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vonHoldt BM, DeCandia AL, Cassidy KA, Stahler EE, Sinsheimer JS, Smith DW, Stahler DR. Patterns of reproduction and autozygosity distinguish the breeding from nonbreeding gray wolves of Yellowstone National Park. J Hered 2024; 115:327-338. [PMID: 37793153 DOI: 10.1093/jhered/esad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding, and genetic diversity of the breeding versus nonreproductive segment of the Yellowstone National Park gray wolf population. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found more than 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time but with minimal loss of observed heterozygosity. Strikingly, the reproductive portion of the population carried a significantly lower genome-wide inbreeding coefficients, autozygosity, and more rapid decay for linkage disequilibrium relative to the nonbreeding population. Breeding wolves had significantly longer lifespans and lower inbreeding coefficients than nonbreeding wolves. Our model revealed that the number of litters was negatively significantly associated with heterozygosity (R = -0.11). Our findings highlight genetic contributions to fitness, and the importance of the reproductively active individuals in a population to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Alexandra L DeCandia
- Department of Biology, Georgetown University, Washington, DC, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Kira A Cassidy
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Erin E Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Janet S Sinsheimer
- Department of Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, CA, United States
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
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2
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Zhang Y, Stern AJ, Nielsen R. The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity. J Hered 2024; 115:373-384. [PMID: 38146994 DOI: 10.1093/jhered/esad079] [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: 06/27/2023] [Revised: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023] Open
Abstract
Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success of GR depends on several factors-such as their demographic history and distribution of dominance effects of mutations-that may vary across populations. While we understand the impact of these factors on the dynamics of GR, their impact on local adaptations remains unclear. To this end, we conduct a population genetics simulation study to evaluate the impact of trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history on the efficacy of GR. We find that the impact on local adaptations depends highly on the mutational load at the time of GR, which is in turn shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. Over time local adaptations are generally restored post-GR, though in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation affecting the trait is replaced by donor variation can vary drastically and is especially high for complex traits. Our results provide insights on the impact of GR on trait evolution and considerations for the practical implementation of GR.
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Affiliation(s)
- Yulin Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Center for Computational Biology, UC Berkeley, Berkeley, CA, United States
| | - Aaron J Stern
- Center for Computational Biology, UC Berkeley, Berkeley, CA, United States
| | - Rasmus Nielsen
- Department of Integrative Biology, UC Berkeley, Berkeley, CA, United States
- Department of Statistics, UC Berkeley, Berkeley, CA, United States
- Center for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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3
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Boughman JW, Brand JA, Brooks RC, Bonduriansky R, Wong BBM. Sexual selection and speciation in the Anthropocene. Trends Ecol Evol 2024; 39:654-665. [PMID: 38503640 DOI: 10.1016/j.tree.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 03/21/2024]
Abstract
Anthropogenic change threatens global biodiversity by causing severe ecological disturbance and extinction. Here, we consider the effects of anthropogenic change on one process that generates biodiversity. Sexual selection (a potent evolutionary force and driver of speciation) is highly sensitive to the environment and, thus, vulnerable to anthropogenic ecological change. Anthropogenic alterations to sexual display and mate preference can make it harder to distinguish between conspecific and heterospecific mates or can weaken divergence via sexual selection, leading to higher rates of hybridization and biodiversity loss. Occasionally, anthropogenically altered sexual selection can abet diversification, but this appears less likely than biodiversity loss. In our rapidly changing world, a full understanding of sexual selection and speciation requires a global change perspective.
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Affiliation(s)
- Janette W Boughman
- Department of Integrative Biology & Evolution, Ecology and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
| | - Jack A Brand
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia; Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Västerbotten, SE-907 36, Sweden
| | - Robert C Brooks
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
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4
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Mugambe J, Ahmed RH, Thaller G, Schmidtmann C. Impact of inbreeding on production, fertility, and health traits in German Holstein dairy cattle utilizing various inbreeding estimators. J Dairy Sci 2024; 107:4714-4725. [PMID: 38310961 DOI: 10.3168/jds.2023-23728] [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: 05/11/2023] [Accepted: 12/29/2023] [Indexed: 02/06/2024]
Abstract
In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (Fped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (Fhat1, Fhat2, Fhat3), VanRaden's first method (FVR1, with observed allele frequencies, and FVR0.5, when allele frequencies are set to 0.5), and one based on runs of homozygosity (Froh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from -0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (Fhat1) to 40.62 kg (Fhat3), 1.18 kg (Fhat2) to 1.70 kg (Fhat3), 0.90 kg (Fhat2) to 1.45 kg (Froh and Fhat3), 0.19 (Fped) to 0.34 d (Fhat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.
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Affiliation(s)
- Julius Mugambe
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany.
| | - Rana H Ahmed
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany
| | - Christin Schmidtmann
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098 Kiel, Germany; IT-Solutions for Animal Production (vit), 27283 Verden, Germany
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5
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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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6
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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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7
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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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8
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Paijmans AJ, Berthelsen AL, Nagel R, Christaller F, Kröcker N, Forcada J, Hoffman JI. Little evidence of inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups. Sci Rep 2024; 14:12610. [PMID: 38824161 PMCID: PMC11144264 DOI: 10.1038/s41598-024-62290-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024] Open
Abstract
Inbreeding depression, the loss of offspring fitness due to consanguineous mating, is generally detrimental for individual performance and population viability. We investigated inbreeding effects in a declining population of Antarctic fur seals (Arctocephalus gazella) at Bird Island, South Georgia. Here, localised warming has reduced the availability of the seal's staple diet, Antarctic krill, leading to a temporal increase in the strength of selection against inbred offspring, which are increasingly failing to recruit into the adult breeding population. However, it remains unclear whether selection operates before or after nutritional independence at weaning. We therefore used microsatellite data from 885 pups and their mothers, and SNP array data from 98 mother-offspring pairs, to quantify the effects of individual and maternal inbreeding on three important neonatal fitness traits: birth mass, survival and growth. We did not find any clear or consistent effects of offspring or maternal inbreeding on any of these traits. This suggests that selection filters inbred individuals out of the population as juveniles during the time window between weaning and recruitment. Our study brings into focus a poorly understood life-history stage and emphasises the importance of understanding the ecology and threats facing juvenile pinnipeds.
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Affiliation(s)
- A J Paijmans
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany.
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany.
| | - A L Berthelsen
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - R Nagel
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- Centre for Biological Diversity, University of St. Andrews, St Andrews, KY16 9TH, UK
| | - F Christaller
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - N Kröcker
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
| | - J Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - J I Hoffman
- Department of Evolutionary Population Genetics, Bielefeld University, 33615, Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501, Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
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9
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Laurent R, Gineau L, Utge J, Lafosse S, Phoeung CL, Hegay T, Olaso R, Boland A, Deleuze JF, Toupance B, Heyer E, Leutenegger AL, Chaix R. Measuring the Efficiency of Purging by non-random Mating in Human Populations. Mol Biol Evol 2024; 41:msae094. [PMID: 38839045 PMCID: PMC11184347 DOI: 10.1093/molbev/msae094] [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: 10/30/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.
