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Lan T, Yang S, Li H, Zhang Y, Li R, Sahu SK, Deng W, Liu B, Shi M, Wang S, Du H, Huang X, Lu H, Liu S, Deng T, Chen J, Wang Q, Han L, Zhou Y, Li Q, Li D, Kristiansen K, Wan QH, Liu H, Fang SG. Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives. Proc Natl Acad Sci U S A 2024; 121:e2406343121. [PMID: 39186654 PMCID: PMC11388402 DOI: 10.1073/pnas.2406343121] [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: 03/28/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.
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Affiliation(s)
- Tianming Lan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shangchen Yang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haimeng Li
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
| | - Yi Zhang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Wenwen Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Boyang Liu
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shiqing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Hanyu Du
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyu Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Haorong Lu
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Shanlin Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Jin Chen
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Lei Han
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yajie Zhou
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Qiye Li
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China
| | - Qiu-Hong Wan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Sheng-Guo Fang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Shock BC, Jones HH, Garrett KB, Hernandez SM, Burchfield HJ, Haman K, Schwantje H, Telford SR, Cunningham MW, Yabsley MJ. Description of B abesia coryicola sp. nov. from Florida pumas ( Puma concolor coryi) from southern Florida, USA. Int J Parasitol Parasites Wildl 2024; 24:100963. [PMID: 39169986 PMCID: PMC11337720 DOI: 10.1016/j.ijppaw.2024.100963] [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: 05/31/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 08/23/2024]
Abstract
Previously, a high prevalence of piroplasms has been reported from Florida pumas (Puma concolor coryi) from southern Florida. In the current study, we describe the biological characteristics of a novel Babesia species in Florida pumas. Ring-stage trophozoites were morphologically similar to trophozoites of numerous small babesids of felids including B. leo, B. felis, and Cytauxzoon felis. Parasitemias in Florida pumas were very low (<1%) and hematologic values of 25 Babesia-infected Florida pumas were within normal ranges for P. concolor. Phylogenetic analysis of near full-length 18S rRNA gene, β-tubulin, cytochrome c oxidase subunit I, cytochrome c oxidase subunit III, and cytochrome b gene sequences indicated that this Babesia species is a member of the Babesia sensu stricto clade and is related to groups of Babesia spp. from carnivores or ungulates, although the closest group varied by gene target. Internal transcribed spacer (ITS)-1 region sequences from this Babesia sp. from 19 Florida pumas were 85.7-99.5% similar to each other and ∼88% similar to B. odocoilei. Similarly, an ITS-2 sequence from one puma was 96% similar to B. bigemina and 92% similar to a Babesia sp. from a red panda (Ailurus fulgens). Infected pumas were positive for antibodies that reacted with B. odocoilei, B. canis, and B. bovis antigens with titers of 1:256, 1:128, and 1:128, respectively. No serologic reactivity was noted for Theileria equi. No molecular evidence of congenital infection was detected in 24 kittens born to 11 Babesia-infected female pumas. Pumas from other populations in the United States [Louisiana (n = 1), North Dakota (n = 5) and Texas (n = 28)], British Columbia, Canada (n = 9), and Costa Rica (n = 2) were negative for this Babesia sp. Collectively, these data provide morphologic, serologic, genetic, and natural history data for this novel Babesia sp. which we propose the name Babesia coryicola sp. nov. sp. This is the first description of a felid-associated Babesia species in North America.
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Affiliation(s)
- Barbara C. Shock
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Håkon H. Jones
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Kayla B. Garrett
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Sonia M. Hernandez
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Holly J. Burchfield
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Katie Haman
- Wildlife Program, Washington Department of Fish and Wildlife, 1111 Washington Street SE, Olympia, WA, 98504, USA
| | - Helen Schwantje
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Nanaimo, British Columbia, Canada
| | - Sam R. Telford
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Mark W. Cunningham
- Florida Fish and Wildlife Conservation Commission, Gainesville, FL, 32601, USA
| | - Michael J. Yabsley
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
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Lott MJ, Frankham GJ, Eldridge MDB, Alquezar‐Planas DE, Donnelly L, Zenger KR, Leigh KA, Kjeldsen SR, Field MA, Lemon J, Lunney D, Crowther MS, Krockenberger MB, Fisher M, Neaves LE. Reversing the decline of threatened koala ( Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes. Ecol Evol 2024; 14:e11700. [PMID: 39091325 PMCID: PMC11289790 DOI: 10.1002/ece3.11700] [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: 02/05/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.
