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Si J, Dai D, Gorkhali NA, Wang M, Wang S, Sapkota S, Kadel RC, Sadaula A, Dhakal A, Faruque MO, Omar AI, Sari EM, Ashari H, Dagong MIA, Yindee M, Rushdi HE, Elregalaty H, Amin A, Radwan MA, Pham LD, Hulugalla WMMP, Silva GLLP, Zheng W, Mansoor S, Ali MB, Vahidi F, Al-Bayatti SA, Pauciullo A, Lenstra JA, Barker JSF, Fang L, Wu DD, Han J, Zhang Y. Complete Genomic Landscape Reveals Hidden Evolutionary History and Selection Signature in Asian Water Buffaloes (Bubalus bubalis). ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2407615. [PMID: 39630943 DOI: 10.1002/advs.202407615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 10/18/2024] [Indexed: 12/07/2024]
Abstract
To identify the genetic determinants of domestication and productivity of Asian water buffaloes (Bubalus bubalis), 470 genomes of domesticated river and swamp buffaloes along with their putative ancestors, the wild water buffaloes (Bubalus arnee) are sequenced and integrated. The swamp buffaloes inherit the morphology of the wild buffaloes. In contrast, most river buffaloes are unique in their morphology, but their genomes cluster with the wild buffaloes. The levels of genomic diversity in Italian river and Indonesian swamp buffaloes decrease at opposite extremes of their distribution range. Purifying selection prevented the accumulation of harmful loss-of-function variants in the Indonesian buffaloes. Genes that evolved rapidly (e.g., GKAP1) following differential selections in the river and swamp buffaloes are involved in their reproduction. Genes related to milk production (e.g., CSN2) and coat color (e.g., MC1R) underwent strong selections in the dairy river buffaloes via soft and hard selective sweeps, respectively. The selective sweeps and single-cell RNA-seq data revealed the luminal cells as the key cell type in response to artificial selection for milk production of the dairy buffaloes. These findings show how artificial selection has been driving the evolutionary divergence and genetic differentiation in morphology and productivity of Asian water buffaloes.
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Affiliation(s)
- Jingfang Si
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dongmei Dai
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Neena Amatya Gorkhali
- National Animal Breeding and Genetics Research Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar, Lalitpur, Nepal
| | - Mingshan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China
| | - Saroj Sapkota
- National Animal Breeding and Genetics Research Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar, Lalitpur, Nepal
| | - Ram Chandra Kadel
- Ministry of Industry, Tourism, Forests and Environment, Government of Gandaki Province, Pokhara, Nepal
| | - Amir Sadaula
- National Trust for Nature Conservation- Biodiversity Conservation Center, Sauraha, Chitwan, Nepal
| | - Aashish Dhakal
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Abdullah Ibne Omar
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Eka Meutia Sari
- Department of Animal Science, Faculty of Agriculture, Syiah Kuala University, Darussalam-Banda Aceh, 23111, Indonesia
| | - Hidayat Ashari
- Department of Animal Science, Faculty of Agriculture, Syiah Kuala University, Darussalam-Banda Aceh, 23111, Indonesia
| | | | - Marnoch Yindee
- Akkhraratchakumari Veterinary College, Walailak University, Thaiburi, 222, Thailand
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, Algammaa Street, Giza, 12613, Egypt
| | - Hussein Elregalaty
- Animal Production Research Institute, Agricultural Research Center, Dokki, Giza, Egypt
| | - Ahmed Amin
- Department of Animal Production, Faculty of Agriculture, Cairo University, Algammaa Street, Giza, 12613, Egypt
| | - Mohamed A Radwan
- Department of Animal Production, Faculty of Agriculture, Cairo University, Algammaa Street, Giza, 12613, Egypt
| | - Lan Doan Pham
- Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Tu Liem, Hanoi, 100000, Vietnam
| | - W M M P Hulugalla
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Sri Lanka
| | - G L L Pradeepa Silva
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Sri Lanka
| | - Wei Zheng
- Guangxi Key Laboratory of Buffalo Genetics, Reproduction and Breeding, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Jamil ur Rehman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Basil Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Farhad Vahidi
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Sahar Ahmed Al-Bayatti
- Medical Laboratory Techniques Department, Al-Farabi University College, Ministry of Higher Education and Scientific Research, Baghdad, Iraq
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco (TO), 10095, Italy
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, Utrecht CM, 3584, The Netherlands
| | - J Stuart F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Lingzhao Fang
- The Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, 8000, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Yi Zhang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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2
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Hoffman JI, Vendrami DLJ, Hench K, Chen RS, Stoffel MA, Kardos M, Amos W, Kalinowski J, Rickert D, Köhrer K, Wachtmeister T, Goebel ME, Bonin CA, Gulland FMD, Dasmahapatra KK. Genomic and fitness consequences of a near-extinction event in the northern elephant seal. Nat Ecol Evol 2024; 8:2309-2324. [PMID: 39333394 PMCID: PMC11618080 DOI: 10.1038/s41559-024-02533-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/07/2024] [Indexed: 09/29/2024]
Abstract
Understanding the genetic and fitness consequences of anthropogenic bottlenecks is crucial for biodiversity conservation. However, studies of bottlenecked populations combining genomic approaches with fitness data are rare. Theory predicts that severe bottlenecks deplete genetic diversity, exacerbate inbreeding depression and decrease population viability. However, actual outcomes are complex and depend on how a species' unique demography affects its genetic load. We used population genetic and veterinary pathology data, demographic modelling, whole-genome resequencing and forward genetic simulations to investigate the genomic and fitness consequences of a near-extinction event in the northern elephant seal. We found no evidence of inbreeding depression within the contemporary population for key fitness components, including body mass, blubber thickness and susceptibility to parasites and disease. However, we detected a genomic signature of a recent extreme bottleneck (effective population size = 6; 95% confidence interval = 5.0-7.5) that will have purged much of the genetic load, potentially leading to the lack of observed inbreeding depression in our study. Our results further suggest that deleterious genetic variation strongly impacted the post-bottleneck population dynamics of the northern elephant seal. Our study provides comprehensive empirical insights into the intricate dynamics underlying species-specific responses to anthropogenic bottlenecks.
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Affiliation(s)
- Joseph I Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- British Antarctic Survey, Cambridge, UK.
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany.
| | - David L J Vendrami
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
| | - Kosmas Hench
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Rebecca S Chen
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Martin A Stoffel
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Alan Turing Institute, British Library, London, UK
| | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - William Amos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jörn Kalinowski
- Department of Microbial Genomics and Biotechnology, CeBiTec, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Daniel Rickert
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Karl Köhrer
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Thorsten Wachtmeister
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Mike E Goebel
- Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Carolina A Bonin
- Department of Marine and Environmental Sciences, Hampton University, Hampton, VA, USA
| | - Frances M D Gulland
- Karen C. Drayer Wildlife Health Center, University of California, Davis, Davis, CA, USA
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3
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Bell DA, Kovach RP, Whiteley AR. Inbreeding avoidance and cost in a small, isolated trout population. Proc Biol Sci 2024; 291:20241164. [PMID: 39500379 PMCID: PMC11537757 DOI: 10.1098/rspb.2024.1164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/14/2024] [Accepted: 09/25/2024] [Indexed: 11/09/2024] Open
Abstract
The persistence of small populations is influenced by the degree and cost of inbreeding, with the degree of inbreeding depending on whether close-kin mating is passively or actively avoided. Few studies have simultaneously studied these factors. We examined inbreeding in a small, isolated population of westslope cutthroat trout using extensive genetic and demographic data. Passive inbreeding avoidance was low, with predicted lifetime dispersal of approximately 36 and 74 m for females and males, respectively. Additionally, we found limited evidence for active inbreeding avoidance during reproduction. Relatives remained spatially clustered into adulthood, and observed relatedness among mate pairs was greater than expected under random mating by 0.09, suggesting that inbreeding is a concern in this population. Further, we examined sex-specific inbreeding depression throughout the life cycle and provide evidence for inbreeding depression in some fitness components, including family size, juvenile survival and reproductive success. Our results suggest that, in an at-risk trout population, limited passive and active inbreeding avoidance lead to a higher degree of inbreeding than expected under random mating. Observed inbreeding, along with evidence for fitness reduction due to inbreeding depression, could put the population at a heightened risk of decline or extirpation.
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Affiliation(s)
- Donovan A. Bell
- Wildlife Biology Program, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
- Montana Fish, Wildlife & Parks, Missoula, MT, USA
| | | | - Andrew R. Whiteley
- Wildlife Biology Program, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
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4
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Martin AM, Johnson JA, Berry RB, Carling M, Martínez Del Rio C. Contrasting Genomic Diversity and Inbreeding Levels Among Two Closely Related Falcon Species With Overlapping Geographic Distributions. Mol Ecol 2024:e17549. [PMID: 39400432 DOI: 10.1111/mec.17549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 09/01/2024] [Accepted: 09/26/2024] [Indexed: 10/15/2024]
Abstract
Genomic resources are valuable to examine historical demographic patterns and their effects to better inform management and conservation of threatened species. We evaluated population trends and genome-wide variation in the near-threatened Orange-breasted Falcon (Falco deiroleucus) and its more common sister species, the Bat Falcon (F. rufigularis), to explore how the two species differ in genomic diversity as influenced by their contrasting long-term demographic histories. We generated and aligned whole genome resequencing data for 12 Orange-breasted Falcons and 9 Bat Falcons to an annotated Gyrfalcon (F. rusticolus) reference genome that retained approximately 22.4 million biallelic autosomal SNPs (chromosomes 1-22). Our analyses indicated much lower genomic diversity in Orange-breasted Falcons compared to Bat Falcons. All sampled Orange-breasted Falcons were significantly more inbred than the sampled Bat Falcons, with values similar to those observed in island-mainland species comparisons. The distribution of runs of homozygosity showed variation suggesting long-term low population size and the possibility of bottlenecks in Orange-breasted Falcons contrasting with consistently larger populations in Bat Falcons. Analysis of genetic load suggests that Orange-breasted Falcons are less likely to experience inbreeding depression than Bat Falcons due to reduced inbreeding load but are at elevated risk from fixation of deleterious gene variants and perhaps a reduced adaptive potential. These genomic analyses highlight differences in the historical demography of two closely related species that have influenced their current genomic diversity and should result in differing strategies for their continued conservation.