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Affiliation(s)
- Romain Laurent
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Laure Gineau
- IRD, MERIT, Université Paris Cité, 75006 Paris, France
| | - José Utge
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Sophie Lafosse
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Tatyana Hegay
- Laboratory of Genome-cell technology, Institute of Immunology and Human genomics, Academy of Sciences, Tashkent, Uzbekistan
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Bruno Toupance
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
- Eco-Anthropologie, Université Paris Cité, 75006 Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Raphaëlle Chaix
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
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10
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Summers J, Cosgrove EJ, Bowman R, Fitzpatrick JW, Chen N. Impacts of increasing isolation and environmental variation on Florida Scrub-Jay demography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575127. [PMID: 38260596 PMCID: PMC10802623 DOI: 10.1101/2024.01.10.575127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understand how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively-breeding Florida Scrub-Jays ( Aphelocoma coerulescens ) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival, and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.
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11
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Taylor BA, Tembrock LR, Sankovitz M, Wilson TM, Looney C, Takahashi J, Gilligan TM, Smith-Pardo AH, Harpur BA. Population genomics of the invasive Northern Giant Hornet Vespa mandarinia in North America and across its native range. Sci Rep 2024; 14:10803. [PMID: 38734771 PMCID: PMC11088652 DOI: 10.1038/s41598-024-61534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024] Open
Abstract
The northern giant hornet Vespa mandarinia (NGH) is a voracious predator of other insect species, including honey bees. NGH's native range spans subtropical and temperate regions across much of east and southeast Asia and, in 2019, exotic populations of the species were discovered in North America. Despite this broad range and invasive potential, investigation of the population genomic structure of NGH across its native and introduced ranges has thus far been limited to a small number of mitochondrial samples. Here, we present analyses of genomic data from NGH individuals collected across the species' native range and from exotic individuals collected in North America. We provide the first survey of whole-genome population variation for any hornet species, covering this species' native and invasive ranges, and in doing so confirm likely origins in Japan and South Korea for the two introductions. We additionally show that, while this introduced population exhibited strongly elevated levels of inbreeding, these signatures of inbreeding are also present in some long-standing native populations, which may indicate that inbreeding depression alone is insufficient to prevent the persistence of NGH populations. As well as highlighting the importance of ongoing monitoring and eradication efforts to limit the spread of this species outside of its natural range, our data will serve as a foundational database for future genomic studies into introduced hornet populations.
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Affiliation(s)
- Benjamin A Taylor
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Madison Sankovitz
- Department of Ecology and Evolutionary Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Telissa M Wilson
- Washington State Department of Agriculture, Olympia, WA, 98501, USA
| | - Chris Looney
- Washington State Department of Agriculture, Olympia, WA, 98501, USA
| | - Junichi Takahashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8047, Japan
| | - Todd M Gilligan
- USDA Animal and Plant Health Inspection Service (APHIS), Fort Collins, CO, 80526-1825, USA
| | - Allan H Smith-Pardo
- USDA Animal and Plant Health Inspection Service (APHIS), Fort Collins, CO, 80526-1825, USA
| | - Brock A Harpur
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA
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12
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Hewett AM, Johnston SE, Morris A, Morris S, Pemberton JM. Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer. Mol Ecol 2024; 33:e17335. [PMID: 38549143 DOI: 10.1111/mec.17335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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13
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Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [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: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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14
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Xu X, Xu Y, Che J, Han X, Wang Z, Wang X, Zhang Q, Li X, Zhang Q, Xiao J, Li X, Zhang Q, Ouyang Y. The genetic basis and process of inbreeding depression in an elite hybrid rice. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2547-2. [PMID: 38679669 DOI: 10.1007/s11427-023-2547-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 05/01/2024]
Abstract
Inbreeding depression refers to the reduced performance arising from increased homozygosity, a phenomenon that is the reverse of heterosis and exists among plants and animals. As a natural self-pollinated crop with strong heterosis, the mechanism of inbreeding depression in rice is largely unknown. To understand the genetic basis of inbreeding depression, we constructed a successive inbreeding population from the F2 to F4 generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each generation. The expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle, 11 for primary branches, and 12 for secondary branches, and these loci constitute the main correlation between heterosis and inbreeding depression. However, the genetic basis of inbreeding depression is also distinct from that of heterosis, such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected depression. Noticeably, two-locus interactions may change the extent and direction of the depression effects of the target loci, and overall interactions would promote inbreeding depression among generations. Using an F2:3 variation population, the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after inbreeding. We found inconsistent or various degrees of background depression from the F2 to F3 generation assuming different genotypes of the target locus, which may affect the actual depression effect of the locus due to epistasis. The results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms, which expand our understanding of the whole-genome architecture of inbreeding depression.
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Affiliation(s)
- Xiaodong Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yawen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Che
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Han
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhengji Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianmeng Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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15
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Rajawat D, Ghildiyal K, Sonejita Nayak S, Sharma A, Parida S, Kumar S, Ghosh AK, Singh U, Sivalingam J, Bhushan B, Dutt T, Panigrahi M. Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle. Gene 2024; 901:148178. [PMID: 38242377 DOI: 10.1016/j.gene.2024.148178] [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: 09/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - 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
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Pharmacology & Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Shive Kumar
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - A K Ghosh
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Umesh Singh
- ICAR Central Institute for Research on Cattle, Meerut, UP, 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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16
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Wilder AP, Steiner CC, Hendricks S, Haller BC, Kim C, Korody ML, Ryder OA. Genetic load and viability of a future restored northern white rhino population. Evol Appl 2024; 17:e13683. [PMID: 38617823 PMCID: PMC11009427 DOI: 10.1111/eva.13683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 04/16/2024] Open
Abstract
As biodiversity loss outpaces recovery, conservationists are increasingly turning to novel tools for preventing extinction, including cloning and in vitro gametogenesis of biobanked cells. However, restoration of populations can be hindered by low genetic diversity and deleterious genetic load. The persistence of the northern white rhino (Ceratotherium simum cottoni) now depends on the cryopreserved cells of 12 individuals. These banked genomes have higher genetic diversity than southern white rhinos (C. s. simum), a sister subspecies that successfully recovered from a severe bottleneck, but the potential impact of genetic load is unknown. We estimated how demographic history has shaped genome-wide genetic load in nine northern and 13 southern white rhinos. The bottleneck left southern white rhinos with more fixed and homozygous deleterious alleles and longer runs of homozygosity, whereas northern white rhinos retained more deleterious alleles masked in heterozygosity. To gauge the impact of genetic load on the fitness of a northern white rhino population restored from biobanked cells, we simulated recovery using fitness of southern white rhinos as a benchmark for a viable population. Unlike traditional restoration, cell-derived founders can be reintroduced in subsequent generations to boost lost genetic diversity and relieve inbreeding. In simulations with repeated reintroduction of founders into a restored population, the fitness cost of genetic load remained lower than that borne by southern white rhinos. Without reintroductions, rapid growth of the restored population (>20-30% per generation) would be needed to maintain comparable fitness. Our results suggest that inbreeding depression from genetic load is not necessarily a barrier to recovery of the northern white rhino and demonstrate how restoration from biobanked cells relieves some constraints of conventional restoration from a limited founder pool. Established conservation methods that protect healthy populations will remain paramount, but emerging technologies hold promise to bolster these tools to combat the extinction crisis.
