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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 PMCID: PMC11235126 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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Wang X, Reid K, Chen Y, Dudgeon D, Merilä J. Ecological genetics of isolated loach populations indicate compromised adaptive potential. Heredity (Edinb) 2024:10.1038/s41437-024-00695-0. [PMID: 38961235 DOI: 10.1038/s41437-024-00695-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/18/2024] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
Many endangered species live in fragmented and isolated populations with low genetic variability, signs of inbreeding, and small effective population sizes - all features elevating their extinction risk. The flat-headed loach (Oreonectes platycephalus), a small noemacheilid fish, is widely across southern China, but only in the headwaters of hillstreams; as a result, they are spatially isolated from conspecific populations. We surveyed single nucleotide polymorphisms in 16 Hong Kong populations of O. platycephalus to determine whether loach populations from different streams were genetically isolated from each other, showed low levels of genetic diversity, signs of inbreeding, and had small contemporary effective population sizes. Estimates of average observed heterozygosity (HO = 0.0473), average weighted nucleotide diversity (πw = 0.0546) and contemporary effective population sizes (Ne = 10.2 ~ 129.8) were very low, and several populations showed clear signs of inbreeding as judged from relatedness estimates. The degree of genetic differentiation among populations was very high (average FST = 0.668), even over short geographic distances (<1.5 km), with clear patterns of isolation by distance. These results suggest that Hong Kong populations of O. platycephalus have experienced strong genetic drift and loss of genetic variability because sea-level rise after the last glaciation reduced connectedness among paleodrainages, isolating populations in headwaters. All this, together with the fact that the levels of genetic diversity and contemporary effective population sizes within O. platycephalus populations are lower than most other freshwater fishes, suggests that they face high local extinction risk and have limited capacity for future adaptation.
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Affiliation(s)
- Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Ying Chen
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - David Dudgeon
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Juha Merilä
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Programme, University of Helsinki, FI-00014 University of Helsinki, Helsinki, Finland.
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3
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Mastretta-Yanes A, da Silva JM, Grueber CE, Castillo-Reina L, Köppä V, Forester BR, Funk WC, Heuertz M, Ishihama F, Jordan R, Mergeay J, Paz-Vinas I, Rincon-Parra VJ, Rodriguez-Morales MA, Arredondo-Amezcua L, Brahy G, DeSaix M, Durkee L, Hamilton A, Hunter ME, Koontz A, Lang I, Latorre-Cárdenas MC, Latty T, Llanes-Quevedo A, MacDonald AJ, Mahoney M, Miller C, Ornelas JF, Ramírez-Barahona S, Robertson E, Russo IRM, Santiago MA, Shaw RE, Shea GM, Sjögren-Gulve P, Spence ES, Stack T, Suárez S, Takenaka A, Thurfjell H, Turbek S, van der Merwe M, Visser F, Wegier A, Wood G, Zarza E, Laikre L, Hoban S. Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework. Ecol Lett 2024; 27:e14461. [PMID: 38953253 DOI: 10.1111/ele.14461] [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: 02/07/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 07/03/2024]
Abstract
Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to reporting the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socio-economic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of the taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators.
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Affiliation(s)
- Alicia Mastretta-Yanes
- Consejo Nacional de Humanidades Ciencias y Tecnología (CONAHCYT), Ciudad de México, Mexico
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Ciudad de México, Mexico
- Wildlife Ecology and Management, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jessica M da Silva
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - Catherine E Grueber
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Luis Castillo-Reina
- Ecology, Evolution and Biodiversity Conservation, Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Fumiko Ishihama
- National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | | | - Joachim Mergeay
- Ecology, Evolution and Biodiversity Conservation, Department of Biology, KU Leuven, Leuven, Belgium
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Université Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, Villeurbanne, France
| | | | | | | | - Gaëlle Brahy
- BIOGECO, INRAE, University of Bordeaux, Cestas, France
| | - Matt DeSaix
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Lily Durkee
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Ashley Hamilton
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
- Center for Tree Science, The Morton Arboretum, Illinois, USA
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, USA
| | - Austin Koontz
- Center for Tree Science, The Morton Arboretum, Illinois, USA
| | - Iris Lang
- Conservatoire d'espaces Naturels d'Occitanie, Montpellier, France
| | - María Camila Latorre-Cárdenas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Tanya Latty
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Alexander Llanes-Quevedo
- Museo de Zoología "Alfonso L. Herrera", Departamento Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México Ciudad de México, Ciudad de Mexico, Mexico
| | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Tasmania, Australia
| | - Meg Mahoney
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, Colorado, USA
| | - Caitlin Miller
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Xalapa, Veracruz, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de Mexico, Mexico
| | - Erica Robertson
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | | | | | - Robyn E Shaw
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Glenn M Shea
- Sydney School of Veterinary Science, B01, University of Sydney, Sydney, New South Wales, Australia
- Australian Museum Research Institute, The Australian Museum, Sydney, New South Wales, Australia
| | - Per Sjögren-Gulve
- Nordic Chapter of the Society for Conservation Biology, Uppsala, Sweden
| | - Emma Suzuki Spence
- Department of Public and Ecosystem Health, Cornell University, Ithaca, New York, USA
| | - Taylor Stack
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sofía Suárez
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Akio Takenaka
- National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Henrik Thurfjell
- Swedish Species Information Center, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Sheela Turbek
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Marlien van der Merwe
- Research Centre for Ecosystem Resilience, Botanic Gardens of Sydney, Sydney, New South Wales, Australia
| | - Fleur Visser
- Conservation Genetics Laboratory, University of Liège, Liège, Belgium
- Zoology & Entomology Department, University of Pretoria, Pretoria, South Africa
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Georgina Wood
- UWA Oceans Institute, University of Western Australia, Crawley, Western Australia, Australia
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Eugenia Zarza
- Consejo Nacional de Humanidades Ciencias y Tecnología (CONAHCYT), Ciudad de México, Mexico
- Departamento de Ciencias de la Sustentabilidad, El Colegio De La Frontera Sur, Tapachula, Chiapas, Mexico
| | | | - Sean Hoban
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
- Center for Tree Science, The Morton Arboretum, Illinois, USA
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4
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Clark MI, Fitzpatrick SW, Bradburd GS. Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species. Evol Appl 2024; 17:e13754. [PMID: 39006005 PMCID: PMC11246600 DOI: 10.1111/eva.13754] [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: 03/20/2024] [Revised: 06/13/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (Ne) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward-time, individual-based simulations with varying mean individual lifespans and extents of generational overlap. We find that age information can be used to aid in the detection of demographic declines when the decline has been severe. When average lifespan is long, comparing young and old individuals from a single timepoint has greater power to detect a recent (within the last 50 years) bottleneck event than comparing individuals sampled at different points in time. Our results demonstrate how longevity and generational overlap can be both a hindrance and a boon to detecting recent demographic declines from population genomic data.
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Affiliation(s)
- Meaghan I Clark
- Department of Integrative Biology Michigan State University East Lansing Michigan USA
- Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan USA
- W.K. Kellogg Biological Station Michigan State University Hickory Corners Michigan USA
| | - Sarah W Fitzpatrick
- Department of Integrative Biology Michigan State University East Lansing Michigan USA
- Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan USA
- W.K. Kellogg Biological Station Michigan State University Hickory Corners Michigan USA
| | - Gideon S Bradburd
- W.K. Kellogg Biological Station Michigan State University Hickory Corners Michigan USA
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan USA
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5
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Lowe WH, Addis BR, Cochrane MM. Outbreeding reduces survival during metamorphosis in a headwater stream salamander. Mol Ecol 2024; 33:e17375. [PMID: 38699973 DOI: 10.1111/mec.17375] [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: 03/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.
