnerová P, Yang C, Rasmussen MS, Schubert M, Dunn RR, Moltke I, Zhang G, Chen L, Wang W, Cao TT, Nguyen HM, Siegismund HR, Albrechtsen A, Gilbert MTP, Heller R. Genomes of critically endangered saola are shaped by population structure and purging. Cell 2025:S0092-8674(25)00390-3. [PMID: 40328258 DOI: 10.1016/j.cell.2025.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 12/20/2024] [Accepted: 03/25/2025] [Indexed: 05/08/2025]
Abstract
The saola is one of the most elusive large mammals, standing at the brink of extinction. We constructed a reference genome and resequenced 26 saola individuals, confirming the saola as a basal member of the Bovini. Despite its small geographic range, we found that the saola is partitioned into two populations with high genetic differentiation (FST = 0.49). We estimate that these populations diverged and started declining 5,000-20,000 years ago, possibly due to climate changes and exacerbated by increasing human activities. The saola has long tracts without genomic diversity; however, most of these tracts are not shared by the two populations. Saolas carry a high genetic load, yet their gradual decline resulted in the purging of the most deleterious genetic variation. Finally, we find that combining the two populations, e.g., in an eventual captive breeding program, would mitigate the genetic load and increase the odds of species survival.
Collapse
Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Copenhagen, Denmark; Bioinformatics Research Centre, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Shanlin Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Minh Duc Le
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, 334 Nguyen Trai Road, Hanoi, Vietnam; Vietnam and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, 19 Le Thanh Tong, Hanoi, Vietnam
| | - Martha M Hurley
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, USA
| | - Hung Dinh Nguyen
- Forest Inventory and Planning Institute, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Dzung Quoc Nguyen
- Forest Inventory and Planning Institute, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Dzung Huy Nguyen
- Forest Inventory and Planning Institute, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Globe Institute, University of Copenhagen, Copenhagen, Denmark; Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | | | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Guanliang Meng
- Zoological Research Museum Alexander Koenig, LIB, Bonn, Germany
| | | | | | | | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guojie Zhang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark; Center of Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lei Chen
- Center for Ecological and Environmental Science, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wen Wang
- Center for Ecological and Environmental Science, Northwestern Polytechnical University, Xi'an 710072, China
| | - Trung Tien Cao
- Institute of Biology, Chemistry and Environment, Vinh University, Vinh, Vietnam
| | - Ha Manh Nguyen
- Center for Nature Conservation and Development, No. 05, 56/119 Tu Lien Street, Hanoi, Vietnam
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
7
|
More KD, Lebrasseur O, Garrido JL, Seguin-Orlando A, Discamps E, Estrada O, Tonasso-Calvière L, Chauvey L, Tressières G, Schiavinato S, Gibert M, Padula H, Chiavazza H, Fernández PM, Guardia NM, Borges C, Bertani S, Contreras-Mancilla J, Allccarima-Crisóstomo D, Fhon M, Barrey E, Charliquart L, Robbe E, de Noblet T, Zhumatayev R, Shakenov S, Vila E, Berthon R, Mashkour M, Khazaeli R, Nikgoftar A, Vahdati AA, Kosintsev P, Houle JL, Bayarsaikhan J, Wilczynski J, Moskal-Del Hoyo M, Nowak M, Taylor W, Bălășescu A, Dobrescu R, Benecke N, Arbuckle B, Steadman S, McMahon G, Šikanjić PR, Buric M, Vukičević TT, Alvarez N, Castel JC, Boudadi-Maligne M, Star B, Post-Melbye JR, Rødsrud CL, Stanton DWG, Charlton S, Mullin VE, Daly KG, Burgos NS, Pablos A, Dalen L, Bradley DG, Frantz L, Larson G, Orlando L. Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals. Mol Ecol Resour 2025:e14112. [PMID: 40202701 DOI: 10.1111/1755-0998.14112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Accepted: 03/20/2025] [Indexed: 04/10/2025]
Abstract
In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.
Collapse
Affiliation(s)
- Kuldeep D More
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Jaime Lira Garrido
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Emmanuel Discamps
- TRACES UMR 5608, CNRS-Université de Toulouse-Jean Jaurès, Toulouse, France
| | - Oscar Estrada
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Laure Tonasso-Calvière
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Loreleï Chauvey
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Gaëtan Tressières
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Stéphanie Schiavinato
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Morgane Gibert
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| | - Horacio Padula
- Centro de Interpretaciòn de Arqueologìa y Paleontologìa 'Mario Silveira', Dirección General de Patrimonio, Museos y Casco Històrico, Buenos Aires, Argentina
| | - Horacio Chiavazza
- Instituto de Arqueología y Etnología, Facultad de Filosofía y Letras, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Pablo M Fernández
- National Institute of Anthropology and Latin American Thought (INAPL), Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Nicolás M Guardia
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Arqueología y Etnología, Facultad de Filosofía y Letras, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Caroline Borges
- Universidade Federal Rural de Pernambuco Recife, Recife, PE, Brazil
| | - Stéphane Bertani
- UMR 152 PHARMADEV, IRD, UPS, Université de Toulouse, Toulouse Cedex 9, France
- International Joint Laboratory of Molecular Anthropological Oncology (LOAM), National Cancer Institute (INEN), Lima, Peru
| | - Juan Contreras-Mancilla
- UMR 152 PHARMADEV, IRD, UPS, Université de Toulouse, Toulouse Cedex 9, France
- International Joint Laboratory of Molecular Anthropological Oncology (LOAM), National Cancer Institute (INEN), Lima, Peru
| | | | | | - Eric Barrey
- Université Paris-Saclay, INRAE, AgroParisTech, Paris, France
| | | | - Emilie Robbe
- Musée de l'Armée, Hôtel Des Invalides, Paris, France
| | | | - Rinat Zhumatayev
- Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Samat Shakenov
- Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | | | - Rémi Berthon
- Centre National de Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique (AASPE), Paris, CP, France
| | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique (AASPE), Paris, CP, France
| | - Roya Khazaeli
- Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, University of Tehran, Tehran, Iran
| | - Ahmad Nikgoftar
- Ministry of Cultural Heritage, Tourism and Handicrafts, Shahr-e Belqays National Research Base, Esfarayen, Iran
| | - Ali A Vahdati
- Ministry of Cultural Heritage, Tourism and Handicrafts, North Khorasan Office, Bojnord, Iran
| | - Pavel Kosintsev
- Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - Jean-Luc Houle
- Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, Kentucky, USA
| | - Jamsranjav Bayarsaikhan
- Max Planck Institute of Geoanthropology, Jena, Germany
- Institute of Archaeology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | - Jaroslaw Wilczynski
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | | | - Marek Nowak
- Institute of Archeology, Jagiellonian University, Kraków, Poland
| | - William Taylor
- Museum of Natural History, University of Colorado-Boulder, Boulder, Colorado, USA
| | | | | | - Norbert Benecke
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Benjamin Arbuckle
- Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon Steadman
- Department of Sociology/Anthropology, College at Cortland, State University of New York, New York, New York, USA
| | - Gregory McMahon
- Classics, Humanities and Italian Studies Department, University of new Hampshire, Durham, New Hampshire, USA
| | | | - Marcel Buric
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Nadir Alvarez
- Geneva Natural History Museum, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Myriam Boudadi-Maligne
- UMR 5199 De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | - David W G Stanton
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - Sophy Charlton
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Kevin G Daly
- School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Nohemi Sala Burgos
- Centro Nacional de Investigación Sobre Evolución Humana (CENIEH), Burgos, Spain
- Centro Mixto UCM-ISCIII de Investigaciòn Sobre Evoluciòn y Comportamiento Humanos, Madrid, Spain
| | - Adrian Pablos
- Centro Nacional de Investigación Sobre Evolución Humana (CENIEH), Burgos, Spain
- Departamento de Geodinamica, Estratigrafía y Paleontología, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Prehistoria y Arqueología, Universidad de Sevilla, Sevilla, Spain
| | - Love Dalen
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CNRS UMR5288/Université de Toulouse), Toulouse, France
| |
Collapse
|
8
|
De Cahsan B, Sandoval Velasco M, Westbury MV, Duchêne DA, Strander Sinding MH, Morales HE, Kalthoff DC, Barnes I, Brace S, Portela Miguez R, Roca AL, Greenwood AD, Johnson RN, Lott MJ, Gilbert MTP. Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala. Mol Biol Evol 2025; 42:msaf057. [PMID: 40129172 PMCID: PMC12014528 DOI: 10.1093/molbev/msaf057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 01/28/2025] [Accepted: 02/24/2025] [Indexed: 03/26/2025] Open
Abstract
Koalas are arboreal herbivorous marsupials, endemic to Australia. During the late 1800s and early 1900s, the number of koalas declined dramatically due to hunting for their furs. In addition, anthropogenic activities have further decimated their available habitat, and decreased population numbers. Here, we utilize 37 historic and 25 modern genomes sampled from across their historic and present geographic range, to gain insights into how their population structure and genetic diversity have changed across time; assess the genetic consequences of the period of intense hunting, and the current genetic status of this iconic Australian species. Our analyses reveal how genome-wide heterozygosity has decreased through time and unveil previously uncharacterized mitochondrial haplotypes and nuclear genotypes in the historic dataset, which are absent from today's koala populations.
Collapse
Affiliation(s)
- Binia De Cahsan
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Marcela Sandoval Velasco
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
- Center for Genome Sciences (CCG), National Autonomous University of Mexico (UNAM), Cuernavaca, Mexico
| | | | - David A Duchêne
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | | | - Hernán E Morales
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, England, UK
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, England, UK
| | | | - Alfred L Roca
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Rebecca N Johnson
- Smithsonian National Museum of Natural History, Washington, D.C. 20560, USA
| | - Matthew J Lott
- Australian Centre for Wildlife Genomics, Australian Museum, Sydney, NSW 2010, Australia
| | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
- Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
| |
Collapse
|
9
|
Eriksen EF, Andrews AJ, Nielsen SV, Persson P, Malca E, Onar V, Aniceti V, Piquès G, Piattoni F, Fontani F, Wiech M, Ferter K, Kersten O, Ferrari G, Cariani A, Tinti F, Cilli E, Atmore LM, Star B. Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA. Heredity (Edinb) 2025; 134:175-185. [PMID: 39920258 PMCID: PMC11977281 DOI: 10.1038/s41437-025-00745-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 01/21/2025] [Accepted: 01/22/2025] [Indexed: 02/09/2025] Open
Abstract
Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.