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Affiliation(s)
- Aryn P. Wilder
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Cynthia C. Steiner
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Sarah Hendricks
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
- Institute for Interdisciplinary Data SciencesUniversity of IdahoMoscowIdahoUSA
| | | | - Chang Kim
- University of CaliforniaSanta Cruz Genomics InstituteSanta CruzCaliforniaUSA
- Department of Neurological SurgeryUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Marisa L. Korody
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Oliver A. Ryder
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
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17
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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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18
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Liu Y, Cai L, Sun W. Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China. BMC PLANT BIOLOGY 2024; 24:200. [PMID: 38500068 PMCID: PMC10949798 DOI: 10.1186/s12870-024-04892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Michelia lacei W.W.Smith (Magnoliaceae), was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both action plans of 2012 and 2021. This evergreen tree is known for its high ornamental and scientific value, but it faces significant threats due to its extremely small population size and narrow geographical distribution. The study aims to understand the genetic structure, diversity, and demographic history of this species to inform its conservation strategies. RESULTS The analysis of transcriptome data from 64 individuals across seven populations of M. lacei identified three distinct genetic clusters and generated 104,616 single-nucleotide polymorphisms (SNPs). The KM ex-situ population, originating from Longling County, exhibited unique genetic features, suggesting limited gene flow. The genetic diversity was substantial, with significant differences between populations, particularly between the KM lineage and the OTHER lineage. Demographic history inferred from the data indicated population experienced three significant population declines during glaciations, followed by periods of recovery. We estimated the effective population size (Ne) of the KM and OTHER lineages 1,000 years ago were 85,851 and 416,622, respectively. Gene flow analysis suggested past gene flow between populations, but the KM ex-situ population showed no recent gene flow. A total of 805 outlier SNPs, associated with four environmental factors, suggest potential local adaptation and showcase the species' adaptive potential. Particularly, the BZ displayed 515 adaptive loci, highlighting its strong potential for adaptation within this group. CONCLUSIONS The comprehensive genomic analysis of M. lacei provides valuable insights into its genetic background and highlights the urgent need for conservation efforts. The study underscores the importance of ex-situ conservation methods, such as seed collection and vegetative propagation, to safeguard genetic diversity and promote population restoration. The preservation of populations like MC and BZ is crucial for maintaining the species' genetic diversity. In-situ conservation measures, including the establishment of in-situ conservation sites and community engagement, are essential to enhance protection awareness and ensure the long-term survival of this threatened plant species.
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Affiliation(s)
- Yang Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations/ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations/ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations/ Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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19
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Biello R, Ghirotto S, Schmidt DJ, Fuselli S, Roberts DT, Espinoza T, Hughes JM, Bertorelle G. Unravelling the mystery of endemic versus translocated populations of the endangered Australian lungfish (Neoceratodus forsteri). Mol Ecol 2024; 33:e17266. [PMID: 38240411 DOI: 10.1111/mec.17266] [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: 02/27/2023] [Revised: 12/24/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024]
Abstract
The Australian lungfish is a primitive and endangered representative of the subclass Dipnoi. The distribution of this species is limited to south-east Queensland, with some populations considered endemic and others possibly descending from translocations in the late nineteenth century shortly after European discovery. Attempts to resolve the historical distribution of this species have met with conflicting results based on descriptive genetic studies. Understanding if all populations are endemic or some are the result of, or influenced by, translocation events, has implications for conservation management. In this work, we analysed the genetic variation at three types of markers (mtDNA genomes, 11 STRs and 5196 nuclear SNPs) using the approximate Bayesian computation (ABC) algorithm to compare several demographic models. We postulated different contributions of Mary River and Burnett River gene pools into the Brisbane River and North Pine River populations, related to documented translocation events. We ran the analysis for each marker type separately, and we also estimated the posterior probabilities of the models combining the markers. Nuclear SNPs have the highest power to correctly identify the true model among the simulated datasets (where the model was known), but different marker types typically provided similar answers. The most supported demographic model able to explain the real dataset implies that an endemic gene pool is still present in the Brisbane and North Pine Rivers and coexists with the gene pools derived from past documented translocation events. These results support the view that ABC modelling can be useful to reconstruct complex historical translocation events with contemporary implications, and will inform ongoing conservation efforts for the endangered and iconic Australian lungfish.
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Affiliation(s)
- Roberto Biello
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Crop Genetics, John Innes Centre, Norwich, UK
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Daniel J Schmidt
- Australian Rivers Institute, Griffith University, Brisbane, Queensland, Australia
| | - Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Tom Espinoza
- Burnett Mary Regional Group, Bargara, Queensland, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Brisbane, Queensland, Australia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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20
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Lange A, Medugorac I, Ali A, Kessler B, Kurome M, Zakhartchenko V, Hammer SE, Hauser A, Denner J, Dobenecker B, Wess G, Tan PLJ, Garkavenko O, Reichart B, Wolf E, Kemter E. Genetic diversity, growth and heart function of Auckland Island pigs, a potential source for organ xenotransplantation. Xenotransplantation 2024; 31:e12858. [PMID: 38646921 DOI: 10.1111/xen.12858] [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: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/28/2024] [Indexed: 04/23/2024]
Abstract
One of the prerequisites for successful organ xenotransplantation is a reasonable size match between the porcine organ and the recipient's organ to be replaced. Therefore, the selection of a suitable genetic background of source pigs is important. In this study, we investigated body and organ growth, cardiac function, and genetic diversity of a colony of Auckland Island pigs established at the Center for Innovative Medical Models (CiMM), LMU Munich. Male and female Auckland Island pig kidney cells (selected to be free of porcine endogenous retrovirus C) were imported from New Zealand, and founder animals were established by somatic cell nuclear transfer (SCNT). Morphologically, Auckland Island pigs have smaller body stature compared to many domestic pig breeds, rendering their organ dimensions well-suited for human transplantation. Furthermore, echocardiography assessments of Auckland Island pig hearts indicated normal structure and functioning across various age groups throughout the study. Single nucleotide polymorphism (SNP) analysis revealed higher runs of homozygosity (ROH) in Auckland Island pigs compared to other domestic pig breeds and demonstrated that the entire locus coding the swine leukocyte antigens (SLAs) was homozygous. Based on these findings, Auckland Island pigs represent a promising genetic background for organ xenotransplantation.
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Affiliation(s)
- Andreas Lange
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Asghar Ali
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Barbara Kessler
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Mayuko Kurome
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
| | - Sabine E Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Andreas Hauser
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Joachim Denner
- Institute of Virology, Free University of Berlin, Berlin, Germany
| | - Britta Dobenecker
- Chair for Animal Nutrition, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Gerhard Wess
- Clinic of Small Animal Medicine, Center for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | | | | | - Bruno Reichart
- Walter-Brendel-Center for Experimental Medicine, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, Munich, Germany
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21
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Kyriazis CC, Lohmueller KE. Constraining models of dominance for nonsynonymous mutations in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.582010. [PMID: 38463985 PMCID: PMC10925099 DOI: 10.1101/2024.02.25.582010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Dominance is a fundamental parameter in genetics, determining the dynamics of natural selection on deleterious and beneficial mutations, the patterns of genetic variation in natural populations, and the severity of inbreeding depression in a population. Despite this importance, dominance parameters remain poorly known, particularly in humans or other non-model organisms. A key reason for this lack of information about dominance is that it is extremely challenging to disentangle the selection coefficient (s) of a mutation from its dominance coefficient (h). Here, we explore dominance and selection parameters in humans by fitting models to the site frequency spectrum (SFS) for nonsynonymous mutations. When assuming a single dominance coefficient for all nonsynonymous mutations, we find that numerous h values can fit the data, so long as h is greater than ~0.15. Moreover, we also observe that theoretically-predicted models with a negative relationship between h and s can also fit the data well, including models with h=0.05 for strongly deleterious mutations. Finally, we use our estimated dominance and selection parameters to inform simulations revisiting the question of whether the out-of-Africa bottleneck has led to differences in genetic load between African and non-African human populations. These simulations suggest that the relative burden of genetic load in non-African populations depends on the dominance model assumed, with slight increases for more weakly recessive models and slight decreases shown for more strongly recessive models. Moreover, these results also demonstrate that models of partially recessive nonsynonymous mutations can explain the observed severity of inbreeding depression in humans, bridging the gap between molecular population genetics and direct measures of fitness in humans. Our work represents a comprehensive assessment of dominance and deleterious variation in humans, with implications for parameterizing models of deleterious variation in humans and other mammalian species.