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Affiliation(s)
- Audrey M Martin
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | | | | | - Matthew Carling
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
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5
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Zhang L, Leonard N, Passaro R, Luan MS, Van Tuyen P, Han LTN, Cam NH, Vogelnest L, Lynch M, Fine AE, Nga NTT, Van Long N, Rawson BM, Behie A, Van Nguyen T, Le MD, Nadler T, Walter L, Marques-Bonet T, Hofreiter M, Li M, Liu Z, Roos C. Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur. Nat Commun 2024; 15:8531. [PMID: 39358348 PMCID: PMC11447269 DOI: 10.1038/s41467-024-52811-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.
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Affiliation(s)
- Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- International Max Planck Research School for Genome Science (IMPRS-GS), University of Göttingen, Göttingen, Germany.
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Neahga Leonard
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Rick Passaro
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Mai Sy Luan
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Pham Van Tuyen
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Le Thi Ngoc Han
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Nguyen Huy Cam
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Larry Vogelnest
- Taronga Conservation Society Australia, Mosman, NSW, Australia
| | - Michael Lynch
- Melbourne Zoo, Zoos Victoria, Parkville, VIC, Australia
| | - Amanda E Fine
- Wildlife Conservation Society (WCS), Health Program, New York, NY, USA
| | | | - Nguyen Van Long
- Wildlife Conservation Society (WCS), Vietnam Country Program, Hanoi, Vietnam
| | - Benjamin M Rawson
- World Wildlife Fund for Nature (WWF) International, Gland, Switzerland
| | - Alison Behie
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
| | - Truong Van Nguyen
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Minh D Le
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Tilo Nadler
- Three Monkeys Wildlife Conservancy, Nho Quan District, Ninh Binh Province, Ninh Binh, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany.
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China.
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
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6
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Patta C, Panthum T, Thatukan C, Wongloet W, Chalermwong P, Wattanadilokchatkun P, Thong T, Srikampa P, Singchat W, Ahmad SF, Noito K, Rasoarahona R, Kraichak E, Muangmai N, Chatchaiphan S, Sriphairoj K, Hatachote S, Chaiyes A, Jantasuriyarat C, Chailertlit V, Suksavate W, Sonongbua J, Prasanpan J, Payungporn S, Han K, Antunes A, Srisapoome P, Koga A, Duengkae P, Matsuda Y, Na-Nakorn U, Srikulnath K. Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand? PLoS One 2024; 19:e0302584. [PMID: 38709757 PMCID: PMC11073742 DOI: 10.1371/journal.pone.0302584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.
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Affiliation(s)
- Chananya Patta
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Chadaphon Thatukan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Phanitada Srikampa
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Kantika Noito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Satid Chatchaiphan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Kednapat Sriphairoj
- Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Sittichai Hatachote
- Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Aingorn Chaiyes
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- School of Agriculture and Cooperatives, Sukhothai Thammathirat Open University, Nonthaburi, Thailand
| | - Chatchawan Jantasuriyarat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Visarut Chailertlit
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division, Department of Fisheries, Pathum Thani, Thailand
| | - Warong Suksavate
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Jumaporn Sonongbua
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Kom Ko, Mueang Nong Khai District, Nong Khai, Thailand
| | - Jiraboon Prasanpan
- Kalasin Fish Hatchery Farm (Betagro), Buaban, Yangtalad District, Kalasin, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Department of Microbiology, Dankook University, Cheonan, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, Korea
- Smart Animal Bio institute, Dankook University, Cheonan, Republic of Korea
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Prapansak Srisapoome
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
| | - Yoichi Matsuda
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand
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7
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Bors MS, Gowri Shankar P, Gruszczyńska J. Current State of Mugger Populations. Animals (Basel) 2024; 14:691. [PMID: 38473076 DOI: 10.3390/ani14050691] [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: 12/27/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
The mugger (Crocodylus palustris) is a medium-sized crocodilian inhabiting South Asia. As a result of intensive hunting, its range declined drastically up till the 1970s. Currently, the world mugger population is fragmented and threatened mainly by habitat loss and the consequences of human-crocodile conflict, being classified as Vulnerable by the IUCN. The goal of this paper is to comprehensively determine the mugger's current range, and assess risks in notable habitats of the species across its range. To determine the range and notable habitats, extensive literature covering surveys, monitoring, population studies and reports of human-crocodile conflict was examined. Habitat suitability and risk assessment were performed by evaluating selected habitats using eight factors: the legal status of the area, elevation, surface water availability, water quality, salinity, availability of nesting and basking sites, interaction with humans and interspecific competition. Based on our findings, the chances of the mugger's survival varies greatly across its range and the threats they face are complex and often site-specific. Defining these threats is the first step for determining suitable risk mitigation efforts, some of which are explored in this review.
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Affiliation(s)
- Milena Sylwia Bors
- Department of Animal Breeding and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
| | | | - Joanna Gruszczyńska
- Department of Animal Breeding and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
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8
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Li W, Wu X, Xiang D, Zhang W, Wu L, Meng X, Huo J, Yin Z, Fu G, Zhao G. Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing. Genes (Basel) 2024; 15:233. [PMID: 38397222 PMCID: PMC10887577 DOI: 10.3390/genes15020233] [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: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.
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Affiliation(s)
- Wenjun Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xudong Wu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Decai Xiang
- Institute of Pig and Animal Research, Yunnan Academy of Animal Husbandry and Veterinary Science, Kunming 650201, China;
| | - Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Lingxiang Wu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xintong Meng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Guowen Fu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
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9
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Hoelzel AR. A need for the wholistic application of genetics to biodiversity conservation; a response to Taylor et al. Trends Ecol Evol 2024; 39:123-124. [PMID: 38177011 DOI: 10.1016/j.tree.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024]
Affiliation(s)
- A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
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10
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [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: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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11
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Shen Y, Tao L, Zhang R, Yao G, Zhou M, Sun W, Ma Y. Genomic insights into endangerment and conservation of the garlic-fruit tree (Malania oleifera), a plant species with extremely small populations. Gigascience 2024; 13:giae070. [PMID: 39311762 PMCID: PMC11417964 DOI: 10.1093/gigascience/giae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/17/2024] [Accepted: 08/22/2024] [Indexed: 09/26/2024] Open
Abstract
BACKGROUND Advanced whole-genome sequencing techniques enable covering nearly all genome nucleotide variations and thus can provide deep insights into protecting endangered species. However, the use of genomic data to make conservation strategies is still rare, particularly for endangered plants. Here we performed comprehensive conservation genomic analysis for Malania oleifera, an endangered tree species with a high amount of nervonic acid. We used whole-genome resequencing data of 165 samples, covering 16 populations across the entire distribution range, to investigate the formation reasons of its extremely small population sizes and to evaluate the possible genomic offsets and changes of ecology niche suitability under future climate change. RESULTS Although M. oleifera maintains relatively high genetic diversity among endangered woody plants (θπ = 3.87 × 10-3), high levels of inbreeding have been observed, which have reduced genetic diversity in 3 populations (JM, NP, and BM2) and caused the accumulation of deleterious mutations. Repeated bottleneck events, recent inbreeding (∼490 years ago), and anthropogenic disturbance to wild habitats have aggravated the fragmentation of M. oleifera and made it endangered. Due to the significant effect of higher average annual temperature, populations distributed in low altitude exhibit a greater genomic offset. Furthermore, ecological niche modeling shows the suitable habitats for M. oleifera will decrease by 71.15% and 98.79% in 2100 under scenarios SSP126 and SSP585, respectively. CONCLUSIONS The basic realizations concerning the threats to M. oleifera provide scientific foundation for defining management and adaptive units, as well as prioritizing populations for genetic rescue. Meanwhile, we highlight the importance of integrating genomic offset and ecological niche modeling to make targeted conservation actions under future climate change. Overall, our study provides a paradigm for genomics-directed conservation.
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Affiliation(s)
- Yuanting Shen
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lidan Tao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Yao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Minjie Zhou
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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12
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Mochales-Riaño G, Fontsere C, de Manuel M, Talavera A, Burriel-Carranza B, Tejero-Cicuéndez H, AlGethami RHM, Shobrak M, Marques-Bonet T, Carranza S. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard ( Panthera pardus nimr). iScience 2023; 26:107481. [PMID: 37601769 PMCID: PMC10432787 DOI: 10.1016/j.isci.2023.107481] [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: 11/23/2022] [Revised: 03/21/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.