Collapse
Affiliation(s)
- Emma Falkeid Eriksen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo, Oslo, Norway.
| | - Adam Jon Andrews
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo, Oslo, Norway
- Norwegian Institute of Water Research, Oslo, Norway
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | | | - Per Persson
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Estrella Malca
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, FL, USA
- NOAA Fisheries, Southeast Fisheries Science Center, Miami, FL, USA
| | - Vedat Onar
- Milas Faculty of Veterinary Medicine, Muğla Sıtkı Kocman University, Muğla, Türkiye
| | - Veronica Aniceti
- Consejo Superior de Investigaciones Científicas, Institució Milà i Fontanals (CSIC-IMF), Barcelona, Spain
| | - Gäel Piquès
- ASM, CNRS, Université Paul Valéry-Montpellier 3, Montpellier, France
| | - Federica Piattoni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Martin Wiech
- Institute of Marine Research, PO Box 1870, N-5817, Bergen, Norway
| | - Keno Ferter
- Institute of Marine Research, PO Box 1870, N-5817, Bergen, Norway
| | - Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo, Oslo, Norway
| | - Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo, Oslo, Norway
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences (IBV), University of Oslo, Oslo, Norway.
| |
Collapse
|
10
|
Jensen EL, Marchisio C, Ochoa A, Gray R, Parra V, Miller JM, Çilingir FG, Caccone A. Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity. Ecol Evol 2025; 15:e71358. [PMID: 40290375 PMCID: PMC12032190 DOI: 10.1002/ece3.71358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 03/26/2025] [Accepted: 04/15/2025] [Indexed: 04/30/2025] Open
Abstract
The utility and importance of whole-genome sequences are recognized across various fields, including evolution and conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high-quality DNA is impossible. In such cases, an alternative may be to employ synteny-based methods using a genome from a closely related taxon to generate more complete genomes. Here we update the reference genome for the Pinta Island Galapagos giant tortoise (Chelonoidis abingdonii) without conducting additional sequencing through rescaffolding against the most closely related chromosome-level genome assembly, the Aldabra giant tortoise (Aldabrachelys gigantea). This effort resulted in a much more contiguous genome, CheloAbing_2.0, with an N50 that is two orders of magnitude longer and large reductions in L50 and the number of gaps. We then examined the impact of the CheloAbing_2.0 genome on estimates of runs of homozygosity (ROH) using genome resequencing data from 37 individual Galapagos giant tortoises from the 13 extant lineages to test the mechanisms by which a fragmented assembly may over- or underestimate the number and extent of ROH. The use of CheloAbing_2.0 resulted in individual estimates of inbreeding, including ROH proportion (FROH), number (NROH), and cumulative length (SROH), that were statistically different from those derived from the earlier genome assembly. This improved genome will serve as a resource for future efforts focusing on the ecology, evolution, and conservation of this species group. More broadly, our results highlight that synteny-based scaffolding is promising for generating contiguous genomes without needing additional data types.
Collapse
Affiliation(s)
- Evelyn L. Jensen
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastleUpon TyneUK
| | - Chiara Marchisio
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastleUpon TyneUK
- Faculty of Health and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Alexander Ochoa
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
| | - Rachel Gray
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastleUpon TyneUK
| | - Vanessa Parra
- Biology DepartmentUniversity of KentuckyLexingtonKentuckyUSA
| | - Joshua M. Miller
- Department of Biological SciencesMacEwan UniversityEdmontonCanada
| | - F. Gözde Çilingir
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Swiss Federal Institute for Research WSLBirmensdorfSwitzerland
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticutUSA
| |
Collapse
|
11
|
Kirkland C, Wang X, Canedo-Ribeiro C, Álvarez-González L, Weisz D, Mena A, St Leger J, Dudchenko O, Aiden EL, Ruiz-Herrera A, Heller R, King T, Farré M. Chromosome-level genomics and historical museum collections reveal new insights into the population structure and chromosome evolution of waterbuck. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.19.644014. [PMID: 40166267 PMCID: PMC11956998 DOI: 10.1101/2025.03.19.644014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Advances in the sequencing and assembly of chromosome-level genome assemblies has enabled the study of non-model animals, providing further insights into the evolution of genomes and chromosomes. Here, we present the waterbuck ( Kobus ellipsiprymnus ) as an emerging model antelope for studying population dynamics and chromosome evolution. Antelope evolutionary history has been shaped by Robertsonian (Rb) fusions, with waterbuck also showing variation in karyotype due to two polymorphic Rb fusions. These polymorphisms are variable between and within the two recognised subspecies, the common and defassa waterbuck. To provide new insights into waterbuck evolution, we firstly assembled a chromosome-level genome assembly for the defassa subspecies using PacBio HiFi and Hi-C sequencing. We then utilised museum collections to carry out whole genome sequencing (WGS) of 24 historical waterbuck skins from both subspecies. Combined with a previous WGS dataset (n = 119), this represents the largest study of waterbuck populations to date. We found novel population structure and gene flow between waterbuck populations and regions across the genome with high genomic differentiation between the two subspecies. Several of these regions were found around the centromeres of fixed and polymorphic Rb fusions, exhibiting signatures of low recombination and local population structure. Interestingly, these regions contain genes involved in development, fertility, and recombination. Our results highlight the importance of assembling genomes to the chromosome-level, the utility and value of historical collections in sampling a wide-ranging species to uncover fine-scale population structure, and the potential impacts of Rb fusions on genomic differentiation and the recombination landscape.
Collapse
|
12
|
Lobo D, Morales HE, Van Oosterhout C, López-Bao JV, Silva P, Llaneza L, Pacheco C, Castro D, Hernández-Alonso G, Pacheco G, Archer J, Gilbert MTP, Ferrand N, Godinho R. Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes. Genome Res 2025; 35:432-445. [PMID: 39952679 PMCID: PMC11960463 DOI: 10.1101/gr.279093.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 02/06/2025] [Indexed: 02/17/2025]
Abstract
Understanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf (Canis lupus signatus), a gray wolf subspecies endemic to the Iberian Peninsula (Portugal and Spain), has uniquely persisted in human-dominated landscapes, unlike many other wolf populations that faced widespread extinction across Europe during the twentieth century. In this study, we conducted a comprehensive genome-wide analysis of 145 historical and contemporary Iberian wolf samples to investigate whether hybridization with domestic dogs resulted in genetic introgression. We identified a dog-derived block on Chromosome 2 in Iberian wolves, displaying signatures consistent with introgression and high nucleotide similarity among introgressed individuals. Additionally, our estimates place the average timing of introgression between 6100 and 3000 years ago, with low sequence divergence to dogs from the Iberian Peninsula suggesting a single local origin for the hybridization event. Using forward genetic simulations, we show that the introgressed haplotype is most likely being maintained in Iberian wolves by selection. The introgressed dog variants are located within the MAST4 gene, which has been linked to neurological disorders, including cognitive and motor developmental delays, hinting at a potential role in cognitive behavior in Iberian wolves. This study uncovers a case of putative adaptive introgression from domestic dogs into wolves, offering new insights into wild canids' adaptation to human-dominated landscapes.
Collapse
Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Cock Van Oosterhout
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, NR4 7TJ Norwich, United Kingdom
| | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias) Oviedo University, E-33600 Mieres, Spain
| | - Pedro Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Luis Llaneza
- A.RE.NA, Asesores en Recursos Naturales, 27003 Lugo, Spain
| | - Carolina Pacheco
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Diana Castro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Germán Hernández-Alonso
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - George Pacheco
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - John Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, 7012 Trondheim, Norway
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, 2006 South Africa
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal;
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, 2006 South Africa
| |
Collapse
|
13
|
Liu S, Gao Y, Long X, Li K, Gutang Q, Xie H, Wang J, Tian J, Liang B, Lin J, Liu W. A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long-Distance-Migratory Marine Fish Scomberomorus niphonius. Mol Ecol Resour 2025:e14103. [PMID: 40084530 DOI: 10.1111/1755-0998.14103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 02/22/2025] [Accepted: 03/05/2025] [Indexed: 03/16/2025]
Abstract
Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not easy for marine fish, especially those with long-distance migration abilities. In this study, we constructed a high-quality reference genome for Japanese Spanish mackerel (Scomberomorus niphonius) and explored its population structure using whole genomic and epigenomic data. Despite the high depth of the sequence data, we failed to identify geographical genetic differentiation of Japanese Spanish mackerel across Chinese coastal waters. However, whole-genome bisulphite sequencing can classify this species into the Bohai-Yellow Sea group and the East China Sea-South China Sea group. Genes involved in embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations and may play important roles as drivers of population structure in Japanese Spanish mackerel. Our study not only provides the first reference genome of the Japanese Spanish mackerel and sheds light on population differentiation at the epigenomic level, but also provides a methylome-based framework for population structure analyses of marine fish with long-distance migration ability. These findings are expected to facilitate the development of scientific programmes for the successful conservation of marine fishery resources.
Collapse
Affiliation(s)
- Sailan Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Yan Gao
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Xinrui Long
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Kunhuan Li
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Qilin Gutang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Huiying Xie
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Jingzhen Wang
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou, China
| | - Jiashen Tian
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Bo Liang
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Jianqing Lin
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
| |
Collapse
|
14
|
Wilson J, Bieker VC, van Boheemen L, Connallon T, Martin MD, Battlay P, Hodgins KA. Copy number variation contributes to parallel local adaptation in an invasive plant. Proc Natl Acad Sci U S A 2025; 122:e2413587122. [PMID: 40030023 PMCID: PMC11912486 DOI: 10.1073/pnas.2413587122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 12/31/2024] [Indexed: 03/19/2025] Open
Abstract
Adaptation is a critical determinant of the diversification, persistence, and geographic range limits of species. Yet the genetic basis of adaptation is often unknown and potentially underpinned by a wide range of mutational types-from single nucleotide changes to large-scale alterations of chromosome structure. Copy number variation (CNV) is thought to be an important source of adaptive genetic variation, as indicated by decades of candidate gene studies that point to CNVs underlying rapid adaptation to strong selective pressures. Nevertheless, population-genomic studies of CNVs face unique logistical challenges not encountered by other forms of genetic variation. Consequently, few studies have systematically investigated the contributions of CNVs to adaptation at a genome-wide scale. We present a genome-wide analysis of CNV contributing to the adaptation of an invasive weed, Ambrosia artemisiifolia. CNVs show clear signatures of parallel local adaptation between North American (native) and European (invaded) ranges, implying widespread reuse of CNVs during adaptation to shared heterogeneous patterns of selection. We used a local principal component analysis (PCA) to genotype CNV regions in whole-genome sequences of samples collected over the last two centuries. We identified 16 large CNV regions of up to 11.85 megabases in length, eight of which show signals of rapid evolutionary change, with pronounced frequency shifts between historic and modern populations. Our results provide compelling genome-wide evidence that CNV underlies rapid adaptation over contemporary timescales of natural populations.
Collapse
Affiliation(s)
- Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, VIC3800, Australia
| | - Vanessa C. Bieker
- Department of Natural History, Norwegian University of Science and Technology University Museum, Norwegian University of Science and Technology, Trondheim7012, Norway
| | - Lotte van Boheemen
- School of Biological Sciences, Monash University, Melbourne, VIC3800, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, VIC3800, Australia
| | - Michael D. Martin
- Department of Natural History, Norwegian University of Science and Technology University Museum, Norwegian University of Science and Technology, Trondheim7012, Norway
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, VIC3800, Australia
| | - Kathryn A. Hodgins
- School of Biological Sciences, Monash University, Melbourne, VIC3800, Australia
| |
Collapse
|
15
|
Liu X, Milesi E, Fontsere C, Owens HL, Heinsohn R, Gilbert MTP, Crates R, Nogués-Bravo D, Morales HE. Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction. Proc Biol Sci 2025; 292:20242480. [PMID: 40132633 PMCID: PMC11936686 DOI: 10.1098/rspb.2024.2480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 01/30/2025] [Accepted: 03/04/2025] [Indexed: 03/27/2025] Open
Abstract
Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.
