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Burriel-Carranza B, Mochales-Riaño G, Talavera A, Els J, Estarellas M, Al Saadi S, Urriago Suarez JD, Olsson PO, Matschiner M, Carranza S. Clinging on the brink: Whole genomes reveal human-induced population declines and severe inbreeding in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus). Mol Ecol 2024:e17451. [PMID: 38970417 DOI: 10.1111/mec.17451] [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: 01/03/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/08/2024]
Abstract
Human-mediated habitat destruction has had a profound impact on increased species extinction rates and population declines worldwide. The coastal development in the United Arab Emirates (UAE) over the last two decades, serves as an example of how habitat transformation can alter the landscape of a country in just a few years. Here, we study the genomic implications of habitat transformation in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus), the only endemic vertebrate of the UAE. We generate a high-quality reference genome for this gecko, representing the first reference genome for the family Phyllodactylidae, and produce whole-genome resequencing data for 23 specimens from 10 different species of leaf-toed geckos. Our results show that A. caudivolvulus has consistently lower genetic diversity than any other Arabian species of Asaccus, suggesting a history of ancient population declines. However, high levels of recent inbreeding are recorded among populations in heavily developed areas, with a more than 50% increase in long runs of homozygosity within a 9-year period. Moreover, results suggest that this species does not effectively purge deleterious mutations, hence making it more vulnerable to future stochastic threats. Overall, results show that A. caudivolvulus is in urgent need of protection, and habitat preservation must be warranted to ensure the species' survival.
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Affiliation(s)
- Bernat Burriel-Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Museu de Ciències Naturals de Barcelona, Barcelona, Spain
| | | | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority, Sharjah, United Arab Emirates
| | - Maria Estarellas
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | | | | | | | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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2
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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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3
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Dehasque M, Morales HE, Díez-Del-Molino D, Pečnerová P, Chacón-Duque JC, Kanellidou F, Muller H, Plotnikov V, Protopopov A, Tikhonov A, Nikolskiy P, Danilov GK, Giannì M, van der Sluis L, Higham T, Heintzman PD, Oskolkov N, Gilbert MTP, Götherström A, van der Valk T, Vartanyan S, Dalén L. Temporal dynamics of woolly mammoth genome erosion prior to extinction. Cell 2024:S0092-8674(24)00577-4. [PMID: 38942016 DOI: 10.1016/j.cell.2024.05.033] [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: 10/02/2023] [Revised: 02/08/2024] [Accepted: 05/17/2024] [Indexed: 06/30/2024]
Abstract
A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.
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Affiliation(s)
- Marianne Dehasque
- 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.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, The 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; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - Foteini Kanellidou
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Héloïse Muller
- Master de Biologie, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon I, Universite de Lyon, 69007 Lyon, France
| | - Valerii Plotnikov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Albert Protopopov
- Academy of Sciences of Sakha Republic, Lenin Avenue 33, Yakutsk, Republic of Sakha (Yakutia), Russia
| | - Alexei Tikhonov
- Zoological Institute of Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences, Moscow, Russia
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 3 University Embankment, Box 199034, Saint-Petersburg, Russia
| | - Maddalena Giannì
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Laura van der Sluis
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Tom Higham
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Peter D Heintzman
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 11418 Stockholm, Sweden
| | - 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; SciLifeLab, Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - 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.
