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Rachmilovitz EN, Shaish L, Douek J, Rinkevich B. Population genetics assessment of two pocilloporid coral species from the northern red sea: Implications for urbanized reef sustainability. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106580. [PMID: 38851082 DOI: 10.1016/j.marenvres.2024.106580] [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: 02/21/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Understanding the genetic makeup of key coral species is vital for effective coral reef management, as heightened genetic diversity directly influences long-term survival and resilience against environmental changes. This study focused on two widespread Indo-Pacific branching corals, Pocillopora damicornis (referred as Pocillopora cf. damicornis (as identified only morphologically) and Seriatopora hystrix, by genotyping 222 and 195 colonies, respectively, from 10 sites in the northern Gulf of Eilat, Red Sea, using six and five microsatellite markers, respectively. Both species exhibited low observed heterozygosity (0.47 for P. cf. damicornis, 0.32 for S. hystrix) and similar expected heterozygosity (0.576 for P. cf. damicornis, 0.578 for S. hystrix). Pocillopora cf. damicornis showed minimal deviations from Hardy-Weinberg equilibrium (HWE) and low but positive F values, indicating high gene flow, while S. hystrix exhibited higher diversion from HWE and positive F values, suggesting isolation by distance and possible non-random mating or genetic drift. As the Gulf of Eilat undergoes rapid urbanization, this study highlights the anthropogenic impacts on the population genetics of key ecosystem engineering species and emphasizes the importance of managing genetics of Marine Protected Areas while implementing active coral reef restoration. The differences in reproductive traits between the two species (S. hystrix being a brooder, while P. cf. damicornis a broadcast spawner), underscore the need for sustainable population genetics management of the coral reefs for the future and resilience of the coral reef ecosystem of the northern Red Sea region.
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Affiliation(s)
- Elad Nehoray Rachmilovitz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel; Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa, 3498838, Israel.
| | - Lee Shaish
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel
| | - Jacob Douek
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel.
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel.
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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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3
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Aitken SN, Jordan R, Tumas HR. Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:707-736. [PMID: 38594931 DOI: 10.1146/annurev-arplant-070523-044239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.
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Affiliation(s)
- Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
| | | | - Hayley R Tumas
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada; ,
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4
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Allendorf FW, Hössjer O, Ryman N. What does effective population size tell us about loss of allelic variation? Evol Appl 2024; 17:e13733. [PMID: 38911263 PMCID: PMC11192967 DOI: 10.1111/eva.13733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/29/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
There are two primary measures of the amount of genetic variation in a population at a locus: heterozygosity and the number of alleles. Effective population size (N e) provides both an expectation of the amount of heterozygosity in a population at drift-mutation equilibrium and the rate of loss of heterozygosity because of genetic drift. In contrast, the number of alleles in a population at drift-mutation equilibrium is a function of both N e and census size (N C). In addition, populations with the same N e can lose allelic variation at very different rates. Allelic variation is generally much more sensitive to bottlenecks than heterozygosity. Expressions used to adjust for the effects of violations of the ideal population on N e do not provide good predictions of the loss of allelic variation. These effects are much greater for loci with many alleles, which are often important for adaptation. We show that there is a linear relationship between the reduction of N C and the corresponding reduction of the expected number of alleles at drift-mutation equilibrium. This makes it possible to predict the expected effect of a bottleneck on allelic variation. Heterozygosity provides good estimates of the rate of adaptive change in the short-term, but allelic variation provides important information about long-term adaptive change. The guideline of long-term N e being greater than 500 is often used as a primary genetic metric for evaluating conservation status. We recommend that this guideline be expanded to take into account allelic variation as well as heterozygosity.
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Affiliation(s)
- Fred W. Allendorf
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Ola Hössjer
- Department of MathematicsStockholm UniversityStockholmSweden
| | - Nils Ryman
- Department of ZoologyStockholm UniversityStockholmSweden
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5
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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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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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7
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Gargiulo R, Decroocq V, González‐Martínez SC, Paz‐Vinas I, Aury J, Lesur Kupin I, Plomion C, Schmitt S, Scotti I, Heuertz M. Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets. Evol Appl 2024; 17:e13691. [PMID: 38707994 PMCID: PMC11069024 DOI: 10.1111/eva.13691] [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: 08/21/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.
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Affiliation(s)
| | | | | | - Ivan Paz‐Vinas
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
- CNRS, ENTPE, UMR5023 LEHNAUniversité Claude Bernard Lyon 1VilleurbanneFrance
| | - Jean‐Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | | | | | - Sylvain Schmitt
- AMAPUniv. Montpellier, CIRAD, CNRS, INRAE, IRDMontpellierFrance
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Leblanc CA, Räsänen K, Morrissey M, Skúlason S, Ferguson M, Kristjánsson BK. Fine scale diversity in the lava: genetic and phenotypic diversity in small populations of Arctic charr Salvelinus alpinus. BMC Ecol Evol 2024; 24:45. [PMID: 38622503 PMCID: PMC11017478 DOI: 10.1186/s12862-024-02232-3] [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: 09/13/2023] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND A major goal in evolutionary biology is to understand the processes underlying phenotypic variation in nature. Commonly, studies have focused on large interconnected populations or populations found along strong environmental gradients. However, studies on small fragmented populations can give strong insight into evolutionary processes in relation to discrete ecological factors. Evolution in small populations is believed to be dominated by stochastic processes, but recent work shows that small populations can also display adaptive phenotypic variation, through for example plasticity and rapid adaptive evolution. Such evolution takes place even though there are strong signs of historical bottlenecks and genetic drift. Here we studied 24 small populations of the freshwater fish Arctic charr (Salvelinus alpinus) found in groundwater filled lava caves. Those populations were found within a few km2-area with no apparent water connections between them. We studied the relative contribution of neutral versus non-neutral evolutionary processes in shaping phenotypic divergence, by contrasting patterns of phenotypic and neutral genetic divergence across populations in relation to environmental measurements. This allowed us to model the proportion of phenotypic variance explained by the environment, taking in to account the observed neutral genetic structure. RESULTS These populations originated from the nearby Lake Mývatn, and showed small population sizes with low genetic diversity. Phenotypic variation was mostly correlated with neutral genetic diversity with only a small environmental effect. CONCLUSIONS Phenotypic diversity in these cave populations appears to be largely the product of neutral processes, fitting the classical evolutionary expectations. However, the fact that neutral processes did not explain fully the phenotypic patterns suggests that further studies can increase our understanding on how neutral evolutionary processes can interact with other forces of selection at early stages of divergence. The accessibility of these populations has provided the opportunity for long-term monitoring of individual fish, allowing tracking how the environment can influence phenotypic and genetic divergence for shaping and maintaining diversity in small populations. Such studies are important, especially in freshwater, as habitat alteration is commonly breaking populations into smaller units, which may or may not be viable.