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Affiliation(s)
- Matthew J. Lott
- Australian Museum Research InstituteSydneyNew South WalesAustralia
| | | | | | | | - Lily Donnelly
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Kellie A. Leigh
- Science for Wildlife LtdMount VictoriaNew South WalesAustralia
| | - Shannon R. Kjeldsen
- Molecular Ecology and Evolutionary Laboratory, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityTownsvilleQueenslandAustralia
- Immunogenomics LabGarvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - John Lemon
- JML Environmental ConsultantsArmidaleNew South WalesAustralia
- School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNew South WalesAustralia
| | - Daniel Lunney
- Australian Museum Research InstituteSydneyNew South WalesAustralia
- Department of Planning and EnvironmentParramattaNew South WalesAustralia
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mathew S. Crowther
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark B. Krockenberger
- Sydney School of Veterinary ScienceUniversity of SydneyCamperdownNew South WalesAustralia
| | - Mark Fisher
- 3D Ecology MappingEmerald BeachNew South WalesAustralia
| | - Linda E. Neaves
- Fenner School of Environment and SocietyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
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4
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Srigyan M, Schubert BW, Bushell M, Santos SHD, Figueiró HV, Sacco S, Eizirik E, Shapiro B. Mitogenomic analysis of a late Pleistocene jaguar from North America. J Hered 2024; 115:424-431. [PMID: 38150503 PMCID: PMC11235123 DOI: 10.1093/jhered/esad082] [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: 08/06/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023] Open
Abstract
The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.
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Affiliation(s)
- Megha Srigyan
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Blaine W Schubert
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Matthew Bushell
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Sarah H D Santos
- Department of Biology, University of Western Ontario, London, ON, Canada
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Henrique Vieira Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Environmental Genomics Group, Vale Institute of Technology, Belem, PA, Brazil
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [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] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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Pozo G, Albuja-Quintana M, Larreátegui L, Gutiérrez B, Fuentes N, Alfonso-Cortés F, Torres MDL. First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (BETHESDA, MD.) 2024; 14:jkae014. [PMID: 38244218 PMCID: PMC10917520 DOI: 10.1093/g3journal/jkae014] [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: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.
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Affiliation(s)
- Gabriela Pozo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Martina Albuja-Quintana
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Lizbeth Larreátegui
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Bernardo Gutiérrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Nathalia Fuentes
- Proyecto Washu/Fundación Naturaleza y Arte, Quito 170521, Ecuador
| | | | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
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7
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Barazandeh M, Kriti D, Fickel J, Nislow C. The Addis Ababa Lions: Whole-Genome Sequencing of a Rare and Precious Population. Genome Biol Evol 2024; 16:evae021. [PMID: 38302110 PMCID: PMC10871700 DOI: 10.1093/gbe/evae021] [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: 05/31/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
Lions are widely known as charismatic predators that once roamed across the globe, but their populations have been greatly affected by environmental factors and human activities over the last 150 yr. Of particular interest is the Addis Ababa lion population, which has been maintained in captivity at around 20 individuals for over 75 yr, while many wild African lion populations have become extinct. In order to understand the molecular features of this unique population, we conducted a whole-genome sequencing study on 15 Addis Ababa lions and detected 4.5 million distinct genomic variants compared with the reference African lion genome. Using functional annotation, we identified several genes with mutations that potentially impact various traits such as mane color, body size, reproduction, gastrointestinal functions, cardiovascular processes, and sensory perception. These findings offer valuable insights into the genetics of this threatened lion population.
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Affiliation(s)
- Marjan Barazandeh
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jörns Fickel
- Institute for Biochemistry and Biology, University Potsdam, Potsdam, Germany
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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9
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Pumpitakkul V, Chetruengchai W, Srichomthong C, Phokaew C, Pootakham W, Sonthirod C, Nawae W, Tongsima S, Wangkumhang P, Wilantho A, Utara Y, Thongpakdee A, Sanannu S, Maikaew U, Khuntawee S, Changpetch W, Phromwat P, Raschasin K, Sarnkhaeveerakul P, Supapannachart P, Buthasane W, Pukazhenthi BS, Koepfli KP, Suriyaphol P, Tangphatsornruang S, Suriyaphol G, Shotelersuk V. Comparative genomics and genome-wide SNPs of endangered Eld's deer provide breeder selection for inbreeding avoidance. Sci Rep 2023; 13:19806. [PMID: 37957263 PMCID: PMC10643696 DOI: 10.1038/s41598-023-47014-x] [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: 05/23/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023] Open
Abstract
Eld's deer, a conserved wildlife species of Thailand, is facing inbreeding depression, particularly in the captive Siamese Eld's deer (SED) subspecies. In this study, we constructed genomes of a male SED and a male Burmese Eld's deer (BED), and used genome-wide single nucleotide polymorphisms to evaluate the genetic purity and the inbreeding status of 35 SED and 49 BED with limited pedigree information. The results show that these subspecies diverged approximately 1.26 million years ago. All SED were found to be purebred. A low proportion of admixed SED genetic material was observed in some BED individuals. Six potential breeders from male SED with no genetic relation to any female SED and three purebred male BED with no relation to more than 10 purebred female BED were identified. This study provides valuable insights about Eld's deer populations and appropriate breeder selection in efforts to repopulate this endangered species while avoiding inbreeding.