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Affiliation(s)
| | - Claudia Fontsere
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raed Hamoud M. AlGethami
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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13
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Kinghorn B, Kinghorn A. Management of diversity and inbreeding when importing new stock into an inbred population. J Hered 2023; 114:492-503. [PMID: 37119054 PMCID: PMC10445517 DOI: 10.1093/jhered/esad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/27/2023] [Indexed: 04/30/2023] Open
Abstract
This article relates to breeding programs that seek to manage genetic diversity. The method maximizes a multicomponent objective function, applicable across breeding scenarios. However, this paper focuses on breeding decisions following immigration of 10 unrelated individuals into a highly inbred simulated population (F ≈ 0.34). We use Optimal Contribution Selection to maximize retention of genetic diversity. However, some treatments add Coancestry Assortative Mating (CAM). This helps to avoid early dilution of immigrant genetic material, maximizing its ability to contribute to genetic diversity in the longer term. After 20 generations, this resulted in considerably increased genetic diversity, with mean coancestries 59% of what random pairing gave. To manage progeny inbreeding, common practice is to reject matings above an upper limit. As a suboptimal rules-based approach, this resulted in 26% decreased genetic diversity and 8% increased inbreeding in the long term, compared with random pairing. In contrast, including mean progeny inbreeding as a continuous variable in the overall objective function decreased final inbreeding by 37% compared with random pairing. Adding some emphasis on selection for a single trait resulted in a similar pattern of effects on coancestry and inbreeding, with 12% higher trait response under CAM. Results indicate the properties of alternative methods, but we encourage users to do their own investigations of particular scenarios, such as including inbreeding depression. Practical implementation of these methods is discussed: they have been widely adopted in domestic animal breeding and are highly flexible to accommodate a wide range of technical and logistical objectives and constraints.
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Affiliation(s)
- Brian Kinghorn
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Alexander Kinghorn
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
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14
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Póvoa O, Lopes V, Barata AM, Farinha N. Monitoring Genetic Erosion of Aromatic and Medicinal Plant Species in Alentejo (South Portugal). PLANTS (BASEL, SWITZERLAND) 2023; 12:2588. [PMID: 37514203 PMCID: PMC10386371 DOI: 10.3390/plants12142588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
The main goal of this work was to study the genetic erosion risk of plants with aromatic, medicinal and gastronomic applications in Portugal, particularly in the Alentejo region. The target species were coriander (Coriandrum sativum L.), hart's pennyroyal (Mentha cervina L.) and pennyroyal (Mentha pulegium L.). The methodology involved direct observations and surveys (2002/2003 and 2011). The GE formula applied in Hammer's studies was used to estimate genetic erosion. The main factors causing genetic erosion were the primary drivers of biodiversity loss: habitat loss, invasive species, and overexploitation influenced by human intervention such as the clearing of watercourses, vegetation control, grazing and desertification. The results indicate a reduction in individuals per species in Alentejo, with a net erosion loss of 11% for M. pulegium, 32% for M. cervina and 33% for C. sativum. The overall loss of accessions (genetic erosion risk) was higher in cultivated accessions (33%) than in wild accessions (11%), with an annual genetic erosion rate of 3.7% and 1.2%, respectively. The annual risk of genetic erosion for M. pulegium accessions collected in a natural habitat was 0.6%, which is much lower than the 3.7% for M. cervina. These results consolidate the importance of collecting and conserving genetic resources.
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Affiliation(s)
- Orlanda Póvoa
- VALORIZA-Centro de Investigação para a Valorização de Recursos Endógenos, Instituto Politécnico de Portalegre, Praça do Município 11, 7300-110 Portalegre, Portugal
- Instituto Politécnico de Portalegre, Praça do Município 11, 7300-110 Portalegre, Portugal
| | - Violeta Lopes
- Banco Português de Germoplasma Vegetal (BPGV), Instituto Nacional de Investigação Agrária e Veterinária, Quinta de S. José, S. Pedro de Merelim, 4700-859 Braga, Portugal
| | - Ana Maria Barata
- Banco Português de Germoplasma Vegetal (BPGV), Instituto Nacional de Investigação Agrária e Veterinária, Quinta de S. José, S. Pedro de Merelim, 4700-859 Braga, Portugal
| | - Noémia Farinha
- Instituto Politécnico de Portalegre, Praça do Município 11, 7300-110 Portalegre, Portugal
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15
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Johnson JA, Athrey G, Anderson CM, Bell DA, Dixon A, Kumazawa Y, Maechtle T, Meeks GW, Mindell D, Nakajima K, Novak B, Talbot S, White C, Zhan X. Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies. Ecol Evol 2023; 13:e10347. [PMID: 37484928 PMCID: PMC10361364 DOI: 10.1002/ece3.10347] [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: 05/14/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
In efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The assumption that all small populations require measures to increase their genetic diversity may be unwarranted, and limited resources for conservation may be better utilized elsewhere. We test this assumption in a case study focused on the peregrine falcon (Falco peregrinus), a cosmopolitan circumpolar species with 19 named subspecies. We used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies. Our analyses revealed extensive variation among subspecies, with many island-restricted and nonmigratory populations possessing lower overall genomic diversity, elevated inbreeding coefficients (F ROH)-among the highest reported, and extensive runs of homozygosity (ROH) compared to mainland and migratory populations. Similarly, the majority of subspecies that are either nonmigratory or restricted to islands show a much longer history of low effective population size (N e). While mutational load analyses indicated an increased proportion of homozygous-derived deleterious variants (i.e., drift load) among nonmigrant and island populations compared to those that are migrant or reside on the mainland, no significant differences in the proportion of heterozygous deleterious variants (i.e., inbreeding load) was observed. Our results provide evidence that high levels of inbreeding may not be an existential threat for some populations or taxa. Additional factors such as the timing and severity of population declines are important to consider in management decisions about extinction potential.
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Affiliation(s)
- Jeff A. Johnson
- Department of Biological SciencesUniversity of North TexasDentonTexasUSA
- Wolf Creek Operating FoundationWolfWyomingUSA
| | - Giridhar Athrey
- Department of Poultry Science & Faculty of Ecology and Evolutionary BiologyTexas A&M UniversityCollege StationTexasUSA
| | | | - Douglas A. Bell
- East Bay Regional Park DistrictOaklandCaliforniaUSA
- California Academy of SciencesSan FranciscoCaliforniaUSA
| | - Andrew Dixon
- The Mohamed Bin Zayed Raptor Conservation FundAbu DhabiUnited Arab Emirates
- International Wildlife ConsultantsCarmarthenUK
| | - Yoshinori Kumazawa
- Research Center for Biological DiversityNagoya City UniversityNagoyaJapan
| | | | - Garrett W. Meeks
- Department of Biological SciencesUniversity of North TexasDentonTexasUSA
| | - David Mindell
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Keiya Nakajima
- Research Center for Biological DiversityNagoya City UniversityNagoyaJapan
- The Japan Falconiformes CenterOwariasahiJapan
| | - Ben Novak
- Revive & RestoreSausalitoCaliforniaUSA
| | - Sandra Talbot
- Far Northwestern Institute of Art and ScienceAnchorageAlaskaUSA
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16
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Horne JB, Frey A, Gaos AR, Martin S, Dutton PH. Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221547. [PMID: 37206959 PMCID: PMC10189603 DOI: 10.1098/rsos.221547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/26/2023] [Indexed: 05/21/2023]
Abstract
Hawksbill sea turtles (Eretmochelys imbricata) from the Hawaiian archipelago form a small and genetically isolated population, consisting of only a few tens of individuals breeding annually. Most females nest on the island of Hawai'i, but little is known about the demographics of this rookery. This study used genetic relatedness, inferred from 135 microhaplotype markers, to determine breeding sex-ratios, estimate female nesting frequency and assess relationships between individuals nesting on different beaches. Samples were collected during the 2017 nesting season and final data included 13 nesting females and 1002 unhatched embryos, salvaged from 41 nests, of which 13 had no observed mother. Results show that most females used a single nesting beach laying 1-5 nests each. From female and offspring alleles, the paternal genotypes of 12 breeding males were reconstructed and many showed high relatedness to their mates. Pairwise relatedness of offspring revealed one instance of polygyny but otherwise suggested a 1 : 1 breeding-sex ratio. Relatedness analysis and spatial-autocorrelation of genotypes indicate that turtles from different nesting areas do not regularly interbreed, suggesting that strong natal homing tendencies in both sexes result in non-random mating across the study area. Complexes of nearby nesting beaches also showed unique patterns of inbreeding across loci, further indicating that Hawaiian hawksbill turtles have demographically discontinuous nesting populations separated by only tens of km.