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Affiliation(s)
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, USA
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, USA
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22
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Naji MM, Gualdrón Duarte JL, Forneris NS, Druet T. Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle. Genet Sel Evol 2024; 56:10. [PMID: 38297209 PMCID: PMC10832232 DOI: 10.1186/s12711-024-00878-7] [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: 06/06/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding. METHODS We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (FPED), on the correlation between uniting gametes (FUNI), on the genomic relationship matrix (FGRM), on excess homozygosity (FHET), or on homozygous-by-descent (HBD) segments (FHBD). RESULTS FUNI and FGRM were sensitive to used allele frequencies, whereas FHET and FHBD were more robust. We detected significant ID for four traits related to height and length; FHBD and FUNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments. CONCLUSIONS Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.
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Affiliation(s)
- Maulana Mughitz Naji
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Quartier Hôpital, Avenue de l'Hôpital, 11, 4000, Liege, Belgium.
| | - José Luis Gualdrón Duarte
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Quartier Hôpital, Avenue de l'Hôpital, 11, 4000, Liege, Belgium
- Walloon Breeders Association (awe groupe), 5590, Ciney, Belgium
| | - Natalia Soledad Forneris
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Quartier Hôpital, Avenue de l'Hôpital, 11, 4000, Liege, Belgium
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Quartier Hôpital, Avenue de l'Hôpital, 11, 4000, Liege, Belgium
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23
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Feng Y, Comes HP, Chen J, Zhu S, Lu R, Zhang X, Li P, Qiu J, Olsen KM, Qiu Y. Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:177-192. [PMID: 37797086 DOI: 10.1111/tpj.16486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.
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Affiliation(s)
- Yu Feng
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Hans Peter Comes
- Department of Environment & Biodiversity, Salzburg University, Salzburg, Austria
| | - Jun Chen
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shanshan Zhu
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xinyi Zhang
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity group, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St Louis, St Louis, Missouri, 63130, USA
| | - Yingxiong Qiu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
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24
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Li S, Yeh C, Jang‐Liaw N, Chang S, Lin Y, Tsai C, Chiu C, Chen C, Ke H, Wang Q, Lu Y, Zheng K, Fan P, Zhang L, Liu Y. Low but highly geographically structured genomic diversity of East Asian Eurasian otters and its conservation implications. Evol Appl 2024; 17:e13630. [PMID: 38288030 PMCID: PMC10824276 DOI: 10.1111/eva.13630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 01/31/2024] Open
Abstract
Populations of Eurasian otters Lutra lutra, one of the most widely distributed apex predators in Eurasia, have been depleted mainly since the 1950s. However, a lack of information about their genomic diversity and how they are organized geographically in East Asia severely impedes our ability to monitor and conserve them in particular management units. Here, we re-sequenced and analyzed 20 otter genomes spanning continental East Asia, including a population at Kinmen, a small island off the Fujian coast, China. The otters form three genetic clusters (one of L. l. lutra in the north and two of L. l. chinensis in the south), which have diverged in the Holocene. These three clusters should be recognized as three conservation management units to monitor and manage independently. The heterozygosity of the East Asian otters is as low as that of the threatened carnivores sequenced. Historical effective population size trajectories inferred from genomic variations suggest that their low genomic diversity could be partially attributed to changes in the climate since the mid-Pleistocene and anthropogenic intervention since the Holocene. However, no evidence of genetic erosion, mutation load, or high level of inbreeding was detected in the presumably isolated Kinmen Island population. Any future in situ conservation efforts should consider this information for the conservation management units.
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Affiliation(s)
- Shou‐Hsien Li
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Chia‐fen Yeh
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | | | - Shih‐Wei Chang
- Division of ZoologyEndemic Species Research InstituteNantouTaiwan
| | - Yu‐Hsiu Lin
- Division of ZoologyEndemic Species Research InstituteNantouTaiwan
| | - Cheng‐En Tsai
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Chi‐Cheng Chiu
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | | | - Hui‐Ru Ke
- Genomics BioSci & Tech Co., Ltd.New Taipei CityTaiwan
| | - Qiaoyun Wang
- State Key Laboratory of Biocontrol, School of Ecology/School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yiwei Lu
- Zhejiang Museum of Natural HistoryZhejiang Biodiversity Research CenterHangzhouChina
| | - Kaidan Zheng
- State Key Laboratory of Biocontrol, School of Ecology/School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Pengfei Fan
- State Key Laboratory of Biocontrol, School of Ecology/School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Lu Zhang
- State Key Laboratory of Biocontrol, School of Ecology/School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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25
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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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26
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Kardos M. Genomes of an endangered rattlesnake show that neutral genetic variation predicts adaptive genetic variation and genetic load. Proc Natl Acad Sci U S A 2023; 120:e2316880120. [PMID: 38011578 PMCID: PMC10710039 DOI: 10.1073/pnas.2316880120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
- Marty Kardos
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA98112
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27
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Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations. Am Nat 2023; 202:737-752. [PMID: 38033186 PMCID: PMC10897732 DOI: 10.1086/726736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).
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28
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Maroso F, Padovani G, Muñoz Mora VH, Giannelli F, Trucchi E, Bertorelle G. Fitness consequences and ancestry loss in the Apennine brown bear after a simulated genetic rescue intervention. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14133. [PMID: 37259604 DOI: 10.1111/cobi.14133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 06/02/2023]
Abstract
Reduction in population size, with its predicted effects on population fitness, is the most alarming anthropogenic impact on endangered species. By introducing compatible individuals, genetic rescue (GR) is a promising but debated approach for reducing the genetic load unmasked by inbreeding and for restoring the fitness of declining populations. Although GR can improve genetic diversity and fitness, it can also produce loss of ancestry, hampering local adaptation, or replace with introduced variants the unique genetic pools evolved in endemic groups. We used forward genetic simulations based on empirical genomic data to assess fitness benefits and loss of ancestry risks of GR in the Apennine brown bear (Ursus arctos marsicanus). There are approximately 50 individuals of this isolated subspecies, and they have lower genetic diversity and higher inbreeding than other European brown bears, and GR has been suggested to reduce extinction risks. We compared 10 GR scenarios in which the number and genetic characteristics of migrants varied with a non-GR scenario of simple demographic increase due to nongenetic factors. The introduction of 5 individuals of higher fitness or lower levels of deleterious mutations than the target Apennine brown bear from a larger European brown bear population produced a rapid 10-20% increase in fitness in the subspecies and up to 22.4% loss of ancestry over 30 generations. Without a contemporary demographic increase, fitness started to decline again after a few generations. Doubling the population size without GR gradually increased fitness to a comparable level, but without losing ancestry, thus resulting in the best strategy for the Apennine brown bear conservation. Our results highlight the importance for management of endangered species of realistic forward simulations grounded in empirical whole-genome data.