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Affiliation(s)
- Camille A Leblanc
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland.
| | - Katja Räsänen
- Department of Biology and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | | | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
- Icelandic Museum of Natural History, Reykjavik, Iceland
| | - Moira Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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9
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Bellis J, Osazuwa-Peters O, Maschinski J, Keir MJ, Parsons EW, Kaye TN, Kunz M, Possley J, Menges E, Smith SA, Roth D, Brewer D, Brumback W, Lange JJ, Niederer C, Turner-Skoff JB, Bontrager M, Braham R, Coppoletta M, Holl KD, Williamson P, Bell T, Jonas JL, McEachern K, Robertson KL, Birnbaum SJ, Dattilo A, Dollard JJ, Fant J, Kishida W, Lesica P, Link SO, Pavlovic NB, Poole J, Reemts CM, Stiling P, Taylor DD, Titus JH, Titus PJ, Adkins ED, Chambers T, Paschke MW, Heineman KD, Albrecht MA. Identifying predictors of translocation success in rare plant species. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14190. [PMID: 37768181 DOI: 10.1111/cobi.14190] [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: 06/08/2023] [Revised: 08/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
The fundamental goal of a rare plant translocation is to create self-sustaining populations with the evolutionary resilience to persist in the long term. Yet, most plant translocation syntheses focus on a few factors influencing short-term benchmarks of success (e.g., survival and reproduction). Short-term benchmarks can be misleading when trying to infer future growth and viability because the factors that promote establishment may differ from those required for long-term persistence. We assembled a large (n = 275) and broadly representative data set of well-documented and monitored (7.9 years on average) at-risk plant translocations to identify the most important site attributes, management techniques, and species' traits for six life-cycle benchmarks and population metrics of translocation success. We used the random forest algorithm to quantify the relative importance of 29 predictor variables for each metric of success. Drivers of translocation outcomes varied across time frames and success metrics. Management techniques had the greatest relative influence on the attainment of life-cycle benchmarks and short-term population trends, whereas site attributes and species' traits were more important for population persistence and long-term trends. Specifically, large founder sizes increased the potential for reproduction and recruitment into the next generation, whereas declining habitat quality and the outplanting of species with low seed production led to increased extinction risks and a reduction in potential reproductive output in the long-term, respectively. We also detected novel interactions between some of the most important drivers, such as an increased probability of next-generation recruitment in species with greater seed production rates, but only when coupled with large founder sizes. Because most significant barriers to plant translocation success can be overcome by improving techniques or resolving site-level issues through early intervention and management, we suggest that by combining long-term monitoring with adaptive management, translocation programs can enhance the prospects of achieving long-term success.
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Affiliation(s)
- Joe Bellis
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, Missouri, USA
- Center for Plant Conservation, Escondido, California, USA
| | - Oyomoare Osazuwa-Peters
- Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joyce Maschinski
- Center for Plant Conservation, Escondido, California, USA
- Fairchild Tropical Botanic Garden, Coral Gables, Florida, USA
| | - Matthew J Keir
- Department of Land and Natural Resources, Hawai'i Division of Forestry and Wildlife, Honolulu, Hawaii, USA
| | - Elliott W Parsons
- Pacific Regional Invasive Species and Climate Change Management Network, University of Hawaii at Mānoa, Honolulu, Hawaii, USA
| | - Thomas N Kaye
- Institute for Applied Ecology, Corvallis, Oregon, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michael Kunz
- North Carolina Botanical Garden, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Eric Menges
- Archbold Biological Station, Venus, Florida, USA
| | - Stacy A Smith
- Archbold Biological Station, Venus, Florida, USA
- Agronomy Department, University of Florida, Gainesville, Florida, USA
| | - Daniela Roth
- New Mexico Energy, Minerals, and Natural Resources Department, Forestry Division, Santa Fe, New Mexico, USA
| | - Debbie Brewer
- Fort Huachuca Environmental and Natural Resources Division, Fort Huachuca, Arizona, USA
| | | | - James J Lange
- Fairchild Tropical Botanic Garden, Coral Gables, Florida, USA
| | | | | | - Megan Bontrager
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Richard Braham
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Karen D Holl
- Environmental Studies Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Paula Williamson
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | | | - Jayne L Jonas
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska, USA
| | - Kathryn McEachern
- U.S. Geological Survey, WERC-Channel Islands Field Station, Ventura, California, USA
| | | | | | - Adam Dattilo
- Tennessee Valley Authority, Knoxville, Tennessee, USA
| | - John J Dollard
- Croatan National Forest, Forest Service, New Bern, North Carolina, USA
| | | | - Wendy Kishida
- Department of Land and Natural Resources, Hawai'i Division of Forestry and Wildlife, Honolulu, Hawaii, USA
| | - Peter Lesica
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Steven O Link
- Department of Natural Resources, Energy and Environmental Sciences Program, Pendleton, Oregon, USA
| | - Noel B Pavlovic
- U.S. Geological Survey, GLSC - Lake Michigan Ecological Research Station, Chesterton, Indiana, USA
| | - Jackie Poole
- Texas Parks & Wildlife Department, Austin, Texas, USA
| | | | - Peter Stiling
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - David D Taylor
- Daniel Boone National Forest, USDA Forest Service, Winchester, Kentucky, USA
| | - Jonathan H Titus
- Biology Department, Science Center, State University of New York, Fredonia, New York, USA
| | | | - Edith D Adkins
- Pacific Cooperative Studies Unit, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Timothy Chambers
- U.S Army Natural Resources Program on Oahu, Schofield Barracks, Hawaii, USA
| | - Mark W Paschke
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, Colorado, USA
| | | | - Matthew A Albrecht
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, Missouri, USA
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10
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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11
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Mujica PC, Martinez V. A purebred South American breed showing high effective population size and independent breed ancestry: The Chilean Terrier. Anim Genet 2023; 54:772-785. [PMID: 37778752 DOI: 10.1111/age.13359] [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: 05/02/2023] [Revised: 08/31/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
The Chilean Terrier is a known breed in Chile that has not been genetically assessed despite its distinctive color patterns, agility, and hardiness across the diversity of climates encountered within the Chilean landscape. The population structure and its relatedness with other breeds, as well as the actual origin of the breed, remain unknown. We estimated several population parameters using samples from individuals representing the distribution of the Chilean Terrier across the country. By utilizing the Illumina HD canine genotyping array, we computed the effective population size (Ne ), individual inbreeding, and relatedness to evaluate the genetic diversity of the breed. The results show that linkage disequilibrium was relatively low and decayed rapidly; in fact, Ne was very high when compared to other breeds, and similar to other American indigenous breeds (such as the Chihuahua with values of Ne near 500). These results are in line with the low estimates of genomic inbreeding and relatedness and the relatively large number of effective chromosome segments (Me = 2467) obtained using the properties of the genomic relationship matrix. Between population analysis (cross-population extended haplotype homozygosity, di ) with other breeds such as the Jack Russell Terrier, the Peruvian-Inca Orchid, and the Chihuahua suggested that candidate regions harboring FGF5, PAX3, and ASIP, probably explained some morphological traits, such as the distinctive color pattern characteristic of the breed. When considering Admixture estimates and phylogenetic analysis, together with other breeds of American and European origin, the Chilean Terrier does not have a recent European ancestry. Overall, the results suggest that the breed has evolved independently in Chile from other terrier breeds, from an unknown European terrier ancestor.