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Affiliation(s)
- Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brett R Addis
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Madaline M Cochrane
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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Clarke SH, Lawrence ER, Matte JM, Gallagher BK, Salisbury SJ, Michaelides SN, Koumrouyan R, Ruzzante DE, Grant JWA, Fraser DJ. Global assessment of effective population sizes: Consistent taxonomic differences in meeting the 50/500 rule. Mol Ecol 2024; 33:e17353. [PMID: 38613250 DOI: 10.1111/mec.17353] [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: 10/01/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal and amphibian populations had a <54% probability of reachingN ̂ e = 50 and a <9% probability of reachingN ̂ e = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller medianN ̂ e than unlisted populations, and this was consistent across all taxonomic groups.N ̂ e was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation ofN ̂ e in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritise assessment of populations from taxa most at risk of failing to meet conservation thresholds.
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Affiliation(s)
- Shannon H Clarke
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Jean-Michel Matte
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Brian K Gallagher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Ramela Koumrouyan
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - James W A Grant
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Dylan J Fraser
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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7
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Kardos M, Waples RS. Low-coverage sequencing and Wahlund effect severely bias estimates of inbreeding, heterozygosity and effective population size in North American wolves. Mol Ecol 2024:e17415. [PMID: 38785346 DOI: 10.1111/mec.17415] [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: 02/16/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
vonHoldt et al. ((2024), Molecular Ecology, 33, e17231) (vH24) used low-coverage (average ~ 7X read depth) restriction site-associated DNA sequence data to estimate individual inbreeding and heterozygosity, and recent effective population size (Ne), in Great Lakes (GL) and Northern Rocky Mountain (RM) wolves. They concluded that RM heterozygosity rapidly declined between 1991 and 2020, and that Ne declined substantially in GL and RM over the last 50 generations. Here, we evaluate the effects of low sequence coverage and sampling strategy on vH24's findings and provide general recommendations for using sequence data to evaluate inbreeding, heterozygosity and Ne. Low-coverage sequencing resulted in downwardly biased estimates of individual inbreeding and heterozygosity, and an erroneous large temporal decline in RM heterozygosity due to declining read depth through time. Additionally, vH24's sampling strategy-which combined individuals from several genetically differentiated populations and across at least eight wolf generations-is expected to have resulted in severe downward bias in estimates of recent Ne for RM. We recommend using high-coverage sequence data (≥ $$ \ge $$ 15-20X) to estimate inbreeding and heterozygosity. Carefully filtering individuals, loci and genotypes, and using genotype imputation or likelihoods can help to minimise bias when low-coverage sequence data must be used. For estimation of contemporary Ne, the marginal benefits of using more than 103-104 loci are small, so aggressive filtering of loci with low average read depth potentially can retain most individuals without sacrificing much precision. Individuals are relatively more valuable than loci because analyses of contemporary Ne should focus on roughly single-generation samples from local breeding populations.
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Affiliation(s)
- Marty Kardos
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Robin S Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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8
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Li WJ, Chen PP, Sui LY, Sun SC. Temporal genetic variation mediated by climate change-induced salinity decline, a study on Artemia (Crustacea: Anostraca) from Kyêbxang Co, a high altitude salt lake on the Qinghai-Tibet Plateau. Gene 2024; 902:148160. [PMID: 38219874 DOI: 10.1016/j.gene.2024.148160] [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: 09/23/2023] [Revised: 12/11/2023] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
The Qinghai-Tibet Plateau is one of the areas the richest in salt lakes and Artemia sites. As a result of climate warming and wetting, the areas of salt lakes on the plateau have been increasing, and the salinities have decreased considerably since 1990s. However, the impact of salinity change on the genetic diversity of Artemia is still unknown. Kyêbxang Co is the highest (4620 m above sea level) salt lake currently with commercial harvesting of Artemia resting eggs in the world, and harbors the largest Artemia population on the plateau. Its salinity had dropped from ∼67 ppt in 1998 to ∼39 ppt in 2019. Using 13 microsatellite markers and the mitochondrial cytochrome oxidase submit I (COI) gene, we analyzed the temporal changes of genetic diversity, effective population size and genetic structure of this Artemia population based on samples collected in 1998, 2007 and 2019. Our results revealed a steady decline of genetic diversity and significant genetic differentiation among the sampling years, which may be a consequence of genetic drift and the selection of decreased salinity. A decline of effective population size was also detected, which may be relative to the fluctuation in census population size, skewed sex ratio, and selection of the declined salinity. In 2007 and 2019, the Artemia population showed an excess of heterozygosity and significant deviation from Hardy-Weinberg Equilibrium (p < 0.001), which may be associated with the heterozygote advantage under low salinity. To comprehensively understand the impact of climate warming and wetting on Artemia populations on the plateau, further investigation with broad and intensive sampling are needed.
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Affiliation(s)
- Wen-Jie Li
- Fisheries College, and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266000, China
| | - Pan-Pan Chen
- Fisheries College, and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266000, China
| | - Li-Ying Sui
- Asian Regional Artemia Reference Center, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shi-Chun Sun
- Fisheries College, and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266000, China.
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9
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Hoelzel AR, Gkafas GA, Kang H, Sarigol F, Le Boeuf B, Costa DP, Beltran RS, Reiter J, Robinson PW, McInerney N, Seim I, Sun S, Fan G, Li S. Genomics of post-bottleneck recovery in the northern elephant seal. Nat Ecol Evol 2024; 8:686-694. [PMID: 38383849 PMCID: PMC11009102 DOI: 10.1038/s41559-024-02337-4] [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: 06/29/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
Populations and species are threatened by human pressure, but their fate is variable. Some depleted populations, such as that of the northern elephant seal (Mirounga angustirostris), recover rapidly even when the surviving population was small. The northern elephant seal was hunted extensively and taken by collectors between the early 1800s and 1892, suffering an extreme population bottleneck as a consequence. Recovery was rapid and now there are over 200,000 individuals. We sequenced 260 modern and 8 historical northern elephant seal nuclear genomes to assess the impact of the population bottleneck on individual northern elephant seals and to better understand their recovery. Here we show that inbreeding, an increase in the frequency of alleles compromised by lost function, and allele frequency distortion, reduced the fitness of breeding males and females, as well as the performance of adult females on foraging migrations. We provide a detailed investigation of the impact of a severe bottleneck on fitness at the genomic level and report on the role of specific gene systems.
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Affiliation(s)
| | - Georgios A Gkafas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Innovation Research Center for Aquatic Mammals, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Burney Le Boeuf
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Daniel P Costa
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Roxanne S Beltran
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Joanne Reiter
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Patrick W Robinson
- Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Nancy McInerney
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington, DC, USA
| | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | | | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Innovation Research Center for Aquatic Mammals, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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10
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Kvalnes T, Flagstad Ø, Våge J, Strand O, Viljugrein H, Sæther B. Harvest and decimation affect genetic drift and the effective population size in wild reindeer. Evol Appl 2024; 17:e13684. [PMID: 38617828 PMCID: PMC11009432 DOI: 10.1111/eva.13684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/29/2024] [Accepted: 03/13/2024] [Indexed: 04/16/2024] Open
Abstract
Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (N e) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate N e of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The N e/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14 years period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2% in 2005-2018 and 44.8% in 2021). Increased harvest rates decreased N e in the simulations, but less sex biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased N e. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to a disease will also depend on population impacts of the disease and how these interact with management actions.