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Affiliation(s)
- Vichayanee Pumpitakkul
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichomthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Wanapinun Nawae
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Pongsakorn Wangkumhang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Alisa Wilantho
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Yongchai Utara
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Ampika Thongpakdee
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Saowaphang Sanannu
- Zoological Park Organization of Thailand, Animal Conservation and Research Institute, Bangkok, 10800, Thailand
| | - Umaporn Maikaew
- Khao Kheow Open Zoo, Zoological Park Organization of Thailand, Chonburi, 20110, Thailand
| | - Suphattharaphonnaphan Khuntawee
- Ubon Ratchathani Zoo, Zoological Park Organization of Thailand, Ubon Ratchathani District, Ubon Ratchathani, 34000, Thailand
| | - Wirongrong Changpetch
- Nakhon Ratchasima Zoo, Zoological Park Organization of Thailand, Nakhon Ratchasima, 30000, Thailand
| | - Phairot Phromwat
- Huai Kha Khaeng Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Uthai Thani, 61160, Thailand
| | - Kacharin Raschasin
- Chulabhorn Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Sisaket, 33140, Thailand
| | - Phunyaphat Sarnkhaeveerakul
- Banglamung Wildlife Breeding Center, Department of National Parks, Wildlife and Plant Conservation, Chonburi, 20150, Thailand
| | - Pannawat Supapannachart
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Wannapol Buthasane
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Budhan S Pukazhenthi
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, 22630, USA
| | - Prapat Suriyaphol
- Office for Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand.
| | - Gunnaporn Suriyaphol
- Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand
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10
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du Plessis SJ, Blaxter M, Koepfli KP, Chadwick EA, Hailer F. Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods. Mol Biol Evol 2023; 40:msad207. [PMID: 37713621 PMCID: PMC10630326 DOI: 10.1093/molbev/msad207] [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: 03/28/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s-1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.
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Affiliation(s)
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Centre for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | | | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, UK
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11
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Yuan J, Wang G, Zhao L, Kitchener AC, Sun T, Chen W, Huang C, Wang C, Xu X, Wang J, Lu H, Xu L, Jiangzuo Q, Murphy WJ, Wu D, Li G. How genomic insights into the evolutionary history of clouded leopards inform their conservation. SCIENCE ADVANCES 2023; 9:eadh9143. [PMID: 37801506 PMCID: PMC10558132 DOI: 10.1126/sciadv.adh9143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Clouded leopards (Neofelis spp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comprehensive investigation of the whole genomes, population genetics, and adaptive evolution of Neofelis. Our results indicate the genus Neofelis arose during the Pleistocene, coinciding with glacial-induced climate changes to the distributions of savannas and rainforests, and signatures of natural selection associated with genes functioning in tooth, pigmentation, and tail development, associated with clouded leopards' unique adaptations. Our study highlights high-altitude adaptation as the main factor driving nontaxonomic population differentiation in Neofelis nebulosa. Population declines and inbreeding have led to reduced genetic diversity and the accumulation of deleterious variation that likely affect reproduction of clouded leopards, highlighting the urgent need for effective conservation efforts.
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Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH9 3PX, UK
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Huimeng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
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12
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Wilder AP, Supple MA, Subramanian A, Mudide A, Swofford R, Serres-Armero A, Steiner C, Koepfli KP, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK, Consortium Z, Ryder OA, Shapiro B. The contribution of historical processes to contemporary extinction risk in placental mammals. Science 2023; 380:eabn5856. [PMID: 37104572 PMCID: PMC10184782 DOI: 10.1126/science.abn5856] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/08/2023] [Indexed: 04/29/2023]
Abstract
Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.