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Affiliation(s)
- John B. Horne
- Southwest Fisheries Science Center, NOAA-Fisheries, La Jolla, CA, USA
| | - Amy Frey
- Southwest Fisheries Science Center, NOAA-Fisheries, La Jolla, CA, USA
| | - Alexander R. Gaos
- Pacific Islands Fisheries Science Center, NOAA-Fisheries, Honolulu, HI, USA
| | - Summer Martin
- Pacific Islands Fisheries Science Center, NOAA-Fisheries, Honolulu, HI, USA
| | - Peter H. Dutton
- Southwest Fisheries Science Center, NOAA-Fisheries, La Jolla, CA, USA
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17
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Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of Seriola lalandi. Animals (Basel) 2023; 13:ani13050913. [PMID: 36899769 PMCID: PMC10000148 DOI: 10.3390/ani13050913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Developing sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as well as a 90 K SNP genotyping array based on different populations of yellowtail kingfish (Seriola lalandi). The minimum and maximum distance between adjacent marker pairs were 0.7 Mb and 13 Mb, respectively, with an average marker spacing of 2 Mb. Weak evidence of the linkage disequilibrium between adjacent marker pairs was found. The results showed high panel performance for parental assignment, with probability exclusion values equaling 1. The rate of false positives when using cross-population data was null. A skewed distribution of genetic contributions by dominant females was observed, thus increasing the risk of higher rates of inbreeding in subsequent captive generations when no parentage data are used. All these results are discussed in the context of breeding program design, using this marker panel to increase the sustainability of this aquaculture resource.
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18
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Zhang L, Lan T, Lin C, Fu W, Yuan Y, Lin K, Li H, Sahu SK, Liu Z, Chen D, Liu Q, Wang A, Wang X, Ma Y, Li S, Zhu Y, Wang X, Ren X, Lu H, Huang Y, Yu J, Liu B, Wang Q, Zhang S, Xu X, Yang H, Liu D, Liu H, Xu Y. Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger. Mol Ecol Resour 2023; 23:330-347. [PMID: 35723950 PMCID: PMC10084155 DOI: 10.1111/1755-0998.13669] [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: 01/07/2022] [Revised: 05/29/2022] [Accepted: 06/10/2022] [Indexed: 01/09/2023]
Abstract
The South China tiger (Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tiger due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first SCT genome and an improved Amur tiger (P. t. altaica, AT) genome named AmyTig1.0 and PanTig2.0. The two genomes are the most continuous and comprehensive among any tiger genomes yet reported at the chromosomal level. By using the two genomes and resequencing data of 15 SCT and 13 AT individuals, we investigated the genomic signature of inbreeding depression of the SCT. The results indicated that the effective population size of SCT experienced three phases of decline, ~5.0-1.0 thousand years ago, 100 years ago, and since captive breeding in 1963. We found 43 long runs of homozygosity fragments that were shared by all individuals in the SCT population and covered a total length of 20.63% in the SCT genome. We also detected a large proportion of identical-by-descent segments across the genome in the SCT population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites and loss-of-function mutations were found across genomes with extensive potential influences, despite a proportion of these loads having been purged by inbreeding depression. Our research provides an invaluable resource for the formulation of genetic management policies for the South China tiger such as developing genome-based breeding and genetic rescue strategy.
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Affiliation(s)
- Le Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen, China
| | - Wenyuan Fu
- Longyan Geopark Protection and Development Center, Longyan, China.,Fujian Meihuashan Institute of South China Tiger Breeding, Longyan, China
| | | | - Kaixiong Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Daqing Chen
- Suzhou Shangfangshan Forest Zoo, Suzhou, China
| | - Qunxiu Liu
- Shanghai Zoological Park, Shanghai, China
| | | | | | - Yue Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shizhou Li
- Shaoguan Research Base of South China Tiger, Shaoguan, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Xiaotong Ren
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Haorong Lu
- China National GeneBank, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | | | - Jieyao Yu
- China National GeneBank, Shenzhen, China
| | - Boyang Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Xun Xu
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Huanming Yang
- Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Dan Liu
- Heilongjiang Siberian Tiger Park, Harbin, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Shenzhen, China.,BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
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19
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Balick DJ. A field theoretic approach to non-equilibrium population genetics in the strong selection regime. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524324. [PMID: 36711507 PMCID: PMC9882232 DOI: 10.1101/2023.01.16.524324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Natural populations are virtually never observed in equilibrium, yet equilibrium approximations comprise the majority of our understanding of population genetics. Using standard tools from statistical physics, a formalism is presented that re-expresses the stochastic equations describing allelic evolution as a partition functional over all possible allelic trajectories ('paths') governed by selection, mutation, and drift. A perturbative field theory is developed for strong additive selection, relevant to disease variation, that facilitates the straightforward computation of closed-form approximations for time-dependent moments of the allele frequency distribution across a wide range of non-equilibrium scenarios; examples are presented for constant population size, exponential growth, bottlenecks, and oscillatory size, all of which align well to simulations and break down just above the drift barrier. Equilibration times are computed and, even for static population size, generically extend beyond the order 1/s timescale associated with exponential frequency decay. Though the mutation load is largely robust to variable population size, perturbative drift-based corrections to the deterministic trajectory are readily computed. Under strong selection, the variance of a new mutation's frequency (related to homozygosity) is dominated by drift-driven dynamics and a transient increase in variance often occurs prior to equilibrating. The excess kurtosis over skew squared is roughly constant (i.e., independent of selection, provided 2Ns ≳ 5) for static population size, and thus potentially sensitive to deviation from equilibrium. These insights highlight the value of such closed-form approximations, naturally generated from Feynman diagrams in a perturbative field theory, which can simply and accurately capture the parameter dependences describing a variety of non-equilibrium population genetic phenomena of interest.
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Affiliation(s)
- Daniel J Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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20
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De Kort H, Legrand S, Honnay O, Buckley J. Transposable elements maintain genome-wide heterozygosity in inbred populations. Nat Commun 2022; 13:7022. [PMID: 36396660 PMCID: PMC9672359 DOI: 10.1038/s41467-022-34795-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding. Capitalizing on the mixed mating system of Arabidopsis lyrata, we assess genome-wide heterozygosity and signatures of selection at single nucleotide polymorphisms near transposable elements across an inbreeding gradient. Under intense inbreeding, we find systematically elevated heterozygosity downstream of several TE superfamilies, associated with signatures of balancing selection. In addition, we demonstrate increased heterozygosity in stress-responsive genes that consistently occur downstream of TEs. We finally reveal that TE superfamilies are associated with specific signatures of selection that are reproducible across independent evolutionary lineages of A. lyrata. Together, our study provides an important hypothesis for the success of self-fertilizing species.
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Affiliation(s)
- Hanne De Kort
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - Sylvain Legrand
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Olivier Honnay
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - James Buckley
- grid.11201.330000 0001 2219 0747School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL1 2BT UK
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21
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von Seth J, van der Valk T, Lord E, Sigeman H, Olsen RA, Knapp M, Kardailsky O, Robertson F, Hale M, Houston D, Kennedy E, Dalén L, Norén K, Massaro M, Robertson BC, Dussex N. Genomic trajectories of a near-extinction event in the Chatham Island black robin. BMC Genomics 2022; 23:747. [PMID: 36357860 PMCID: PMC9647977 DOI: 10.1186/s12864-022-08963-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation. RESULTS We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations. CONCLUSION Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.
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Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Edana Lord
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
- Ecology and Genetics Research Unit, University of Oulu, 90014, Oulu, Finland
| | - Remi-André Olsen
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17121, Solna, Sweden
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
- Coastal People Southern Skies Centre of Research Excellence, University of Otago, PO Box 56, Dunedin, 9054, Aotearoa, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin, 9054, New Zealand
| | - Marie Hale
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Dave Houston
- Department of Conservation, Biodiversity Group, Auckland, New Zealand
| | - Euan Kennedy
- Department of Conservation, Science and Capability, Christchurch, New Zealand
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - Melanie Massaro
- School of Agricultural, Environmental and Veterinary Sciences and Gulbali Institute, Charles Sturt University, PO Box 789, Albury, NSW, Australia
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden.
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22
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Reproductive biology and population structure of the endangered shrub Grevillea bedggoodiana (Proteaceae). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01480-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractNarrowly endemic species are particularly vulnerable to catastrophic events. Compared to widespread species, they may also be less capable of adapting to shifts in environmental pressures as a result of specialisation on a narrow range of local condition and limited ability to disperse. However, life-history traits, such as preferential outcrossing and high fecundity can maintain genetic diversity and evolutionary potential, and boost species resilience. The endangered Grevillea bedggoodiana (Enfield Grevillea) is an understorey shrub restricted to an area of ca. 150 km2 in south-eastern Australia with a legacy of large-scale anthropogenic disturbance. Prior to this study little was known about its biology and population structure. Here, its breeding system was assessed through a controlled pollination experiment at one of its central populations, and eight populations were sampled for genetic analysis with microsatellite markers. The species was found to be preferentially outcrossing, with no evidence of pollination limitation. In most populations, allelic richness, observed heterozygosity and gene diversity were high (Ar: 3.8–6.3; Ho: 0.45–0.65, He: 0.60 − 0.75). However, the inbreeding coefficients were significant in at least four populations, ranging from Fi -0.061 to 0.259 despite high outcrossing rates. Estimated reproductive rates varied among sampled populations but were independent of gene diversity and inbreeding. Despite its small geographic range, the species’ populations showed moderate differentiation (AMOVA: FST = 0.123), which was largely attributable to isolation by distance. We interpret these results as suggesting that G. bedggoodiana is reproductively healthy and has maintained high levels of genetic diversity despite recent disturbance.
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23
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Charmouh AP, Reid JM, Bilde T, Bocedi G. Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations. Evolution 2022; 76:2482-2497. [PMID: 36117269 PMCID: PMC9828521 DOI: 10.1111/evo.14620] [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: 03/24/2022] [Revised: 06/01/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting local extinction, and recolonization through evolving dispersal facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favor increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.