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4
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Steux C, Szpiech ZA. The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques. Genome Biol Evol 2024; 16:evae115. [PMID: 38795368 PMCID: PMC11157460 DOI: 10.1093/gbe/evae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/25/2024] [Accepted: 05/22/2024] [Indexed: 05/27/2024] Open
Abstract
Understanding how deleterious variation is shaped and maintained in natural populations is important in conservation and evolutionary biology, as decreased fitness caused by these deleterious mutations can potentially lead to an increase in extinction risk. It is known that demographic processes can influence these patterns. For example, population bottlenecks and inbreeding increase the probability of inheriting identical-by-descent haplotypes from a recent common ancestor, creating long tracts of homozygous genotypes called runs of homozygosity (ROH), which have been associated with an accumulation of mildly deleterious homozygotes. Counterintuitively, positive selection can also maintain deleterious variants in a population through genetic hitchhiking. Here, we analyze the whole genomes of 79 wild Chinese rhesus macaques across five subspecies and characterize patterns of deleterious variation with respect to ROH and signals of recent positive selection. We show that the fraction of homozygotes occurring in long ROH is significantly higher for deleterious homozygotes than tolerated ones, whereas this trend is not observed for short and medium ROH. This confirms that inbreeding, by generating these long tracts of homozygosity, is the main driver of the high burden of homozygous deleterious alleles in wild macaque populations. Furthermore, we show evidence that homozygous LOF variants are being purged. Next, we identify seven deleterious variants at high frequency in regions putatively under selection near genes involved with olfaction and other processes. Our results shed light on how evolutionary processes can shape the distribution of deleterious variation in wild nonhuman primates.
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Affiliation(s)
- Camille Steux
- Department of Biology, Pennsylvania State University, University Park, USA
- Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3—Paul Sabatier (UT3), Toulouse, France
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, USA
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5
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Wang Y, Yang Y, Han Z, Li J, Luo J, Yang H, Kuang J, Wu D, Wang S, Tso S, Ju T, Liu J, Renner SS, Kangshan M. Efficient purging of deleterious mutations contributes to the survival of a rare conifer. HORTICULTURE RESEARCH 2024; 11:uhae108. [PMID: 38883334 PMCID: PMC11179848 DOI: 10.1093/hr/uhae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/01/2024] [Indexed: 06/18/2024]
Abstract
Cupressaceae is a conifer family rich in plants of horticultural importance, including Cupressus, Chamaecyparis, Juniperus, and Thuja, yet genomic surveys are lacking for this family. Cupressus gigantea, one of the many rare conifers that are threatened by climate change and anthropogenic habitat fragmentation, plays an ever-increasing role in ecotourism in Tibet. To infer how past climate change has shaped the population evolution of this species, we generated a de novo chromosome-scale genome (10.92 Gb) and compared the species' population history and genetic load with that of a widespread close relative, C. duclouxiana. Our demographic analyses, based on 83 re-sequenced individuals from multiple populations of the two species, revealed a sharp decline of population sizes during the first part of the Quaternary. However, populations of C. duclouxiana then started to recover, while C. gigantea populations continued to decrease until recently. The total genomic diversity of C. gigantea is smaller than that of C. duclouxiana, but contrary to expectations, C. gigantea has fewer highly and mildly deleterious mutations than C. duclouxiana, and simulations and statistical tests support purifying selection during prolonged inbreeding as the explanation. Our results highlight the evolutionary consequences of decreased population size on the genetic burden of a long-lived endangered conifer with large genome size and suggest that genetic purging deserves more attention in conservation management.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Zhitong Han
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Jian Luo
- Xizang Key Laboratory of Forest Ecology in Plateau Area of Ministry of Education, National Key Station of Field Scientific Observation & Experiment of Alpine Forest Ecology System in Nyingchi, Research Institute of Xizang Plateau Ecology, Xizang Agriculture & Animal Husbandry University, Nyingchi 860000, China
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Jingge Kuang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Dayu Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Shiyang Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Sonam Tso
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Tsam Ju
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Mao Kangshan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
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6
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Ewart KM, Ho SYW, Chowdhury AA, Jaya FR, Kinjo Y, Bennett J, Bourguignon T, Rose HA, Lo N. Pervasive relaxed selection in termite genomes. Proc Biol Sci 2024; 291:20232439. [PMID: 38772424 DOI: 10.1098/rspb.2023.2439] [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: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/23/2024] Open
Abstract
Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we analysed nine genomes, including newly sequenced genomes from three non-eusocial cockroaches. Using a phylogenomic approach, we found that termite genomes have experienced lower rates of synonymous substitutions than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of non-synonymous substitutions in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24-31% of the genes analysed) compared with the latter (2-4%). We infer that this is due to reductions in effective population size, rather than gene-specific effects (e.g. indirect selection of caste-biased genes). We found no obvious signature of increased genetic load in termites, and postulate efficient purging of deleterious alleles at the colony level. Additionally, we identified genomic adaptations that may underpin caste differentiation, such as genes involved in post-translational modifications. Our results provide insights into the evolution of termites and the genomic consequences of eusociality more broadly.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Frederick R Jaya
- Ecology & Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Yukihiro Kinjo
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Okinawa International University, Okinawa, Japan
| | - Juno Bennett
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Harley A Rose
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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7
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Steux C, Szpiech ZA. The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.04.560901. [PMID: 38712222 PMCID: PMC11071285 DOI: 10.1101/2023.10.04.560901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Understanding how deleterious variation is shaped and maintained in natural populations is important in conservation and evolutionary biology, as decreased fitness caused by these deleterious mutations can potentially lead to an increase in extinction risk. It is known that demographic processes can influence these patterns. For example, population bottlenecks and inbreeding increase the probability of inheriting identical-by-descent haplotypes from a recent common ancestor, creating long tracts of homozygous genotypes called runs of homozygosity (ROH), which have been associated with an accumulation of mildly deleterious homozygotes. Counter intuitively, positive selection can also maintain deleterious variants in a population through genetic hitchhiking. Here we analyze the whole genomes of 79 wild Chinese rhesus macaques across five subspecies and characterize patterns of deleterious variation with respect to ROH and signals of recent positive selection. We show that the fraction of homozygotes occurring in long ROH is significantly higher for deleterious homozygotes than tolerated ones, whereas this trend is not observed for short and medium ROH. This confirms that inbreeding, by generating these long tracts of homozygosity, is the main driver of the high burden of homozygous deleterious alleles in wild macaque populations. Furthermore, we show evidence that homozygous LOF variants are being purged. Next, we identify 7 deleterious variants at high frequency in regions putatively under selection near genes involved with olfaction and other processes. Our results shed light on how evolutionary processes can shape the distribution of deleterious variation in wild non-human primates.
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Affiliation(s)
- Camille Steux
- Department of Biology, Pennsylvania State University, USA
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France
- Département de Biologie, École Normale Supérieure, PSL Université Paris, Paris, France
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, USA
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8
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Jiang J, Xu YC, Zhang ZQ, Chen JF, Niu XM, Hou XH, Li XT, Wang L, Zhang YE, Ge S, Guo YL. Forces driving transposable element load variation during Arabidopsis range expansion. THE PLANT CELL 2024; 36:840-862. [PMID: 38036296 PMCID: PMC10980350 DOI: 10.1093/plcell/koad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.
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Affiliation(s)
- Juan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhi-Qin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Fu Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Min Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xin-Tong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yong E Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Taylor RS, Manseau M, Keobouasone S, Liu P, Mastromonaco G, Solmundson K, Kelly A, Larter NC, Gamberg M, Schwantje H, Thacker C, Polfus J, Andrew L, Hervieux D, Simmons D, Wilson PJ. High genetic load without purging in caribou, a diverse species at risk. Curr Biol 2024; 34:1234-1246.e7. [PMID: 38417444 DOI: 10.1016/j.cub.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/17/2023] [Accepted: 02/01/2024] [Indexed: 03/01/2024]
Abstract
High intra-specific genetic diversity is associated with adaptive potential, which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging of deleterious variation has been demonstrated in some threatened species. However, less is known about the costs of declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that are expected to undergo population declines. Caribou is a species of ecological and cultural significance in North America with a wide distribution supporting extensive phenotypic variation but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole-genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We found highly divergent levels of inbreeding across individuals, including the loss of alleles by drift but not increased purging in inbred individuals, which had more homozygous deleterious alleles. We also found comparable frequencies of homozygous deleterious alleles between lineages regardless of nucleotide diversity. Thus, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the "double-edged sword" of genetic diversity that may be representative of other species atrisk affected by anthropogenic activities.