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Affiliation(s)
- Thomas Kvalnes
- Norwegian Institute for Nature Research (NINA)TrondheimNorway
- Centre for Biodiversity Dynamics (CBD), Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | | | - Jørn Våge
- Norwegian Veterinary InstituteÅsNorway
| | - Olav Strand
- Norwegian Institute for Nature Research (NINA)TrondheimNorway
| | | | - Bernt‐Erik Sæther
- Centre for Biodiversity Dynamics (CBD), Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Gjærevoll Center for Biodiversity Foresight AnalysesNorwegian University of Science and Technology (NTNU)TrondheimNorway
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11
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Furlan EM, Baumgartner LJ, Duncan M, Ellis I, Gruber B, Harrisson K, Michie L, Thiem JD, Stuart I. Swinging back from the brink? Polygamous mating strategies revealed for an iconic threatened freshwater fish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170808. [PMID: 38336046 DOI: 10.1016/j.scitotenv.2024.170808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Catastrophic fish death events are increasing in frequency and severity globally. A series of major recent fish deaths in the semi-arid lower Darling-Baaka river system (LDBR) of Australia are emblematic of these issues with tens of millions of native fish perishing. In 2018-2019 there was a major death event for Australia's largest freshwater fish, Murray cod (Maccullochella peelii). To aid the recovery and guide restoration activities of local Murray cod populations, it is essential to gather information on the mating strategies and effective population size following the fish death event. After the fish deaths, we collected larvae during the 2020 and 2021 breeding seasons and used single nucleotide polymorphisms (SNPs) to provide insight mating strategies and to estimate effective population size. Larvae were detected in both years along the entire length of the LDBR. Sixteen percent of the inferred breeding individuals were found to contribute to multiple pairings, confirming a complex and polygamous mating system. A high frequency of polygamy was evident both within and between years with 100 % polygamy identified among parents that produced offspring in both 2020 and 2021 and 95 % polygamy identified among parents involved in multiple spawning events within years. Post-larval Murray cod samples collected between 2016 and 2021 were co-analysed to further inform kinship patterns. Again, monogamy was rare with no confirmed cases of the same male-female pair contributing to multiple breeding events within or between seasons. Effective population size based on Murray cod collected after the fish death event was estimated at 721.6 (CI 471-1486), though this has likely declined following a subsequent catastrophic fish death event in the LDBR in March 2023. Our data provide insight into the variability of Murray cod mating strategies, and we anticipate that this knowledge will assist in planning conservation actions to ultimately help recover a species in crisis.
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Affiliation(s)
- Elise M Furlan
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, University Drive, Bruce, ACT 2617, Australia; Gulbali Institute for Agriculture, Water and Environment, Charles Sturt University, P.O. Box 789, Albury, NSW 2640, Australia.
| | - Lee J Baumgartner
- Gulbali Institute for Agriculture, Water and Environment, Charles Sturt University, P.O. Box 789, Albury, NSW 2640, Australia
| | - Meaghan Duncan
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
| | - Iain Ellis
- Department of Primary Industries, Buronga, New South Wales, Australia
| | - Bernd Gruber
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, University Drive, Bruce, ACT 2617, Australia
| | - Katherine Harrisson
- Department of Environment and Genetics, La Trobe University, Melbourne, Australia; Research Centre for Future Landscapes, La Trobe University, Melbourne, Australia; Arthur Rylah Institute for Environmental Research, Department of Energy, Environment and Climate Action, Victoria, Australia
| | - Laura Michie
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
| | - Jason D Thiem
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
| | - Ivor Stuart
- Gulbali Institute for Agriculture, Water and Environment, Charles Sturt University, P.O. Box 789, Albury, NSW 2640, Australia
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12
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Sévêque A, Lonsinger RC, Waits LP, Brzeski KE, Komoroske LM, Ott-Conn CN, Mayhew SL, Norton DC, Petroelje TR, Swenson JD, Morin DJ. Sources of bias in applying close-kin mark-recapture to terrestrial game species with different life histories. Ecology 2024; 105:e4244. [PMID: 38272487 DOI: 10.1002/ecy.4244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/18/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024]
Abstract
Close-kin mark-recapture (CKMR) is a method analogous to traditional mark-recapture but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used to identify related individuals in one or more sampling occasions, which enables the opportunistic use of samples from harvested wildlife. To apply the method accurately, it is important to build appropriate CKMR models that do not violate assumptions linked to the species' and population's biology and sampling methods. In this study, we evaluated the implications of fitting overly simplistic CKMR models to populations with complex reproductive success dynamics or selective sampling. We used forward-in-time, individual-based simulations to evaluate the accuracy and precision of CKMR abundance and survival estimates in species with different longevities, mating systems, and sampling strategies. Simulated populations approximated a range of life histories among game species of North America with lethal sampling to evaluate the potential of using harvested samples to estimate population size. Our simulations show that CKMR can yield nontrivial biases in both survival and abundance estimates, unless influential life history traits and selective sampling are explicitly accounted for in the modeling framework. The number of kin pairs observed in the sample, in combination with the type of kinship used in the model (parent-offspring pairs and/or half-sibling pairs), can affect the precision and/or accuracy of the estimates. CKMR is a promising method that will likely see an increasing number of applications in the field as costs of genetic analysis continue to decline. Our work highlights the importance of applying population-specific CKMR models that consider relevant demographic parameters, individual covariates, and the protocol through which individuals were sampled.
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Affiliation(s)
- Anthony Sévêque
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Mississippi, USA
| | - Robert C Lonsinger
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Resources, University of Idaho, Moscow, Idaho, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Caitlin N Ott-Conn
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - Sarah L Mayhew
- Wildlife Division, Michigan Department of Natural Resources, Lansing, Michigan, USA
| | - D Cody Norton
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - Tyler R Petroelje
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - John D Swenson
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Dana J Morin
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Mississippi, USA
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13
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Kessler C, Shafer ABA. Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid. Mol Biol Evol 2024; 41:msae038. [PMID: 38378172 PMCID: PMC10917209 DOI: 10.1093/molbev/msae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.
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Affiliation(s)
- Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
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14
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Bors MS, Gowri Shankar P, Gruszczyńska J. Current State of Mugger Populations. Animals (Basel) 2024; 14:691. [PMID: 38473076 DOI: 10.3390/ani14050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
The mugger (Crocodylus palustris) is a medium-sized crocodilian inhabiting South Asia. As a result of intensive hunting, its range declined drastically up till the 1970s. Currently, the world mugger population is fragmented and threatened mainly by habitat loss and the consequences of human-crocodile conflict, being classified as Vulnerable by the IUCN. The goal of this paper is to comprehensively determine the mugger's current range, and assess risks in notable habitats of the species across its range. To determine the range and notable habitats, extensive literature covering surveys, monitoring, population studies and reports of human-crocodile conflict was examined. Habitat suitability and risk assessment were performed by evaluating selected habitats using eight factors: the legal status of the area, elevation, surface water availability, water quality, salinity, availability of nesting and basking sites, interaction with humans and interspecific competition. Based on our findings, the chances of the mugger's survival varies greatly across its range and the threats they face are complex and often site-specific. Defining these threats is the first step for determining suitable risk mitigation efforts, some of which are explored in this review.
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Affiliation(s)
- Milena Sylwia Bors
- Department of Animal Breeding and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
| | | | - Joanna Gruszczyńska
- Department of Animal Breeding and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
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15
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Popovic I, Bergeron LA, Bozec YM, Waldvogel AM, Howitt SM, Damjanovic K, Patel F, Cabrera MG, Wörheide G, Uthicke S, Riginos C. High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator. PLoS Genet 2024; 20:e1011129. [PMID: 38346089 PMCID: PMC10861045 DOI: 10.1371/journal.pgen.1011129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Lewontin's paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π and Nc are found for highly abundant marine invertebrates. Yet, the influences of new mutations on π relative to extrinsic processes such as Nc fluctuations are unknown. Here, we provide the first germline mutation rate (μ) estimate for a marine invertebrate in corallivorous crown-of-thorns sea stars (Acanthaster cf. solaris). We use high-coverage whole-genome sequencing of 14 parent-offspring trios alongside empirical estimates of Nc in Australia's Great Barrier Reef to jointly examine the determinants of π in populations undergoing extreme Nc fluctuations. The A. cf. solaris mean μ was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08), exceeding estimates for other invertebrates and showing greater concordance with vertebrate mutation rates. Lower-than-expected Ne (~70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated weak influences of population outbreaks on long-term π. Our findings are consistent with elevated μ evolving in response to reduced Ne and generation time length, with important implications for explaining high mutational loads and the determinants of genetic diversity in marine invertebrate taxa.