Collapse
Affiliation(s)
- Xufen Liu
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ester Milesi
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Hannah L. Owens
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Informatics Department, University of Florida, Gainesville, FL, USA
| | - Robert Heinsohn
- Fenner School of Environment and Society, Australian National University, Canberra, Australia
| | - M. Thomas P. Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Trøndelag, Norway
| | - Ross Crates
- Fenner School of Environment and Society, Australian National University, Canberra, Australia
| | | | - Hernán E. Morales
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
16
|
Battlay P, Craig S, Putra AR, Monro K, De Silva NP, Wilson J, Bieker VC, Kabir S, Shamaya N, van Boheemen L, Rieseberg LH, Stinchcombe JR, Fournier-Level A, Martin MD, Hodgins KA. Rapid Parallel Adaptation in Distinct Invasions of Ambrosia Artemisiifolia Is Driven by Large-Effect Structural Variants. Mol Biol Evol 2025; 42:msae270. [PMID: 39812008 PMCID: PMC11733498 DOI: 10.1093/molbev/msae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 11/21/2024] [Accepted: 12/17/2024] [Indexed: 01/16/2025] Open
Abstract
When introduced to multiple distinct ranges, invasive species provide a compelling natural experiment for understanding the repeatability of adaptation. Ambrosia artemisiifolia is an invasive, noxious weed, and chief cause of hay fever. Leveraging over 400 whole-genome sequences spanning the native-range in North America and 2 invasions in Europe and Australia, we inferred demographically distinct invasion histories on each continent. Despite substantial differences in genetic source and effective population size changes during introduction, scans of both local climate adaptation and divergence from the native-range revealed genomic signatures of parallel adaptation between invasions. Disproportionately represented among these parallel signatures are 37 large haploblocks-indicators of structural variation-that cover almost 20% of the genome and exist as standing genetic variation in the native-range. Many of these haploblocks are associated with traits important for adaptation to local climate, like size and the timing of flowering, and have rapidly reformed native-range clines in invaded ranges. Others show extreme frequency divergence between ranges, consistent with a response to divergent selection on different continents. Our results demonstrate the key role of large-effect standing variants in rapid adaptation during range expansion, a pattern that is robust to diverse invasion histories.
Collapse
Affiliation(s)
- Paul Battlay
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Samuel Craig
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Andhika R Putra
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Nissanka P De Silva
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Saila Kabir
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Nawar Shamaya
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Lotte van Boheemen
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada
| | | | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
17
|
Battilani D, Gargiulo R, Caniglia R, Fabbri E, Madrigal JR, Fontsere C, Ciucani MM, Gopalakrishnan S, Girardi M, Fracasso I, Mastroiaco M, Ciucci P, Vernesi C. Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf. J Hered 2025; 116:10-23. [PMID: 39189963 DOI: 10.1093/jhered/esae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/15/2024] [Indexed: 08/28/2024] Open
Abstract
Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of 13 individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e. Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.
Collapse
Affiliation(s)
- Daniele Battilani
- Department of Biology and Biotechnologies "Charles Darwin", Università di Roma La Sapienza, Roma, Italy
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Roberta Gargiulo
- Ecosystem Stewardship, Royal Botanical Gardens, Kew, United Kingdom
| | - Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Jazmín Ramos- Madrigal
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marta Maria Ciucani
- 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
| | - Matteo Girardi
- Research and Innovation Centre-Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Ilaria Fracasso
- Research and Innovation Centre-Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Matteo Mastroiaco
- Department of Biology and Biotechnologies "Charles Darwin", Università di Roma La Sapienza, Roma, Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnologies "Charles Darwin", Università di Roma La Sapienza, Roma, Italy
| | - Cristiano Vernesi
- Research and Innovation Centre-Fondazione Edmund Mach, S. Michele all'Adige, Italy
| |
Collapse
|
18
|
Bon C. [Paleoepigenetics: when DNA damages become epigenetic traces]. Med Sci (Paris) 2024; 40:965-970. [PMID: 39705568 DOI: 10.1051/medsci/2024171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2024] Open
Affiliation(s)
- Céline Bon
- UMR7206 Éco-Anthropologie (EA), CNRS, Muséum national d'Histoire naturelle, Université Paris-Cité, Paris, France
| |
Collapse
|
19
|
Atmore LM, van der Jagt I, Boilard A, Häberle S, Blevis R, Dierickx K, Quinlan LM, Orton DC, Hufthammer AK, Barrett JH, Star B. The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA. GLOBAL CHANGE BIOLOGY 2024; 30:e70010. [PMID: 39723543 DOI: 10.1111/gcb.70010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 11/22/2024] [Accepted: 12/09/2024] [Indexed: 12/28/2024]
Abstract
Small pelagic fish support profitable fisheries and are important for food security around the world. Yet, their sustainable management can be hindered by the indiscriminate impacts of simultaneous exploitation of fish from multiple distinct biological populations over extended periods of time. The quantification of such impacts is greatly facilitated by recently developed molecular tools-including diagnostic single nucleotide polymorphism (SNP) panels for mixed-stock analysis (MSA)-that can accurately detect the population identity of individual fish. However, the biological relevance of such tools over longer periods of time remains unknown. Here, we demonstrate that diagnostic SNP panels designed for contemporary MSA in Atlantic herring have a millennium-long biological relevance and applicability. We assign the population identity of ancient Atlantic herring specimens-obtained through famously profitable historic fisheries-up to 1300 years old from eight archaeological sites across Europe. Analyzing contemporary and ancient whole-genome data, we obtain evidence for the long-term mixed-stock exploitation of Atlantic herring. Despite such mixed-stock exploitation, we exclusively identify autumn-spawning herring amongst these archaeological remains, indicative of a specific biological availability or cultural preference for certain herring ecotypes in the past. Moreover, our results show that herring demographic patterns were relatively stable until the dramatic disruptions and stock collapses during the 20th century. We find small but significant reductions in genetic diversity over time, indicating long-term evolutionary consequences from 20th-century stock declines. The long-term applicability of diagnostic SNP panels underscores their biological relevance and cost-effective application for the genetic monitoring of herring stocks and highlights the utility of ancient DNA to obtain insights in herring ecology and population dynamics.
Collapse
Affiliation(s)
- Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Institute of Biosciences, University of Oslo, Oslo, Norway
- Department of Anthropology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Inge van der Jagt
- Cultural Heritage Agency of the Netherlands, Amersfoort, The Netherlands
| | - Aurélie Boilard
- Centre for Ecological and Evolutionary Synthesis, Institute of Biosciences, University of Oslo, Oslo, Norway
| | - Simone Häberle
- Integrative Prehistory and Archaeological Science, Department of Environmental Sciences, Basel University, Basel, Switzerland
| | - Rachel Blevis
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Katrien Dierickx
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Archaeology, University of York, York, UK
| | - Liz M Quinlan
- Department of Archaeology, University of York, York, UK
| | - David C Orton
- Department of Archaeology, University of York, York, UK
| | | | - James H Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Institute of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
20
|
Wang X, Pedersen CET, Athanasiadis G, Garcia-Erill G, Hanghøj K, Bertola LD, Rasmussen MS, Schubert M, Liu X, Li Z, Lin L, Balboa RF, Jørsboe E, Nursyifa C, Liu S, Muwanika V, Masembe C, Chen L, Wang W, Moltke I, Siegismund HR, Albrechtsen A, Heller R. Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model. Syst Biol 2024; 73:979-994. [PMID: 39140829 PMCID: PMC11637686 DOI: 10.1093/sysbio/syae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 03/22/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024] Open
Abstract
African antelope diversity is a globally unique vestige of a much richer world-wide Pleistocene megafauna. Despite this, the evolutionary processes leading to the prolific radiation of African antelopes are not well understood. Here, we sequenced 145 whole genomes from both subspecies of the waterbuck (Kobus ellipsiprymnus), an African antelope believed to be in the process of speciation. We investigated genetic structure and population divergence and found evidence of a mid-Pleistocene separation on either side of the eastern Great Rift Valley, consistent with vicariance caused by a rain shadow along the so-called "Kingdon's Line." However, we also found pervasive evidence of both recent and widespread historical gene flow across the Rift Valley barrier. By inferring the genome-wide landscape of variation among subspecies, we found 14 genomic regions of elevated differentiation, including a locus that may be related to each subspecies' distinctive coat pigmentation pattern. We investigated these regions as candidate speciation islands. However, we observed no significant reduction in gene flow in these regions, nor any indications of selection against hybrids. Altogether, these results suggest a pattern whereby climatically driven vicariance is the most important process driving the African antelope radiation and suggest that reproductive isolation may not set in until very late in the divergence process. This has a significant impact on taxonomic inference, as many taxa will be in a gray area of ambiguous systematic status, possibly explaining why it has been hard to achieve consensus regarding the species status of many African antelopes. Our analyses demonstrate how population genetics based on low-depth whole genome sequencing can provide new insights that can help resolve how far lineages have gone along the path to speciation.
Collapse
Affiliation(s)
- Xi Wang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Casper-Emil Tingskov Pedersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820, Gentofte, Denmark
| | - Georgios Athanasiadis
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Av. Diagonal, 643, Les Corts, 08028, Barcelona,Spain
| | - Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Malthe Sebro Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Emil Jørsboe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, 2200, Copenhagen, Denmark
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, OX3 7LF, Regne Unit, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Old Road Campus, Headington, OX3 7LF, Regne Unit, Oxford, UK
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, 2934+RXP, Haidian District, 100193, Beijing, China
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, Wandegeya, Makerere, PO Box 7062, Kampala, Uganda
| | - Charles Masembe
- Department of Biology, Makerere University, Wandegeya, Makerere, PO Box 7062, Kampala, Uganda
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| |
Collapse
|
21
|
Zhur KV, Sharko FS, Leonova MV, Mey A, Prokhortchouk EB, Trifonov VA. Human DNA from the oldest Eneolithic cemetery in Nalchik points the spread of farming from the Caucasus to the Eastern European steppes. iScience 2024; 27:110963. [PMID: 39569382 PMCID: PMC11576401 DOI: 10.1016/j.isci.2024.110963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/30/2024] [Accepted: 09/11/2024] [Indexed: 11/22/2024] Open
Abstract
The Darkveti-Meshoko culture (c.5000-3500/3300 BCE) is the earliest known farming community in the Northern Caucasus, but its contribution to the genetic profile of the neighboring steppe herders has remained unclear. We present analysis of human DNA from the Nalchik cemetery-the oldest Eneolithic site in the Northern Caucasus-which shows a link with the LowerVolga's first herders of the Khvalynsk culture. The Nalchik male genotype combines the genes of the Caucasus hunter-gatherers, the Eastern hunter-gatherers and the Pre-Pottery Neolithic (PPN) farmers of western Asia. Improved comparative analysis suggests that the genetic profile of certain Khvalynsk individuals shares the genetic ancestry of the Unakozovo-Nalchik type population of the Northern Caucasus' Eneolithic. Therefore, it seems that in the first half of the 5th millennium BCE, cultural and mating networks helped agriculture and pastoralism spread from West Asia across the Caucasian, into the steppes between the Don and the Volga in Eastern Europe.
Collapse
Affiliation(s)
- K V Zhur
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow, Russian Federation
| | - F S Sharko
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow, Russian Federation
| | - M V Leonova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow, Russian Federation
| | - A Mey
- A.MEY Eventmanagement GmbH & Co. KG, Salzatal, Germany
| | - E B Prokhortchouk
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow, Russian Federation
| | - V A Trifonov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow, Russian Federation
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| |
Collapse
|
22
|
Martínez-García L, Pulido A, Ferrari G, Hufthammer AK, Vedeler M, Hirons A, Kneale C, Barrett JH, Star B. Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA. Proc Biol Sci 2024; 291:20242019. [PMID: 39592000 PMCID: PMC11597396 DOI: 10.1098/rspb.2024.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 11/04/2024] [Accepted: 11/04/2024] [Indexed: 11/28/2024] Open
Abstract
Marine resources have been important for the survival and economic development of coastal human communities across northern Europe for millennia. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes (δ13C, δ15N, non-exchangeable δ2H and δ34S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different geographical populations, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade increased during the thirteenth to fourteenth centuries. The genomic assignments of specimens to different populations coincide with significantly different δ13C values between those same specimens, indicating that multiple Atlantic cod populations living in different environments were exploited. This research provides novel information about the exploitation timeline of specific Atlantic cod stocks and highlights the utility of combining ancient DNA (aDNA) methods and stable isotope analysis to describe the development of medieval and post-medieval marine fisheries.