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Affiliation(s)
- Aryn P. Wilder
- Conservation Genetics, San Diego Zoo Wildlife Alliance; Escondido, CA 92027, USA
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz; Santa Cruz, CA 95064, USA
| | | | | | - Ross Swofford
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
| | - Aitor Serres-Armero
- Institute of Evolutionary Biology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra; Barcelona, 08003, Spain
| | - Cynthia Steiner
- Conservation Genetics, San Diego Zoo Wildlife Alliance; Escondido, CA 92027, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University; Front Royal, VA 22630, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park; Washington, DC, 30008, USA
- Computer Technologies Laboratory, ITMO University; St. Petersburg, 197101, Russia
| | | | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University; Uppsala, 751 32, Sweden
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra; Barcelona, 08003, Spain
- Catalan Institution of Research and Advanced Studies; Barcelona, 08010, Spain
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology; Barcelona, 08028, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona; Barcelona, 08193, Spain
| | - Violeta Munoz Fuentes
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus; Hinxton, UK
| | - Kathleen Foley
- College of Law, University of Iowa; Iowa City, IA 52242, USA
- Lehigh University, Biological Sciences; Bethlehem, PA 18015, USA
| | - Wynn K. Meyer
- Lehigh University, Biological Sciences; Bethlehem, PA 18015, USA
| | | | - Oliver A. Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance; Escondido, CA 92027, USA
- Department of Evolution, Behavior and Ecology, Division of Biology, University of California, San Diego; La Jolla, CA 92039 USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz; Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz; Santa Cruz, CA 95064, USA
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13
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Li A, Yang Q, Li R, Dai X, Cai K, Lei Y, Jia K, Jiang Y, Zan L. Chromosome-level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity. Mol Ecol 2023; 32:1323-1334. [PMID: 35467052 DOI: 10.1111/mec.16483] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/29/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The takin (Budorcas taxicolor) is one of the largest bovid herbivores in the subfamily Caprinae. The takin is at high risk of extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed the first reference genome of Bu. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb, which were anchored onto 25+XY chromosomes. We found that the takin was more closely related to muskox than to other Caprinae species. Compared to the common ancestral karyotype of bovidae (2n = 60), we found the takin (2n = 52) experienced four chromosome fusions and one large translocation. Furthermore, we resequenced nine golden takins from the main distribution area, the Qinling Mountains, and identified 3.3 million single nucleotide polymorphisms. The genetic diversity of takin was very low (θπ = 0.00028 and heterozygosity =0.00038), among the lowest detected in domestic and wild mammals. Takin genomes showed a high inbreeding coefficient (FROH =0.217), suggesting severe inbreeding depression. The demographic history showed that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into their evolution.
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Affiliation(s)
- Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qimeng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuelei Dai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Keli Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinghu Lei
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Kangsheng Jia
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
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14
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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15
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Genomes of endangered great hammerhead and shortfin mako sharks reveal historic population declines and high levels of inbreeding in great hammerhead. iScience 2022; 26:105815. [PMID: 36632067 PMCID: PMC9826928 DOI: 10.1016/j.isci.2022.105815] [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: 08/08/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and <1% in ROH > 1 Mbp. Both these sharks experienced precipitous declines in effective population size (Ne) over the last 250 thousand years. While shortfin mako exhibited a large historical Ne that may have enabled the retention of higher genetic variation, the genomic data suggest a possibly more concerning picture for the great hammerhead, and a need for evaluation with additional individuals.
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16
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Cockerill CA, Hasselgren M, Dussex N, Dalén L, von Seth J, Angerbjörn A, Wallén JF, Landa A, Eide NE, Flagstad Ø, Ehrich D, Sokolov A, Sokolova N, Norén K. Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox ( Vulpes lagopus). Genes (Basel) 2022; 13:2124. [PMID: 36421799 PMCID: PMC9690288 DOI: 10.3390/genes13112124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck in the late 19th century. The future persistence of the entire Scandinavian population is highly dependent on the northernmost Fennoscandian subpopulations (Scandinavia and the Kola Peninsula), to provide a link to the viable Siberian population. By analyzing 43 arctic fox genomes, we quantified genomic variation and inbreeding in these populations. Signatures of genome erosion increased from Siberia to northern Sweden indicating a stepping-stone model of connectivity. In northern Fennoscandia, runs of homozygosity (ROH) were on average ~1.47-fold longer than ROH found in Siberia, stretching almost entire scaffolds. Moreover, consistent with recent inbreeding, northern Fennoscandia harbored more homozygous deleterious mutations, whereas Siberia had more in heterozygous state. This study underlines the value of documenting genome erosion following population fragmentation to identify areas requiring conservation priority. With the increasing fragmentation and isolation of Arctic habitats due to global warming, understanding the genomic and demographic consequences is vital for maintaining evolutionary potential and preventing local extinctions.
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Affiliation(s)
| | - Malin Hasselgren
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Nicolas Dussex
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
| | - Love Dalén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
| | - Johanna von Seth
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Johan F. Wallén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Arild Landa
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Nina E. Eide
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | | | - Dorothee Ehrich
- Department of Arctic and Marine Biology, UiT Arctic University of Tromsø, 9037 Tromsø, Norway
| | - Aleksandr Sokolov
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str. 21, 629400 Labytnangi, Russia
| | - Natalya Sokolova
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str. 21, 629400 Labytnangi, Russia
| | - Karin Norén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
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17
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Zink RM, Klicka LB. The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.971280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.
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18
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Ochoa A, Onorato DP, Roelke-Parker ME, Culver M, Fitak RR. Give and Take: Effects of Genetic Admixture on Mutation Load in Endangered Florida Panthers. J Hered 2022; 113:491-499. [PMID: 35930593 DOI: 10.1093/jhered/esac037] [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: 01/19/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.