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Affiliation(s)
- Rebecca S Taylor
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Micheline Manseau
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Sonesinh Keobouasone
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Peng Liu
- Landscape Science and Technology, Environment and Climate Change Canada, Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | | | - Kirsten Solmundson
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, ON K9L 1Z8, Canada
| | - Allicia Kelly
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Nicholas C Larter
- Department of Environment and Natural Resources, Government of Northwest Territories, PO Box 900, Fort Smith, NT X0E 0P0, Canada
| | - Mary Gamberg
- Gamberg Consulting, Jarvis Street, Whitehorse, YK Y1A 2J2, Canada
| | - Helen Schwantje
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Caeley Thacker
- British Columbia Ministry of Forest, Lands, Natural Resource Operations, and Rural Development, Labieux Road, Nanaimo, BC V9T 6E9, Canada
| | - Jean Polfus
- Canadian Wildlife Service - Pacific Region, Environment and Climate Change Canada, 1238 Discovery Avenue, Kelowna, BC V1V 1V9, Canada
| | - Leon Andrew
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Dave Hervieux
- Alberta Ministry of Environment and Protected Areas, Government of Alberta, 10320-99 Street, Grande Prairie, AB T8V 6J4, Canada
| | - Deborah Simmons
- Ɂehdzo Got'ı̨nę Gots'ę́ Nákedı (Sahtú Renewable Resources Board), P.O. Box 134, Tulít'a, NT X0E 0K0, Canada
| | - Paul J Wilson
- Biology Department, Trent University, East Bank Drive, Peterborough, ON K9L 1Z8, Canada
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10
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Lucena-Perez M, Paijmans JLA, Nocete F, Nadal J, Detry C, Dalén L, Hofreiter M, Barlow A, Godoy JA. Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx. Nat Ecol Evol 2024; 8:282-292. [PMID: 38225424 DOI: 10.1038/s41559-023-02267-7] [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: 06/30/2022] [Accepted: 11/10/2023] [Indexed: 01/17/2024]
Abstract
Genetic diversity is lost in small and isolated populations, affecting many globally declining species. Interspecific admixture events can increase genetic variation in the recipient species' gene pool, but empirical examples of species-wide restoration of genetic diversity by admixture are lacking. Here we present multi-fold coverage genomic data from three ancient Iberian lynx (Lynx pardinus) approximately 2,000-4,000 years old and show a continuous or recurrent process of interspecies admixture with the Eurasian lynx (Lynx lynx) that increased modern Iberian lynx genetic diversity above that occurring millennia ago despite its recent demographic decline. Our results add to the accumulating evidence for natural admixture and introgression among closely related species and show that this can result in an increase of species-wide genetic diversity in highly genetically eroded species. The strict avoidance of interspecific sources in current genetic restoration measures needs to be carefully reconsidered, particularly in cases where no conspecific source population exists.
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Affiliation(s)
- Maria Lucena-Perez
- Department of Ecology and Evolution, Estación Biológica de Doñana, CSIC, Seville, Spain
| | - Johanna L A Paijmans
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Francisco Nocete
- Grupo de Investigación MIDAS, Departamento Historia I (Prehistoria), Universidad de Huelva, Huelva, Spain
| | - Jordi Nadal
- SERP, Departament de Prehistoria, Historia Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Cleia Detry
- UNIARQ - Centro de Arqueologia da Faculdade de Letras da Universidade de Lisboa, Alameda da Universidade, Lisbon, Portugal
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, UK
| | - José A Godoy
- Department of Ecology and Evolution, Estación Biológica de Doñana, CSIC, Seville, Spain.