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Affiliation(s)
- Paola C Mujica
- FAVET-INBIOGEN Laboratory, Faculty of Veterinary Sciences, Universidad de Chile, Santiago, Chile
| | - Víctor Martinez
- FAVET-INBIOGEN Laboratory, Faculty of Veterinary Sciences, Universidad de Chile, Santiago, Chile
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12
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Dussex N, Kurland S, Olsen RA, Spong G, Ericsson G, Ekblom R, Ryman N, Dalén L, Laikre L. Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose. Commun Biol 2023; 6:1035. [PMID: 37848497 PMCID: PMC10582009 DOI: 10.1038/s42003-023-05385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden.
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.
- Norwegian University of Science and Technology, University Museum, Trondheim, NO-7491, Norway.
| | - Sara Kurland
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21, Solna, Sweden
| | - Göran Spong
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Göran Ericsson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, SE-106 48, Stockholm, Sweden
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
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13
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Nistelberger HM, Roycroft E, Macdonald AJ, McArthur S, White LC, Grady PGS, Pierson J, Sims C, Cowen S, Moseby K, Tuft K, Moritz C, Eldridge MDB, Byrne M, Ottewell K. Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur. Mol Ecol 2023. [PMID: 37715549 DOI: 10.1111/mec.17119] [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: 04/10/2023] [Revised: 07/11/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre-decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single-source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre-decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.
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Affiliation(s)
- Heidi M Nistelberger
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Emily Roycroft
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anna J Macdonald
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shelley McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Lauren C White
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer Pierson
- Australian Wildlife Conservancy, Subiaco, Western Australia, Australia
| | - Colleen Sims
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Saul Cowen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Moseby
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mark D B Eldridge
- Terrestrial Vertebrates, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
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14
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Hössjer O, Laikre L, Ryman N. Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes. Acta Biotheor 2023; 71:19. [PMID: 37458852 PMCID: PMC10352448 DOI: 10.1007/s10441-023-09470-w] [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: 11/08/2021] [Accepted: 06/28/2023] [Indexed: 07/20/2023]
Abstract
The variance effective population size ([Formula: see text]) is frequently used to quantify the expected rate at which a population's allele frequencies change over time. The purpose of this paper is to find expressions for the global [Formula: see text] of a spatially structured population that are of interest for conservation of species. Since [Formula: see text] depends on allele frequency change, we start by dividing the cause of allele frequency change into genetic drift within subpopulations (I) and a second component mainly due to migration between subpopulations (II). We investigate in detail how these two components depend on the way in which subpopulations are weighted as well as their dependence on parameters of the model such a migration rates, and local effective and census sizes. It is shown that under certain conditions the impact of II is eliminated, and [Formula: see text] of the metapopulation is maximized, when subpopulations are weighted proportionally to their long term reproductive contributions. This maximal [Formula: see text] is the sought for global effective size, since it approximates the gene diversity effective size [Formula: see text], a quantifier of the rate of loss of genetic diversity that is relevant for conservation of species and populations. We also propose two novel versions of [Formula: see text], one of which (the backward version of [Formula: see text]) is most stable, exists for most populations, and is closer to [Formula: see text] than the classical notion of [Formula: see text]. Expressions for the optimal length of the time interval for measuring genetic change are developed, that make it possible to estimate any version of [Formula: see text] with maximal accuracy.
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Affiliation(s)
- Ola Hössjer
- Division of Mathematical Statistics, Department of Mathematics, Stockholm University, 106 91 Stockholm, Sweden
| | - Linda Laikre
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Nils Ryman
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
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15
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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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16
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Carrier A, Gilbert I, Leclerc P, Duchesne M, Robert C. Characterization of the genetic pool of the Canadienne dairy cattle breed. Genet Sel Evol 2023; 55:32. [PMID: 37161364 PMCID: PMC10170705 DOI: 10.1186/s12711-023-00793-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/15/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Canadienne cattle are the oldest breed of dairy cattle in North America. The Canadienne breed originates from cattle that were brought to America by the mid-seventeenth century French settlers. The herd book was established in 1886 and the current breed characteristics include dark coat color, small size compared to the modern Holstein breed, and overall rusticity shaped by the harsh environmental conditions that were prevalent during the settlement of North America. The Canadienne breed is an invaluable genetic resource due to its high resilience, longevity and fertility. However, it is heavily threatened with a current herd limited to an estimated 1200 registered animals, of which less than 300 are fullblood. To date, no effort has been made to document the genetic pool of this heritage breed in order to preserve it. RESULTS In this project, we used genomic data, which allow a precise description of the genetic makeup of a population, to provide valuable information on the genetic diversity of this heritage breed and suggest management options for its long-term viability. Using a panel that includes 640,000 single nucleotide polymorphisms (SNPs), we genotyped 190 animals grouped into six purity ranges. Unsupervised clustering analyses revealed three genetically distinct groups among those with the higher levels of purity. The observed heterozygosity was higher than expected even in the 100% purebreds. Comparison with Holstein genotypes showed significantly shorter runs of homozygosity for the Canadienne breed, which was unexpected due to the high inbreeding value calculated from pedigree data. CONCLUSIONS Overall, our data indicate that the fullblood gene pool of the Canadienne breed is more diversified than expected and that bloodline management could promote breed sustainability. In its current state, the Canadienne is not a dead-end breed but remains highly vulnerable due to its small population size.
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Affiliation(s)
- Alexandra Carrier
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
| | - Isabelle Gilbert
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
| | - Pierre Leclerc
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Dé̇partement d'obstétrique, gynécologie et reproduction, Faculté de médecine, Université Laval, QC, Québec, Canada
| | - Mario Duchesne
- Association de Mise en Valeur de La Race Bovine Canadienne (AVRBC), Québec, QC, Canada
| | - Claude Robert
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada.
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada.
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
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17
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Horne JB, Frey A, Gaos AR, Martin S, Dutton PH. Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221547. [PMID: 37206959 PMCID: PMC10189603 DOI: 10.1098/rsos.221547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/26/2023] [Indexed: 05/21/2023]
Abstract
Hawksbill sea turtles (Eretmochelys imbricata) from the Hawaiian archipelago form a small and genetically isolated population, consisting of only a few tens of individuals breeding annually. Most females nest on the island of Hawai'i, but little is known about the demographics of this rookery. This study used genetic relatedness, inferred from 135 microhaplotype markers, to determine breeding sex-ratios, estimate female nesting frequency and assess relationships between individuals nesting on different beaches. Samples were collected during the 2017 nesting season and final data included 13 nesting females and 1002 unhatched embryos, salvaged from 41 nests, of which 13 had no observed mother. Results show that most females used a single nesting beach laying 1-5 nests each. From female and offspring alleles, the paternal genotypes of 12 breeding males were reconstructed and many showed high relatedness to their mates. Pairwise relatedness of offspring revealed one instance of polygyny but otherwise suggested a 1 : 1 breeding-sex ratio. Relatedness analysis and spatial-autocorrelation of genotypes indicate that turtles from different nesting areas do not regularly interbreed, suggesting that strong natal homing tendencies in both sexes result in non-random mating across the study area. Complexes of nearby nesting beaches also showed unique patterns of inbreeding across loci, further indicating that Hawaiian hawksbill turtles have demographically discontinuous nesting populations separated by only tens of km.