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Affiliation(s)
- Anders P. Charmouh
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUnited Kingdom
| | - Jane M. Reid
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUnited Kingdom,Centre for Biodiversity DynamicsInstitutt for Biologi, NTNUTrondheim7491Norway
| | - Trine Bilde
- Department of BiologyAarhus UniversityAarhus C8000Denmark
| | - Greta Bocedi
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUnited Kingdom
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24
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Carley LN, Morris WF, Walsh R, Riebe D, Mitchell‐Olds T. Are genetic variation and demographic performance linked? Evol Appl 2022; 15:1888-1906. [PMID: 36426131 PMCID: PMC9679243 DOI: 10.1111/eva.13487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Quantifying relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. To empirically test whether and how genetic variation and population dynamics are related, we present one such paired approach. First, we use eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λ S) and extinction risk of each population. We then combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, standing genetic variation and demography are weakly positively correlated. However, the inbreeding coefficient was not strongly correlated with demographic performance, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than less inbred populations. A contemporary re-census of these populations revealed that neither genetic nor demographic parameters were consistently strong predictors of current population density, although populations showing lower probabilities of extinction in demographic models had larger population sizes at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.
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Affiliation(s)
- Lauren N. Carley
- University Program in EcologyDuke UniversityDurhamNorth CarolinaUSA
- Biology DepartmentDuke UniversityDurhamNorth CarolinaUSA
- Department of Plant and Microbial BiologyUniversity of Minnesota Twin CitiesSt. PaulMinnesotaUSA
| | | | - Roberta Walsh
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Donna Riebe
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Tom Mitchell‐Olds
- Biology DepartmentDuke UniversityDurhamNorth CarolinaUSA
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
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25
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Banos G, Talenti A, Chatziplis D, Sánchez-Molano E. Genomic analysis of the rare British Lop pig and identification of distinctive genomic markers. PLoS One 2022; 17:e0271053. [PMID: 35960784 PMCID: PMC9374264 DOI: 10.1371/journal.pone.0271053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/22/2022] [Indexed: 11/19/2022] Open
Abstract
Concentration of production on a few commercial pig breeds has led to the marginalization of many native, numerically small breeds, increasing their risk of endangerment. In the UK, one such rare breed is the British Lop, a lop-eared breed, of similar origin to the Welsh breed. The objective of the present study was to address the genomic status of the British Lop and its relationship with other breeds and identify a small set of genomic markers that uniquely characterize and distinguish British Lop animals. Results have shown that the British Lop is a relatively distinct population with reduced genomic diversity and effective size consistent with its status as a rare breed. Furthermore, we demonstrated the genetic closeness of the British Lop to phenotypically similar breeds such as Landrace and Welsh as well Large White, Middle White and Pietrain. Finally, a set of 75 Single Nucleotide Polymorphisms distributed across multiple chromosomes were identified and validated as markers that can consistently distinguish British Lops from other closely related breeds. Results may inform breeding and management strategies aiming to enhance diversity as well as the development of a breed purity test.
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Affiliation(s)
- Georgios Banos
- Scotland’s Rural College (SRUC), Department of Animal and Veterinary Sciences, The Roslin Institute Building, Edinburgh, United Kingdom
| | - Andrea Talenti
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Dimitrios Chatziplis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Sindos, Greece
| | - Enrique Sánchez-Molano
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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26
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Pérez‐Pereira N, López‐Cortegano E, García‐Dorado A, Caballero A. Prediction of fitness under different breeding designs in conservation programs. Anim Conserv 2022. [DOI: 10.1111/acv.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. Pérez‐Pereira
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - E. López‐Cortegano
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - A. García‐Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas Universidad Complutense Madrid Spain
| | - A. Caballero
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
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27
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Hooper AK, Bonduriansky R. Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly. J Evol Biol 2022; 35:803-816. [PMID: 35514040 PMCID: PMC9325454 DOI: 10.1111/jeb.14014] [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: 07/26/2021] [Accepted: 03/14/2022] [Indexed: 12/02/2022]
Abstract
Condition is assumed to reflect both genes and environment, enabling condition‐dependent signals to reveal genetic quality. However, because the phenotypic effects of variation in genetic quality could be masked by environmental heterogeneity, the contribution of genetic quality to phenotypic variation in fitness‐related traits and condition‐dependent signals remains unclear. We compared effects of ecologically relevant manipulations of environmental quality (nutrient dilution in the larval diet) and genetic quality (one generation of inbreeding) on male and female morphology, life history and reproductive performance in the neriid fly Telostylinus angusticollis. We found that larval diet quality had strong, positive effects on male and female body size, male secondary sexual traits, and aspects of male and female reproductive performance. By contrast, inbreeding had weak effects on most traits, and no trait showed clear and consistent effects of both environmental and genetic quality. Indeed, inbreeding effects on body size and male competitive performance were of opposite sign in rich vs. poor larval diet treatment groups. Our results suggest that environmental quality strongly affects condition, but the effects of genetic quality are subtle and environment‐dependent in this species. These findings raise questions about the genetic architecture of condition and the potential for condition‐dependent traits to function as signals of genetic quality.
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Affiliation(s)
- Amy K Hooper
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Cisternas‐Fuentes A, Jogesh T, Broadhead GT, Raguso RA, Skogen KA, Fant JB. Evolution of selfing syndrome and its influence on genetic diversity and inbreeding: A range-wide study in Oenothera primiveris. AMERICAN JOURNAL OF BOTANY 2022; 109:789-805. [PMID: 35596689 PMCID: PMC9320852 DOI: 10.1002/ajb2.1861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 06/15/2023]
Abstract
PREMISE To avoid inbreeding depression, plants have evolved diverse breeding systems to favor outcrossing, such as self-incompatibility. However, changes in biotic and abiotic conditions can result in selective pressures that lead to a breakdown in self-incompatibility. The shift to increased selfing is commonly associated with reduced floral features, lower attractiveness to pollinators, and increased inbreeding. We tested the hypothesis that the loss of self-incompatibility, a shift to self-fertilization (autogamy), and concomitant evolution of the selfing syndrome (reduction in floral traits associated with cross-fertilization) will lead to increased inbreeding and population differentiation in Oenothera primiveris. Across its range, this species exhibits a shift in its breeding system and floral traits from a self-incompatible population with large flowers to self-compatible populations with smaller flowers. METHODS We conducted a breeding system assessment, evaluated floral traits in the field and under controlled conditions, and measured population genetic parameters using RADseq data. RESULTS Our results reveal a bimodal transition to the selfing syndrome from the west to the east of the range of O. primiveris. This shift includes variation in the breeding system and the mating system, a reduction in floral traits (flower diameter, herkogamy, and scent production), a shift to greater autogamy, reduced genetic diversity, and increased inbreeding. CONCLUSIONS The observed variation highlights the importance of range-wide studies to understand breeding system variation and the evolution of the selfing syndrome within populations and species.
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Affiliation(s)
- Anita Cisternas‐Fuentes
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
- Plant Biology and ConservationNorthwestern University2205 Tech DriveEvanstonIllinois60208USA
- Department of Biological ScienceClemson University132 Long HallClemsonSouth Carolina29631USA
| | - Tania Jogesh
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
| | - Geoffrey T. Broadhead
- Department of Entomology and NematologyUniversity of Florida1881 Natural Area DriveGainesvilleFlorida32611USA
| | - Robert A. Raguso
- Department of Neurobiology and BehaviorCornell UniversityW361 Mudd HallIthacaNew York14853USA
| | - Krissa A. Skogen
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
- Plant Biology and ConservationNorthwestern University2205 Tech DriveEvanstonIllinois60208USA
| | - Jeremie B. Fant
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60035USA
- Plant Biology and ConservationNorthwestern University2205 Tech DriveEvanstonIllinois60208USA
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Genetic load: genomic estimates and applications in non-model animals. Nat Rev Genet 2022; 23:492-503. [PMID: 35136196 DOI: 10.1038/s41576-022-00448-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/11/2022]
Abstract
Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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Saura M, Caballero A, Santiago E, Fernández A, Morales-González E, Fernández J, Cabaleiro S, Millán A, Martínez P, Palaiokostas C, Kocour M, Aslam ML, Houston RD, Prchal M, Bargelloni L, Tzokas K, Haffray P, Bruant JS, Villanueva B. Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes. Genet Sel Evol 2021; 53:85. [PMID: 34742227 PMCID: PMC8572424 DOI: 10.1186/s12711-021-00680-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 10/22/2021] [Indexed: 11/15/2022] Open
Abstract
Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. Methods Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00680-9.