Collapse
Affiliation(s)
- Lourdes Martínez-García
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, OsloNO-0371, Norway
| | - Angélica Pulido
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, OsloNO-0371, Norway
- Department of Ecology and Evolution, University of Lausanne, LausanneCH-1015, Switzerland
| | - Giada Ferrari
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, OsloNO-0371, Norway
| | - Anne Karin Hufthammer
- Department of Natural History, The University Museum, University of Bergen, BergenNO-5020, Norway
| | - Marianne Vedeler
- Museum of Cultural History, University of Oslo, OsloNO-0164, Norway
| | - Alex Hirons
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, CambridgeCB2 3DZ, UK
| | - Catherine Kneale
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, CambridgeCB2 3DZ, UK
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology, TrondheimNO-7012, Norway
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, OsloNO-0371, Norway
| |
Collapse
|
23
|
Pan J, Liu X, Baca M, Calvière-Tonasso L, Schiavinato S, Chauvey L, Tressières G, Perdereau A, Aury JM, Oliveira PH, Wincker P, Abdykanova A, Arsuaga JL, Bayarsaikhan J, Belinskiy AB, Carbonell E, Davoudi H, Lira Garrido J, Gilbert AS, Hermes T, Warinner C, Kalmykov AA, Lordkipanidze D, Mackiewicz P, Mohaseb AF, Richter K, Sayfullaev N, Shapiro B, Shnaider S, Southon J, Stefaniak K, Summers GD, van Asperen EN, Vanishvili N, Hill EA, Kuznetsov P, Reinhold S, Hansen S, Mashkour M, Berthon R, Taylor WTT, Houle JL, Hekkala E, Popović D, Orlando L. Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses. Mol Ecol 2024; 33:e17527. [PMID: 39279684 DOI: 10.1111/mec.17527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/08/2024] [Accepted: 09/03/2024] [Indexed: 09/18/2024]
Abstract
The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.
Collapse
Affiliation(s)
- Jianfei Pan
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuexue Liu
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
| | - Mateusz Baca
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Laure Calvière-Tonasso
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
| | - Gaétan Tressières
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
| | - Aude Perdereau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Pedro H Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Aida Abdykanova
- Anthropology Department, American University of Central Asia, Bishkek, Kyrgyzstan
| | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
- Departamento de Geodinámica, Estratigrafía y Paleontología. Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Jamsranjav Bayarsaikhan
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- National Museum of Mongolia, Ulaanbaatar, Mongolia
| | | | - Eudald Carbonell
- Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona, Spain
- Institut Català de Paleoecologia Humana I Evolució Social (IPHES-CERCA), Tarragona, Spain
| | - Hossein Davoudi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, Tehran, Iran
| | - Jaime Lira Garrido
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
| | - Allan S Gilbert
- Department of Sociology and Anthropology, Fordham University, New York, New York, USA
| | - Taylor Hermes
- Department of Anthropology, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, Massachusetts, USA
| | | | - David Lordkipanidze
- Georgian National Museum, Tbilisi, Tbilisi, Georgia
- Tbilisi State University Tbilisi I. Chavchavadze Avenue 1, Tbilisi, Georgia
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Azadeh F Mohaseb
- UMR 7209 'Archéozoologie, Archéobotanique: sociétés, Pratiques et Environnements', CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Kristine Richter
- Department of Anthropology, Harvard University, Cambridge, Massachusetts, USA
| | - Nuritdin Sayfullaev
- Donish Institute of History, Archaeology and Ethnography, Dushanbe, Tajikistan
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Svetlana Shnaider
- International Laboratory "Archaeozoology in Siberia and Central Asia" ZooSCAn, IRL 2013, National Center for Scientific Research - Institute of Archeology and Ethnography SB RAS, Novosibirsk, Russia
| | - John Southon
- Earth System Science Department, University of California, Irvine, California, USA
| | | | - Geoffrey D Summers
- Ecole Nationale Supérieure d'Architecture de Nantes-Mauritius, Pierrefonds, Mauritius
- The Oriental Institute, Chicago University, Chicago, Illinois, USA
| | | | - Nikoloz Vanishvili
- Department of Vertebrate Paleontology, L. Davitashvili Institute of Paleobiology, Georgian National Museum, Tbilisi, Georgia
| | - Eden A Hill
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pavel Kuznetsov
- The Museum of Archeology of the Volga Region Samara State University of Social Sciences and Education, Samara, Russia
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Marjan Mashkour
- UMR 7209 'Archéozoologie, Archéobotanique: sociétés, Pratiques et Environnements', CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Rémi Berthon
- UMR 7209 'Archéozoologie, Archéobotanique: sociétés, Pratiques et Environnements', CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - William Timothy Treal Taylor
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Anthropology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Jean-Luc Houle
- Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, Kentucky, USA
| | - Evon Hekkala
- Department Biological Sciences, Fordham University, New York, New York, USA
| | - Danijela Popović
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR5288, Université Paul Sabatier, Toulouse, France
| |
Collapse
|
24
|
Ruiz-Puerta EJ, Jarrett G, McCarthy ML, Pan SE, Keighley X, Aiken M, Zampirolo G, Loonen MJJE, Gotfredsen AB, Howse LR, Szpak P, Pálsson S, Rufolo S, Malmquist HJ, Desjardins SPA, Olsen MT, Jordan PD. Greenland Norse walrus exploitation deep into the Arctic. SCIENCE ADVANCES 2024; 10:eadq4127. [PMID: 39331710 PMCID: PMC11430631 DOI: 10.1126/sciadv.adq4127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/26/2024] [Indexed: 09/29/2024]
Abstract
Walrus ivory was a prized commodity in medieval Europe and was supplied by Norse intermediaries who expanded across the North Atlantic, establishing settlements in Iceland and Greenland. However, the precise sources of the traded ivory have long remained unclear, raising important questions about the sustainability of commercial walrus harvesting, the extent to which Greenland Norse were able to continue mounting their own long-range hunting expeditions, and the degree to which they relied on trading ivory with the various Arctic Indigenous peoples that they were starting to encounter. We use high-resolution genomic sourcing methods to track walrus artifacts back to specific hunting grounds, demonstrating that Greenland Norse obtained ivory from High Arctic waters, especially the North Water Polynya, and possibly from the interior Canadian Arctic. These results substantially expand the assumed range of Greenland Norse ivory harvesting activities and support intriguing archaeological evidence for substantive interactions with Thule Inuit, plus possible encounters with Tuniit (Late Dorset Pre-Inuit).
Collapse
Affiliation(s)
- Emily J Ruiz-Puerta
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, DK-1353 Copenhagen K, Denmark
- Arctic Centre and Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, NL-9700 AS Groningen, Netherlands
| | - Greer Jarrett
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, 223 62 Lund, Sweden
| | - Morgan L McCarthy
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, DK-1353 Copenhagen K, Denmark
| | - Shyong En Pan
- Palaeobiology Section, Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - Xénia Keighley
- The Bureau of Meteorology, The Treasury Building, Parkes Place West, Parkes, ACT 2600, Australia
| | - Magie Aiken
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, DK-1353 Copenhagen K, Denmark
| | - Giulia Zampirolo
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, DK-1353 Copenhagen K, Denmark
| | - Maarten J J E Loonen
- Arctic Centre and Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, NL-9700 AS Groningen, Netherlands
| | - Anne Birgitte Gotfredsen
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Lesley R Howse
- Inuit Heritage Trust Inc., 2425 Abe Okpik, Iqaluit, Nunavut X0A 2H0, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, 1600 West Bank Drive, Peterborough, Ontario K9L 0G2, Canada
| | - Snæbjörn Pálsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7, 101 Reykjavik, Iceland
| | - Scott Rufolo
- Arctic Centre and Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, NL-9700 AS Groningen, Netherlands
- Palaeobiology Section, Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - Hilmar J Malmquist
- Icelandic Museum of Natural History, Suðurlandsbraut 24, 108 Reykjavík, Iceland
| | - Sean P A Desjardins
- Arctic Centre and Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, PO Box 716, NL-9700 AS Groningen, Netherlands
- Palaeobiology Section, Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, Ontario K1P 6P4, Canada
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5-7, DK-1353 Copenhagen K, Denmark
| | - Peter D Jordan
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, 223 62 Lund, Sweden
- Global Station for Indigenous Studies and Cultural Diversity (GSI), GI-CoRE, Hokkaido University, Sapporo, Japan
| |
Collapse
|
25
|
Sun Y, Lorenzen ED, Westbury MV. Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation. BMC Genomics 2024; 25:826. [PMID: 39278943 PMCID: PMC11403954 DOI: 10.1186/s12864-024-10617-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/12/2024] [Indexed: 09/18/2024] Open
Abstract
The polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many traits adapted for cold temperatures, movement across snow, ice and open water, and for consuming highly lipid-dense prey species. The divergence of polar bears from brown bears (Ursus arctos) and their adaptation to their Arctic lifestyle is a well-known example of rapid evolution. Previous research investigating whole genomes uncovered twelve key genes that are highly differentiated between polar and brown bears, show signatures of selection in the polar bear lineage, and are associated with polar bear adaptation to the Arctic environment. Further research suggested fixed derived alleles in these genes arose from selection on both standing variation and de novo mutations in the evolution of polar bears. Here, we reevaluate these findings based on a larger and geographically more representative dataset of 119 polar bears and 135 brown bears, and assess the timing of derived allele fixation in polar bears by incorporating the genomes of two Late Pleistocene individuals (aged 130-100,000 years old and 100-70,000 years old). In contrast with previous results, we found no evidence of derived alleles fixed in present-day polar bears within the key genes arising from de novo mutation. Most derived alleles fixed in present-day polar bears were also fixed in the Late Pleistocene polar bears, suggesting selection occurred prior to 70,000 years ago. However, some derived alleles fixed in present-day polar bears were not fixed in the two Late Pleistocene polar bears, including at sites within APOB, LYST, and TTN. These three genes are associated with cardiovascular function, metabolism, and pigmentation, suggesting selection may have acted on different loci at different times.
Collapse
Affiliation(s)
- Yulin Sun
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- School of The Environment, The University of Queensland, Brisbane, QLD, Australia
| | | | | |
Collapse
|
26
|
Slimak L, Vimala T, Seguin-Orlando A, Metz L, Zanolli C, Joannes-Boyau R, Frouin M, Arnold LJ, Demuro M, Devièse T, Comeskey D, Buckley M, Camus H, Muth X, Lewis JE, Bocherens H, Yvorra P, Tenailleau C, Duployer B, Coqueugniot H, Dutour O, Higham T, Sikora M. Long genetic and social isolation in Neanderthals before their extinction. CELL GENOMICS 2024; 4:100593. [PMID: 39265525 PMCID: PMC11480857 DOI: 10.1016/j.xgen.2024.100593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 11/23/2023] [Accepted: 06/05/2024] [Indexed: 09/14/2024]
Abstract
Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations' structure that mostly indicates that late European Neanderthals belonged to a single metapopulation with no significant evidence of population structure. Here, we report the discovery of a late Neanderthal individual, nicknamed "Thorin," from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of Neanderthal final technological traditions in this region ∼50-42 thousand years ago. Thorin's genome reveals a relatively early divergence of ∼105 ka with other late Neanderthals. Thorin belonged to a population with a small group size that showed no genetic introgression with other known late European Neanderthals, revealing some 50 ka of genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the disappearance of the Neanderthals.