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Affiliation(s)
- Francesco Maroso
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Giada Padovani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Francesco Giannelli
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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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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Nordstrom SW, Hufbauer RA, Olazcuaga L, Durkee LF, Melbourne BA. How density dependence, genetic erosion and the extinction vortex impact evolutionary rescue. Proc Biol Sci 2023; 290:20231228. [PMID: 37989246 PMCID: PMC10688442 DOI: 10.1098/rspb.2023.1228] [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] [Accepted: 10/23/2023] [Indexed: 11/23/2023] Open
Abstract
Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity and the fixation of maladaptive alleles, hindered adaptation and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.
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Affiliation(s)
- Scott W. Nordstrom
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Ruth A. Hufbauer
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Laure Olazcuaga
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Lily F. Durkee
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Brett A. Melbourne
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
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Justinski C, Wilkens J, Distl O. Inbreeding Depression and Purging for Meat Performance Traits in German Sheep Breeds. Animals (Basel) 2023; 13:3547. [PMID: 38003164 PMCID: PMC10668769 DOI: 10.3390/ani13223547] [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: 09/30/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
This study provides estimates on genetic parameters, inbreeding depression and purging for meat performance measures from 25 German sheep breeds. All German meat, merino sheep breeds and breeds of other breeding directions with a sufficient number of pedigree and performance data were included in this study. Phenotypic traits retrieved from the national database OviCap were evaluated: daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness. We employed animal models to estimate heritability, variance and covariance components for these meat performance traits as well as inbreeding depression and purging. The heritabilities, on average, reached estimates of 0.55, 0.34, 0.53 and 0.61 for daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness, respectively. We estimated the linear regression slopes for the individual rate of inbreeding, new and ancestral inbreeding, as well as the inbreeding coefficient and its interaction with the inbreeding coefficient of Ballou, employing animal models with non-genetic effects and the additive genetic effect of the animal. Across all breeds, inbreeding was only significant for daily weight gain, whereas for all other traits, estimates were not significant. Within sheep breeds, we found significant inbreeding depression for daily weight gain in German Mutton Merino and German Blackheaded Mutton as well as for the meatiness score in German Whiteheaded Mutton. Significant effects for purging, based on ancestral inbreeding and the interaction effect of the classical inbreeding coefficient with the inbreeding coefficient of Ballou, were not obvious either across or within any sheep breed. A 1% increase in inbreeding significantly decreased the phenotypic trait median of daily weight gain across all sheep breeds by 0.50% and 0.70% of phenotypic and genetic standard deviation, respectively. Purging effects due to ancestral inbreeding were not significant in any breed or across breeds. The results of this study may indicate that inbreeding depression may be more harmful in traits under stronger selection than in traits that exert low selection pressure. The results of this study demonstrate the different effects that result in meat performance traits due to inbreeding. With increasing rates of inbreeding and critical effective population sizes, selection intensity for breeding objectives has to be critically reviewed for each sheep breed. Inbreeding depression and purging should be evaluated in order to prevent a decrease in trait means due to inbreeding and to determine whether detrimental alleles are eliminated.
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Affiliation(s)
- Cathrin Justinski
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
| | - Jens Wilkens
- VIT—Vereinigte Informationssysteme Tierhaltung w.V., Heinrich-Schröder-Weg 1, 27283 Verden, Germany;
| | - Ottmar Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
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Zimmermann E, Ros KB, Pfarrer C, Distl O. Historic Horse Family Displaying Malformations of the Cervicothoracic Junction and Their Connection to Modern German Warmblood Horses. Animals (Basel) 2023; 13:3415. [PMID: 37958170 PMCID: PMC10650596 DOI: 10.3390/ani13213415] [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: 09/19/2023] [Revised: 10/18/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Malformations of the equine cervicothoracic junction affect the C6 and C7 cervical vertebrae, the T1 thoracic vertebra and in variable extent the first and second sternal ribs. To date, the clinical impact of this malformation, its prevalence and mode of inheritance in equine populations are not yet determined. We examined five skeletons for signs of malformation of the cervicothoracic junction, including three skeletons from widely used Thoroughbred stallions affected with the malformation and two skeletons serving as a comparison. The three affected historical horses were the Thoroughbred stallions Der Loewe XX, Birkhahn XX and their common great grandsire Dark Ronald XX. Malformations of C6 and C7 showed a large variation between the three stallions, as Dark Ronald XX, Der Loewe XX and Birkhahn XX were affected uni-laterally at C6 and C7, uni-laterally at C6 and bi-laterally at C6 and C7, respectively, with varying grades. In order to evaluate whether or not these malformations are incidental, we took a random sample of 20 living German Warmblood horses, which are distant descendants of these stallions. This sample consisted of ten controls and ten horses with malformations of C6/C7. Blood proportions of the historical sires in the modern Warmblood horses ranged from 0.10 to 6.25%. The contribution to inbreeding in each individual horse of our selected horse group by those sires was expressed as a percentage of the total inbreeding coefficient and ranged from 0.01 to 17.96%, demonstrating their influence on the modern Warmblood. In the present study, we were able to describe the variability of the malformation of C6/C7 within a horse family including historic and modern horses. Additionally, we detected variations appearing in connection with malformations of the cervicothoracic junction that have not been described in the literature yet. This is the first time that the malformations of C6 and C7 have been described within a familial context, providing hints on inheritance in Thoroughbreds and Warmbloods. It is worthwhile to carry out further studies in a larger setting to gain more comprehensive insights into the inheritance of the malformation and the role of important ancestors.
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Affiliation(s)
- Elisa Zimmermann
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
| | | | - Christiane Pfarrer
- Institute for Anatomy, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
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Tsheten G, Fuerst-Waltl B, Pfeiffer C, Sölkner J, Bovenhuis H, Mészáros G. Inbreeding depression and its effect on sperm quality traits in Pietrain pigs. J Anim Breed Genet 2023; 140:653-662. [PMID: 37409752 DOI: 10.1111/jbg.12816] [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: 07/13/2022] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (FPED ) and genomic data based on runs of homozygosity (ROH) in the genome (FROH ) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree-based inbreeding coefficients were lower than ROH-based inbreeding values. The correlations between pedigree and ROH-based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree-based inbreeding affected only sperm motility while ROH-based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (FPED10 ) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised.