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Affiliation(s)
- Iva Popovic
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Lucie A. Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yves-Marie Bozec
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Samantha M. Howitt
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Frances Patel
- Australian Institute of Marine Science, Townsville, Australia
| | | | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
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16
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Osborne MJ, Archdeacon TP, Yackulic CB, Dudley RK, Caeiro-Dias G, Turner TF. Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14154. [PMID: 37489292 DOI: 10.1111/cobi.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/08/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas P Archdeacon
- U.S. Fish and Wildlife Service, New Mexico Fish and Wildlife Conservation Office, Albuquerque, New Mexico, USA
| | - Charles B Yackulic
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, USA
| | - Robert K Dudley
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
- American Southwest Ichthyological Researchers, Albuquerque, New Mexico, USA
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
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17
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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18
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Sidlauskas BL, Mathur S, Aydoğan H, Monzyk FR, Black AN. Genetic approaches reveal a healthy population and an unexpectedly recent origin for an isolated desert spring fish. BMC Ecol Evol 2024; 24:2. [PMID: 38177987 PMCID: PMC10765885 DOI: 10.1186/s12862-023-02191-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Foskett Spring in Oregon's desert harbors a historically threatened population of Western Speckled Dace (Rhinichthys klamathensis). Though recently delisted, the dace's recruitment depends upon regular removal of encroaching vegetation. Previous studies assumed that Foskett Dace separated from others in the Warner Valley about 10,000 years ago, thereby framing an enigma about the population's surprising ability to persist for so long in a tiny habitat easily overrun by plants. To investigate that persistence and the effectiveness of interventions to augment population size, we assessed genetic diversity among daces inhabiting Foskett Spring, a refuge at Dace Spring, and three nearby streams. Analysis revealed a robust effective population size (Ne) of nearly 5000 within Foskett Spring, though Ne in the Dace Spring refuge is just 10% of that value. Heterozygosity is slightly lower than expected based on random mating at all five sites, indicating mild inbreeding, but not at a level of concern. These results confirm the genetic health of Foskett Dace. Unexpectedly, genetic differentiation reveals closer similarity between Foskett Dace and a newly discovered population from Nevada's Coleman Creek than between Foskett Dace and dace elsewhere in Oregon. Demographic modeling inferred Coleman Creek as the ancestral source of Foskett Dace fewer than 1000 years ago, much more recently than previously suspected and possibly coincident with the arrival of large herbivores whose grazing may have maintained open water suitable for reproduction. These results solve the enigma of persistence by greatly shortening the duration over which Foskett Dace have inhabited their isolated spring.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA.
| | - Samarth Mathur
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, 318 W 12th Ave, Columbus, OH, 43210, USA
| | - Hakan Aydoğan
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, 104 Nash Hall, Corvallis, OR, 97331, USA
| | - Fred R Monzyk
- Oregon Department of Fish and Wildlife, Corvallis Research Lab, 28655 OR-34, Corvallis, OR, 97333, USA
| | - Andrew N Black
- Center for Quantitative Life Sciences, Oregon State University, 2750 SW Campus Way, Corvallis, OR, 97331, USA
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19
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Santiago E, Caballero A, Köpke C, Novo I. Estimation of the contemporary effective population size from SNP data while accounting for mating structure. Mol Ecol Resour 2024; 24:e13890. [PMID: 37937674 DOI: 10.1111/1755-0998.13890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
A new method is developed to estimate the contemporary effective population size (Ne ) from linkage disequilibrium (LD) between SNPs without information on their location, which is the usual scenario in non-model species. The general theory of linkage disequilibrium is extended to include the contribution of full-sibs to the measure of LD, leading naturally to the estimation of Ne in monogamous and polygamous mating systems, as well as in multiparous species, and with non-random distributions of full-sib family size due to selection or other causes. Prediction of confidence intervals for Ne estimates was solved using a small artificial neural network trained on a dataset of over 105 simulation results. The method, implemented in a user-friendly and fast software (currentNe), is able to estimate Ne even in problematic scenarios with large population sizes or small sample sizes and provides confidence intervals that are more consistent than resampling methods.
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Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Armando Caballero
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | | | - Irene Novo
- Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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20
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Hoelzel AR. Where to now with the evolutionarily significant unit? Trends Ecol Evol 2023; 38:1134-1142. [PMID: 37596130 DOI: 10.1016/j.tree.2023.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/20/2023]
Abstract
The designation of units for conservation has been a necessary but challenging objective since conservation efforts began. Most species are divided, typically by environment, into populations with independent evolutionary trajectories. There are practical conservation objectives for defining these boundaries. Separate genetic clusters provide future evolutionary potential as environments change, and individuals in isolated populations may lose fitness when population size is reduced. The history of the effort to define units is briefly reviewed here, but I focus on finding a process that may facilitate uniform and effective application at a time when conservation urgency is great. I propose a refinement of the designated unit concept, distinguishing between conservation units (CUs) and evolutionarily sustaining conservation units (ESCUs).
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Affiliation(s)
- A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
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21
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Bergman J, Pedersen RØ, Lundgren EJ, Lemoine RT, Monsarrat S, Pearce EA, Schierup MH, Svenning JC. Worldwide Late Pleistocene and Early Holocene population declines in extant megafauna are associated with Homo sapiens expansion rather than climate change. Nat Commun 2023; 14:7679. [PMID: 37996436 PMCID: PMC10667484 DOI: 10.1038/s41467-023-43426-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32-76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92-95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.
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Affiliation(s)
- Juraj Bergman
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark.
| | - Rasmus Ø Pedersen
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Erick J Lundgren
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Rhys T Lemoine
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Sophie Monsarrat
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Rewilding Europe, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
| | - Elena A Pearce
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Jens-Christian Svenning
- Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, DK-8000, Aarhus C, Denmark
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22
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Schmidt C, Hoban S, Jetz W. Conservation macrogenetics: harnessing genetic data to meet conservation commitments. Trends Genet 2023; 39:816-829. [PMID: 37648576 DOI: 10.1016/j.tig.2023.08.002] [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: 05/05/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
Genetic biodiversity is rapidly gaining attention in global conservation policy. However, for almost all species, conservation relevant, population-level genetic data are lacking, limiting the extent to which genetic diversity can be used for conservation policy and decision-making. Macrogenetics is an emerging discipline that explores the patterns and processes underlying population genetic composition at broad taxonomic and spatial scales by aggregating and reanalyzing thousands of published genetic datasets. Here we argue that focusing macrogenetic tools on conservation needs, or conservation macrogenetics, will enhance decision-making for conservation practice and fill key data gaps for global policy. Conservation macrogenetics provides an empirical basis for better understanding the complexity and resilience of biological systems and, thus, how anthropogenic drivers and policy decisions affect biodiversity.
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Affiliation(s)
- Chloé Schmidt
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT, USA; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Sean Hoban
- The Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT, USA
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23
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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24
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Sparks MM, Schraidt CE, Yin X, Seeb LW, Christie MR. Rapid genetic adaptation to a novel ecosystem despite a large founder event. Mol Ecol 2023. [PMID: 37668092 DOI: 10.1111/mec.17121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/17/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023]
Abstract
Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72-a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation.
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Affiliation(s)
- Morgan M Sparks
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Claire E Schraidt
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
| | - Xiaoshen Yin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, USA
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25
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Zhao YJ, Yin GS, Gong X. RAD-sequencing improves the genetic characterization of a threatened tree peony ( Paeonia ludlowii) endemic to China: Implications for conservation. PLANT DIVERSITY 2023; 45:513-522. [PMID: 37936813 PMCID: PMC10625974 DOI: 10.1016/j.pld.2022.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2023]
Abstract
Compared with traditional genetic markers, genomic approaches have proved valuable to the conservation of endangered species. Paeonia ludlowii having rarely and pure yellow flowers, is one of the world's most famous tree peonies. However, only several wild populations remain in the Yarlung Zangbo Valley (Nyingchi and Shannan regions, Xizang) in China due to increasing anthropogenic impact on the natural habitats. We used genome-wide single nucleotide polymorphisms to elucidate the spatial pattern of genetic variation, population structure and demographic history of P. ludlowii from the fragmented region comprising the entire range of this species, aiming to provide a basis for conserving the genetic resources of this species. Unlike genetic uniformity among populations revealed in previous studies, we found low but varied levels of intra-population genetic diversity, in which lower genetic diversity was detected in the population in Shannan region compared to those in Nyingzhi region. These spatial patterns may be likely associated with different population sizes caused by micro-environment differences in these two regions. Additionally, low genetic differentiation among populations (Fst = 0.0037) were detected at the species level. This line of evidence, combined with the result of significant genetic differentiation between the two closest populations and lack of isolation by distance, suggested that shared ancestry among now remnant populations rather than contemporary genetic connectivity resulted in subtle population structure. Demographic inference suggested that P. ludlowii probably experienced a temporal history of sharp population decline during the period of Last Glacial Maximum, and a subsequent bottleneck event resulting from prehistoric human activities on the Qinghai-Tibet Plateau. All these events, together with current habitat fragment and excavation might contribute to the endangered status of P. ludlowii. Our study improved the genetic characterization of the endangered tree peony (P. ludlowii) in China, and these genetic inferences should be considered when making different in situ and ex situ conservation actions for P. ludlowii in this evolutionary hotspot region.