Collapse
Affiliation(s)
- Ludovic Slimak
- Centre d'Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Faculté de Santé, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France.
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Faculté de Santé, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France; Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Laure Metz
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, BP 647, 5 rue du Château de l'Horloge, 13094 Aix-en-Provence Cedex 2, France; University of Connecticut, College of Liberal Arts and Sciences, 215 Glenbrook Road, U-4098, Storrs, CT 06269-4098, USA
| | - Clément Zanolli
- Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, 33600 Pessac, France
| | - Renaud Joannes-Boyau
- Geoarchaeology & Archaeometry Research Group (GARG), Southern Cross University, Military Rd., Lismore, NSW 2480, Australia
| | - Marine Frouin
- Department of Geosciences, Stony Brook University, 255 Earth and Space Sciences Building, Stony Brook, NY 11794-2100, USA; Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA
| | - Lee J Arnold
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Martina Demuro
- School of Physical Sciences, Environment Institute, Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Thibaut Devièse
- CEREGE, Aix-Marseille University, CNRS, IRD, INRAE, Collège de France, Technopôle de l'Arbois, Aix-en-Provence, France
| | - Daniel Comeskey
- Syft Technologies Ltd., 3 Craft Place, Middleton, PO Box 28 149, Christchurch 8242, New Zealand
| | - Michael Buckley
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Hubert Camus
- PROTEE-EXPERT, 4 rue des Aspholdèles, 34750 Villeneuve-lès-Maguelone, France
| | - Xavier Muth
- Get in Situ, 1091 Bourg-en-Lavaux, Switzerland
| | - Jason E Lewis
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794-4364, USA; Chronicle Heritage, 319 E Palm Lane, Phoenix, AZ 85004, USA
| | - Hervé Bocherens
- Fachbereich Geowissenschaften Forschungsbereich Paläobiologie - Biogeologie Senckenberg, Centre for Human Evolution and Palaeoenvironment (SHEP), Universität Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany
| | - Pascale Yvorra
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, BP 647, 5 rue du Château de l'Horloge, 13094 Aix-en-Provence Cedex 2, France
| | - Christophe Tenailleau
- Centre Inter-Universitaire de Recherche et d'Ingénierie des Matériaux, UMR 5085 CNRS-Université de Toulouse (Paul Sabatier), 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Benjamin Duployer
- Centre Inter-Universitaire de Recherche et d'Ingénierie des Matériaux, UMR 5085 CNRS-Université de Toulouse (Paul Sabatier), 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Hélène Coqueugniot
- École Pratique des Hautes Études - Paris Sciences et Lettres University, 4-14 rue Ferrus, 75014 Paris, France; University of Bordeaux-Montaigne, CNRS, EPHE, Archéosciences, UMR 6034, 33607 Pessac, France
| | - Olivier Dutour
- École Pratique des Hautes Études - Paris Sciences et Lettres University, 4-14 rue Ferrus, 75014 Paris, France; University of Bordeaux-Montaigne, CNRS, EPHE, Archéosciences, UMR 6034, 33607 Pessac, France
| | - Thomas Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences Forschungsverbund, University of Vienna, Vienna 1090, Austria
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, 1350K Copenhagen, Denmark.
| |
Collapse
|
27
|
Skovrind M, Louis M, Ferguson SH, Glazov DM, Litovka DI, Loseto L, Meschersky IG, Miller MM, Petr M, Postma L, Rozhnov VV, Scott M, Westbury MV, Szpak P, Friesen TM, Lorenzen ED. Elucidating the sustainability of 700 y of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada. Proc Natl Acad Sci U S A 2024; 121:e2405993121. [PMID: 39136992 PMCID: PMC11348011 DOI: 10.1073/pnas.2405993121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/08/2024] [Indexed: 08/29/2024] Open
Abstract
Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remain unknown. Here, we integrate paleogenomics, genetic simulations, and stable δ13C and δ15N isotope analysis to investigate 700 y of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which is based on radiocarbon dating, span three time periods (1290 to 1440 CE; 1450 to 1650 CE; 1800 to 1870 CE), indicates shifts across time in the sex ratio of the harvested belugas. The equal number of females and males harvested in 1450 to 1650 CE versus more males harvested in the two other time periods may reflect changes in hunting practices or temporal shifts in beluga availability. We find temporal shifts and sex-based differences in δ13C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. We uncovered distinct mitochondrial diversity unique to the Mackenzie Delta belugas, but found no changes in nuclear genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 y surveyed, indicating the impact of Inuvialuit subsistence harvests on the genetic diversity of contemporary beluga individuals has been negligible.
Collapse
Affiliation(s)
- Mikkel Skovrind
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen1350, Denmark
| | - Marie Louis
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen1350, Denmark
- Greenland Institute of Natural Resources, Nuuk3900, Greenland
| | | | - Dmitry M. Glazov
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Science, Moscow119071, Russia
| | - Dennis I. Litovka
- Autonomous nonprofit organisation “Chukotka Arctic Scientific Center”, Anadyr689000, Russia
| | - Lisa Loseto
- Fisheries and Oceans Canada, Winnipeg, MBR3T 2N6, Canada
- Department of Environment and Geography, Centre for Earth Observation Science, University of Manitoba, Winnipeg, MBR3T 2N2, Canada
| | - Ilya G. Meschersky
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Science, Moscow119071, Russia
| | - Mariah M. Miller
- Department of Anthropology, Trent University, Peterborough, ONK9L 0G2, Canada
| | - Martin Petr
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen1350, Denmark
| | - Lianne Postma
- Fisheries and Oceans Canada, Winnipeg, MBR3T 2N6, Canada
| | - Viatcheslav V. Rozhnov
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Science, Moscow119071, Russia
| | - Michael Scott
- Department of Anthropology, Trent University, Peterborough, ONK9L 0G2, Canada
| | - Michael V. Westbury
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen1350, Denmark
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, ONK9L 0G2, Canada
| | - T. Max Friesen
- Department of Anthropology, University of Toronto, Toronto, ONM5S 2S2, Canada
| | - Eline D. Lorenzen
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen1350, Denmark
| |
Collapse
|
28
|
Przelomska NAS, Diaz RA, Ávila FA, Ballen GA, Cortés-B R, Kistler L, Chitwood DH, Charitonidou M, Renner SS, Pérez-Escobar OA, Antonelli A. Morphometrics and Phylogenomics of Coca (Erythroxylum spp.) Illuminate Its Reticulate Evolution, With Implications for Taxonomy. Mol Biol Evol 2024; 41:msae114. [PMID: 38982580 PMCID: PMC11233275 DOI: 10.1093/molbev/msae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 07/11/2024] Open
Abstract
South American coca (Erythroxylum coca and E. novogranatense) has been a keystone crop for many Andean and Amazonian communities for at least 8,000 years. However, over the last half-century, global demand for its alkaloid cocaine has driven intensive agriculture of this plant and placed it in the center of armed conflict and deforestation. To monitor the changing landscape of coca plantations, the United Nations Office on Drugs and Crime collects annual data on their areas of cultivation. However, attempts to delineate areas in which different varieties are grown have failed due to limitations around identification. In the absence of flowers, identification relies on leaf morphology, yet the extent to which this is reflected in taxonomy is uncertain. Here, we analyze the consistency of the current naming system of coca and its four closest wild relatives (the "coca clade"), using morphometrics, phylogenomics, molecular clocks, and population genomics. We include name-bearing type specimens of coca's closest wild relatives E. gracilipes and E. cataractarum. Morphometrics of 342 digitized herbarium specimens show that leaf shape and size fail to reliably discriminate between species and varieties. However, the statistical analyses illuminate that rounder and more obovate leaves of certain varieties could be associated with the subtle domestication syndrome of coca. Our phylogenomic data indicate extensive gene flow involving E. gracilipes which, combined with morphometrics, supports E. gracilipes being retained as a single species. Establishing a robust evolutionary-taxonomic framework for the coca clade will facilitate the development of cost-effective genotyping methods to support reliable identification.
Collapse
Affiliation(s)
- Natalia A S Przelomska
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Rudy A Diaz
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | | | - Gustavo A Ballen
- Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Rocío Cortés-B
- Herbario Forestal Universidad Distrital, Campus El Vivero, CR 5E 15-82 Bogotá, Colombia
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560, USA
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Martha Charitonidou
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, SE 41319 Göteborg, Sweden
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| |
Collapse
|
29
|
Librado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, et alLibrado P, Tressières G, Chauvey L, Fages A, Khan N, Schiavinato S, Calvière-Tonasso L, Kusliy MA, Gaunitz C, Liu X, Wagner S, Der Sarkissian C, Seguin-Orlando A, Perdereau A, Aury JM, Southon J, Shapiro B, Bouchez O, Donnadieu C, Collin YRH, Gregersen KM, Jessen MD, Christensen K, Claudi-Hansen L, Pruvost M, Pucher E, Vulic H, Novak M, Rimpf A, Turk P, Reiter S, Brem G, Schwall C, Barrey É, Robert C, Degueurce C, Horwitz LK, Klassen L, Rasmussen U, Kveiborg J, Johannsen NN, Makowiecki D, Makarowicz P, Szeliga M, Ilchyshyn V, Rud V, Romaniszyn J, Mullin VE, Verdugo M, Bradley DG, Cardoso JL, Valente MJ, Telles Antunes M, Ameen C, Thomas R, Ludwig A, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Granado J, Schlumbaum A, Deschler-Erb S, Mráz MS, Boulbes N, Gardeisen A, Mayer C, Döhle HJ, Vicze M, Kosintsev PA, Kyselý R, Peške L, O'Connor T, Ananyevskaya E, Shevnina I, Logvin A, Kovalev AA, Iderkhangai TO, Sablin MV, Dashkovskiy PK, Graphodatsky AS, Merts I, Merts V, Kasparov AK, Pitulko VV, Onar V, Öztan A, Arbuckle BS, McColl H, Renaud G, Khaskhanov R, Demidenko S, Kadieva A, Atabiev B, Sundqvist M, Lindgren G, López-Cachero FJ, Albizuri S, Trbojević Vukičević T, Rapan Papeša A, Burić M, Rajić Šikanjić P, Weinstock J, Asensio Vilaró D, Codina F, García Dalmau C, Morer de Llorens J, Pou J, de Prado G, Sanmartí J, Kallala N, Torres JR, Maraoui-Telmini B, Belarte Franco MC, Valenzuela-Lamas S, Zazzo A, Lepetz S, Duchesne S, Alexeev A, Bayarsaikhan J, Houle JL, Bayarkhuu N, Turbat T, Crubézy É, Shingiray I, Mashkour M, Berezina NY, Korobov DS, Belinskiy A, Kalmykov A, Demoule JP, Reinhold S, Hansen S, Wallner B, Roslyakova N, Kuznetsov PF, Tishkin AA, Wincker P, Kanne K, Outram A, Orlando L. Widespread horse-based mobility arose around 2200 BCE in Eurasia. Nature 2024; 631:819-825. [PMID: 38843826 PMCID: PMC11269178 DOI: 10.1038/s41586-024-07597-5] [Show More Authors] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/23/2024] [Indexed: 07/19/2024]
Abstract
Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.