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Affiliation(s)
- John B. Horne
- Southwest Fisheries Science Center, NOAA-Fisheries, La Jolla, CA, USA
| | - Amy Frey
- Southwest Fisheries Science Center, NOAA-Fisheries, La Jolla, CA, USA
| | - Alexander R. Gaos
- Pacific Islands Fisheries Science Center, NOAA-Fisheries, Honolulu, HI, USA
| | - Summer Martin
- Pacific Islands Fisheries Science Center, NOAA-Fisheries, Honolulu, HI, USA
| | - Peter H. Dutton
- Southwest Fisheries Science Center, NOAA-Fisheries, La Jolla, CA, USA
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18
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Ryman N, Laikre L, Hössjer O. Variance effective population size is affected by census size in sub-structured populations. Mol Ecol Resour 2023. [PMID: 37122118 DOI: 10.1111/1755-0998.13804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023]
Abstract
Measurement of allele frequency shifts between temporally spaced samples has long been used for assessment of effective population size (Ne ), and this 'temporal method' provides estimates of Ne referred to as variance effective size (NeV ). We show that NeV of a local population that belongs to a sub-structured population (a metapopulation) is determined not only by genetic drift and migration rate (m), but also by the census size (Nc ). The realized NeV of a local population can either increase or decrease with increasing m, depending on the relationship between Ne and Nc in isolation. This is shown by explicit mathematical expressions for the factors affecting NeV derived for an island model of migration. We verify analytical results using high-resolution computer simulations, and show that the phenomenon is not restricted to the island model migration pattern. The effect of Nc on the realized NeV of a local subpopulation is most pronounced at high migration rates. We show that Nc only affects local NeV , whereas NeV for the metapopulation as a whole, inbreeding (NeI ), and linkage disequilibrium (NeLD ) effective size are all independent of Nc . Our results provide a possible explanation to the large variation of Ne /Nc ratios reported in the literature, where Ne is frequently estimated by NeV . They are also important for the interpretation of empirical Ne estimates in genetic management where local NeV is often used as a substitute for inbreeding effective size, and we suggest an increased focus on metapopulation NeV as a proxy for NeI .
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Affiliation(s)
- Nils Ryman
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Ola Hössjer
- Department of Mathematics, Stockholm University, Stockholm, Sweden
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19
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Zhou C, Xia S, Wen Q, Song Y, Jia Q, Wang T, Liu L, Ouyang T. Genetic structure of an endangered species Ormosia henryi in southern China, and implications for conservation. BMC PLANT BIOLOGY 2023; 23:220. [PMID: 37098472 PMCID: PMC10131447 DOI: 10.1186/s12870-023-04231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/15/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The evergreen broadleaved forest (EBLF) is an iconic vegetation type of East Asia, and it contributes fundamentally to biodiversity-based ecosystem functioning and services. However, the native habitat of EBLFs keeps on decreasing due to anthropogenic activities. Ormosia henryi is a valuable rare woody species in EBLFs that is particularly sensitive to habitat loss. In this study, ten natural populations of O. henryi in southern China were sampled, and then genotyping by sequencing (GBS) was applied to elucidate the standing genetic variation and population structure of this endangered species. RESULTS In ten O. henryi populations, 64,158 high-quality SNPs were generated by GBS. Based on these markers, a relatively low level of genetic diversity was found with the expected heterozygosity (He) ranging from 0.2371 to 0.2901. Pairwise FST between populations varied from 0.0213 to 0.1652, indicating a moderate level of genetic differentiation. However, contemporary gene flow between populations were rare. Assignment test and principal component analysis (PCA) both supported that O. henryi populations in southern China could be divided into four genetic groups, and prominent genetic admixture was found in those populations located in southern Jiangxi Province. Mantel tests and multiple matrix regression with randomization (MMRR) analyses suggested that isolation by distance (IBD) could be the possible reason for describing the current population genetic structure. In addition, the effective population size (Ne) of O. henryi was extremely small, and showed a continuous declining trend since the Last Glacial Period. CONCLUSIONS Our results indicate that the endangered status of O. henryi is seriously underestimated. Artificial conservation measures should be applied as soon as possible to prevent O. henryi from the fate of extinction. Further studies are needed to elucidate the mechanism that leading to the continuous loss of genetic diversity in O. henryi and help to develop a better conservation strategy.
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Affiliation(s)
- Chengchuan Zhou
- Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, Jiangxi Academy of Forestry, Nanchang, China
| | - Shiqi Xia
- Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, Jiangxi Academy of Forestry, Nanchang, China
| | - Qiang Wen
- Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, Jiangxi Academy of Forestry, Nanchang, China
| | - Ying Song
- Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, Jiangxi Academy of Forestry, Nanchang, China
| | - Quanquan Jia
- Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, Jiangxi Academy of Forestry, Nanchang, China
| | - Tian Wang
- Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, Jiangxi Academy of Forestry, Nanchang, China
| | - Liting Liu
- Identification and Evaluation Center for Forest Germplasm Resources in Jiangxi Province, Jiangxi Academy of Forestry, Nanchang, China.
| | - Tianlin Ouyang
- Jiangxi Provincial Forestry Science and Technology Experiment Center, Ganzhou, China.
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Kurland S, Ryman N, Hössjer O, Laikre L. Effects of subpopulation extinction on effective size (Ne) of metapopulations. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01510-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
AbstractPopulation extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis.
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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: 2] [Impact Index Per Article: 2.0] [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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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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Thompson LM, Thurman LL, Cook CN, Beever EA, Sgrò CM, Battles A, Botero CA, Gross JE, Hall KR, Hendry AP, Hoffmann AA, Hoving C, LeDee OE, Mengelt C, Nicotra AB, Niver RA, Pérez‐Jvostov F, Quiñones RM, Schuurman GW, Schwartz MK, Szymanski J, Whiteley A. Connecting research and practice to enhance the evolutionary potential of species under climate change. CONSERVATION SCIENCE AND PRACTICE 2023. [DOI: 10.1111/csp2.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Laura M. Thompson
- U.S. Geological Survey (USGS), National Climate Adaptation Science Center and the University of Tennessee Knoxville Tennessee USA
| | | | - Carly N. Cook
- School of Biological Sciences Monash University Melbourne Australia
| | - Erik A. Beever
- USGS, Northern Rocky Mountain Science Center and Montana State University Bozeman Montana USA
| | - Carla M. Sgrò
- School of Biological Sciences Monash University Melbourne Australia
| | | | | | - John E. Gross
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | | | | | | | | | - Olivia E. LeDee
- USGS, Midwest Climate Adaptation Science Center Saint Paul Minnesota USA
| | | | | | - Robyn A. Niver
- U.S. Fish and Wildlife Service (USFWS), Branch of Listing and Policy Support Bailey's Crossroads Virginia USA
| | | | - Rebecca M. Quiñones
- Massachusetts Division of Fisheries and Wildlife Westborough Massachusetts USA
| | - Gregor W. Schuurman
- National Park Service (NPS) Climate Change Response Program Fort Collins Colorado USA
| | - Michael K. Schwartz
- U.S. Forest Service, National Genomics Center for Wildlife and Fish Conservation Missoula Montana USA
| | - Jennifer Szymanski
- USFWS, Branch of SSA Science Support, Division of Endangered Species Onalaska Wisconsin USA
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Andersson A, Karlsson S, Ryman N, Laikre L. Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator. Mol Ecol 2022; 31:6422-6439. [PMID: 36170147 PMCID: PMC10091952 DOI: 10.1111/mec.16710] [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: 11/29/2021] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST , respectively) and assess the effective population size (Ne -indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.