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Affiliation(s)
- Yu-Juan Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, Yunnan, China
| | - Gen-Shen Yin
- Kunming University, Institute of Agriculture and Life Sciences, Kunming 650214, Yunnan, China
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Wild Plant Resources, Kunming 650201, Yunnan, China
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26
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Yamamichi M, Ellner SP, Hairston NG. Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics. Ecol Lett 2023; 26 Suppl 1:S16-S21. [PMID: 37840027 DOI: 10.1111/ele.14197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/18/2023] [Accepted: 02/20/2023] [Indexed: 10/17/2023]
Abstract
Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Stephen P Ellner
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Nelson G Hairston
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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27
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Bender AN, Krause DJ, Goebel ME, Hoffman JI, Lewallen EA, Bonin CA. Genetic diversity and demographic history of the leopard seal: A Southern Ocean top predator. PLoS One 2023; 18:e0284640. [PMID: 37566609 PMCID: PMC10420386 DOI: 10.1371/journal.pone.0284640] [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: 04/03/2023] [Accepted: 06/14/2023] [Indexed: 08/13/2023] Open
Abstract
Leopard seals (Hydrurga leptonyx) are top predators that can exert substantial top-down control of their Antarctic prey species. However, population trends and genetic diversity of leopard seals remain understudied, limiting our understanding of their ecological role. We investigated the genetic diversity, effective population size and demographic history of leopard seals to provide fundamental data that contextualizes their predatory influence on Antarctic ecosystems. Ninety leopard seals were sampled from the northern Antarctic Peninsula during the austral summers of 2008-2019 and a 405bp segment of the mitochondrial control region was sequenced for each individual. We uncovered moderate levels of nucleotide (π = 0.013) and haplotype (Hd = 0.96) diversity, and the effective population size was estimated at around 24,000 individuals (NE = 24,376; 95% CI: 16,876-33,126). Consistent with findings from other ice-breeding pinnipeds, Bayesian skyline analysis also revealed evidence for population expansion during the last glacial maximum, suggesting that historical population growth may have been boosted by an increase in the abundance of sea ice. Although leopard seals can be found in warmer, sub-Antarctic locations, the species' core habitat is centered on the Antarctic, making it inherently vulnerable to the loss of sea ice habitat due to climate change. Therefore, detailed assessments of past and present leopard seal population trends are needed to inform policies for Antarctic ecosystems.
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Affiliation(s)
- Arona N. Bender
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
| | - Douglas J. Krause
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA, United States of America
| | - Michael E. Goebel
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- British Antarctic Survey, Cambridge, United Kingdom
| | - Eric A. Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
| | - Carolina A. Bonin
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
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28
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King E, McPhee MV, Vulstek SC, Cunningham CJ, Russell JR, Tallmon DA. Alternative life-history strategy contributions to effective population size in a naturally spawning salmon population. Evol Appl 2023; 16:1472-1482. [PMID: 37622095 PMCID: PMC10445090 DOI: 10.1111/eva.13580] [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: 12/15/2022] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 08/26/2023] Open
Abstract
Alternative life-history tactics are predicted to affect within-population genetic processes but have received little attention. For example, the impact of precocious males on effective population size (N e) has not been quantified directly in Pacific salmon Oncorhynchus spp., even though they can make up a large percentage of the total male spawners. We investigated the contribution of precocial males ("jacks") to N e in a naturally spawning population of Coho Salmon O. kisutch from the Auke Creek watershed in Juneau, Alaska. Mature adults that returned from 2009 to 2019 (~8000 individuals) were genotyped at 259 single-nucleotide polymorphism (SNP) loci for parentage analysis. We used demographic and genetic methods to estimate the effective number of breeders per year (N b). Jack contribution to N b was assessed by comparing values of N b calculated with and without jacks and their offspring. Over a range of N b values (108-406), the average jack contribution to N b from 2009 to 2015 was 12.9% (SE = 3.8%). Jacks consistently made up over 20% of the total male spawners. The presence of jacks did not seem to influence N b/N. The linkage disequilibrium N e estimate was lower than the demographic estimate, possibly due to immigration effects on population genetic processes: based on external marks and parentage data, we estimated that immigrant spawners produced 4.5% of all returning offspring. Our results demonstrate that jacks can influence N b and N e and can make a substantial contribution to population dynamics and conservation of threatened stocks.
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Affiliation(s)
- Erika King
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
| | - Megan V. McPhee
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
| | | | - Curry J. Cunningham
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
| | | | - David A. Tallmon
- College of Fisheries and Ocean SciencesUniversity of AlaskaFairbanksAlaskaUSA
- Biology and Marine Biology ProgramUniversity of Alaska SoutheastJuneauAlaskaUSA
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29
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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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30
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Kim KR, Kwak YH, Sung MS, Cho SJ, Bang IC. Population structure and genetic diversity of the endangered fish black shinner Pseudopungtungia nigra (Cyprinidae) in Korea: a wild and restoration population. Sci Rep 2023; 13:9692. [PMID: 37322262 PMCID: PMC10272174 DOI: 10.1038/s41598-023-36569-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
The black shinner Pseudopungtungia nigra Mori, 1935 is an endangered fish endemic to Korea. It lives in the narrow basin of the Geumgang River, Mangyeonggang River, and Ungcheoncheon Stream, which flow into the West Sea of Korea. One population of P. nigra in Ungcheoncheon Stream has been locally exterminated once; it is now inhabiting the upper reaches of the dam through a restoration program. Efforts to identify and understand the genetic structure of these populations are important for conservation planning. Here, we analyzed genetic diversity using 21 microsatellite markers for 9 populations. The mean number of alleles ranged from 4.4 to 8.1, mean allelic richness ranged from 4.6 to 7.8, mean observed heterozygosity ranged from 0.519 to 0.702, and mean expected heterozygosity ranged from 0.540 to 0.763. All groups had recent and historical bottlenecks (P < 0.05, M-ratio < 0.68). Three groups [YD (2019), OC and UC] had significant inbreeding index values, suggesting that they were engaged in inbreeding. We observed a moderate level of genetic differentiation between MG and the rest of the population (FST = 0.135 to 0.168, P < 0.05). The genetic structure exhibited a fitting constant K = 2, along with separation between MG and the remaining populations. With respect to genetic flow, YD (2019), OC, CG, and ND shifted to the UC population (0.263 to 0.278). The genetic flow of each population was transferred only within the population; there was no gene flow among populations, except for the Ungcheoncheon Stream population. This study shows that the Ungcheoncheon Stream population needs conservation efforts to increase its genetic diversity, and the Geumgang River populations needs a conservation plan that considers the possibility of conservation and evolution through gene exchange among the populations.
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Affiliation(s)
- Kang-Rae Kim
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Yeong-Ho Kwak
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Mu-Sung Sung
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | | | - In-Chul Bang
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea.