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Affiliation(s)
- Gyembo Tsheten
- Department of Livestock, Ministry of Agriculture and Livestock, Thimphu, Bhutan
| | - Birgit Fuerst-Waltl
- University of Natural Resources and Life Sciences, Division of Livestock Sciences, Vienna, Austria
| | | | - Johann Sölkner
- University of Natural Resources and Life Sciences, Division of Livestock Sciences, Vienna, Austria
| | - Henk Bovenhuis
- Wageningen University and Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Division of Livestock Sciences, Vienna, Austria
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Justinski C, Wilkens J, Distl O. Effect of Individual Rate of Inbreeding, Recent and Ancestral Inbreeding on Wool Quality, Muscling Conformation and Exterior in German Sheep Breeds. Animals (Basel) 2023; 13:3329. [PMID: 37958084 PMCID: PMC10648841 DOI: 10.3390/ani13213329] [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: 09/19/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
This study provides comprehensive results on the current status of inbreeding depression for traits upon which sheep are selected for the herdbook in Germany. A total of 30 sheep breeds from the OviCap national database met the inclusion criteria for the present analysis regarding the depth and completeness of pedigrees and the number of animals with phenotypic data. We analyzed heritabilities and inbreeding depression for the three breeding objective traits of wool quality, muscling conformation and exterior. Heritabilities were across all breeds of moderate size, with estimates of 0.18 for wool quality and muscling conformation and of 0.14 for exterior. The models employed to estimate linear regression slopes for individual and ancestral inbreeding rates also account for non-genetic effects and the additive genetic effect of the animal. Inbreeding depression was obvious for all three traits when we averaged the estimates across all 30 sheep breeds. Inbreeding depression was significant for wool quality for only a few breeds, whereas for muscling conformation, 14/30 breeds achieved significant estimates. A 1% increase in inbreeding decreased the mean of all three traits across all sheep breeds by 0.33% of their standard deviation. Positive effects due to ancestral inbreeding were only significant in very few breeds in the different traits. Across all 30 sheep breeds, there were indications that purging effects (a reduction in negative effects of inbreeding depression due to selection for heterozygotes) may play a role for the exterior. The results of this study should help for reviewing breeding programs, particularly for sheep breeds with critical effective population sizes and increasing rates of inbreeding, with regard to the selection policy and selection intensity applied.
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Affiliation(s)
- Cathrin Justinski
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
| | - Jens Wilkens
- vit—Vereinigte Informationssysteme Tierhaltung w.V., Heinrich-Schröder-Weg 1, 27283 Verden, Germany;
| | - Ottmar Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
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35
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Dussex N, Tørresen OK, van der Valk T, Le Moullec M, Veiberg V, Tooming-Klunderud A, Skage M, Garmann-Aarhus B, Wood J, Rasmussen JA, Pedersen ÅØ, Martin SL, Røed KH, Jakobsen KS, Dalén L, Hansen BB, Martin MD. Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer. iScience 2023; 26:107811. [PMID: 37744038 PMCID: PMC10514459 DOI: 10.1016/j.isci.2023.107811] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/24/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Typically much smaller in number than their mainland counterparts, island populations are ideal systems to investigate genetic threats to small populations. The Svalbard reindeer (Rangifer tarandus platyrhynchus) is an endemic subspecies that colonized the Svalbard archipelago ca. 6,000-8,000 years ago and now shows numerous physiological and morphological adaptations to its arctic habitat. Here, we report a de-novo chromosome-level assembly for Svalbard reindeer and analyze 133 reindeer genomes spanning Svalbard and most of the species' Holarctic range, to examine the genomic consequences of long-term isolation and small population size in this insular subspecies. Empirical data, demographic reconstructions, and forward simulations show that long-term isolation and high inbreeding levels may have facilitated the reduction of highly deleterious-and to a lesser extent, moderately deleterious-variation. Our study indicates that long-term reduced genetic diversity did not preclude local adaptation to the High Arctic, suggesting that even severely bottlenecked populations can retain evolutionary potential.
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Affiliation(s)
- Nicolas Dussex
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Tom van der Valk
- Centre for PalaeoGenetics, Svante Arrhenius väg 20C, SE 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE 104 05 Stockholm, Sweden
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), NO 7491 Trondheim, Norway
| | - Vebjørn Veiberg
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), NO 7034 Trondheim, Trondheim, Norway
| | - Ave Tooming-Klunderud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Morten Skage
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Benedicte Garmann-Aarhus
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
- Natural History Museum, University of Oslo, NO 0318 Oslo, Norway
| | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA Cambridge, UK
| | - Jacob A. Rasmussen
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
- Globe Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Sarah L.F. Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
| | - Knut H. Røed
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, N-0316 Oslo, Norway
| | - Love Dalén
- Centre for PalaeoGenetics, Svante Arrhenius väg 20C, 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
| | - Brage B. Hansen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), NO 7491 Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), NO 7034 Trondheim, Trondheim, Norway
| | - Michael D. Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), NO 7491 Trondheim, Norway
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36
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Dussex N, Kurland S, Olsen RA, Spong G, Ericsson G, Ekblom R, Ryman N, Dalén L, Laikre L. Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose. Commun Biol 2023; 6:1035. [PMID: 37848497 PMCID: PMC10582009 DOI: 10.1038/s42003-023-05385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden.
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.
- Norwegian University of Science and Technology, University Museum, Trondheim, NO-7491, Norway.
| | - Sara Kurland
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21, Solna, Sweden
| | - Göran Spong
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Göran Ericsson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, SE-106 48, Stockholm, Sweden
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
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37
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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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Sallam AM, Reyer H, Wimmers K, Bertolini F, Aboul-Naga A, Braz CU, Rabee AE. Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds. BMC Genomics 2023; 24:573. [PMID: 37752425 PMCID: PMC10521497 DOI: 10.1186/s12864-023-09679-6] [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: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
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Affiliation(s)
- Ahmed M Sallam
- Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
| | - Henry Reyer
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6b, 18059, Rostock, Germany
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Adel Aboul-Naga
- Animal Production Research Institute, Agricultural Research Center, Dokki, Cairo, Egypt
| | - Camila U Braz
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Egypt
| | - Alaa Emara Rabee
- Department of Animal Sciences, University of Illinois Urbana-Champaign, 1207 Gregory Dr, Urbana, 61801, USA
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39
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Nigenda-Morales SF, Lin M, Nuñez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urbán R J, Archer FI, Viloria-Gómora L, Pérez-Álvarez MJ, Poulin E, Lohmueller KE, Moreno-Estrada A, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations. Nat Commun 2023; 14:5465. [PMID: 37699896 PMCID: PMC10497599 DOI: 10.1038/s41467-023-40052-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/10/2023] [Indexed: 09/14/2023] Open
Abstract
Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged ~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, 92096, USA.
| | - Meixi Lin
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
| | - Paulina G Nuñez-Valencia
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Aaron P Ragsdale
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico
- Department of Integrative Biology, University of Wisconsin, Madison, WI, 53706, USA
| | - Jorge Urbán R
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - Frederick I Archer
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, La Jolla, CA, 92037, USA
| | - Lorena Viloria-Gómora
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur (UABCS), La Paz, Baja California Sur, Mexico
| | - María José Pérez-Álvarez
- Escuela de Medicina Veterinaria, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad de Chile, Santiago, Chile
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | - Andrés Moreno-Estrada
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, 36824, Mexico.
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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40
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Burnett HA, Bieker VC, Le Moullec M, Peeters B, Rosvold J, Pedersen ÅØ, Dalén L, Loe LE, Jensen H, Hansen BB, Martin MD. Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer. Evol Appl 2023; 16:1531-1548. [PMID: 37752961 PMCID: PMC10519417 DOI: 10.1111/eva.13585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.