Collapse
Affiliation(s)
- Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Spain.
| | - Gaetan Tressières
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Lorelei Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Zoological institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Mariya A Kusliy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Charleen Gaunitz
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xuexue Liu
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Stefanie Wagner
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- INRAE Division Ecology and Biodiversity (ECODIV), Plant Genomic Resources Center (CNRGV), Castanet Tolosan Cedex, France
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Aude Perdereau
- Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - John Southon
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Yvette Running Horse Collin
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Taku Skan Skan Wasakliyapi: Global Institute for Traditional Sciences, Rapid City, SD, USA
| | | | - Mads Dengsø Jessen
- Department for Prehistory Middle Ages and Renaissance, National Museum of Denmark, Copenhagen K, Denmark
| | | | | | - Mélanie Pruvost
- UMR 5199 De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cédex, France
| | | | | | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | - Peter Turk
- Narodni muzej Slovenije, Ljubljana, Slovenia
| | - Simone Reiter
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Schwall
- Leibniz-Zentrum für Archäologie (LEIZA), Mainz, Germany
- Department of Prehistory & Western Asian/Northeast African Archaeology, Austrian Archaeological Institute (OeAI), Austrian Academy of Sciences (OeAW), Vienna, Austria
| | - Éric Barrey
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
| | - Céline Robert
- Université Paris-Saclay, AgroParisTech, INRAE GABI UMR1313, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | | | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem, Israel
| | | | - Uffe Rasmussen
- Department of Archaeology, Moesgaard Museum, Højbjerg, Denmark
| | - Jacob Kveiborg
- Department of Archaeological Science and Conservation, Moesgaard Museum, Højbjerg, Denmark
| | | | - Daniel Makowiecki
- Institute of Archaeology, Faculty of History, Nicolaus Copernicus University, Toruń, Poland
| | | | - Marcin Szeliga
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Vasyl Ilchyshyn
- Kremenetsko-Pochaivskii Derzhavnyi Istoriko-arkhitekturnyi Zapovidnik, Kremenets, Ukraine
| | - Vitalii Rud
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Jan Romaniszyn
- Faculty of Archaeology, Adam Mickiewicz University, Poznań, Poland
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - João L Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro, Portugal
- Universidade Aberta, Lisbon, Portugal
| | - Maria J Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Carly Ameen
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Richard Thomas
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | | | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan, Italy
| | - José Granado
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Angela Schlumbaum
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Sabine Deschler-Erb
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Monika Schernig Mráz
- Department of Environmental Sciences, Integrative Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris/UMR 7194 HNHP, MNHN-CNRS-UPVD/EPCC Centre Européen de Recherche Préhistorique, Tautavel, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditeranéennes, Archimède IA-ANR-11-LABX-0032-01, CNRS UMR 5140, Université Paul Valéry, Montpellier, France
| | - Christian Mayer
- Department for Digitalization and Knowledge Transfer, Federal Monuments Authority Austria, Vienna, Austria
| | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, Halle (Saale), Germany
| | - Magdolna Vicze
- National Institute of Archaeology, Hungarian National Museum, Budapest, Hungary
| | - Pavel A Kosintsev
- Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - René Kyselý
- Department of Natural Sciences and Archaeometry, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Elina Ananyevskaya
- Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Irina Shevnina
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Andrey Logvin
- Laboratory for Archaeological Research, Akhmet Baitursynuly Kostanay Regional University, Kostanay, Kazakhstan
| | - Alexey A Kovalev
- Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russia
| | - Tumur-Ochir Iderkhangai
- Department of Innovation and Technology, Ulaanbaatar Science and Technology Park, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Petr K Dashkovskiy
- Department of Russian Regional Studies, National and State-confessional Relations, Altai State University, Barnaul, Russia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Ilia Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Viktor Merts
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Aleksei K Kasparov
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir V Pitulko
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St Petersburg, Russia
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul, Türkiye
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara, Türkiye
| | - Benjamin S Arbuckle
- Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Ruslan Khaskhanov
- Kh. Ibragimov Complex Institute of the Russian Academy of Sciences (CI RAS), Grozny, Russia
| | - Sergey Demidenko
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kadieva
- Department of Archaeological Monuments, State Historical Museum, Moscow, Russian Federation
| | | | | | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - F Javier López-Cachero
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Albizuri
- Institut d'Arqueologia de la Universitat de Barcelona (IAUB), Seminari d'Estudis i Recerques Prehistoriques (SERP-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Tajana Trbojević Vukičević
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Marcel Burić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Jaco Weinstock
- Faculty of Arts and Humanities (Archaeology), University of Southampton, Southampton, UK
| | - David Asensio Vilaró
- Secció de Prehistòria i Arqueologia, IAUB Institut d'Arqueologia de la Universitat de Barcelona, Barcelona, Spain
| | - Ferran Codina
- C/Major, 20, Norfeu, Arqueologia Art i Patrimoni S.C., La Tallada d'Empordà, Spain
| | | | | | - Josep Pou
- Ajuntament de Calafell, Calafell (Tarragona), Spain
| | - Gabriel de Prado
- Museu d'Arqueologia de Catalunya (MAC-Ullastret), Ullastret, Spain
| | - Joan Sanmartí
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- Departament d'Història i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Nabil Kallala
- Ecole Tunisienne d'Histoire et d'Anthropologie, Tunis, Tunisia
- University of Tunis, Institut National du Patrimoine, Tunis, Tunisia
| | | | | | - Maria-Carme Belarte Franco
- IEC-Institut d'Estudis Catalans (Union Académique Internationale), Barcelona, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- ICAC (Catalan Institute of Classical Archaeology), Tarragona, Spain
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
- UNIARQ - Unidade de Arqueologia, Universidade de Lisboa, Alameda da Universidade, Lisboa, Portugal
| | - Antoine Zazzo
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sébastien Lepetz
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sylvie Duchesne
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | - Anatoly Alexeev
- Institute for Humanities Research and Indigenous Studies of the North (IHRISN), Yakutsk, Russia
| | - Jamsranjav Bayarsaikhan
- Max Planck Institute of Geoanthropology, Jena, Germany
- Institute of Archaeology, Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | - Jean-Luc Houle
- Department of Folk Studies and Anthropology, Western Kentucky University, Bowling Green, KY, USA
| | - Noost Bayarkhuu
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tsagaan Turbat
- Archaeological Research Center and Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Éric Crubézy
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France
| | | | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
- Central Laboratory, Bioarchaeology Laboratory, Archaeozoology section, University of Tehran, Tehran, Iran
| | - Natalia Ya Berezina
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy S Korobov
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Jean-Paul Demoule
- UMR du CNRS 8215 Trajectoires, Institut d'Art et Archéologie, Paris, France
| | - Sabine Reinhold
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Natalia Roslyakova
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel F Kuznetsov
- Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Katherine Kanne
- Department of Archaeology and History, University of Exeter, Exeter, UK
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Alan Outram
- Department of Archaeology and History, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5288, Université Paul Sabatier, Faculté de Médecine Purpan, Toulouse, France.
| |
Collapse
|
30
|
Cavill EL, Morales HE, Sun X, Westbury MV, van Oosterhout C, Accouche W, Zora A, Schulze MJ, Shah N, Adam P, Brooke MDL, Sweet P, Gopalakrishnan S, Gilbert MTP. When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine. Evol Appl 2024; 17:e13739. [PMID: 38948538 PMCID: PMC11212007 DOI: 10.1111/eva.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 07/02/2024] Open
Abstract
The Seychelles magpie-robin's (SMR) five island populations exhibit some of the lowest recorded levels of genetic diversity among endangered birds, and high levels of inbreeding. These populations collapsed during the 20th century, and the species was listed as Critically Endangered in the IUCN Red List in 1994. An assisted translocation-for-recovery program initiated in the 1990s increased the number of mature individuals, resulting in its downlisting to Endangered in 2005. Here, we explore the temporal genomic erosion of the SMR based on a dataset of 201 re-sequenced whole genomes that span the past ~150 years. Our sample set includes individuals that predate the bottleneck by up to 100 years, as well as individuals from contemporary populations established during the species recovery program. Despite the SMR's recent demographic recovery, our data reveal a marked increase in both the genetic load and realized load in the extant populations when compared to the historical samples. Conservation management may have reduced the intensity of selection by increasing juvenile survival and relaxing intraspecific competition between individuals, resulting in the accumulation of loss-of-function mutations (i.e. severely deleterious variants) in the rapidly recovering population. In addition, we found a 3-fold decrease in genetic diversity between temporal samples. While the low genetic diversity in modern populations may limit the species' adaptability to future environmental changes, future conservation efforts (including IUCN assessments) may also need to assess the threats posed by their high genetic load. Our computer simulations highlight the value of translocations for genetic rescue and show how this could halt genomic erosion in threatened species such as the SMR.
Collapse
Affiliation(s)
- Emily L. Cavill
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Xin Sun
- The Globe Institute, University of CopenhagenCopenhagenDenmark
| | | | - Cock van Oosterhout
- School of Environmental SciencesUniversity of East Anglia, Norwich Research ParkNorwichUK
| | | | - Anna Zora
- Fregate Island Sanctuary LtdVictoriaSeychelles
| | | | | | | | | | - Paul Sweet
- American Museum of Natural HistoryNew YorkUSA
| | | | - M. Thomas P. Gilbert
- The Globe Institute, University of CopenhagenCopenhagenDenmark
- University Museum, Norwegian University of Science and TechnologyTrondheimNorway
| |
Collapse
|
31
|
Zhu S, Zhang N, Zhang J, Shao X, Guo Y, Cai D. Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China. Genes (Basel) 2024; 15:790. [PMID: 38927726 PMCID: PMC11203007 DOI: 10.3390/genes15060790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.
Collapse
Affiliation(s)
- Siqi Zhu
- Department of Archaeology, School of History, Wuhan University, Wuhan 430072, China;
| | - Naifan Zhang
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
- National Centre for Archaeology, Beijing 100013, China
| | - Jie Zhang
- Xinjiang Institute of Cultural Relics and Archaeology, Ürümqi 830011, China;
| | - Xinyue Shao
- Department of Archaeology, University of Southampton, Avenue Campus, Southampton SO17 1BF, UK;
| | - Yaqi Guo
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
| | - Dawei Cai
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
| |
Collapse
|
32
|
Rayo E, Ulrich GF, Zemp N, Greeff M, Schuenemann VJ, Widmer A, Fischer MC. Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens. Sci Rep 2024; 14:12875. [PMID: 38834639 DOI: 10.1038/s41598-024-63587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, Melitaea diamina, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.
Collapse
Affiliation(s)
- Enrique Rayo
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
- Institut Für Veterinärpathologie, University of Zurich, Zurich, Switzerland
| | - Gabriel F Ulrich
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Michael Greeff
- Institute of Agricultural Sciences (IAS), ETH Zurich, Zurich, Switzerland
| | - Verena J Schuenemann
- Department of Environmental Sciences (DUW), University of Basel, Basel, Switzerland
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Martin C Fischer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
33
|
Fegraeus K, Rosengren MK, Naboulsi R, Orlando L, Åbrink M, Jouni A, Velie BD, Raine A, Egner B, Mattsson CM, Lång K, Zhigulev A, Björck HM, Franco-Cereceda A, Eriksson P, Andersson G, Sahlén P, Meadows JRS, Lindgren G. An endothelial regulatory module links blood pressure regulation with elite athletic performance. PLoS Genet 2024; 20:e1011285. [PMID: 38885195 PMCID: PMC11182536 DOI: 10.1371/journal.pgen.1011285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024] Open
Abstract
The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.