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31
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Jops K, O'Dwyer JP. Life history complementarity and the maintenance of biodiversity. Nature 2023:10.1038/s41586-023-06154-w. [PMID: 37286601 DOI: 10.1038/s41586-023-06154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Life history, the schedule of when and how fast organisms grow, die and reproduce, is a critical axis along which species differ from each other1-4. In parallel, competition is a fundamental mechanism that determines the potential for species coexistence5-8. Previous models of stochastic competition have demonstrated that large numbers of species can persist over long timescales, even when competing for a single common resource9-12, but how life history differences between species increase or decrease the possibility of coexistence and, conversely, whether competition constrains what combinations of life history strategies complement each other remain open questions. Here we show that specific combinations of life history strategy optimize the persistence times of species competing for a single resource before one species overtakes its competitors. This suggests that co-occurring species would tend to have such complementary life history strategies, which we demonstrate using empirical data for perennial plants.
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Affiliation(s)
- Kenneth Jops
- Department of Plant Biology, University of Illinois, Urbana, IL, USA.
| | - James P O'Dwyer
- Department of Plant Biology, University of Illinois, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
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32
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PVA-based assessment of resiliency, redundancy, and representation in an imperiled freshwater turtle. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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33
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Brooks GC, Wendt A, Haas CA, Roberts JH. Comparing estimates of census and effective population size in an endangered amphibian. Anim Conserv 2023. [DOI: 10.1111/acv.12871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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34
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Schleimer A, Frantz AC, Richart L, Mehnert J, Semiadi G, Rode‐Margono J, Mittelbronn M, Young S, Drygala F. Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago. DIVERS DISTRIB 2023. [DOI: 10.1111/ddi.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Affiliation(s)
- Anna Schleimer
- Musée National d'Histoire Naturelle Luxembourg Luxembourg
| | | | - Lorraine Richart
- National Center of Pathology (NCP) Laboratoire National de Santé (LNS) Dudelange Luxembourg
- Luxembourg Center of Neuropathology (LCNP) Dudelange Luxembourg
- Department of Oncology (DONC) Luxembourg Institute of Health (LIH) Luxembourg Luxembourg
- Doctoral School in Science and Engineering (DSSE) 25 University of Luxembourg (UL) Esch‐sur‐Alzette Luxembourg
| | - Jörg Mehnert
- Association for Nature and Biodiversity (ANB) Frankfurt am Main Germany
| | - Gono Semiadi
- Research Centre for Applied Zoology National Research and Innovation Agency Cibinong Indonesia
| | | | - Michel Mittelbronn
- National Center of Pathology (NCP) Laboratoire National de Santé (LNS) Dudelange Luxembourg
- Luxembourg Center of Neuropathology (LCNP) Dudelange Luxembourg
- Department of Oncology (DONC) Luxembourg Institute of Health (LIH) Luxembourg Luxembourg
- Faculty of Science, Technology and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Department of Life Sciences and Medicine (DLSM) University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Stuart Young
- The North of England Zoological Society/Chester Zoo Upton‐by‐Chester Chester UK
| | - Frank Drygala
- Musée National d'Histoire Naturelle Luxembourg Luxembourg
- Association for Nature and Biodiversity (ANB) Frankfurt am Main Germany
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When Theory Meets Practice: Balancing Genetic Diversity and Behaviour When Choosing Founders for a Recently Reintroduced Bison (Bison bison) Herd in Banff National Park, Canada. DIVERSITY 2023. [DOI: 10.3390/d15030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The tragic decline of plains bison (Bison bison bison) in North America is well known. By the turn of the 20th century, plains bison, once numbering in the tens of millions, were extirpated from the wild in Canada. Banff National Park, AB, Canada, is within the original range of bison in North America, and still contains suitable habitat for the species. In 2017, we used measures of genetic diversity, as well as age and reproductive status, to select 16 plains bison for reintroduction to an unoccupied corner of their former historic range in Banff National Park. However, five of the preferred founders from this genetically diverse group needed to be substituted for less ideal candidates when aggressive behavior was observed, which could have compromised animal welfare during translocation. The level of genetic diversity in the founding population was therefore lower than if all proposed founders had been used, although the difference was not substantial. As expected, adults in this small, reintroduced herd had lower observed heterozygosity and number of alleles than the larger source herd, but expected heterozygosity was higher, likely a result of preferentially choosing individuals with rare alleles. Another substantial contribution to genetic diversity was in unborn fetuses: sired by males that were not translocated, the calves born a few months later provided a boost to the genetic diversity of this small founder herd. Where opportunities allow, the inclusion of pregnant females can significantly increase the genetic diversity of small founder populations. When compared to other founded herds of bison, the techniques described here have ensured that the newly established Banff NP herd is one of the most diverse bison herds in Canada, despite its relatively small number of founders.
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Gargiulo R, Waples RS, Grow AK, Shefferson RP, Viruel J, Fay MF, Kull T. Effective population size in a partially clonal plant is not predicted by the number of genetic individuals. Evol Appl 2023; 16:750-766. [PMID: 36969138 PMCID: PMC10033856 DOI: 10.1111/eva.13535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/22/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Estimating effective population size (N e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N e. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected N e. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary N e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on N e confidence intervals. The magnitude of N e/N ramets and N e/N genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N e. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.
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Affiliation(s)
| | - Robin S. Waples
- NOAA Fisheries, Northwest Fisheries Science Center Seattle Washington USA
- University of Washington Seattle Washington USA
| | - Adri K. Grow
- Department of Biological Sciences Smith College Northampton Massachusetts USA
| | | | | | - Michael F. Fay
- Royal Botanic Gardens, Kew Richmond UK
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Tiiu Kull
- Estonian University of Life Sciences Tartu Estonia
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37
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Löytynoja A, Rastas P, Valtonen M, Kammonen J, Holm L, Olsen MT, Paulin L, Jernvall J, Auvinen P. Fragmented habitat compensates for the adverse effects of genetic bottleneck. Curr Biol 2023; 33:1009-1018.e7. [PMID: 36822202 DOI: 10.1016/j.cub.2023.01.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/01/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023]
Abstract
In the face of the human-caused biodiversity crisis, understanding the theoretical basis of conservation efforts of endangered species and populations has become increasingly important. According to population genetics theory, population subdivision helps organisms retain genetic diversity, crucial for adaptation in a changing environment. Habitat topography is thought to be important for generating and maintaining population subdivision, but empirical cases are needed to test this assumption. We studied Saimaa ringed seals, landlocked in a labyrinthine lake and recovering from a drastic bottleneck, with additional samples from three other ringed seal subspecies. Using whole-genome sequences of 145 seals, we analyzed the distribution of variation and genetic relatedness among the individuals in relation to the habitat shape. Despite a severe history of genetic bottlenecks with prevalent homozygosity in Saimaa ringed seals, we found evidence for the population structure mirroring the subregions of the lake. Our genome-wide analyses showed that the subpopulations had retained unique variation and largely complementary patterns of homozygosity, highlighting the significance of habitat connectivity in conservation biology and the power of genomic tools in understanding its impact. The central role of the population substructure in preserving genetic diversity at the metapopulation level was confirmed by simulations. Integration of genetic analyses in conservation decisions gives hope to Saimaa ringed seals and other endangered species in fragmented habitats.
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Affiliation(s)
- Ari Löytynoja
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland.
| | - Pasi Rastas
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Mia Valtonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Juhana Kammonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Liisa Holm
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland; Organismal and Evolutionary Biology Research Program, Faculty of Biosciences, University of Helsinki, Helsinki 00014, Finland
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute and University of Copenhagen, Copenhagen 1350, Denmark
| | - Lars Paulin
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Jukka Jernvall
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland; Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Petri Auvinen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
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38
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Fitz KS, Montes HR, Thompson DM, Pinsky ML. Isolation-by-distance and isolation-by-oceanography in Maroon Anemonefish ( Amphiprion biaculeatus). Evol Appl 2023; 16:379-392. [PMID: 36793687 PMCID: PMC9923474 DOI: 10.1111/eva.13448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/27/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
Obtaining dispersal estimates for a species is key to understanding local adaptation and population dynamics and to implementing conservation actions. Genetic isolation-by-distance (IBD) patterns can be used for estimating dispersal, and these patterns are especially useful for marine species in which few other methods are available. In this study, we genotyped coral reef fish (Amphiprion biaculeatus) at 16 microsatellite loci across eight sites across 210 km in the central Philippines to generate fine-scale estimates of dispersal. All sites except for one followed IBD patterns. Using IBD theory, we estimated a larval dispersal kernel spread of 8.9 km (95% confidence interval of 2.3-18.4 km). Genetic distance to the remaining site correlated strongly with the inverse probability of larval dispersal from an oceanographic model. Ocean currents were a better explanation for genetic distance at large spatial extents (sites greater than 150 km apart), while geographic distance remained the best explanation for spatial extents less than 150 km. Our study demonstrates the utility of combining IBD patterns with oceanographic simulations to understand connectivity in marine environments and to guide marine conservation strategies.