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Affiliation(s)
- Alexander Ochoa
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL
| | - Melody E Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD
| | - Melanie Culver
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, and School of Natural Resources and the Environment, University of Arizona, Tucson, AZ
| | - Robert R Fitak
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
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19
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Weaver S, McGaugh SE, Kono TJY, Macip-Rios R, Gluesenkamp AG. Assessing genomic and ecological differentiation among subspecies of the Rough-footed Mud Turtle, Kinosternon hirtipes. J Hered 2022; 113:538-551. [PMID: 35922036 DOI: 10.1093/jhered/esac036] [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: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Combining genetic and ecological measures of differentiation can provide compelling evidence for ecological and genetic divergence among lineages. The Rough-footed Mud Turtle, Kinosternon hirtipes, is distributed from the Trans-Pecos region of Texas to the highlands of Central Mexico and contains six described subspecies, five of which are extant. We use ddRAD sequencing and species distribution models to assess levels of ecological and genetic differentiation among these subspecies. We also predict changes in climatically suitable habitat under different climate change scenarios and assess levels of genetic diversity and inbreeding within each lineage. Our results show that there is strong genetic and ecological differentiation among multiple lineages within K. hirtipes, and that this differentiation appears to be the result of vicariance associated with the Trans-Mexican Volcanic Belt. We propose changes to subspecies designations to more accurately reflect the evolutionary relationships among populations and assess threats to each subspecies.
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Affiliation(s)
- Sam Weaver
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Thomas J Y Kono
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Rodrigo Macip-Rios
- Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex Hacienda de San José de la Huerta, CP 58190 Morelia, Michoacán, México.,Laboratorio Nacional de Síntesis Ecológica, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex Hacienda de San José de la Huerta, CP 58190 Morelia, Michoacán, México
| | - Andrew G Gluesenkamp
- Center for Conservation and Research, San Antonio Zoo, 3903 N. St. Mary's Street, San Antonio, Texas 78212 USA
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20
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Alvarez‐Estape M, Fontsere C, Serres‐Armero A, Kuderna LFK, Dobrynin P, Guidara H, Pukazhenthi BS, Koepfli K, Marques‐Bonet T, Moreno E, Lizano E. Insights from the rescue and breeding management of Cuvier's gazelle ( Gazella cuvieri) through whole-genome sequencing. Evol Appl 2022; 15:351-364. [PMID: 35386395 PMCID: PMC8965372 DOI: 10.1111/eva.13336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022] Open
Abstract
Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier's gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. Here, we aim to determine the genetic consequences of this reintroduction event by assessing the genetic diversity of the founder stock as well as of their descendants. We present the first whole-genome sequencing dataset of 30 Cuvier's gazelles including captive-bred animals, animals born in Tunisia after a reintroduction and individuals from a genetically unrelated Moroccan population. Our analyses revealed no difference between the founder and the offspring cohorts in genome-wide heterozygosity and inbreeding levels, and in the amount and length of runs of homozygosity. The captive but unmanaged Moroccan gazelles have the lowest genetic diversity of all genomes analysed. Our findings demonstrate that the Cuvier's gazelle captive breeding programme can serve as source populations for future reintroductions of this species. We believe that this study can serve as a starting point for global applications of genomics to the conservation plan of this species.
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Affiliation(s)
| | | | | | | | - Pavel Dobrynin
- Computer Technologies LaboratoryITMO UniversitySt. PetersburgRussian Federation
- Center for Species SurvivalNational Zoological ParkSmithsonian Conservation Biology InstituteFront RoyalVirginiaUSA
- Center for Species SurvivalNational Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
| | | | - Budhan S. Pukazhenthi
- Center for Species SurvivalNational Zoological ParkSmithsonian Conservation Biology InstituteFront RoyalVirginiaUSA
- Center for Species SurvivalNational Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
| | - Klaus‐Peter Koepfli
- Computer Technologies LaboratoryITMO UniversitySt. PetersburgRussian Federation
- Center for Species SurvivalNational Zoological ParkSmithsonian Conservation Biology InstituteFront RoyalVirginiaUSA
- Center for Species SurvivalNational Zoological ParkSmithsonian Conservation Biology InstituteWashingtonDistrict of ColumbiaUSA
- Smithsonian‐Mason School of ConservationFront RoyalVirginiaUSA
| | - Tomas Marques‐Bonet
- Institute of Evolutionary Biology, (UPF‐CSIC)PRBBBarcelonaSpain
- CNAG‐CRGCentre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Universitat Autònoma de Barcelona (UAB)Edifici ICTA‐ICPInstitut Català de Paleontologia Miquel CrusafontBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
| | - Eulalia Moreno
- Dept. Ecología Funcional y EvolutivaEstación Experimental de Zonas Áridas‐CSICAlmeríaSpain
| | - Esther Lizano
- Institute of Evolutionary Biology, (UPF‐CSIC)PRBBBarcelonaSpain
- Universitat Autònoma de Barcelona (UAB)Edifici ICTA‐ICPInstitut Català de Paleontologia Miquel CrusafontBarcelonaSpain
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21
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Lu CW, Yao CT, Hung CM. Domestication obscures genomic estimates of population history. Mol Ecol 2021; 31:752-766. [PMID: 34779057 DOI: 10.1111/mec.16277] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022]
Abstract
Domesticated species are valuable models to examine phenotypic evolution, and knowledge on domestication history is critical for understanding the trajectories of evolutionary changes. Sequentially Markov Coalescent models are often used to infer domestication history. However, domestication practices may obscure the signal left by population history, affecting demographic inference. Here we assembled the genomes of a recently domesticated species-the society finch-and its parent species-the white-rumped munia-to examine its domestication history. We applied genomic analyses to two society finch breeds and white-rumped munias to test whether domestication of the former resulted from inbreeding or hybridization. The society finch showed longer and more runs of homozygosity and lower genomic heterozygosity than the white-rumped munia, supporting an inbreeding origin in the former. Blocks of white-rumped munia and other ancestry in society finch genomes showed similar genetic distance between the two taxa, inconsistent with the hybridization origin hypothesis. We then applied two Sequentially Markov Coalescent models-psmc and smc++-to infer the demographic histories of both. Surprisingly, the two models did not reveal a recent population bottleneck, but instead the psmc model showed a specious, dramatic population increase in the society finch. Subsequently, we used simulated genomes based on an array of demographic scenarios to demonstrate that recent inbreeding, not hybridization, caused the distorted psmc population trajectory. Such analyses could have misled our understanding of the domestication process. Our findings stress caution when interpreting the histories of recently domesticated species inferred by psmc, arguing that these histories require multiple analyses to validate.