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Affiliation(s)
- María Saura
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain.
| | - Armando Caballero
- Centro de Investigación Mariña, Facultade de Bioloxía, Universidade de Vigo, 36310, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Universidad de Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
| | | | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
| | - Santiago Cabaleiro
- CETGA, Cluster de Acuicultura de Galicia, Punta do Couso s/n, 15695, Aguiño-Ribeira, Spain
| | | | - Paulino Martínez
- Departament of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Christos Palaiokostas
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Martin Kocour
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | | | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Martin Prchal
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Luca Bargelloni
- Universitá degli Studi di Padova, Via 8 Febbraio 1848, 2, 35122, Padova, PD, Italy
| | - Kostas Tzokas
- Andromeda Group SA, Leof. Lavriou 99, 190 02, Peania, Greece
| | - Pierrick Haffray
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
| | | | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
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Li SH, Liu Y, Yeh CF, Fu Y, Yeung CKL, Lee CC, Chiu CC, Kuo TH, Chan FT, Chen YC, Ko WY, Yao CT. Not out of the woods yet: Signatures of the prolonged negative genetic consequences of a population bottleneck in a rapidly re-expanding wader, the black-faced spoonbill Platalea minor. Mol Ecol 2021; 31:529-545. [PMID: 34726290 DOI: 10.1111/mec.16260] [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: 06/30/2021] [Revised: 09/27/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022]
Abstract
The long-term persistence of a population which has suffered a bottleneck partly depends on how historical demographic dynamics impacted its genetic diversity and the accumulation of deleterious mutations. Here we provide genomic evidence for the genetic effect of a recent population bottleneck in the endangered black-faced spoonbill (Platalea minor) after its rapid population recovery. Our data suggest that the bird's effective population size, Ne , had been relatively stable (7500-9000) since 22,000 years ago; however, a recent brief yet severe bottleneck (Ne = 20) which we here estimated to occur around the 1940s wiped out >99% of its historical Ne in roughly three generations. Despite a >15-fold population recovery since 1988, we found that black-faced spoonbill population has higher levels of inbreeding (7.4 times more runs of homozygosity) than its sister species, the royal spoonbill (P. regia), which is not thought to have undergone a marked population contraction. Although the two spoonbills have similar levels of genome-wide genetic diversity, our results suggest that selection on more genes was relaxed in the black-faced spoonbill; moreover individual black-faced spoonbills carry more putatively deleterious mutations (Grantham's score > 50), and may therefore express more deleterious phenotypic effects than royal spoonbills. Here we demonstrate the value of using genomic indices to monitor levels of genetic erosion, inbreeding and mutation load in species with conservation concerns. To mitigate the prolonged negative genetic effect of a population bottleneck, we recommend that all possible measures should be employed to maintain population growth of a threatened species.
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Affiliation(s)
- Shou-Hsien Li
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Guangzhou, China
| | - Chia-Fen Yeh
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Yuchen Fu
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | | | - Chun-Cheng Lee
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chi-Cheng Chiu
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | | | - Fang-Tse Chan
- Division of Zoology, Taiwan Endemic Species Research Institute, Nantou, Taiwan
| | - Yu-Chia Chen
- Department of Life Sciences, National Yanming Medical University, Taipei, Taiwan
| | - Wen-Ya Ko
- Department of Life Sciences, National Yanming Medical University, Taipei, Taiwan
| | - Cheng-Te Yao
- High Altitude Research Station, Taiwan Endemic Species Research Institute, Nantou, Taiwan
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33
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López-Cortegano E, Moreno E, García-Dorado A. Genetic purging in captive endangered ungulates with extremely low effective population sizes. Heredity (Edinb) 2021; 127:433-442. [PMID: 34584227 PMCID: PMC8551332 DOI: 10.1038/s41437-021-00473-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023] Open
Abstract
Inbreeding threatens the survival of small populations by producing inbreeding depression, but also exposes recessive deleterious effects in homozygosis allowing for genetic purging. Using inbreeding-purging theory, we analyze early survival in four pedigreed captive breeding programs of endangered ungulates where population growth was prioritized so that most adult females were allowed to contribute offspring according to their fitness. We find evidence that purging can substantially reduce inbreeding depression in Gazella cuvieri (with effective population size Ne = 14) and Nanger dama (Ne = 11). No purging is detected in Ammotragus lervia (Ne = 4), in agreement with the notion that drift overcomes purging under fast inbreeding, nor in G. dorcas (Ne = 39) where, due to the larger population size, purging is slower and detection is expected to require more generations. Thus, although smaller populations are always expected to show smaller fitness (as well as less adaptive potential) than larger ones due to higher homozygosis and deleterious fixation, our results show that a substantial fraction of their inbreeding load and inbreeding depression can be purged when breeding contributions are governed by natural selection. Since management strategies intended to maximize the ratio from the effective to the actual population size tend to reduce purging, the search for a compromise between these strategies and purging could be beneficial in the long term. This could be achieved either by allowing some level of random mating and some role of natural selection in determining breeding contributions, or by undertaking reintroductions into the wild at the earliest opportunity.
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Affiliation(s)
- Eugenio López-Cortegano
- grid.4305.20000 0004 1936 7988Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, UK
| | - Eulalia Moreno
- grid.466639.80000 0004 0547 1725Estación Experimental de Zonas Áridas (CSIC), 04120 Almería, Spain
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34
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Abstract
AbstractGenetic rescue is increasingly considered a promising and underused conservation strategy to reduce inbreeding depression and restore genetic diversity in endangered populations, but the empirical evidence supporting its application is limited to a few generations. Here we discuss on the light of theory the role of inbreeding depression arising from partially recessive deleterious mutations and of genetic purging as main determinants of the medium to long-term success of rescue programs. This role depends on two main predictions: (1) The inbreeding load hidden in populations with a long stable demography increases with the effective population size; and (2) After a population shrinks, purging tends to remove its (partially) recessive deleterious alleles, a process that is slower but more efficient for large populations than for small ones. We also carry out computer simulations to investigate the impact of genetic purging on the medium to long term success of genetic rescue programs. For some scenarios, it is found that hybrid vigor followed by purging will lead to sustained successful rescue. However, there may be specific situations where the recipient population is so small that it cannot purge the inbreeding load introduced by migrants, which would lead to increased fitness inbreeding depression and extinction risk in the medium to long term. In such cases, the risk is expected to be higher if migrants came from a large non-purged population with high inbreeding load, particularly after the accumulation of the stochastic effects ascribed to repeated occasional migration events. Therefore, under the specific deleterious recessive mutation model considered, we conclude that additional caution should be taken in rescue programs. Unless the endangered population harbors some distinctive genetic singularity whose conservation is a main concern, restoration by continuous stable gene flow should be considered, whenever feasible, as it reduces the extinction risk compared to repeated occasional migration and can also allow recolonization events.
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35
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Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (BETHESDA, MD.) 2021; 11:jkab307. [PMID: 34542587 PMCID: PMC8527487 DOI: 10.1093/g3journal/jkab307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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Affiliation(s)
- Yasmin Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brodie J Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Tracey Van Stijn
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - John C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | | | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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Pérez-Pereira N, Pouso R, Rus A, Vilas A, López-Cortegano E, García-Dorado A, Quesada H, Caballero A. Long-term exhaustion of the inbreeding load in Drosophila melanogaster. Heredity (Edinb) 2021; 127:373-383. [PMID: 34400819 PMCID: PMC8478893 DOI: 10.1038/s41437-021-00464-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.