Collapse
Affiliation(s)
- Kim Fegraeus
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Maria K. Rosengren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Rakan Naboulsi
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institute, Stockholm
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CNRS UMR 5288), Université Paul Sabatier, Toulouse, France
| | - Magnus Åbrink
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ahmad Jouni
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Brandon D. Velie
- School of Life & Environmental Sciences, University of Sydney, Sydney, Australia
| | - Amanda Raine
- Department of Medical Sciences, Science for life laboratory, Uppsala University, Sweden
| | - Beate Egner
- Department of Cardio-Vascular Research, Veterinary Academy of Higher Learning, Babenhausen, Germany
| | - C Mikael Mattsson
- Silicon Valley Exercise Analytics (svexa), MenloPark, CA, United States of America
| | - Karin Lång
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Artemy Zhigulev
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Hanna M. Björck
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Anders Franco-Cereceda
- Section of Cardiothoracic Surgery, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Per Eriksson
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Göran Andersson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences Uppsala, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| |
Collapse
|
34
|
Borry M, Forsythe A, Andrades Valtueña A, Hübner A, Ibrahim A, Quagliariello A, White AE, Kocher A, Vågene ÅJ, Bartholdy BP, Spurīte D, Ponce-Soto GY, Neumann G, Huang IT, Light I, Velsko IM, Jackson I, Frangenberg J, Serrano JG, Fumey J, Özdoğan KT, Blevins KE, Daly KG, Lopopolo M, Moraitou M, Michel M, van Os M, Bravo-Lopez MJ, Sarhan MS, Dagtas ND, Oskolkov N, Smith OS, Lebrasseur O, Rozwalak P, Eisenhofer R, Wasef S, Ramachandran SL, Vanghi V, Warinner C, Fellows Yates JA. Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000Res 2024; 12:926. [PMID: 39262445 PMCID: PMC11387932 DOI: 10.12688/f1000research.134798.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/07/2024] [Indexed: 09/13/2024] Open
Abstract
Background Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir. Results AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community. Conclusions Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.
Collapse
Affiliation(s)
- Maxime Borry
- Cluster of Excellence "Balance of the Microverse", Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
| | - Adrian Forsythe
- Department of Animal Zoology, Uppsala Universitet, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
| | - Alexander Hübner
- Cluster of Excellence "Balance of the Microverse", Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, Universita degli Studi di Padova, Viale dell'Università 16, Legnaro, Padova, 350250, Italy
| | - Anna E White
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Øster Farimagsgade 5, Copenhagen K, 1353, Denmark
- BioArCh, Department of Archaeology, University of York, York, England, YO10 5DD, UK
| | - Arthur Kocher
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for Geoanthropology, Kahlaische Str. 10, Jena, Thuringia, 07745, Germany
| | - Åshild J Vågene
- Section for Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Oester Voldgade 44747, Copenhagen K, 1350, Denmark
| | - Bjørn Peare Bartholdy
- Department of Archaeological Sciences, Universiteit Leiden, Einsteinweg 2, Leiden, 2333 CC, The Netherlands
| | - Diāna Spurīte
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Institute of Ecology and Evolution, Friedrich-Schiller-Universität Jena, Jena, Thuringia, 07743, Germany
| | - Gabriel Yaxal Ponce-Soto
- Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France
| | - Gunnar Neumann
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
| | - I-Ting Huang
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, Massachusetts, 02138, USA
| | - Ian Light
- Max Planck Institute for Infection Biology, Virchowweg 12, Berlin, Berlin, 10117, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
| | - Iseult Jackson
- SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, H91 TK33, Ireland
- Smurfit Institute of Genetics, The University of Dublin Trinity College, Dublin, Leinster, D02 VF25, Ireland
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
| | - Javier G Serrano
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38200, Spain
| | - Julien Fumey
- Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France
| | - Kadir T Özdoğan
- Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland, 6700 AA, The Netherlands
- Department of History and Art History, Universiteit Utrecht, Drift 6, Utrecht, Utrecht, 3512 BS, The Netherlands
| | - Kelly E Blevins
- Center for Bioarchaeological Research, Arizona State University, Candy Mall, Tempe, Arizona, 85281, USA
- Department of Archaeology, Durham University, South Road, Durham, County Durham, England, DH1 3LE, UK
| | - Kevin G Daly
- Smurfit Institute of Genetics, The University of Dublin Trinity College, Dublin, Leinster, D02 VF25, Ireland
| | - Maria Lopopolo
- Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France
| | - Markella Moraitou
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, Scotland, EH9 3FL, UK
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Department of Human Evolutionary Biology, Harvard University, Divinity Avenue 11, Cambridge, Massachusetts, 02138, USA
| | - Meriam van Os
- Department of Anatomy, University of Otago, 270 Great King St, Dunedin, Otago, 9016, New Zealand
| | - Miriam J Bravo-Lopez
- International Laboratory for Human Genome Research (LIIGH), Universidad Nacional Autonoma de Mexico, La Mesa 3001, Juriquilla, Queretaro, 76230, Mexico
- Center for Genomic Sciences (CCG), Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210, Mexico
| | - Mohamed S Sarhan
- Institute for Mummy Studies, Eurac Research, Drususallee 1, Bolzano/Bozen, Autonome Provinz Bozen, 39100, Italy
- Centre for Integrative Biology (CIBIO), Universita degli Studi di Trento, Via Sommarive 9, Povo, Trentino, 38123, Italy
| | - Nihan D Dagtas
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv-Yafo, 69978, Israel
| | - Nikolay Oskolkov
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Tomtebodavägen 23, Stockholm, 17165, Sweden
- Department of Biology, Lunds Universitet, Sölvegatan 35, Lund, 223 62, Sweden
| | - Olivia S Smith
- Department of Integrative Biology, The University of Texas at Austin, Speedway 2415, Austin, Texas, 78712, USA
| | - Ophélie Lebrasseur
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, 3 de Febrero 1370 (1426), Ciudad Autónoma de Buenos Aires, C1426BJN CABA, Argentina
- Center for Anthropobiology and Genomics of Toulouse, CNRS/Universite Toulouse III Paul Sabatier, Allées Jules Guesde 37, Toulouse, Occitanie, 31000, France
| | - Piotr Rozwalak
- Department of Computational Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznanskiego 6, Poznań, Wielkopolska, 61-614, Poland
| | - Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, Københavns Universitet, ester Voldgade 44747, Copenhagen, Copenhagen K, 1350, Denmark
| | - Sally Wasef
- Defence Genomics, Centre for Genomics and Personalised Health, Queensland University of Technology, Musk Ave 60, Kelvin Grove, Queensland, 4059, Australia
| | - Shreya L Ramachandran
- Department of Human Genetics, The University of Chicago, E. 58th St. 920, Chicago, Illinois, 60637, USA
| | - Valentina Vanghi
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv-Yafo, 69978, Israel
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
- Department of Anthropology, Harvard University, Divinity Avenue 11, Cambridge, Massachusetts, 02138, USA
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich-Schiller-Universität Jena, Neugasse 25, Jena, Thuringia, 07743, Germany
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
| |
Collapse
|
35
|
Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, Funder S, Gotfredsen AB, Gregersen KM, Hansen CH, Ilsøe PC, Klassen L, Kristensen IK, Ravnholt GB, Marin F, Der Sarkissian C. Advancing responsible genomic analyses of ancient mollusc shells. PLoS One 2024; 19:e0302646. [PMID: 38709766 PMCID: PMC11073703 DOI: 10.1371/journal.pone.0302646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
The analysis of the DNA entrapped in ancient shells of molluscs has the potential to shed light on the evolution and ecology of this very diverse phylum. Ancient genomics could help reconstruct the responses of molluscs to past climate change, pollution, and human subsistence practices at unprecedented temporal resolutions. Applications are however still in their infancy, partly due to our limited knowledge of DNA preservation in calcium carbonate shells and the need for optimized methods for responsible genomic data generation. To improve ancient shell genomic analyses, we applied high-throughput DNA sequencing to 27 Mytilus mussel shells dated to ~111-6500 years Before Present, and investigated the impact, on DNA recovery, of shell imaging, DNA extraction protocols and shell sub-sampling strategies. First, we detected no quantitative or qualitative deleterious effect of micro-computed tomography for recording shell 3D morphological information prior to sub-sampling. Then, we showed that double-digestion and bleach treatment of shell powder prior to silica-based DNA extraction improves shell DNA recovery, also suggesting that DNA is protected in preservation niches within ancient shells. Finally, all layers that compose Mytilus shells, i.e., the nacreous (aragonite) and prismatic (calcite) carbonate layers, with or without the outer organic layer (periostracum) proved to be valuable DNA reservoirs, with aragonite appearing as the best substrate for genomic analyses. Our work contributes to the understanding of long-term molecular preservation in biominerals and we anticipate that resulting recommendations will be helpful for future efficient and responsible genomic analyses of ancient mollusc shells.
Collapse
Affiliation(s)
- Raphaël Martin-Roy
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Jakob Thyrring
- Department of Ecoscience, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Xavier Mata
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| | - Pernille Bangsgaard
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Ole Bennike
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | | | - Svend Funder
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Peter Carsten Ilsøe
- Globe Institute, Section for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Frédéric Marin
- Biogéosciences, UMR6282, CNRS-EPHE-uB, University of Burgundy, EPHE, Dijon, France
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Paul Sabatier, Toulouse, France
| |
Collapse
|
36
|
Hempel E, Faith JT, Preick M, de Jager D, Barish S, Hartmann S, Grau JH, Moodley Y, Gedman G, Pirovich KM, Bibi F, Kalthoff DC, Bocklandt S, Lamm B, Dalén L, Westbury MV, Hofreiter M. Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size. Curr Biol 2024; 34:2020-2029.e6. [PMID: 38614080 DOI: 10.1016/j.cub.2024.03.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/09/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.
Collapse
Affiliation(s)
- Elisabeth Hempel
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany.
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108, USA; Department of Anthropology, University of Utah, 260 South Central Campus Drive, Salt Lake City, UT 84112, USA; Origins Centre, University of the Witwatersrand, 2000 Johannesburg, Republic of South Africa
| | - Michaela Preick
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Deon de Jager
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Stefanie Hartmann
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - José H Grau
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA; Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | | | - Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Daniela C Kalthoff
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 10405 Stockholm, Sweden
| | | | - Ben Lamm
- Colossal Biosciences, Dallas, TX 75247, USA
| | - Love Dalén
- Swedish Museum of Natural History, Department of Bioinformatics and Genetics, Box 50007, 10405 Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20c, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Michael V Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| |
Collapse
|
37
|
Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024; 15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.
Collapse
Affiliation(s)
- Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Rui Resende Pinto
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jonas Meisner
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Research Centre for Mental Health, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Rute R da Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
38
|
Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024; 34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.
Collapse
Affiliation(s)
- Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bøggild
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mumbi Chege
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands; Wildlife Research and Training Institute, Naivasha, Kenya
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morris Agaba
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road, Arusha, Tanzania
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P O. Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
39
|
Sosale MS, Roelke-Parker M, Machange GA, Edwards CW, Figueiró HV, Koepfli KP. The complete mitochondrial genome of Meller's mongoose ( Rhynchogale melleri). Mitochondrial DNA B Resour 2024; 9:432-436. [PMID: 38586507 PMCID: PMC10993741 DOI: 10.1080/23802359.2024.2333567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Meller's mongoose (Rhynchogale melleri) is a member of the family Herpestidae (Mammalia: Carnivora) and the sole species in the genus Rhynchogale. It is primarily found in savannas and open woodlands of eastern sub-Saharan Africa. Here, we report the first complete mitochondrial genome for a female Meller's mongoose collected in Tanzania, generated using a genome-skimming approach. The mitogenome had a final length of 16,644 bp and a total of 37 annotated genes. Phylogenetic analysis validated the placement of this species in the herpestid subfamily Herpestinae. Ultimately, the outcomes of this research offer a genetic foundation for future studies of Meller's mongoose.