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Affiliation(s)
- Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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22
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Lucena-Perez M, Kleinman-Ruiz D, Marmesat E, Saveljev AP, Schmidt K, Godoy JA. Bottleneck-associated changes in the genomic landscape of genetic diversity in wild lynx populations. Evol Appl 2021; 14:2664-2679. [PMID: 34815746 PMCID: PMC8591332 DOI: 10.1111/eva.13302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 01/06/2023] Open
Abstract
Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole-genome diversity patterns in populations with and without severe recent documented declines of Iberian (Lynx pardinus, n = 31) and Eurasian lynx (Lynx lynx, n = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher θ W diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low-frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra-conserved elements can be used as a sensitive and easy-to-apply signature of genetic erosion in wild populations.
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Affiliation(s)
- Maria Lucena-Perez
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Daniel Kleinman-Ruiz
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
- Departamento de Genética Facultad de Biología Universidad Complutense Madrid Spain
| | - Elena Marmesat
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - Alexander P Saveljev
- Department of Animal Ecology Russian Research Institute of Game Management and Fur Farming Kirov Russia
| | - Krzysztof Schmidt
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - José A Godoy
- Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain
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23
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Tamazian G, Dobrynin P, Zhuk A, Zhernakova DV, Perelman PL, Serdyukova NA, Graphodatsky AS, Komissarov A, Kliver S, Cherkasov N, Scott AF, Mohr DW, Koepfli KP, O'Brien SJ, Krasheninnikova K. Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi. J Hered 2021; 112:540-548. [PMID: 34146095 PMCID: PMC8558579 DOI: 10.1093/jhered/esab036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/17/2021] [Indexed: 11/12/2022] Open
Abstract
The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification.
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Affiliation(s)
- Gaik Tamazian
- Faculty of Biology, Saint Petersburg State University, St. Petersburg, Russia
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
| | - Anna Zhuk
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
| | - Daria V Zhernakova
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | | | | | - Aleksey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, St. Petersburg, Russia
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Novosibirsk, Russia
| | - Nikolay Cherkasov
- Faculty of Biology, Saint Petersburg State University, St. Petersburg, Russia.,Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, St. Petersburg, Russia
| | - Alan F Scott
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David W Mohr
- Genetic Resources Core Facility, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, VA, USA.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Stephen J O'Brien
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia.,Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Ksenia Krasheninnikova
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia.,Wellcome Trust Sanger Institute, Cambridge, UK
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24
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Schultz DT, Francis WR, McBroome JD, Christianson LM, Haddock SHD, Green RE. A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis. G3 (BETHESDA, MD.) 2021; 11:jkab302. [PMID: 34545398 PMCID: PMC8527503 DOI: 10.1093/g3journal/jkab302] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/18/2021] [Indexed: 11/12/2022]
Abstract
Here, we present a karyotype, a chromosome-scale genome assembly, and a genome annotation from the ctenophore Hormiphora californensis (Ctenophora: Cydippida: Pleurobrachiidae). The assembly spans 110 Mb in 44 scaffolds and 99.47% of the bases are contained in 13 scaffolds. Chromosome micrographs and Hi-C heatmaps support a karyotype of 13 diploid chromosomes. Hi-C data reveal three large heterozygous inversions on chromosome 1, and one heterozygous inversion shares the same gene order found in the genome of the ctenophore Pleurobrachia bachei. We find evidence that H. californensis and P. bachei share thirteen homologous chromosomes, and the same karyotype of 1n = 13. The manually curated PacBio Iso-Seq-based genome annotation reveals complex gene structures, including nested genes and trans-spliced leader sequences. This chromosome-scale assembly is a useful resource for ctenophore biology and will aid future studies of metazoan evolution and phylogenetics.