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Affiliation(s)
- Noelia Pérez-Pereira
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ramón Pouso
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Rus
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Vilas
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Eugenio López-Cortegano
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain ,grid.4305.20000 0004 1936 7988Present Address: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Aurora García-Dorado
- grid.4795.f0000 0001 2157 7667Facultad de Ciencias Biológicas, Departamento de Genética, Universidad Complutense, Madrid, Spain
| | - Humberto Quesada
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Armando Caballero
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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Dussex N, van der Valk T, Morales HE, Wheat CW, Díez-del-Molino D, von Seth J, Foster Y, Kutschera VE, Guschanski K, Rhie A, Phillippy AM, Korlach J, Howe K, Chow W, Pelan S, Mendes Damas JD, Lewin HA, Hastie AR, Formenti G, Fedrigo O, Guhlin J, Harrop TW, Le Lec MF, Dearden PK, Haggerty L, Martin FJ, Kodali V, Thibaud-Nissen F, Iorns D, Knapp M, Gemmell NJ, Robertson F, Moorhouse R, Digby A, Eason D, Vercoe D, Howard J, Jarvis ED, Robertson BC, Dalén L. Population genomics of the critically endangered kākāpō. CELL GENOMICS 2021; 1:100002. [PMID: 36777713 PMCID: PMC9903828 DOI: 10.1016/j.xgen.2021.100002] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/23/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022]
Abstract
The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden,Department of Zoology, Stockholm University, 10691 Stockholm, Sweden,Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand,Corresponding author
| | - Tom van der Valk
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Hernán E. Morales
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - David Díez-del-Molino
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden,Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Yasmin Foster
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Verena E. Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Katerina Guschanski
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK,Department of Ecology and Genetics, Animal Ecology, Uppsala University, 75236 Uppsala, Sweden
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonas Korlach
- Pacific Biosciences, 1305 O’Brien Drive, Menlo Park, CA 94025, USA
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Joanna D. Mendes Damas
- Department of Evolution and Ecology and the UC Davis Genome Center, 4321 Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA
| | - Harris A. Lewin
- Department of Evolution and Ecology and the UC Davis Genome Center, 4321 Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA
| | - Alex R. Hastie
- Bionano Genomics, 9540 Towne Centre Drive, San Diego, CA 92121, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA,Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
| | - Joseph Guhlin
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
| | - Thomas W.R. Harrop
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
| | - Marissa F. Le Lec
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
| | - Peter K. Dearden
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vamsi Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand
| | - Neil J. Gemmell
- Department of Anatomy, University of Otago, PO Box 913, Dunedin 9016, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ron Moorhouse
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
| | - Andrew Digby
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
| | - Daryl Eason
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery, Department of Conservation, PO Box 743, Invercargill 9840, New Zealand
| | - Jason Howard
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA,BioSkryb Genomics, 701 W Main Street, Suite 200, Durham, NC 27701, USA
| | - Erich D. Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA,Laboratory of Neurogenetics of Language, Box 54, The Rockefeller University, New York, NY 10065, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA,Corresponding author
| | - Bruce C. Robertson
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand,Corresponding author
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden,Department of Zoology, Stockholm University, 10691 Stockholm, Sweden,Corresponding author
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38
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Manoel RO, Rossini BC, Cornacini MR, Moraes MLT, Cambuim J, Alcântara MAM, Silva AM, Sebbenn AM, Marino CL. Landscape barriers to pollen and seed flow in the dioecious tropical tree Astronium fraxinifolium in Brazilian savannah. PLoS One 2021; 16:e0255275. [PMID: 34339479 PMCID: PMC8336915 DOI: 10.1371/journal.pone.0255275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/14/2021] [Indexed: 11/19/2022] Open
Abstract
Gene flow studies provide information on gene exchange between populations, which is essential for developing genetic conservation strategies. Such analyses enable a better understanding of the life history and seed and pollen dispersal mechanisms of plant species. In this study, we investigate pollen and seed flow in a regenerant population of the pioneer species Astronium fraxinifolium in an area degraded during the construction of a hydroelectric dam. We mapped, sampled, sexed, and genotyped 386 individuals in the regenerant population (RP), as well as 128 adult trees located along two highways adjacent to the degraded area; one in Mato Grosso do Sul State (MS) and other in São Paulo State (SP). Parentage analyses was carried out for 370 individuals of the RP population, using as putative parents 348 individuals from RP and all 128 individuals sampled in MS and SP. Based on parentage analysis and eight microsatellite loci, our analyses revealed that for individuals of the RP with an identified father (pollen donor), 1.1% of the pollen was dispersed up to 532 m, while for those with an identified mother (seed donor), 0.5% of seeds were dispersed up to 4,782 m. However, a large proportion of pollen (76.5%) and seeds (57%) immigrated from trees outside the sampled populations. Pollen and seeds were dispersed through a pattern of isolation by distance. Genetic diversity was significantly similar between adults of both highway populations and individuals from RP, with significant levels of inbreeding detected only in RP. Our results demonstrate that the nearest trees contributed pollen and seeds for the recovery of the degraded area, indicating reproductive spatial isolation among the sampled populations due to the damming of the river. Such results help to understand the process of regeneration for A. fraxinifolium in regenerant populations to inform strategies for conservation and environmental recovery with this species.
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Affiliation(s)
| | | | | | - Mário L. T. Moraes
- Faculdade de Engenharia de Ilha Solteira/UNESP, Ilha Solteira, São Paulo,
Brazil
| | - José Cambuim
- Faculdade de Engenharia de Ilha Solteira/UNESP, Ilha Solteira, São Paulo,
Brazil
| | | | - Alexandre M. Silva
- Faculdade de Engenharia de Ilha Solteira/UNESP, Ilha Solteira, São Paulo,
Brazil
| | - Alexandre M. Sebbenn
- Departamento de Melhoramento e Conservação Genética, Instituto Florestal
de São Paulo, Piracicaba, São Paulo, Brazil
| | - Celso L. Marino
- Instituto de Biotecnologia/ UNESP, Botucatu, São Paulo,
Brazil
- Instituto de Biociências/ UNESP, Botucatu, São Paulo,
Brazil
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39
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Duntsch L, Whibley A, Brekke P, Ewen JG, Santure AW. Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi. Mol Ecol 2021; 30:6006-6020. [PMID: 34242449 DOI: 10.1111/mec.16068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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40
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Baduel P, Leduque B, Ignace A, Gy I, Gil J, Loudet O, Colot V, Quadrana L. Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biol 2021; 22:138. [PMID: 33957946 PMCID: PMC8101250 DOI: 10.1186/s13059-021-02348-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/09/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we leverage publicly available multi-omic and bio-climatic data for more than 1000 wild Arabidopsis thaliana accessions to determine the rate of transposable element (TE) mobilization and its potential to create adaptive variation in natural settings. RESULTS We demonstrate that TE insertions arise at almost the same rate as base substitutions. Mobilization activity of individual TE families varies greatly between accessions, in association with genetic and environmental factors as well as through complex gene-environment interactions. Although the distribution of TE insertions across the genome is ultimately shaped by purifying selection, reflecting their typically strong deleterious effects when located near or within genes, numerous recent TE-containing alleles show signatures of positive selection. Moreover, high rates of transposition appear positively selected at the edge of the species' ecological niche. Based on these findings, we predict through mathematical modeling higher transposition activity in Mediterranean regions within the next decades in response to global warming, which in turn should accelerate the creation of large-effect alleles. CONCLUSIONS Our study reveals that TE mobilization is a major generator of genetic variation in A. thaliana that is finely modulated by genetic and environmental factors. These findings and modeling indicate that TEs may be essential genomic players in the demise or rescue of native populations in times of climate crises.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Basile Leduque
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Amandine Ignace
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - José Gil
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
- Present Address: Institut Curie, 26 rue d'Ulm, 75005, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Vincent Colot
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
| | - Leandro Quadrana
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
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41
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von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, Steiner CC, Liu S, Gilbert MTP, Sinding MHS, Prost S, Guschanski K, Nathan SKSS, Brace S, Chan YL, Wheat CW, Skoglund P, Ryder OA, Goossens B, Götherström A, Dalén L. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations. Nat Commun 2021; 12:2393. [PMID: 33896938 PMCID: PMC8071806 DOI: 10.1038/s41467-021-22386-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
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Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cynthia C Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Shanlin Liu
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yvonne L Chan
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Benoit Goossens
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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42
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Teixeira JC, Huber CD. The inflated significance of neutral genetic diversity in conservation genetics. Proc Natl Acad Sci U S A 2021; 118:e2015096118. [PMID: 33608481 PMCID: PMC7958437 DOI: 10.1073/pnas.2015096118] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies.
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Affiliation(s)
- João C Teixeira
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia;
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, 5005 SA, Australia
| | - Christian D Huber
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005 SA, Australia;
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43
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Liu L, Bosse M, Megens H, de Visser M, A. M. Groenen M, Madsen O. Genetic consequences of long-term small effective population size in the critically endangered pygmy hog. Evol Appl 2021; 14:710-720. [PMID: 33767746 PMCID: PMC7980308 DOI: 10.1111/eva.13150] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/24/2022] Open
Abstract
Increasing human disturbance and climate change have a major impact on habitat integrity and size, with far-reaching consequences for wild fauna and flora. Specifically, population decline and habitat fragmentation result in small, isolated populations. To what extend different endangered species can cope with small population size is still largely unknown. Studies on the genomic landscape of these species can shed light on past demographic dynamics and current genetic load, thereby also providing guidance for conservation programs. The pygmy hog (Porcula salvania) is the smallest and rarest wild pig in the world, with current estimation of only a few hundred living in the wild. Here, we analyzed whole-genome sequencing data of six pygmy hogs, three from the wild and three from a captive population, along with 30 pigs representing six other Suidae. First, we show that the pygmy hog had a very small population size with low genetic diversity over the course of the past ~1 million years. One indication of historical small effective population size is the absence of mitochondrial variation in the six sequenced individuals. Second, we evaluated the impact of historical demography. Runs of homozygosity (ROH) analysis suggests that the pygmy hog population has gone through past but not recent inbreeding. Also, the long-term, extremely small population size may have led to the accumulation of harmful mutations suggesting that the accumulation of deleterious mutations is exceeding purifying selection in this species. Thus, care has to be taken in the conservation program to avoid or minimize the potential for further inbreeding depression, and guard against environmental changes in the future.