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Affiliation(s)
- Hamish A. Burnett
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Vanessa C. Bieker
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Jørgen Rosvold
- Department of Terrestrial BiodiversityNorwegian Institute for Nature Research (NINA)TrondheimNorway
| | | | - Love Dalén
- Centre for PalaeogeneticsStockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
- Department of ZoologyStockholm UniversityStockholmSweden
| | - Leif Egil Loe
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesAasNorway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Brage B. Hansen
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Terrestrial EcologyNorwegian Institute for Nature Research (NINA)TrondheimNorway
| | - Michael D. Martin
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
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41
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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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42
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Hudson DW, McKinley TJ, Benton CH, Delahay R, McDonald RA, Hodgson DJ. Multi-locus homozygosity promotes actuarial senescence in a wild mammal. J Anim Ecol 2023; 92:1881-1892. [PMID: 37427855 DOI: 10.1111/1365-2656.13979] [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: 11/07/2022] [Accepted: 06/05/2023] [Indexed: 07/11/2023]
Abstract
Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value. Here we infer associations between multi-locus homozygosity (MLH), sex, disease and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers Meles meles in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis [bTB]). We find important effects of MLH on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later life. Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bTB. These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.
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Affiliation(s)
- Dave W Hudson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Clare H Benton
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Richard Delahay
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Robbie A McDonald
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Dave J Hodgson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
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43
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Charmouh AP, Bocedi G, Hartfield M. Inferring the distributions of fitness effects and proportions of strongly deleterious mutations. G3 (BETHESDA, MD.) 2023; 13:jkad140. [PMID: 37337692 PMCID: PMC10468728 DOI: 10.1093/g3journal/jkad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
The distribution of fitness effects is a key property in evolutionary genetics as it has implications for several evolutionary phenomena including the evolution of sex and mating systems, the rate of adaptive evolution, and the prevalence of deleterious mutations. Despite the distribution of fitness effects being extensively studied, the effects of strongly deleterious mutations are difficult to infer since such mutations are unlikely to be present in a sample of haplotypes, so genetic data may contain very little information about them. Recent work has attempted to correct for this issue by expanding the classic gamma-distributed model to explicitly account for strongly deleterious mutations. Here, we use simulations to investigate one such method, adding a parameter (plth) to capture the proportion of strongly deleterious mutations. We show that plth can improve the model fit when applied to individual species but underestimates the true proportion of strongly deleterious mutations. The parameter can also artificially maximize the likelihood when used to jointly infer a distribution of fitness effects from multiple species. As plth and related parameters are used in current inference algorithms, our results are relevant with respect to avoiding model artifacts and improving future tools for inferring the distribution of fitness effects.
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Affiliation(s)
- Anders P Charmouh
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
- Bioinformatics Research Centre Aarhus University, University City 81, building 1872, 3rd floor. DK-8000 Aarhus C, Denmark
| | - Greta Bocedi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Matthew Hartfield
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh EH9 3FL, UK
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44
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Wirth A, Duda J, Distl O. Impact of Inbreeding and Ancestral Inbreeding on Longevity Traits in German Brown Cows. Animals (Basel) 2023; 13:2765. [PMID: 37685029 PMCID: PMC10486702 DOI: 10.3390/ani13172765] [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: 07/03/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
A recent study on the population structure of the German Brown population found increasing levels of classical and ancestral inbreeding coefficients. Thus, the aim of this study was to determine the effects of inbreeding depression and purging on longevity traits using classical and ancestral inbreeding coefficients according to Kalinowski (2002) (Fa_Kal, FNew), Ballou (1997) (Fa_Bal), and Baumung (2015) (Ahc). For this purpose, uncensored data of 480,440 cows born between 1990 and 2001 were available. We analyzed 17 longevity traits, including herd life, length of productive life, number of calvings, lifetime and effective lifetime production for milk, fat, and protein yield, the survival to the 2nd, 4th, 6th, 8th, and 10th lactation number, and the culling frequencies due to infertility, or udder and foot and leg problems. Inbreeding depression was significant and negative for all traits but for culling due to udder and to foot and leg problems. When expressed in percentages of genetic standard deviations, inbreeding depression per 1% increase in inbreeding was -3.61 to -10.98%, -2.42 to -2.99%, -2.21 to -4.58%, and 5.13% for lifetime production traits, lifetime traits, survival rates, and culling due to infertility, respectively. Heterosis and recombination effects due to US Brown Swiss genes were positive and counteracted inbreeding depression. The effects of FNew were not significantly different from zero, while Fa_Kal had negative effects on lifetime and lifetime production traits. Similarly, the interaction of F with Fa_Bal was significantly negative. Thus, purging effects could not be shown for longevity traits in German Brown. A possible explanation may be seen in the breed history of the German Brown, that through the introgression of US Brown Swiss bulls ancestral inbreeding increased and longevity decreased. Our results show, that reducing a further increase in inbreeding in mating plans is advisable to prevent a further decline in longevity due to inbreeding depression, as purging effects were very unlikely in this population.
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Affiliation(s)
- Anna Wirth
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
| | - Jürgen Duda
- Landeskuratorium der Erzeugerringe für Tierische Veredelung in Bayern e.V. (LKV), 80687 München, Germany;
| | - Ottmar Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany;
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45
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Afonso RO, Pina-Martins F, Friesen V, Sun Z, Campioni L, Madeiros J, Silva MC. No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow). J Hered 2023; 114:459-469. [PMID: 37162284 DOI: 10.1093/jhered/esad030] [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: 10/28/2022] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950s, the population has been recovering aided by the implementation of an ongoing conservation plan. However, it still faces several threats, and negative genetic effects resulting from that drastic decline are to be expected, including inbreeding and genetic drift. We studied genetic diversity and levels of inbreeding, and their effects on individual fitness and mating choice. We also tested for a genetic signature of the recent demographic bottleneck. For this, we analyzed variation in thousands of nuclear single-nucleotide polymorphisms derived from double digest restriction site-associated DNA sequencing and 1 mitochondrial gene (cytochrome oxidase I). The results revealed that the Bermuda petrel suffered a recent genetic bottleneck and shows low mitochondrial diversity compared with other petrel species. Conversely, nuclear diversity was similar to that of other endangered petrels. Inbreeding levels were not high overall, although some individuals were highly inbred. However, we found no evidence that individual inbreeding or relatedness between mates affected hatching success, or that mate choice is influenced by kinship in this very small population.
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Affiliation(s)
- Rita O Afonso
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Pina-Martins
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Vicki Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Letizia Campioni
- MARE-Marine and Environmental Sciences Centre, Ispa-Instituto Universitário, Lisboa, Portugal
| | - Jeremy Madeiros
- Department of Environment and Natural Resources, Government of Bermuda, Hamilton, Bermuda
| | - Mónica C Silva
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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46
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Sun S, Wang B, Li C, Xu G, Yang J, Hufford MB, Ross-Ibarra J, Wang H, Wang L. Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding. Mol Biol Evol 2023; 40:msad170. [PMID: 37494285 PMCID: PMC10414807 DOI: 10.1093/molbev/msad170] [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] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
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Affiliation(s)
- Shichao Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
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47
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Doña J, Johnson KP. Host body size, not host population size, predicts genome-wide effective population size of parasites. Evol Lett 2023; 7:285-292. [PMID: 37475749 PMCID: PMC10355176 DOI: 10.1093/evlett/qrad026] [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: 10/31/2022] [Revised: 04/19/2023] [Accepted: 05/18/2023] [Indexed: 07/22/2023] Open
Abstract
The effective population size (Ne) of an organism is expected to be generally proportional to the total number of individuals in a population. In parasites, we might expect the effective population size to be proportional to host population size and host body size, because both are expected to increase the number of parasite individuals. However, among other factors, parasite populations are sometimes so extremely subdivided that high levels of inbreeding may distort these predicted relationships. Here, we used whole-genome sequence data from dove parasites (71 feather louse species of the genus Columbicola) and phylogenetic comparative methods to study the relationship between parasite effective population size and host population size and body size. We found that parasite effective population size is largely explained by host body size but not host population size. These results suggest the potential local population size (infrapopulation or deme size) is more predictive of the long-term effective population size of parasites than is the total number of potential parasite infrapopulations (i.e., host individuals).