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Affiliation(s)
- Anastasia Andersson
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
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25
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Development and characterization of 148 SNP markers in the caribbean symmetrical brain coral Pseudodiploria strigosa. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01294-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AbstractAs coral reefs decline, restoring lost coral populations has been hampered due to the paucity of genetic information available for many coral species. In the Caribbean, the symmetrical brain coral Pseudodiploria strigosa, a prominent framework builder of the reef, has experienced an accelerated decline due to stony coral tissue loss disease (SCTLD). Colonies of P. strigosa gene-banked in response to the threat of SCTLD in Florida, USA, were sampled to develop 148 novel single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.008 to 0.888 and 0.018 to 0.500, respectively. Deviations from Hardy–Weinberg equilibrium within populations, measured by the inbreeding coefficient index (Fis), ranged from − 0.799 to 0.923. In total, 96 SNPs were found to deviate significantly from Hardy–Weinberg (p < 0.05). These SNPs can be used for genetic population analysis to assist management and restoration of P. strigosa.
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Alvarez-Aleman A, Hunter ME, Frazer TK, Powell JA, Alfonso EG, Austin JD. The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba. Genetica 2022; 150:327-341. [PMID: 36271978 DOI: 10.1007/s10709-022-00172-8] [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: 04/20/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
Abstract
The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites HE = 0.44, and SNP HE = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite FIS = 0.12, SNP FIS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all Ne < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.
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Affiliation(s)
- Anmari Alvarez-Aleman
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA. .,Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16 # 114 Entre 1ra y 3ra Plaza, Havana, Cuba. .,Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA.
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Thomas K Frazer
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,College of Marine Science, University of South Florida, 140 Seventh Avenue South, KRC 3109, St. Petersburg, FL, 33701, USA
| | - James A Powell
- Clearwater Marine Aquarium Research Institute, Clearwater Marine Aquarium, Clearwater, FL, USA
| | - Eddy Garcia Alfonso
- Refugio de Fauna Lanzanillo-Pajonal-Fragoso, Empresa Provincial para la Protección de la Flora y la Fauna, Villa Clara, Cuba
| | - James D Austin
- School of Natural Resources and Environment, University of Florida, 2035 McCarty hall D, Gainesville, FL, 32611, USA.,Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
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Bosse M, van Loon S. Challenges in quantifying genome erosion for conservation. Front Genet 2022; 13:960958. [PMID: 36226192 PMCID: PMC9549127 DOI: 10.3389/fgene.2022.960958] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.
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Affiliation(s)
- Mirte Bosse
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mirte Bosse,
| | - Sam van Loon
- Amsterdam Institute for Life and Environment (A-LIFE), Section Ecology and Evolution, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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Lepais O, Aissi A, Véla E, Beghami Y. Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations. Heredity (Edinb) 2022; 129:169-182. [PMID: 35725763 PMCID: PMC9411615 DOI: 10.1038/s41437-022-00550-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/25/2022] Open
Abstract
Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.
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Affiliation(s)
- Olivier Lepais
- Univ. Bordeaux, INRAE, BIOGECO, F-33610, Cestas, France.
| | | | - Errol Véla
- AMAP, Université de Montpellier/CIRAD/CNRS/INRA/IRD, Montpellier, France
| | - Yassine Beghami
- LAPAPEZA, Université Batna 1 Hadj Lakhdar, ISVSA, Batna, Algeria
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29
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A decade of genetic monitoring reveals increased inbreeding for the Endangered western leopard toad, Sclerophrys pantherina. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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The tails of two invasive species: genetic responses to acute and chronic bottlenecks. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractGenetic diversity can affect population viability and can be reduced by both acute and chronic mechanisms. Using the history of the establishment and management of two invasive rat species on Tetiaroa atoll, French Polynesia, we investigated the intensity and longevity of contrasting population bottleneck mechanisms on genetic diversity and bottleneck signal. Using microsatellite loci we show how both a chronic reduction over approximately 50 years of a Rattus exulans population caused by the arrival of its competitor R. rattus, and an acute reduction in a R. rattus population caused by a failed eradication approximately 10 years ago, caused similar magnitudes of genetic diversity loss. Furthermore, these strong bottleneck signals were in addition to the lasting signal from initial colonisation by each species many decades to centuries earlier, characterising a genetic paradox of biological invasion. These findings have implications for the study of population genetics of invasive species, and underscore how important historical context of population dynamics is when interpreting snapshots of genetic diversity.
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Global protected areas seem insufficient to safeguard half of the world's mammals from human-induced extinction. Proc Natl Acad Sci U S A 2022; 119:e2200118119. [PMID: 35666869 PMCID: PMC9214487 DOI: 10.1073/pnas.2200118119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protected areas are vital for conserving global biodiversity, but we lack information on the extent to which the current global protected area network is able to prevent local extinctions. Here we investigate this by assessing the potential size of individual populations of nearly 4,000 terrestrial mammals within protected areas. We find that many existing protected areas are too small or too poorly connected to provide robust and resilient protection for almost all mammal species that are threatened with extinction and for over 1,000 species that are not currently threatened. These results highlight that global biodiversity targets must reflect ecological realities by incorporating spatial structure and estimates of population viability, rather than relying simply on the total area of land protected. Protected areas (PAs) are a cornerstone of global conservation and central to international plans to minimize global extinctions. During the coming century, global ecosystem destruction and fragmentation associated with increased human population and economic activity could make the long-term survival of most terrestrial vertebrates even more dependent on PAs. However, the capacity of the current global PA network to sustain species for the long term is unknown. Here, we explore this question for all nonvolant terrestrial mammals for which we found sufficient data, ∼4,000 species. We first estimate the potential population size of each such mammal species in each PA and then use three different criteria to estimate if solely the current global network of PAs might be sufficient for their long-term survival. Our analyses suggest that current PAs may fail to provide robust protection for about half the species analyzed, including most species currently listed as threatened with extinction and a third of species not currently listed as threatened. Hundreds of mammal species appear to have no viable protected populations. Underprotected species were found across all body sizes, taxonomic groups, and geographic regions. Large-bodied mammals, endemic species, and those in high-biodiversity tropical regions were particularly poorly protected by existing PAs. As new international biodiversity targets are formulated, our results suggest that the global network of PAs must be greatly expanded and most importantly that PAs must be located in diverse regions that encompass species not currently protected and must be large enough to ensure that protected species can persist for the long term.