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Affiliation(s)
- Langqing Liu
- Animal Breeding and GenomicsWageningen University & ResearchWageningenthe Netherlands
| | - Mirte Bosse
- Animal Breeding and GenomicsWageningen University & ResearchWageningenthe Netherlands
| | - Hendrik‐Jan Megens
- Animal Breeding and GenomicsWageningen University & ResearchWageningenthe Netherlands
| | - Manon de Visser
- Animal Breeding and GenomicsWageningen University & ResearchWageningenthe Netherlands
| | - Martien A. M. Groenen
- Animal Breeding and GenomicsWageningen University & ResearchWageningenthe Netherlands
| | - Ole Madsen
- Animal Breeding and GenomicsWageningen University & ResearchWageningenthe Netherlands
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44
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Kyriazis CC, Wayne RK, Lohmueller KE. Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression. Evol Lett 2021; 5:33-47. [PMID: 33552534 PMCID: PMC7857301 DOI: 10.1002/evl3.209] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/10/2020] [Accepted: 11/21/2020] [Indexed: 11/08/2022] Open
Abstract
Human-driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by recessive deleterious mutations becoming homozygous due to inbreeding. The typical approach for managing these populations is to maintain high genetic diversity, increasingly by translocating individuals from large populations to initiate a "genetic rescue." However, the limitations of this approach have recently been highlighted by the demise of the gray wolf population on Isle Royale, which declined to the brink of extinction soon after the arrival of a migrant from the large mainland wolf population. Here, we use a novel population genetic simulation framework to investigate the role of genetic diversity, deleterious variation, and demographic history in mediating extinction risk due to inbreeding depression in small populations. We show that, under realistic models of dominance, large populations harbor high levels of recessive strongly deleterious variation due to these mutations being hidden from selection in the heterozygous state. As a result, when large populations contract, they experience a substantially elevated risk of extinction after these strongly deleterious mutations are exposed by inbreeding. Moreover, we demonstrate that, although genetic rescue is broadly effective as a means to reduce extinction risk, its effectiveness can be greatly increased by drawing migrants from small or moderate-sized source populations rather than large source populations due to smaller populations harboring lower levels of recessive strongly deleterious variation. Our findings challenge the traditional conservation paradigm that focuses on maximizing genetic diversity in small populations in favor of a view that emphasizes minimizing strongly deleterious variation. These insights have important implications for managing small and isolated populations in the increasingly fragmented landscape of the Anthropocene.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCalifornia90095
- Interdepartmental Program in BioinformaticsUniversity of CaliforniaLos AngelesCalifornia90095
- Department of Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCalifornia90095
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45
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White KS, Levi T, Breen J, Britt M, Meröndun J, Martchenko D, Shakeri YN, Porter B, Shafer ABA. Integrating Genetic Data and Demographic Modeling to Facilitate Conservation of Small, Isolated Mountain Goat Populations. J Wildl Manage 2021. [DOI: 10.1002/jwmg.21978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin S. White
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Taal Levi
- Department of Fish and Wildlife Oregon State University Corvallis OR 97331 USA
| | - Jessica Breen
- Forensics Program, Trent University Peterborough ON K9J 7B8 Canada
| | - Meghan Britt
- Forensics Program, Trent University Peterborough ON K9J 7B8 Canada
| | - Justin Meröndun
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
| | - Daria Martchenko
- Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
| | - Yasaman N. Shakeri
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Boyd Porter
- Division of Wildlife Conservation Alaska Department of Fish and Game Juneau AK 99811 USA
| | - Aaron B. A. Shafer
- Forensic Science Program and Environmental and Life Sciences Graduate Program Trent University Peterborough ON K9J 7B8 Canada
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46
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Caballero A, Villanueva B, Druet T. On the estimation of inbreeding depression using different measures of inbreeding from molecular markers. Evol Appl 2021; 14:416-428. [PMID: 33664785 PMCID: PMC7896712 DOI: 10.1111/eva.13126] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/09/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
The inbreeding coefficient (F) of individuals can be estimated from molecular marker data, such as SNPs, using measures of homozygosity of individual markers or runs of homozygosity (ROH) across the genome. These different measures of F can then be used to estimate the rate of inbreeding depression (ID) for quantitative traits. Some recent simulation studies have investigated the accuracy of this estimation with contradictory results. Whereas some studies suggest that estimates of inbreeding from ROH account more accurately for ID, others suggest that inbreeding measures from SNP-by-SNP homozygosity giving a large weight to rare alleles are more accurate. Here, we try to give more light on this issue by carrying out a set of computer simulations considering a range of population genetic parameters and population sizes. Our results show that the previous studies are indeed not contradictory. In populations with low effective size, where relationships are more tight and selection is relatively less intense, F measures based on ROH provide very accurate estimates of ID whereas SNP-by-SNP-based F measures with high weight to rare alleles can show substantial upwardly biased estimates of ID. However, in populations of large effective size, with more intense selection and trait allele frequencies expected to be low if they are deleterious for fitness because of purifying selection, average estimates of ID from SNP-by-SNP-based F values become unbiased or slightly downwardly biased and those from ROH-based F values become slightly downwardly biased. The noise attached to all these estimates, nevertheless, can be very high in large-sized populations. We also investigate the relationship between the different F measures and the homozygous mutation load, which has been suggested as a proxy of inbreeding depression.
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Affiliation(s)
- Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC ExperimentaisUniversidade de VigoVigoSpain
| | - Beatriz Villanueva
- Departamento de Mejora GenéticaInstituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadridSpain
| | - Tom Druet
- Unit of Animal GenomicsGIGA‐R & Faculty of Veterinary MedicineUniversity of LiègeLiègeBelgium
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47
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Multiple life-stage inbreeding depression impacts demography and extinction risk in an extinct-in-the-wild species. Sci Rep 2021; 11:682. [PMID: 33436770 PMCID: PMC7804286 DOI: 10.1038/s41598-020-79979-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Inbreeding can depress individuals’ fitness traits and reduce population viability. However, studies that directly translate inbreeding depression on fitness traits into consequences for population viability, and further, into consequences for management choices, are lacking. Here, we estimated impacts of inbreeding depression (B, lethal equivalents) across life-history stages for an extinct-in-the-wild species, the sihek (Guam kingfisher, Todiramphus cinnamominus). We then projected population growth under different management alternatives with our B estimates incorporated, as well as without inbreeding depression (B = 0) or with a conventional default B. We found that inbreeding depression severely impacted multiple life-history stages, and directly translated into an effect on population viability under management alternatives. Simulations including our B estimates indicated rapid population decline, whereas projections without inbreeding depression or with default B suggested very gradual population decline. Further, our results demonstrate that incorporation of B across life-history stages can influence management decisions, as projections with our B estimates suggested a need to switch to increased breeding management to avoid species extinction and support wild releases. Our results demonstrate that magnitude of B across life-history stages can translate into demographic consequences, such that incorporation of multiple life-stage B into population models can be important for informed conservation management decision-making.
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Curik I, Kövér G, Farkas J, Szendrő Z, Romvári R, Sölkner J, Nagy I. Inbreeding depression for kit survival at birth in a rabbit population under long-term selection. Genet Sel Evol 2020; 52:39. [PMID: 32640975 PMCID: PMC7346452 DOI: 10.1186/s12711-020-00557-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Background Accumulation of detrimental mutations in small populations leads to inbreeding depression of fitness traits and a higher frequency of genetic defects, thus increasing risk of extinction. Our objective was to quantify the magnitude of inbreeding depression for survival at birth, in a closed rabbit population under long-term selection. Methods We used an information theory-based approach and multi-model inference to estimate inbreeding depression and its purging with respect to the trait ‘kit survival at birth’ over a 25-year period in a closed population of Pannon White rabbits, by analysing 22,718 kindling records. Generalised linear mixed models based on the logit link function were applied, which take polygenic random effects into account. Results Our results indicated that inbreeding depression occurred during the period 1992–1997, based on significant estimates of the z-standardised classical inbreeding coefficient z.FL (CI95% − 0.12 to − 0.03) and of the new inbreeding coefficient of the litter z.FNEWL (CI95% − 0.13 to − 0.04) as well as a 59.2% reduction in contributing founders. Inbreeding depression disappeared during the periods 1997–2007 and 2007–2017. For the period 1992–1997, the best model resulted in a significantly negative standardised estimate of the new inbreeding coefficient of the litter and a significantly positive standardised estimate of Kalinowski’s ancestral inbreeding coefficient of the litter (CI95% 0.01 to 0.17), which indicated purging of detrimental load. Kindling season and parity had effects on survival at birth that differed across the three periods of 1992–1997, 1997–2007 and 2007–2017. Conclusions Our results support the existence of inbreeding depression and its purging with respect to kit survival at birth in this Pannon White rabbit population. However, we were unable to exclude possible confounding from the effects of parity and potentially other environmental factors during the study period, thus our results need to be extended and confirmed in other populations.
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Affiliation(s)
- Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.
| | - György Kövér
- Institute of Methodology, Faculty of Economic Science, Kaposvár University, Kaposvár, Hungary
| | - János Farkas
- Institute of Methodology, Faculty of Economic Science, Kaposvár University, Kaposvár, Hungary
| | - Zsolt Szendrő
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary
| | - Róbert Romvári
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Istvan Nagy
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary.
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Domínguez-García S, García C, Quesada H, Caballero A. Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster. Heredity (Edinb) 2019; 123:709-722. [PMID: 31477803 PMCID: PMC6834575 DOI: 10.1038/s41437-019-0263-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 01/21/2023] Open
Abstract
Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.
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Affiliation(s)
- Sara Domínguez-García
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Carlos García
- CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain. .,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain.
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Origin and Evolution of Deleterious Mutations in Horses. Genes (Basel) 2019; 10:genes10090649. [PMID: 31466279 PMCID: PMC6769756 DOI: 10.3390/genes10090649] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023] Open
Abstract
Domestication has changed the natural evolutionary trajectory of horses by favoring the reproduction of a limited number of animals showing traits of interest. Reduced breeding stocks hampered the elimination of deleterious variants by means of negative selection, ultimately inflating mutational loads. However, ancient genomics revealed that mutational loads remained steady during most of the domestication history until a sudden burst took place some 250 years ago. To identify the factors underlying this trajectory, we gather an extensive dataset consisting of 175 modern and 153 ancient genomes previously published, and carry out the most comprehensive characterization of deleterious mutations in horses. We confirm that deleterious variants segregated at low frequencies during the last 3500 years, and only spread and incremented their occurrence in the homozygous state during modern times, owing to inbreeding. This independently happened in multiple breeds, following both the development of closed studs and purebred lines, and the deprecation of horsepower in the 20th century, which brought many draft breeds close to extinction. Our work illustrates the paradoxical effect of some conservation and improvement programs, which reduced the overall genomic fitness and viability.
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