Collapse
Affiliation(s)
- Medhini S. Sosale
- Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, Virginia, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Melody Roelke-Parker
- Laboratory Animal Science Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Cody W. Edwards
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Department of Biology, George Mason University, Fairfax, Virginia, USA
| | - Henrique V. Figueiró
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, Virginia, USA
| |
Collapse
|
40
|
Cobb L, de Muinck E, Kollias S, Skage M, Gilfillan GD, Sydenham MAK, Qiao SW, Star B. High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method. PLoS One 2024; 19:e0300865. [PMID: 38517905 PMCID: PMC10959394 DOI: 10.1371/journal.pone.0300865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.
Collapse
Affiliation(s)
- Lauren Cobb
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Erik de Muinck
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Spyros Kollias
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Morten Skage
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Gregor D. Gilfillan
- Department of Medical Genetics, Oslo University Hospital Ullevål and University of Oslo, Oslo, Norway
| | | | - Shuo-Wang Qiao
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
41
|
Kellner FL, Le Moullec M, Ellegaard MR, Rosvold J, Peeters B, Burnett HA, Pedersen ÅØ, Brealey JC, Dussex N, Bieker VC, Hansen BB, Martin MD. A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies. Mol Ecol 2024; 33:e17274. [PMID: 38279681 DOI: 10.1111/mec.17274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.
Collapse
Affiliation(s)
- Fabian L Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Mammals and Birds, Greenland Institute of Natural Resources (GINR), Nuuk, Greenland
| | - Martin R Ellegaard
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jørgen Rosvold
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hamish A Burnett
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nicolas Dussex
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Brage B Hansen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| |
Collapse
|
42
|
Lin C, Lu Y, Liu S, Wang Z, Yao L, Yin Y, Jiao L. Retrieving complete plastid genomes of endangered Guibourtia timber using hybridization capture for forensic identification and phylogenetic analysis. Forensic Sci Int Genet 2024; 69:103006. [PMID: 38171223 DOI: 10.1016/j.fsigen.2023.103006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/25/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
The high economic value and increased demand for timber have led to illegal logging and overexploitation, threatening wild populations. In this context, there is an urgent need to develop effective and accurate forensic tools for identifying endangered Guibourtia timber species to protect forest ecosystem resources and regulate their trade. In this study, a hybridization capture method was developed and applied to explore the feasibility of retrieving complete plastid genomes from Guibourtia sapwood and heartwood specimens stored in a xylarium (wood collection). We then carried out forensic identification and phylogenetic analyses of Guibourtia within the subfamily Detarioideae. This study is the first to successfully retrieve high-quality plastid genomes from xylarium specimens, with 76.95-99.97% coverage. The enrichment efficiency, sequence depth, and coverage of plastid genomes from sapwood were 16.73 times, 70.47 times and 1.14 times higher, respectively, than those from heartwood. Although the DNA capture efficiency of heartwood was lower than that of sapwood, the hybridization capture method used in this study is still suitable for heartwood DNA analysis. Based on the complete plastid genome, we identified six endangered or commonly traded Guibourtia woods at the species level. This technique also has the potential for geographical traceability, especially for Guibourtia demeusei and Guibourtia ehie. Meanwhile, Bayesian phylogenetic analysis suggested that these six Guibourtia species diverged from closely related species within the subfamily Detarioideae ca. 18 Ma during the Miocene. The DNA reference database established based on the xylarium specimens provides admissible evidence for diversity conservation and evolutionary analyses of endangered Guibourtia species.
Collapse
Affiliation(s)
- Chuanyang Lin
- College of Material Science and Art Design, Inner Mongolia Agricultural University, Hohhot 010018, China; Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yang Lu
- Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China; Wood Collection of Chinese Academy of Forestry, Beijing 100091, China
| | - Shoujia Liu
- Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China; Wood Collection of Chinese Academy of Forestry, Beijing 100091, China
| | - Zhaoshan Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lihong Yao
- College of Material Science and Art Design, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Yafang Yin
- Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China; Wood Collection of Chinese Academy of Forestry, Beijing 100091, China
| | - Lichao Jiao
- Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing 100091, China; Wood Collection of Chinese Academy of Forestry, Beijing 100091, China; China-Central Asia "the Belt and Road" Joint Laboratory on Human and Environment Research, Key Laboratory of Cultural Heritage Research and Conservation, Collaborative Research Centre for Archaeology of the Silk Roads, School of Culture Heritage, Northwest University, Xi'an 710127, China.
| |
Collapse
|
43
|
Verry AJF, Mas-Carrió E, Gibb GC, Dutoit L, Robertson BC, Waters JM, Rawlence NJ. Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho. Mol Ecol 2024; 33:e17227. [PMID: 38018770 DOI: 10.1111/mec.17227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/05/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.
Collapse
Affiliation(s)
- Alexander J F Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Eduard Mas-Carrió
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Gillian C Gibb
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Jonathan M Waters
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| |
Collapse
|
44
|
Gavriil M, Proietto M, Paczia N, Ginolhac A, Halder R, Valceschini E, Sauter T, Linster CL, Sinkkonen L. 2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition. Life Sci Alliance 2024; 7:e202302333. [PMID: 38011998 PMCID: PMC10681907 DOI: 10.26508/lsa.202302333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
2-Hydroxyglutarate (2-HG) is an oncometabolite that accumulates in certain cancers. Gain-of-function mutations in isocitrate dehydrogenase lead to 2-HG accumulation at the expense of alpha-ketoglutarate. Elevated 2-HG levels inhibit histone and DNA demethylases, causing chromatin structure and gene regulation changes with tumorigenic consequences. We investigated the effects of elevated 2-HG levels in Saccharomyces cerevisiae, a yeast devoid of DNA methylation and heterochromatin-associated histone methylation. Our results demonstrate genetic background-dependent gene expression changes and altered H3K4 and H3K36 methylation at specific loci. Analysis of histone demethylase deletion strains indicated that 2-HG inhibits Rph1 sufficiently to induce extensive gene expression changes. Rph1 is the yeast homolog of human KDM4 demethylases and, among the yeast histone demethylases, was the most sensitive to the inhibitory effect of 2-HG in vitro. Interestingly, Rph1 deficiency favors gene repression and leads to further down-regulation of already silenced genes marked by low H3K4 and H3K36 trimethylation, but abundant in H3K36 dimethylation. Our results provide novel insights into the genome-wide effects of 2-HG and highlight Rph1 as its preferential demethylase target.
Collapse
Affiliation(s)
- Marios Gavriil
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Marco Proietto
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Nicole Paczia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Aurelien Ginolhac
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Elena Valceschini
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| |
Collapse
|
45
|
Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C, Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol 2024; 33:e16859. [PMID: 36748324 PMCID: PMC7615563 DOI: 10.1111/mec.16859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/08/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023]
Abstract
Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.
Collapse
Affiliation(s)
- Stefanie Wagner
- Plant Genomic Resources Center (CNRGV), INRAE, Castanet-Tolosan, France
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| | | | - Thibault Leroy
- IRHS UMR1345, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | | | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Patrick Wincker
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | | | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse, France
| |
Collapse
|
46
|
Segawa T, Rey-Iglesia A, Lorenzen ED, Westbury MV. The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations. Proc Biol Sci 2024; 291:20232411. [PMID: 38264778 PMCID: PMC10806438 DOI: 10.1098/rspb.2023.2411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.
Collapse
Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Chuo, Yamanashi, Japan
| | | | | | | |
Collapse
|
47
|
Lebrasseur O, More KD, Orlando L. Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus Evol 2024; 10:vead087. [PMID: 38465241 PMCID: PMC10924538 DOI: 10.1093/ve/vead087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/27/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024] Open
Abstract
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health.
Collapse
Affiliation(s)
- Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, 3 de Febrero 1370 (1426), Ciudad Autónoma de Buenos Aires, Argentina
| | - Kuldeep Dilip More
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
| |
Collapse
|
48
|
Swain T, Pflueger C, Freytag S, Poppe D, Pflueger J, Nguyen T, Li J, Lister R. A modular dCas9-based recruitment platform for combinatorial epigenome editing. Nucleic Acids Res 2024; 52:474-491. [PMID: 38000387 PMCID: PMC10783489 DOI: 10.1093/nar/gkad1108] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Targeted epigenome editing tools allow precise manipulation and investigation of genome modifications, however they often display high context dependency and variable efficacy between target genes and cell types. While systems that simultaneously recruit multiple distinct 'effector' chromatin regulators can improve efficacy, they generally lack control over effector composition and spatial organisation. To overcome this we have created a modular combinatorial epigenome editing platform, called SSSavi. This system is an interchangeable and reconfigurable docking platform fused to dCas9 that enables simultaneous recruitment of up to four different effectors, allowing precise control of effector composition and spatial ordering. We demonstrate the activity and specificity of the SSSavi system and, by testing it against existing multi-effector targeting systems, demonstrate its comparable efficacy. Furthermore, we demonstrate the importance of the spatial ordering of the recruited effectors for effective transcriptional regulation. Together, the SSSavi system enables exploration of combinatorial effector co-recruitment to enhance manipulation of chromatin contexts previously resistant to targeted editing.
Collapse
Affiliation(s)
- Tessa Swain
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Saskia Freytag
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Trung Viet Nguyen
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Ji Kevin Li
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| |
Collapse
|
49
|
Bennasar-Figueras A. The Natural and Clinical History of Plague: From the Ancient Pandemics to Modern Insights. Microorganisms 2024; 12:146. [PMID: 38257973 PMCID: PMC10818976 DOI: 10.3390/microorganisms12010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The human pathogen Yersinia pestis is responsible for bubonic, septicemic, and pneumonic plague. A deeply comprehensive overview of its historical context, bacteriological characteristics, genomic analysis based on ancient DNA (aDNA) and modern strains, and its impact on historical and actual human populations, is explored. The results from multiple studies have been synthesized to investigate the origins of plague, its transmission, and effects on different populations. Additionally, molecular interactions of Y. pestis, from its evolutionary origins to its adaptation to flea-born transmission, and its impact on human and wild populations are considered. The characteristic combinations of aDNA patterns, which plays a decisive role in the reconstruction and analysis of ancient genomes, are reviewed. Bioinformatics is fundamental in identifying specific Y. pestis lineages, and automated pipelines are among the valuable tools in implementing such studies. Plague, which remains among human history's most lethal infectious diseases, but also other zoonotic diseases, requires the continuous investigation of plague topics. This can be achieved by improving molecular and genetic screening of animal populations, identifying ecological and social determinants of outbreaks, increasing interdisciplinary collaborations among scientists and public healthcare providers, and continued research into the characterization, diagnosis, and treatment of these diseases.
Collapse
Affiliation(s)
- Antoni Bennasar-Figueras
- Microbiologia—Departament de Biologia, Universitat de les Illes Balears (UIB), Campus UIB, Carretera de Valldemossa, Km 7.5, 07122 Palma de Mallorca, Spain; ; Tel.: +34-971172778
- Facultat de Medicina, Hospital Universitari Son Espases (HUSE), Universitat de les Illes Balears (UIB), Carretera de Valldemossa, 79, 07122 Palma de Mallorca, Spain
| |
Collapse
|
50
|
Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
Collapse
Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077, Göttingen, Germany
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|