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11
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Nagy I, Nguyen TA. Characterizing and Eliminating the Inbreeding Load. Vet Sci 2023; 11:8. [PMID: 38250914 PMCID: PMC10819885 DOI: 10.3390/vetsci11010008] [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: 10/29/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
The authors evaluated the relevant literature related to purging, which is the interaction between selection and inbreeding in which the population may eliminate its inbreeding load at least partially. According to the relevant literature, the inbreeding load and the process of purging were evaluated via pedigree methods based on ancestral inbreeding, the inbreeding-purging model, and expressed opportunity of purging, along with genomic methods. Most ancestral inbreeding-related studies were performed in zoos, where only a small proportion of the studied populations show signs of purging. The inbreeding-purging model was developed with Drosophila, and it was used to evaluate different zoo ungulates and Pannon white rabbits. Purging was detected in both studies. The expressed opportunity of purging was applied in Jersey cattle and Pannon white rabbits. In the Jersey cattle, it had an effect of 12.6% for fitness, while in the Pannon white rabbits, the inbreeding load was between 40% and 80% of its original value. The genomic studies also signalled purging, but they also made it clear that, contrary to the detected purging, the evaluated populations still suffered from inbreeding depression. Therefore, especially for domesticated animals, it can be concluded that deliberate inbreeding with the purpose of generating purging is not advocated.
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Affiliation(s)
- István Nagy
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary;
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12
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Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
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Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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13
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Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
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Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
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14
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Dussex N, Morales HE, Grossen C, Dalén L, van Oosterhout C. Purging and accumulation of genetic load in conservation. Trends Ecol Evol 2023; 38:961-969. [PMID: 37344276 DOI: 10.1016/j.tree.2023.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.
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Affiliation(s)
- Nicolas Dussex
- Department of Natural History, NTNU University Museum, Erling Skakkes Gate 47A, 7012 Trondheim, Norway.
| | - Hernán E Morales
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christine Grossen
- WSL Swiss Federal Research Institute, CH-8903 Birmensdorf, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91 Stockholm, Sweden
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, UK
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15
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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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16
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Rougemont Q, Leroy T, Rondeau EB, Koop B, Bernatchez L. Allele surfing causes maladaptation in a Pacific salmon of conservation concern. PLoS Genet 2023; 19:e1010918. [PMID: 37683018 PMCID: PMC10545117 DOI: 10.1371/journal.pgen.1010918] [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: 11/11/2022] [Revised: 10/02/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations, is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.
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Affiliation(s)
- Quentin Rougemont
- Centre d’Ecologie Fonctionnelle et Evolutive, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Auzeville- Tolosane, France
| | - Eric B. Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, Canada
| | - Ben Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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17
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Qi J, Pan H, Wang X, Xuan Z, Pan X, Li X, Shen Y, Yang J, Zhang J, Li M. Genomic insights into the postintroduction failure of the Asian icefish Protosalanx chinensis in China. Mol Ecol 2023. [PMID: 37160724 DOI: 10.1111/mec.16979] [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: 01/10/2022] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
Biological introductions provide a natural ecological experiment unfolding in a recent historical timeframe to elucidate how evolutionary processes (such as founder effects, genetic diversity and adaptation) shape the genomic landscape of populations postintroduction. The Asian icefish, Protosalanx chinensis, is an economically important fishery resource, deliberately introduced into dozens of provinces across China for decades. However, while invading and disturbing the local ecosystem, many introduced populations declined, disappearing mysteriously in a very short time. The way in which various evolutionary forces integrate to result in invasion failure of an introduced population remains unknown. Here, we performed whole-genome sequencing of 10 species from the Salangidae family and 70 Asian icefish (Protosalanx chinensis) individuals from 7 geographic populations in China, aiming to characterize the evolutionary fate of introduced populations. Our results show that compared to other Salangidae species, P. chinensis has low genetic diversity, potentially due to the long-lasting decline in population size. In a recently introducted population, Lugu lake, severe sampling effects and a strong bottleneck further deteriorated the genomic landscape. Although the introduced population showed signs of reduced genetic load, the purging selection efficiency was low. Our selective sweep analysis revealed site frequency changes in candidate genes, including gata1a and hoxd4b, which could be associated with a decrease in dissolved oxygen in the deep-water plateau lake. These findings caution against the widespread introduction of P. chinensis in China and lay the groundwork for future use of this economically species.