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Tanaka MM, Wahl LM. Surviving environmental change: when increasing population size can increase extinction risk. Proc Biol Sci 2022; 289:20220439. [PMID: 35642362 PMCID: PMC9156903 DOI: 10.1098/rspb.2022.0439] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Populations threatened by an abrupt environmental change-due to rapid climate change, pathogens or invasive competitors-may survive if they possess or generate genetic combinations adapted to the novel, challenging condition. If these genotypes are initially rare or non-existent, the emergence of lineages that allow a declining population to survive is known as 'evolutionary rescue'. By contrast, the genotypes required for survival could, by chance, be common before the environmental change. Here, considering both of these possibilities, we find that the risk of extinction can be lower in very small or very large populations, but peaks at intermediate population sizes. This pattern occurs when the survival genotype has a small deleterious effect before the environmental change. Since mildly deleterious mutations constitute a large fraction of empirically measured fitness effects, we suggest that this unexpected result-an intermediate size that puts a population at a greater risk of extinction-may not be unusual in the face of environmental change.
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Affiliation(s)
- Mark M. Tanaka
- University of New South Wales, Sydney, NSW 2052, Australia
| | - Lindi M. Wahl
- Western University, London, Ontario, Canada, N6A 5B7
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Genetic diversity and structure of an endangered medicinal plant species (Pilocarpus microphyllus) in eastern Amazon: implications for conservation. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01454-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Bérces S, Fülöp D, Samu F. Life history adaptations of Carabus populations in a suburban park: A capture-recapture case study. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Andrello M, D'Aloia C, Dalongeville A, Escalante MA, Guerrero J, Perrier C, Torres-Florez JP, Xuereb A, Manel S. Evolving spatial conservation prioritization with intraspecific genetic data. Trends Ecol Evol 2022; 37:553-564. [PMID: 35450706 DOI: 10.1016/j.tree.2022.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022]
Abstract
Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change.
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Affiliation(s)
- Marco Andrello
- Institute for the study of Anthropic impacts and Sustainability in the marine environment, National Research Council, CNR-IAS, Rome, Italy.
| | - Cassidy D'Aloia
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | | | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jimena Guerrero
- Sociedad Científica de Investigación Transdisciplinaria y Especialización (SCITE), Calimaya, México
| | - Charles Perrier
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade, Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Santos, Brazil
| | - Amanda Xuereb
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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Lee JH, Ong HG, Kim BY, Kim YI, Jung EK, Chung MG, Kim YD. Population genomics study for the conservation management of the endangered shrub Abeliophyllum distichum. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01447-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractNatural monuments are IUCN Category III protected areas that play an important role in biodiversity conservation as they provide species refuge and allow species migration. Despite their status, natural monuments are often confined to cultural and fragmented landscapes due to anthropogenic land-use demands. In this population genomic study, we surveyed 11 populations of the endemic shrub Abeliophyllum distichum Nakai (Oleaceae), including five natural monument habitats, covering its range-wide distribution in South Korea. Using 2,254 SNPs as markers, our results showed a mean expected heterozygosity (He) of 0.319, with populations in the central distribution showing significantly higher He than those at the periphery. There was no significant heterozygote deficiency and inbreeding among studied populations overall (FIS = −0.098), except for a single natural monument population (GS-NM147). Population structure and differentiation was moderate to high (FST = 0.196), while recent gene flow between populations appeared weak, which can be attributed to the fragmented distribution and the outcrossing mating system of the heterostylous plant. Based on these findings, we provide suggestions for the population conservation and management of this endangered species.
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Shafer CL. A greater yellowstone ecosystem grizzly bear case study: genetic reassessment for managers. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractThere are five grizzly bear (Ursus arctos horribilis) populations in the lower 48 states of the United States. My goal in this Commentary was to ascertain whether genetic diversity is being lost from the isolated GYE grizzly bear population and to better understand any viability implications. I reviewed the scientific literature, including two key genetic studies that the US Fish and Wildlife Service (USFWS) relied upon for their 2007 and current 2017 GYE grizzly bear genetics policy. I discovered that some studies reveal a loss of heterozygosity in the GYE bear population, both historically and in recent decades. Some had a statistically significant depletion rate. My review took place periodically between 2010 and 2021 and indicates that the genome of the GYE grizzly bear population is too small for long-term adaptation. The paper includes a discussion about evolutionary adaptation which invokes time frames rarely considered by nature conservation planners. I also examined genetic statements in the USFWS’s 2017 GYE grizzly bear delisting regulations and highlighted those that seem incongruent with current scientific thought. If this paper is read by some scientists, land managers, administrators, environmentalists, and others with some genetics background, they will better understand some USFWS decisions and policy statements. This case study illustrates that land management agencies can provide a one-sided treatment of some science when writing regulations about genetics.
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Hoban S, Archer FI, Bertola LD, Bragg JG, Breed MF, Bruford MW, Coleman MA, Ekblom R, Funk WC, Grueber CE, Hand BK, Jaffé R, Jensen E, Johnson JS, Kershaw F, Liggins L, MacDonald AJ, Mergeay J, Miller JM, Muller-Karger F, O'Brien D, Paz-Vinas I, Potter KM, Razgour O, Vernesi C, Hunter ME. Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition. Biol Rev Camb Philos Soc 2022; 97:1511-1538. [PMID: 35415952 PMCID: PMC9545166 DOI: 10.1111/brv.12852] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
Abstract
Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (Ne). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.
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Affiliation(s)
- Sean Hoban
- Center for Tree Science, The Morton Arboretum, 4100 Illinois Rt 53, Lisle, IL, 60532, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, NOAA/NMFS, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Laura D Bertola
- City College of New York, 160 Convent Avenue, New York, NY, 10031, USA
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, University Drive, Bedford Park, SA, 5042, Australia
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, Wales, UK
| | - Melinda A Coleman
- Department of Primary Industries, New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, Blekholmsterrassen 36, Stockholm, SE-106 48, Sweden
| | - W Chris Funk
- Department of Biology, Graduate Degree in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523-1878, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Carslaw Building, Sydney, NSW, 2006, Australia
| | - Brian K Hand
- Flathead Lake Biological Station, 32125 Bio Station Ln, Polson, MT, 59860, USA
| | - Rodolfo Jaffé
- Exponent, 15375 SE 30th Place, Suite 250, Bellevue, WA, 98007, USA
| | - Evelyn Jensen
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, Newcastle Upon Tyne, NE1 7RU, UK
| | - Jeremy S Johnson
- Department of Environmental Studies, Prescott College, 220 Grove Avenue, Prescott, AZ, 86303, USA
| | - Francine Kershaw
- Natural Resources Defense Council, 40 West 20th Street, New York, NY, 10011, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Ōtehā Rohe campus, Gate 4 Albany Highway, Auckland, Aotearoa, 0745, New Zealand
| | - Anna J MacDonald
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium.,Aquatic Ecology, Evolution and Conservation, KULeuven, Charles Deberiotstraat 32, box 2439, 3000, Leuven, Belgium
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, 10700 104 Avenue, Edmonton, AB, T5J 4S2, Canada
| | - Frank Muller-Karger
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, Florida, 33701, USA
| | - David O'Brien
- NatureScot, Great Glen House, Leachkin Road, Inverness, IV3 8NW, UK
| | - Ivan Paz-Vinas
- Laboratoire Evolution et Diversité Biologique, Université de Toulouse, CNRS, IRD, UPS, UMR-5174 EDB, 118 route de Narbonne, Toulouse, 31062, France
| | - Kevin M Potter
- Department of Forestry and Environmental Resources, North Carolina State University, 3041 Cornwallis Road, Research Triangle Park, NC, 27709, USA
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK
| | - Cristiano Vernesi
- Forest Ecology Unit, Research and Innovation Centre- Fondazione Edmund Mach, Via E. Mach, 1, San Michele all'Adige, 38010, (TN), Italy
| | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
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Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations. Heredity (Edinb) 2022; 128:364-376. [PMID: 35246618 PMCID: PMC9076905 DOI: 10.1038/s41437-022-00515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (~1000 ind.), suggesting that the evolutionary potential of the species is not assured.