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Affiliation(s)
- Darrin T Schultz
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Warren R Francis
- Department of Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Jakob D McBroome
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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25
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Assisted gene flow using cryopreserved sperm in critically endangered coral. Proc Natl Acad Sci U S A 2021; 118:2110559118. [PMID: 34493583 PMCID: PMC8463791 DOI: 10.1073/pnas.2110559118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/06/2021] [Indexed: 12/30/2022] Open
Abstract
Global change threatens the genetic diversity of economically important and foundational ecosystem-building species such as corals. We tested whether cryopreserved coral sperm could be used to transfer genetic diversity among genetically isolated populations of the critically endangered Caribbean elkhorn coral, Acropora palmata. Here we report successful assisted gene flow (AGF) in corals using cryopreserved sperm, yielding the largest living wildlife population ever created from cryopreserved cells. Furthermore, we produced direct evidence that genetically distinct populations of Caribbean coral can interbreed. Thus, we demonstrated that sperm cryopreservation can enable efficient, large-scale AGF in corals. This form of assisted genetic migration can enhance genetic diversity and help critically endangered species adapt to local environments in the face of rapid global change. Assisted gene flow (AGF) is a conservation intervention to accelerate species adaptation to climate change by importing genetic diversity into at-risk populations. Corals exemplify both the need for AGF and its technical challenges; corals have declined in abundance, suffered pervasive reproductive failures, and struggled to adapt to climate change, yet mature corals cannot be easily moved for breeding, and coral gametes lose viability within hours. Here, we report the successful demonstration of AGF in corals using cryopreserved sperm that was frozen for 2 to 10 y. We fertilized Acropora palmata eggs from the western Caribbean (Curaçao) with cryopreserved sperm from genetically distinct populations in the eastern and central Caribbean (Florida and Puerto Rico, respectively). We then confirmed interpopulation parentage in the Curaçao–Florida offspring using 19,696 single-nucleotide polymorphism markers. Thus, we provide evidence of reproductive compatibility of a Caribbean coral across a recognized barrier to gene flow. The 6-mo survival of AGF offspring was 42%, the highest ever achieved in this species, yielding the largest wildlife population ever raised from cryopreserved material. By breeding a critically endangered coral across its range without moving adults, we show that AGF using cryopreservation is a viable conservation tool to increase genetic diversity in threatened marine populations.
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26
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Ochoa A, Gibbs HL. Genomic signatures of inbreeding and mutation load in a threatened rattlesnake. Mol Ecol 2021; 30:5454-5469. [PMID: 34448259 DOI: 10.1111/mec.16147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their genetic load, but recent work suggests that the impact of load may be minimized by purging resulting from long-term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use individual genome resequencing data to compare levels of inbreeding, levels of genetic load (estimated as mutation load) and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus), which exist in small isolated populations, and closely related yet outbred Western massasauga rattlesnakes (Sistrurus tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of runs of homozygosity of varying sizes, indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of mutation load in the form of greater numbers of derived deleterious mutations compared to S. catenatus, presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped species-level drift effects within S. catenatus populations were in general more frequent and more often found in homozygous genotypes than in S. tergeminus, suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations for most mutations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present, which impacts implementation of conservation actions such as genetic rescue.
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Affiliation(s)
- Alexander Ochoa
- Department of Evolution, Ecology, and Organismal Biology, Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, Ohio, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, Ohio, USA
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Saremi NF, Oppenheimer J, Vollmers C, O'Connell B, Milne SA, Byrne A, Yu L, Ryder OA, Green RE, Shapiro B. An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus. J Hered 2021; 112:377-384. [PMID: 33882130 PMCID: PMC8280923 DOI: 10.1093/jhered/esab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
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Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Christopher Vollmers
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Brendan O'Connell
- Department of Medical and Molecular Genetics, Oregon Health & Science University, Portland, OR
| | - Shard A Milne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Byrne
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | | | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
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Escoda L, Castresana J. The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species. Evol Appl 2021; 14:1898-1913. [PMID: 34295371 PMCID: PMC8288019 DOI: 10.1111/eva.13249] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 01/23/2023] Open
Abstract
The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.
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Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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Hasselgren M, Dussex N, von Seth J, Angerbjörn A, Olsen RA, Dalén L, Norén K. Genomic and fitness consequences of inbreeding in an endangered carnivore. Mol Ecol 2021; 30:2790-2799. [PMID: 33955096 DOI: 10.1111/mec.15943] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 12/28/2022]
Abstract
Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower FROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.