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Affiliation(s)
- Jorge Doña
- Corresponding authors: Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, United States.
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, United States.
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48
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Nishio M, Inoue K, Ogawa S, Ichinoseki K, Arakawa A, Fukuzawa Y, Okamura T, Kobayashi E, Taniguchi M, Oe M, Ishii K. Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle. BMC Genomics 2023; 24:376. [PMID: 37403068 DOI: 10.1186/s12864-023-09480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and depression. Recently, many measures have been used for genome-based inbreeding coefficients; however, with no consensus on which is the most appropriate. Therefore, we compared the pedigree- ([Formula: see text]) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ([Formula: see text]), correlation between uniting gametes ([Formula: see text]), the observed vs expected number of homozygous genotypes ([Formula: see text]), runs of homozygosity (ROH) segments ([Formula: see text]) and heterozygosity by descent segments ([Formula: see text]). We quantified inbreeding depression from estimating regression coefficients of inbreeding coefficients on three reproductive traits: age at first calving (AFC), calving difficulty (CD) and gestation length (GL) in Japanese Black cattle. RESULTS The highest correlations with [Formula: see text] were for [Formula: see text] (0.86) and [Formula: see text] (0.85) whereas [Formula: see text] and [Formula: see text] provided weak correlations with [Formula: see text], with range 0.33-0.55. Except for [Formula: see text] and [Formula: see text], there were strong correlations among genome-based inbreeding coefficients ([Formula: see text] 0.94). The estimates of regression coefficients of inbreeding depression for [Formula: see text] was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but [Formula: see text] had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than [Formula: see text]. In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for [Formula: see text] had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, [Formula: see text] provided significant effects at chromosomal level in four chromosomes for AFC, three chromosomes for CD, and two chromosomes for GL. In addition, similar results were obtained for [Formula: see text]. CONCLUSIONS Genome-based inbreeding coefficients can capture more phenotypic variation than [Formula: see text]. In particular, [Formula: see text] and [Formula: see text] can be considered good estimators for quantifying inbreeding level and identifying inbreeding depression at the chromosome level. These findings might improve the quantification of inbreeding and breeding programs using genome-based inbreeding coefficients.
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Affiliation(s)
- Motohide Nishio
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan.
| | - Keiichi Inoue
- University of Miyazaki, Miyazaki, Miyazaki, 889-2192, Japan
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Shinichiro Ogawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Kasumi Ichinoseki
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Aisaku Arakawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Yo Fukuzawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Toshihiro Okamura
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Eiji Kobayashi
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Masaaki Taniguchi
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Mika Oe
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Kazuo Ishii
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
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Solmundson K, Bowman J, Manseau M, Taylor RS, Keobouasone S, Wilson PJ. Genomic population structure and inbreeding history of Lake Superior caribou. Ecol Evol 2023; 13:e10278. [PMID: 37424935 PMCID: PMC10326607 DOI: 10.1002/ece3.10278] [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: 03/06/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/11/2023] Open
Abstract
Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), 1 of the 12 Designatable Units, has lost approximately half of its historic range in the last 150 years, particularly along the southern edge of its distribution. Despite this overall northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the continuous boreal caribou range in Ontario, along the coast and nearshore islands of Lake Superior. The population history of caribou along Lake Superior remains unclear. It appears that these caribou likely represent a remnant distribution at the trailing edge of the receding population of boreal caribou, but they may also exhibit local adaptation to the coastal environment. A better understanding of the population structure and history of caribou along Lake Superior is important for their conservation and management. Here, we use high-coverage whole genomes (N = 20) from boreal, eastern migratory, and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate population structure and inbreeding histories. We discovered that caribou from the Lake Superior range form a distinct group but also found some evidence of gene flow with the continuous boreal caribou range. Notably, caribou along Lake Superior demonstrated relatively high levels of inbreeding (measured as runs of homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between ranges. Despite inbreeding, caribou along Lake Superior retained high heterozygosity, particularly in genomic regions without ROH. These results suggest that they present distinct genomic characteristics but also some level of gene flow with the continuous range. Our study provides key insights into the genomics of the southernmost range of caribou in Ontario, beginning to unravel the evolutionary history of these small, isolated caribou populations.
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Affiliation(s)
- Kirsten Solmundson
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
| | - Jeff Bowman
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and ForestryTrent UniversityPeterboroughOntarioCanada
| | - Micheline Manseau
- Environmental & Life Sciences Graduate ProgramTrent UniversityPeterboroughOntarioCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Rebecca S. Taylor
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Sonesinh Keobouasone
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaOntarioCanada
| | - Paul J. Wilson
- Biology DepartmentTrent UniversityPeterboroughOntarioCanada
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50
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Pérez‐Pereira N, Quesada H, Caballero A. An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions. Evol Appl 2023; 16:1302-1315. [PMID: 37492144 PMCID: PMC10363801 DOI: 10.1111/eva.13568] [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: 12/14/2022] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 07/27/2023] Open
Abstract
Inbreeding depression (ID), the reduction in fitness due to inbreeding, is typically measured by the regression of the phenotypic values of individuals for a particular trait on their corresponding inbreeding coefficients (F). While genealogical records can provide these coefficients, they may be unavailable or incomplete, making molecular markers a useful alternative. The power to detect ID and its accuracy depend on the variation of F values of individuals, the sample sizes available, and the accuracy in the estimation of individual fitness traits and F values. In this study, we used Drosophila melanogaster to evaluate the effectiveness of molecular markers in estimating ID under suboptimal conditions. We generated two sets of 100 pairs of unrelated individuals from a large panmictic population and mated them for two generations to produce non-inbred and unrelated individuals (F = 0) and inbred individuals (full-sib progeny; F = 0.25). Using these expected genealogical F values, we calculated inbreeding depression for two fitness-related traits, pupae productivity and competitive fitness. We then sequenced the males from 17 non-inbred pairs and 17 inbred pairs to obtain their genomic inbreeding coefficients and estimate ID for the two traits. The scenario assumed was rather restrictive in terms of estimation of ID because: (1) the individuals belonged to the same generation of a large panmictic population, leading to low variation in individual F coefficients; (2) the sample sizes were small; and (3) the traits measured depended on both males and females while only males were sequenced. Despite the challenging conditions of our study, we found that molecular markers provided estimates of ID that were comparable to those obtained from simple pedigree estimations with larger sample sizes. The results therefore suggest that genomic measures of inbreeding are useful to provide estimates of inbreeding depression even under very challenging scenarios.
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Affiliation(s)
- Noelia Pérez‐Pereira
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Humberto Quesada
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
| | - Armando Caballero
- Centro de Investigación MariñaUniversidade de Vigo, Facultade de BioloxíaVigoSpain
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