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Demographic and Evolutionary History of Pallid and Shovelnose Sturgeon in the Upper Missouri River. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2022. [DOI: 10.3996/jfwm-21-035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Natural-origin pallid sturgeon Scaphirhynchus albus in the upper Missouri River are predicted to become extirpated as early as 2024. To aid in recovery efforts for this endangered species, we used genetic data from 17 microsatellite loci to infer demographic and evolutionary history of pallid sturgeon and a sympatric shovelnose sturgeon S. platorynchus . A recent sundering of geneflow between these species was indicated by overlapping allele size distributions at all loci and low level of genetic divergence ( F ST = 0.10). Tests for recent bottlenecks, using heterozygosity excess or allele frequency mode-shift tests indicated demographic stability for both species while the M-Ratio identified historic bottlenecks had occurred in both species. Estimates of historical effective population size ( N e ), based on coalescent modeling of allele size distribution, suggested the geographic expansion of these species into the upper Missouri River during the late Pleistocene was associated with 10 to 19 fold reductions in N e . In contrast estimates of contemporary estimates of N e based on linkage disequilibrium revealed that shovelnose sturgeon ( N e = 2983) had approximately 10 times greater N e than pallid sturgeon ( N e = 254). Our results are consistent with the recent collapse of pallid sturgeon being caused by dam construction which occurred between 1930 and 1965. Fortunately, genetic diversity remaining in this long-lived species has provided an opportunity to conserve pre-dam pallid sturgeon genetic diversity via a successful captive breeding program. We provide recommendations to address key conservation needs including how to incorporate our estimate of N e / adult census size of 0.26 (95% CI: 0.16 – 0.47) into setting demographic recovery goals for pallid sturgeon.
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Mularo AJ, Bernal XE, DeWoody JA. Dominance can increase genetic variance after a population bottleneck: a synthesis of the theoretical and empirical evidence. J Hered 2022; 113:257-271. [PMID: 35143665 DOI: 10.1093/jhered/esac007] [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: 09/26/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on two theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.
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Affiliation(s)
- Andrew J Mularo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ximena E Bernal
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
| | - J Andrew DeWoody
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
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Wahl LM, Tanaka MM. Hazardous Loss of Genetic Diversity through Selective Sweeps in Asexual Populations. Am Nat 2022; 199:313-329. [DOI: 10.1086/717813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | - Mark M. Tanaka
- School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, University of New South Wales, Sydney, Australia
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Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes. FISHES 2021. [DOI: 10.3390/fishes6040078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This study evaluates the genetic diversity of different meagre broodstocks sampled in Greece. A multiplex of twelve microsatellite markers was used to genotype 946 fish from eleven stocks and batches used for broodstock selection, and the genetic data was used to calculate genetic population parameters as well as to investigate the genetic differentiation between stocks. The results from a relatedness analysis were used as the guiding lines for a fine-tuned and overall evaluation of the genetic distance between stocks, and the choice of candidate breeders from some of them. The approach implemented in this study uses well-established population genetics methods to evaluate the selection of breeder candidates in aquaculture commercial conditions utilizing a descriptive genetic data set based on microsatellite analyses, and to outline an efficient methodology for establishing the basis of new breeding schemes.
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Khan A, Patel K, Shukla H, Viswanathan A, van der Valk T, Borthakur U, Nigam P, Zachariah A, Jhala YV, Kardos M, Ramakrishnan U. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proc Natl Acad Sci U S A 2021; 118:e2023018118. [PMID: 34848534 PMCID: PMC8670471 DOI: 10.1073/pnas.2023018118] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 01/03/2023] Open
Abstract
Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.
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Affiliation(s)
- Anubhab Khan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | - Kaushalkumar Patel
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Harsh Shukla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ashwin Viswanathan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Nature Conservation Foundation, Mysore 570017, India
| | | | | | - Parag Nigam
- Wildlife Institute of India, Dehradun 248001, India
| | | | | | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112;
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
- Department of Biotechnology-Wellcome Trust India Alliance, Hyderabad 500034, India
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Ledoux J, Ghanem R, Horaud M, López‐Sendino P, Romero‐Soriano V, Antunes A, Bensoussan N, Gómez‐Gras D, Linares C, Machordom A, Ocaña O, Templado J, Leblois R, Ben Souissi J, Garrabou J. Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jean‐Baptiste Ledoux
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Institut de Ciències del Mar CSIC Barcelona Spain
| | - Raouia Ghanem
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
| | | | | | | | - Agostinho Antunes
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | | | | | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals Institut de Recerca de la Biodiversitat (IRBIO) Universitat de Barcelona Barcelona Spain
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Oscar Ocaña
- Departamento de Oceanografía Biológica y Biodiversidad Fundación Museo del Mar de Ceuta Ceuta Spain
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Raphaêl Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
| | - Jamila Ben Souissi
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
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López-Cortegano E, Moreno E, García-Dorado A. Genetic purging in captive endangered ungulates with extremely low effective population sizes. Heredity (Edinb) 2021; 127:433-442. [PMID: 34584227 PMCID: PMC8551332 DOI: 10.1038/s41437-021-00473-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 02/07/2023] Open
Abstract
Inbreeding threatens the survival of small populations by producing inbreeding depression, but also exposes recessive deleterious effects in homozygosis allowing for genetic purging. Using inbreeding-purging theory, we analyze early survival in four pedigreed captive breeding programs of endangered ungulates where population growth was prioritized so that most adult females were allowed to contribute offspring according to their fitness. We find evidence that purging can substantially reduce inbreeding depression in Gazella cuvieri (with effective population size Ne = 14) and Nanger dama (Ne = 11). No purging is detected in Ammotragus lervia (Ne = 4), in agreement with the notion that drift overcomes purging under fast inbreeding, nor in G. dorcas (Ne = 39) where, due to the larger population size, purging is slower and detection is expected to require more generations. Thus, although smaller populations are always expected to show smaller fitness (as well as less adaptive potential) than larger ones due to higher homozygosis and deleterious fixation, our results show that a substantial fraction of their inbreeding load and inbreeding depression can be purged when breeding contributions are governed by natural selection. Since management strategies intended to maximize the ratio from the effective to the actual population size tend to reduce purging, the search for a compromise between these strategies and purging could be beneficial in the long term. This could be achieved either by allowing some level of random mating and some role of natural selection in determining breeding contributions, or by undertaking reintroductions into the wild at the earliest opportunity.