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Affiliation(s)
| | - Nicolas Dussex
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Johanna von Seth
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
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30
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Zecherle LJ, Nichols HJ, Bar‐David S, Brown RP, Hipperson H, Horsburgh GJ, Templeton AR. Subspecies hybridization as a potential conservation tool in species reintroductions. Evol Appl 2021; 14:1216-1224. [PMID: 34025762 PMCID: PMC8127701 DOI: 10.1111/eva.13191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/11/2020] [Accepted: 12/27/2020] [Indexed: 11/30/2022] Open
Abstract
Reintroductions are a powerful tool for the recovery of endangered species. However, their long-term success is strongly influenced by the genetic diversity of the reintroduced population. The chances of population persistence can be improved by enhancing the population's adaptive ability through the mixing of individuals from different sources. However, where source populations are too diverse the reintroduced population could also suffer from outbreeding depression or unsuccessful admixture due to behavioural or genetic barriers. For the reintroduction of Asiatic wild ass Equus hemionus ssp. in Israel, a breeding core was created from individuals of two different subspecies (E. h. onager & E. h. kulan). Today the population comprises approximately 300 individuals and displays no signs of outbreeding depression. The aim of this study was a population genomic evaluation of this conservation reintroduction protocol. We used maximum likelihood methods and genetic clustering analyses to investigate subspecies admixture and test for spatial autocorrelation based on subspecies ancestry. Further, we analysed heterozygosity and effective population sizes in the breeding core prior to release and the current wild population. We discovered high levels of subspecies admixture in the breeding core and wild population, consistent with a significant heterozygote excess in the breeding core. Furthermore, we found no signs of spatial autocorrelation associated with subspecies ancestry in the wild population. Inbreeding and variance effective population size estimates were low. Our results indicate no genetic or behavioural barriers to admixture between the subspecies and suggest that their hybridization has led to greater genetic diversity in the reintroduced population. The study provides rare empirical evidence of the successful application of subspecies hybridization in a reintroduction. It supports use of intraspecific hybridization as a tool to increase genetic diversity in conservation translocations.
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Affiliation(s)
- Lilith J. Zecherle
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | | | - Shirli Bar‐David
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Richard P. Brown
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Gavin J. Horsburgh
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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32
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Novak BJ, Phelan R, Weber M. U.S. conservation translocations: Over a century of intended consequences. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Pečnerová P, Garcia-Erill G, Liu X, Nursyifa C, Waples RK, Santander CG, Quinn L, Frandsen P, Meisner J, Stæger FF, Rasmussen MS, Brüniche-Olsen A, Hviid Friis Jørgensen C, da Fonseca RR, Siegismund HR, Albrechtsen A, Heller R, Moltke I, Hanghøj K. High genetic diversity and low differentiation reflect the ecological versatility of the African leopard. Curr Biol 2021; 31:1862-1871.e5. [PMID: 33636121 DOI: 10.1016/j.cub.2021.01.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
Large carnivores are generally sensitive to ecosystem changes because their specialized diet and position at the top of the trophic pyramid is associated with small population sizes. Accordingly, low genetic diversity at the whole-genome level has been reported for all big cat species, including the widely distributed leopard. However, all previous whole-genome analyses of leopards are based on the Far Eastern Amur leopards that live at the extremity of the species' distribution and therefore are not necessarily representative of the whole species. We sequenced 53 whole genomes of African leopards. Strikingly, we found that the genomic diversity in the African leopard is 2- to 5-fold higher than in other big cats, including the Amur leopard, likely because of an exceptionally high effective population size maintained by the African leopard throughout the Pleistocene. Furthermore, we detected ongoing gene flow and very low population differentiation within African leopards compared with those of other big cats. We corroborated this by showing a complete absence of an otherwise ubiquitous equatorial forest barrier to gene flow. This sets the leopard apart from most other widely distributed large African mammals, including lions. These results revise our understanding of trophic sensitivity and highlight the remarkable resilience of the African leopard, likely because of its extraordinary habitat versatility and broad dietary niche.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Ryan K Waples
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Copenhagen Zoo, Research and Conservation, Roskildevej 32, 2000 Frederiksberg, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Frederik Filip Stæger
- 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
| | - Anna Brüniche-Olsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark; Department of Forestry and Natural Resources, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | | | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, 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.
| | - Ida Moltke
- 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.
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Tarlinton RE, Fabijan J, Hemmatzadeh F, Meers J, Owen H, Sarker N, Seddon JM, Simmons G, Speight N, Trott DJ, Woolford L, Emes RD. Transcriptomic and genomic variants between koala populations reveals underlying genetic components to disorders in a bottlenecked population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01340-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractHistorical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.
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35
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Hohenlohe PA, Funk WC, Rajora OP. Population genomics for wildlife conservation and management. Mol Ecol 2020; 30:62-82. [PMID: 33145846 PMCID: PMC7894518 DOI: 10.1111/mec.15720] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
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36
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A comparative genomics multitool for scientific discovery and conservation. Nature 2020; 587:240-245. [PMID: 33177664 PMCID: PMC7759459 DOI: 10.1038/s41586-020-2876-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity. A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.
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