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Affiliation(s)
- Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Huijuan Pan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiaochen Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhongya Xuan
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xiaofu Pan
- State key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xuanzhao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
- College of Life Sciences, Hebei University, Baoding, China
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Jian Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Fishery Ecological Environment Assessment and Resource Conservation in Middle and Lower Reaches of the Yangtze River, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jie Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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18
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Wang X, Peischl S, Heckel G. Demographic history and genomic consequences of 10,000 generations of isolation in a wild mammal. Curr Biol 2023; 33:2051-2062.e4. [PMID: 37178689 DOI: 10.1016/j.cub.2023.04.042] [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: 12/20/2022] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
Increased human activities caused the isolation of populations in many species-often associated with genetic depletion and negative fitness effects. The effects of isolation are predicted by theory, but long-term data from natural populations are scarce. We show, with full genome sequences, that common voles (Microtus arvalis) in the Orkney archipelago have remained genetically isolated from conspecifics in continental Europe since their introduction by humans over 5,000 years ago. Modern Orkney vole populations are genetically highly differentiated from continental conspecifics as a result of genetic drift processes. Colonization likely started on the biggest Orkney island and vole populations on smaller islands were gradually split off, without signs of secondary admixture. Despite having large modern population sizes, Orkney voles are genetically depauperate and successive introductions to smaller islands resulted in further reduction of genetic diversity. We detected high levels of fixation of predicted deleterious variation compared with continental populations, particularly on smaller islands, yet the fitness effects realized in nature are unknown. Simulations showed that predominantly mildly deleterious mutations were fixed in populations, while highly deleterious mutations were purged early in the history of the Orkney population. Relaxation of selection overall due to benign environmental conditions on the islands and the effects of soft selection may have contributed to the repeated, successful establishment of Orkney voles despite potential fitness loss. Furthermore, the specific life history of these small mammals, resulting in relatively large population sizes, has probably been important for their long-term persistence in full isolation.
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Affiliation(s)
- Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Stephan Peischl
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Institute of Bioinformatics, Amphipôle, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland.
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19
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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20
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Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious Variation in Natural Populations and Implications for Conservation Genetics. Annu Rev Anim Biosci 2023; 11:93-114. [PMID: 36332644 PMCID: PMC9933137 DOI: 10.1146/annurev-animal-080522-093311] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.
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Affiliation(s)
- Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, California, USA;
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Stella C Yuan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , , .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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21
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Abstract
Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.
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Affiliation(s)
- Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden;
| | - Alexis Beaurepaire
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Eckart Stolle
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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22
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Kyriazis CC, Beichman AC, Brzeski KE, Hoy SR, Peterson RO, Vucetich JA, Vucetich LM, Lohmueller KE, Wayne RK. Genomic Underpinnings of Population Persistence in Isle Royale Moose. Mol Biol Evol 2023; 40:7024794. [PMID: 36729989 PMCID: PMC9927576 DOI: 10.1093/molbev/msad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.
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Affiliation(s)
| | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Sarah R Hoy
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Rolf O Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Leah M Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
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23
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Gajdárová B, Belotti E, Bufka L, Volfová J, Wölfl S, Mináriková T, Hollerbach L, Duľa M, Kleven O, Kutal M, Nowak C, Ozoliņš J, Tám B, Bryja J, Koubek P, Krojerová-Prokešová J. Long-term genetic monitoring of a reintroduced Eurasian lynx population does not indicate an ongoing loss of genetic diversity. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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24
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Smeds L, Ellegren H. From high masked to high realized genetic load in inbred Scandinavian wolves. Mol Ecol 2022; 32:1567-1580. [PMID: 36458895 DOI: 10.1111/mec.16802] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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25
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Abstract
SignificanceThe dynamics of deleterious variation under contrasting demographic scenarios remain poorly understood in spite of their relevance in evolutionary and conservation terms. Here we apply a genomic approach to study differences in the burden of deleterious alleles between the endangered Iberian lynx (Lynx pardinus) and the widespread Eurasian lynx (Lynx lynx). Our analysis unveils a significantly lower deleterious burden in the former species that should be ascribed to genetic purging, that is, to the increased opportunities of selection against recessive homozygotes due to the inbreeding caused by its smaller population size, as illustrated by our analytical predictions. This research provides theoretical and empirical evidence on the evolutionary relevance of genetic purging under certain demographic conditions.
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