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Affiliation(s)
- Eugenio López-Cortegano
- grid.4305.20000 0004 1936 7988Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, UK
| | - Eulalia Moreno
- grid.466639.80000 0004 0547 1725Estación Experimental de Zonas Áridas (CSIC), 04120 Almería, Spain
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Dalapicolla J, Alves R, Jaffé R, Vasconcelos S, Pires ES, Nunes GL, Pereira JBDS, Guimarães JTF, Dias MC, Fernandes TN, Scherer D, dos Santos FMG, Castilho A, Santos MP, Calderón EN, Martins RL, da Fonseca RN, Esteves FDA, Caldeira CF, Oliveira G. Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon. Ecol Evol 2021; 11:10119-10132. [PMID: 34367563 PMCID: PMC8328431 DOI: 10.1002/ece3.7812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
The quillwort Isoëtes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (N e) are expected for narrow endemic species (NES). Conservation biology studies centered in a single species show some limitations, but they are still useful considering the limited time and resources available for protection of species at risk of extinction. Here, we evaluated the genetic diversity, population structure, N e, and minimum viable population (MVP) of I. cangae to provide information for effective conservation programs. Our analyses were based on 55 individuals collected from the Amendoim Lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and N e in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential and that all individuals should be treated as one demographic unit. These results provide essential information to optimize ex situ conservation efforts and genetic diversity monitoring, which are currently applied to guide I. cangae conservation plans.
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Affiliation(s)
| | | | - Rodolfo Jaffé
- Instituto Tecnológico ValeBelémBrazil
- ExponentBellevueWAUSA
| | | | | | | | | | | | - Mariana C. Dias
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Daniela Scherer
- VALE S/AGerência de Estudos AmbientaisLicenciamento e EspeleologiaNova LimaBrazil
| | | | - Alexandre Castilho
- VALE S/AGerência de Estudos AmbientaisLicenciamento e EspeleologiaNova LimaBrazil
| | - Mirella Pupo Santos
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Emiliano Nicolas Calderón
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Rodrigo Lemes Martins
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Rodrigo Nunes da Fonseca
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
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Conroy GC, Lamont RW, Bridges L, Stephens D, Wardell-Johnson A, Ogbourne SM. Conservation concerns associated with low genetic diversity for K'gari-Fraser Island dingoes. Sci Rep 2021; 11:9503. [PMID: 33947920 PMCID: PMC8097078 DOI: 10.1038/s41598-021-89056-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
The dingo population on world heritage-listed K'gari-Fraser Island (K'gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K'gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K'gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.
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Affiliation(s)
- G C Conroy
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia. .,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
| | - R W Lamont
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - L Bridges
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - D Stephens
- Zoological Genetics, Inglewood, Adelaide, SA, 5133, Australia
| | - A Wardell-Johnson
- Senior Professional Fellow, Curtin University, Bentley, WA, Australia
| | - S M Ogbourne
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
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Giglio RM, Rocke TE, Osorio JE, Latch EK. Characterizing patterns of genomic variation in the threatened Utah prairie dog: Implications for conservation and management. Evol Appl 2021; 14:1036-1051. [PMID: 33897819 PMCID: PMC8061279 DOI: 10.1111/eva.13179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/30/2022] Open
Abstract
Utah prairie dogs (Cynomys parvidens) are federally threatened due to eradication campaigns, habitat destruction, and outbreaks of plague. Today, Utah prairie dogs exist in small, isolated populations, making them less demographically stable and more susceptible to erosion of genetic variation by genetic drift. We characterized patterns of genetic structure at neutral and putatively adaptive loci in order to evaluate the relative effects of genetic drift and local adaptation on population divergence. We sampled individuals across the Utah prairie dog species range and generated 2955 single nucleotide polymorphisms using double digest restriction site-associated DNA sequencing. Genetic diversity was lower in low-elevation sites compared to high-elevation sites. Population divergence was high among sites and followed an isolation-by-distance model. Our results indicate that genetic drift plays a substantial role in the population divergence of the Utah prairie dog, and colonies would likely benefit from translocation of individuals between recovery units, which are characterized by distinct elevations, despite the detection of environmental associations with outlier loci. By understanding the processes that shape genetic structure, better informed decisions can be made with respect to the management of threatened species to ensure that adaptation is not stymied.
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Affiliation(s)
- Rachael M. Giglio
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
| | | | - Jorge E. Osorio
- Department of Pathobiological SciencesSchool of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Emily K. Latch
- Department of Biological SciencesUniversity of Wisconsin‐MilwaukeeMilwaukeeWIUSA
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O’Reilly C, Turner P, O’Mahony DT, Twining JP, Tosh DG, Smal C, McAney K, Powell C, Power J, O’Meara DB. Not out of the woods yet: genetic insights related to the recovery of the pine marten (Martes martes) in Ireland. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
In this study, the history of the pine marten (Martes martes) in Ireland is reviewed, revealing that the population has undergone several retractions and expansions over the last few hundred years. Here, we consider the genetic legacy of this flux in fortunes and its likely impacts upon the conservation and future recovery of the species. Using nuclear DNA markers (microsatellites), we found that the genetic diversity present in Ireland today is like that of other Irish carnivores, but there is evidence of a genetic bottleneck and low effective population size that might result in further reductions of diversity in the future. There is a lack of genetic structure, showing that the population has not been fragmented genetically, despite the low percentage of woodland in Ireland. We also reviewed the mitochondrial DNA diversity present in the Irish population and showed that there is only one contemporary and one extinct haplotype present; a reduced diversity relative to other Irish carnivores. The Irish haplotypes, both extant and extinct, are shared or are genetically similar to haplotypes commonly present in southern Europe today. We discuss the possibility of reinforcing the Irish population with animals from these sources to help supplement and maintain genetic diversity for future generations.
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Affiliation(s)
- Catherine O’Reilly
- Molecular Ecology Research Group, Eco-innovation Research Centre, School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
| | - Peter Turner
- Molecular Ecology Research Group, Eco-innovation Research Centre, School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
| | | | - Joshua P Twining
- School of Biological Sciences, Queen’s University of Belfast, Belfast, Northern Ireland, UK
| | - David G Tosh
- National Museums Northern Ireland, Northern Ireland, UK
| | - Christopher Smal
- Ecological Solutions, Rathdown Upper, Greystones, County Wicklow, Ireland
| | - Kate McAney
- Vincent Wildlife Trust, Donaghpatrick, Headford, County Galway, Ireland
| | - Ciara Powell
- Molecular Ecology Research Group, Eco-innovation Research Centre, School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
| | - John Power
- Molecular Ecology Research Group, Eco-innovation Research Centre, School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
| | - Denise B O’Meara
- Molecular Ecology Research Group, Eco-innovation Research Centre, School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
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