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Affiliation(s)
- Kyra S Fitz
- Department of Ecology, Evolution and Natural Resources Rutgers University New Brunswick New Jersey USA
| | - Humberto R Montes
- Institute of Tropical Ecology and Environmental Management Visayas State University Baybay City Philippines
| | - Diane M Thompson
- Department of Geosciences University of Arizona Tucson Arizona USA
| | - Malin L Pinsky
- Department of Ecology, Evolution and Natural Resources Rutgers University New Brunswick New Jersey USA
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39
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Peres PA, Mantelatto FL. Demographic changes and life-history strategies predict the genetic diversity in crabs. J Evol Biol 2023; 36:432-443. [PMID: 36537369 DOI: 10.1111/jeb.14138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analysed across 150 species (16 992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.
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Affiliation(s)
- Pedro A Peres
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Fernando L Mantelatto
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
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40
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Kyriazis CC, Beichman AC, Brzeski KE, Hoy SR, Peterson RO, Vucetich JA, Vucetich LM, Lohmueller KE, Wayne RK. Genomic Underpinnings of Population Persistence in Isle Royale Moose. Mol Biol Evol 2023; 40:7024794. [PMID: 36729989 PMCID: PMC9927576 DOI: 10.1093/molbev/msad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.
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Affiliation(s)
| | | | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Sarah R Hoy
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Rolf O Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
| | - Leah M Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI
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41
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Stojanovic D, McLennan E, Olah G, Cobden M, Heinsohn R, Manning AD, Alves F, Hogg C, Rayner L. Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities. Anim Conserv 2023. [DOI: 10.1111/acv.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- D. Stojanovic
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - E. McLennan
- School of Life & Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - G. Olah
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - M. Cobden
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - R. Heinsohn
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - A. D. Manning
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - F. Alves
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - C. Hogg
- School of Life & Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - L. Rayner
- ACT Parks and Conservation Service, Australian Capital Territory Government Canberra Australia
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42
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Hansen CCR, Láruson ÁJ, Rasmussen JA, Ballesteros JAC, Sinding MHS, Hallgrimsson GT, von Schmalensee M, Stefansson RA, Skarphédinsson KH, Labansen AL, Leivits M, Sonne C, Dietz R, Skelmose K, Boertmann D, Eulaers I, Martin MD, Helgason AS, Gilbert MTP, Pálsson S. Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla). Mol Ecol 2023; 32:1925-1942. [PMID: 36680370 DOI: 10.1111/mec.16858] [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: 10/12/2021] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023]
Abstract
Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: (1) Isolation of refugia during the last glacial period 110-115,000 years ago, (2) population divergence following the colonization of the deglaciated areas ~10,000 years ago, (3) human population expansion, which led to the settlement in Iceland ~1100 years ago, and (4) human persecution and exposure to toxic pollutants during the last two centuries.
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Affiliation(s)
| | - Áki Jarl Láruson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Jacob Agerbo Rasmussen
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesus Adrian Chimal Ballesteros
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Mikkel-Holger S Sinding
- Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Gunnar T Hallgrimsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | - Madis Leivits
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Christian Sonne
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Rune Dietz
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Kim Skelmose
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David Boertmann
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Igor Eulaers
- Department of Ecoscience, Aarhus University, Roskilde, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Agnar S Helgason
- Department of Anthropology, University of Iceland, Reykjavik, Iceland.,deCODE Genetics, Reykjavik, Iceland
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Center for Evolutionary Hologenomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Snaebjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
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43
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Conservation genomics reveals fine-scale population structuring and recent declines in the Critically Endangered Australian Kuranda Treefrog. CONSERV GENET 2023. [DOI: 10.1007/s10592-022-01499-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
AbstractThe Kuranda Treefrog occurs in tropical north-east Australia and is listed as Critically Endangered due to its small distribution and population size, with observed declines due to drought and human-associated impacts to habitat. Field surveys identified marked population declines in the mid-2000s, culminating in very low abundance at most sites in 2005 and 2006, followed by limited recovery. Here, samples from before (2001–2004) and after (2007–2009) this decline were analysed using 7132 neutral genome-wide SNPs to assess genetic connectivity among breeding sites, genetic erosion, and effective population size. We found a high level of genetic connectivity among breeding sites, but also structuring between the population at the eastern end of the distribution (Jumrum Creek) versus all other sites. Despite finding no detectable sign of genetic erosion between the two times periods, we observed a marked decrease in effective population size (Ne), from 1720 individuals pre-decline to 818 post-decline. This mirrors the decline detected in the field census data, but the magnitude of the decline suggested by the genetic data is greater. We conclude that the current effective population size for the Kuranda Treefrog remains around 800 adults, split equally between Jumrum Creek and all other sites combined. The Jumrum Creek habitat requires formal protection. Connectivity among all other sites must be maintained and improved through continued replanting of rainforest, and it is imperative that impacts to stream flow and water quality are carefully managed to maintain or increase population sizes and prevent genetic erosion.
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44
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Liebgold EB, Dickey MJ, Lamb SM, Howell HJ, Ransom TS. (Not) far from home: No sex bias in dispersal, but limited genetic patch size, in an endangered species, the Spotted Turtle ( Clemmys guttata). Ecol Evol 2023; 13:e9734. [PMID: 36620419 PMCID: PMC9812832 DOI: 10.1002/ece3.9734] [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: 10/22/2021] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Sex-biased dispersal is common in many animals, with male-biased dispersal often found in studies of mammals and reptiles, including interpretations of spatial genetic structure, ostensibly as a result of male-male competition and a lack of male parental care. Few studies of sex-biased dispersal have been conducted in turtles, but a handful of studies, in saltwater turtles and in terrestrial turtles, have detected male-biased dispersal as expected. We tested for sex-biased dispersal in the endangered freshwater turtle, the spotted turtle (Clemmys guttata) by investigating fine-scale genetic spatial structure of males and females. We found significant spatial genetic structure in both sexes, but the patterns mimicked each other. Both males and females typically had higher than expected relatedness at distances <25 km, and in many distance classes greater than 25 km, less than expected relatedness. Similar patterns were apparent whether we used only loci in Hardy-Weinberg equilibrium (n = 7) or also included loci with potential null alleles (n = 5). We conclude that, contrary to expectations, sex-biased dispersal is not occurring in this species, possibly related to the reverse sexual dimorphism in this species, with females having brighter colors. We did, however, detect significant spatial genetic structure in males and females, separate and combined, showing philopatry within a genetic patch size of <25 km in C. guttata, which is concerning for an endangered species whose populations are often separated by distances greater than the genetic patch size.
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Affiliation(s)
- Eric B. Liebgold
- Department of Biological SciencesSalisbury UniversitySalisburyMarylandUSA
| | - Myra J. Dickey
- Department of EntomologyTexas A & M UniversityCollege StationTexasUSA
| | - Stephanie M. Lamb
- Department of Biological SciencesSalisbury UniversitySalisburyMarylandUSA
| | | | - Tami S. Ransom
- Department of Environmental StudiesSalisbury UniversitySalisburyMarylandUSA
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45
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Beichman AC, Kalhori P, Kyriazis CC, DeVries AA, Nigenda-Morales S, Heckel G, Schramm Y, Moreno-Estrada A, Kennett DJ, Hylkema M, Bodkin J, Koepfli KP, Lohmueller KE, Wayne RK. Genomic analyses reveal range-wide devastation of sea otter populations. Mol Ecol 2023; 32:281-298. [PMID: 34967471 PMCID: PMC9875727 DOI: 10.1111/mec.16334] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/02/2021] [Accepted: 12/23/2021] [Indexed: 01/28/2023]
Abstract
The genetic consequences of species-wide declines are rarely quantified because the timing and extent of the decline varies across the species' range. The sea otter (Enhydra lutris) is a unique model in this regard. Their dramatic decline from thousands to fewer than 100 individuals per population occurred range-wide and nearly simultaneously due to the 18th-19th century fur trade. Consequently, each sea otter population represents an independent natural experiment of recovery after extreme population decline. We designed sequence capture probes for 50 Mb of sea otter exonic and neutral genomic regions. We sequenced 107 sea otters from five populations that span the species range to high coverage (18-76×) and three historical Californian samples from ~1500 and ~200 years ago to low coverage (1.5-3.5×). We observe distinct population structure and find that sea otters in California are the last survivors of a divergent lineage isolated for thousands of years and therefore warrant special conservation concern. We detect signals of extreme population decline in every surviving sea otter population and use this demographic history to design forward-in-time simulations of coding sequence. Our simulations indicate that this decline could lower the fitness of recovering populations for generations. However, the simulations also demonstrate how historically low effective population sizes prior to the fur trade may have mitigated the effects of population decline on genetic health. Our comprehensive approach shows how demographic inference from genomic data, coupled with simulations, allows assessment of extinction risk and different models of recovery.
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Affiliation(s)
- Annabel C. Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Pooneh Kalhori
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Amber A. DeVries
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Sergio Nigenda-Morales
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Gisela Heckel
- Centro de Investigación Científica y de Educación Superior de Ensenada (Ensenada Center for Scientific Research and Higher Education), Ensenada, Baja California 22860, Mexico
| | - Yolanda Schramm
- Universidad Autónoma de Baja California (Autonomous University of Baja California), Ensenada, Baja California 22860, Mexico
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Mark Hylkema
- Cultural Resources Program Manager and Tribal Liaison/Archaeologist, Santa Cruz District, California State Parks, Santa Cruz, California, USA
| | - James Bodkin
- Retired, Alaska Science Center, US Geological Survey, Anchorage Alaska, 99503, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, D.C., 20008, USA
- ITMO University, Computer Technologies Laboratory, St. Petersburg 197101, Russia
| | - 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
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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46
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Recent Changes in Genetic Diversity, Structure, and Gene Flow in a Passerine Experiencing a Rapid Population Decline, the Dupont’s Lark (Chersophilus duponti). DIVERSITY 2022. [DOI: 10.3390/d14121120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.
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47
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Kimble SJA, Unger SD, Williams RN. Genetically derived effective population size estimates of herpetofaunal species should be used with caution. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Shem D. Unger
- Department of Biology Wingate University Wingate NC 28174 USA
| | - Rod N. Williams
- Department of Forestry and Natural Resources Purdue University West Lafayette IN 47907 USA
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48
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Gompert Z, Flaxman SM, Feder JL, Chevin LM, Nosil P. Laplace's demon in biology: Models of evolutionary prediction. Evolution 2022; 76:2794-2810. [PMID: 36193839 DOI: 10.1111/evo.14628] [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: 09/15/2021] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 01/22/2023]
Abstract
Our ability to predict natural phenomena can be limited by incomplete information. This issue is exemplified by "Laplace's demon," an imaginary creature proposed in the 18th century, who knew everything about everything, and thus could predict the full nature of the universe forward or backward in time. Quantum mechanics, among other things, has cast doubt on the possibility of Laplace's demon in the full sense, but the idea still serves as a useful metaphor for thinking about the extent to which prediction is limited by incomplete information on deterministic processes versus random factors. Here, we use simple analytical models and computer simulations to illustrate how data limits can be captured in a Bayesian framework, and how they influence our ability to predict evolution. We show how uncertainty in measurements of natural selection, or low predictability of external environmental factors affecting selection, can greatly reduce predictive power, often swamping the influence of intrinsic randomness caused by genetic drift. Thus, more accurate knowledge concerning the causes and action of natural selection is key to improving prediction. Fortunately, our analyses and simulations show quantitatively that reasonable improvements in data quantity and quality can meaningfully increase predictability.
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Affiliation(s)
| | | | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Luis-Miguel Chevin
- CEFE, Univ Montpellier, Montpellier, France.,CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Patrik Nosil
- CEFE, Univ Montpellier, Montpellier, France.,CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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49
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Sequeira F, Aguilar FF, Madeira FM, Teixeira J, Crespo E, Ferrand N, Rebelo R. What can genetics tell us about the history of a human-mediated introduction of the golden-striped salamander south of its native range? EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01628-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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50
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Schacht R, Beissinger SR, Wedekind C, Jennions MD, Geffroy B, Liker A, Kappeler PM, Weissing FJ, Kramer KL, Hesketh T, Boissier J, Uggla C, Hollingshaus M, Székely T. Adult sex ratios: causes of variation and implications for animal and human societies. Commun Biol 2022; 5:1273. [PMID: 36402823 PMCID: PMC9675760 DOI: 10.1038/s42003-022-04223-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022] Open
Abstract
Converging lines of inquiry from across the social and biological sciences target the adult sex ratio (ASR; the proportion of males in the adult population) as a fundamental population-level determinant of behavior. The ASR, which indicates the relative number of potential mates to competitors in a population, frames the selective arena for competition, mate choice, and social interactions. Here we review a growing literature, focusing on methodological developments that sharpen knowledge of the demographic variables underlying ASR variation, experiments that enhance understanding of the consequences of ASR imbalance across societies, and phylogenetic analyses that provide novel insights into social evolution. We additionally highlight areas where research advances are expected to make accelerating contributions across the social sciences, evolutionary biology, and biodiversity conservation.
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Affiliation(s)
- Ryan Schacht
- grid.255364.30000 0001 2191 0423Department of Anthropology, East Carolina University, Greenville, NC USA
| | - Steven R. Beissinger
- grid.47840.3f0000 0001 2181 7878Department of Environmental Science, Policy and Management and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720 USA
| | - Claus Wedekind
- grid.9851.50000 0001 2165 4204Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael D. Jennions
- grid.1001.00000 0001 2180 7477Ecology & Evolution, Research School of Biology, The Australian National University, Acton, Canberra 2601 Australia
| | - Benjamin Geffroy
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - András Liker
- grid.7336.10000 0001 0203 5854ELKH-PE Evolutionary Ecology Research Group, University of Pannonia, 8210 Veszprém, Hungary ,grid.7336.10000 0001 0203 5854Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, 8210 Veszprém, Hungary
| | - Peter M. Kappeler
- grid.418215.b0000 0000 8502 7018Behavioral Ecology and Sociobiology Unit, German Primate Center, Leibniz Institute of Primate Biology, 37077 Göttingen, Germany ,grid.7450.60000 0001 2364 4210Department of Sociobiology/Anthropology, University of Göttingen, 37077 Göttingen, Germany
| | - Franz J. Weissing
- grid.4830.f0000 0004 0407 1981Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Karen L. Kramer
- grid.223827.e0000 0001 2193 0096Department of Anthropology, University of Utah, Salt Lake City, UT USA
| | - Therese Hesketh
- grid.83440.3b0000000121901201Institute of Global Health, University College London, London, UK ,grid.13402.340000 0004 1759 700XCentre for Global Health, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Jérôme Boissier
- grid.4444.00000 0001 2112 9282IHPE Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - Caroline Uggla
- grid.10548.380000 0004 1936 9377Stockholm University Demography Unit, Sociology Department, Stockholm University, 106 91 Stockholm, Sweden
| | - Mike Hollingshaus
- grid.223827.e0000 0001 2193 0096Kem C. Gardner Policy Institute, David Eccles School of Business, University of Utah, Salt Lake City, UT USA
| | - Tamás Székely
- grid.7340.00000 0001 2162 1699Milner Centre for Evolution, University of Bath, Bath, BA2 7AY UK ,grid.7122.60000 0001 1088 8582ELKH-DE Reproductive Strategies Research Group, Department of Zoology and Human Biology, University of Debrecen, H-4032 Debrecen, Hungary
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