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Hoffman JI, Vendrami DLJ, Hench K, Chen RS, Stoffel MA, Kardos M, Amos W, Kalinowski J, Rickert D, Köhrer K, Wachtmeister T, Goebel ME, Bonin CA, Gulland FMD, Dasmahapatra KK. Genomic and fitness consequences of a near-extinction event in the northern elephant seal. Nat Ecol Evol 2024:10.1038/s41559-024-02533-2. [PMID: 39333394 DOI: 10.1038/s41559-024-02533-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/07/2024] [Indexed: 09/29/2024]
Abstract
Understanding the genetic and fitness consequences of anthropogenic bottlenecks is crucial for biodiversity conservation. However, studies of bottlenecked populations combining genomic approaches with fitness data are rare. Theory predicts that severe bottlenecks deplete genetic diversity, exacerbate inbreeding depression and decrease population viability. However, actual outcomes are complex and depend on how a species' unique demography affects its genetic load. We used population genetic and veterinary pathology data, demographic modelling, whole-genome resequencing and forward genetic simulations to investigate the genomic and fitness consequences of a near-extinction event in the northern elephant seal. We found no evidence of inbreeding depression within the contemporary population for key fitness components, including body mass, blubber thickness and susceptibility to parasites and disease. However, we detected a genomic signature of a recent extreme bottleneck (effective population size = 6; 95% confidence interval = 5.0-7.5) that will have purged much of the genetic load, potentially leading to the lack of observed inbreeding depression in our study. Our results further suggest that deleterious genetic variation strongly impacted the post-bottleneck population dynamics of the northern elephant seal. Our study provides comprehensive empirical insights into the intricate dynamics underlying species-specific responses to anthropogenic bottlenecks.
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Affiliation(s)
- Joseph I Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- British Antarctic Survey, Cambridge, UK.
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany.
| | - David L J Vendrami
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
| | - Kosmas Hench
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Rebecca S Chen
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Department of Animal Behaviour, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Martin A Stoffel
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Alan Turing Institute, British Library, London, UK
| | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - William Amos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jörn Kalinowski
- Department of Microbial Genomics and Biotechnology, CeBiTec, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Daniel Rickert
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Karl Köhrer
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Thorsten Wachtmeister
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Mike E Goebel
- Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Carolina A Bonin
- Department of Marine and Environmental Sciences, Hampton University, Hampton, VA, USA
| | - Frances M D Gulland
- Karen C. Drayer Wildlife Health Center, University of California, Davis, Davis, CA, USA
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2
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Crossman CA, Hamilton PK, Brown MW, Conger LA, George RC, Jackson KA, Radvan SN, Frasier TR. Effects of inbreeding on reproductive success in endangered North Atlantic right whales. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240490. [PMID: 39086821 PMCID: PMC11289666 DOI: 10.1098/rsos.240490] [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: 03/25/2024] [Accepted: 05/24/2024] [Indexed: 08/02/2024]
Abstract
Only approximately 356 North Atlantic right whales (Eubalaena glacialis) remain. With extremely low levels of genetic diversity, limited options for mates, and variation in reproductive success across females, there is concern regarding the potential for genetic limitations of population growth from inbreeding depression. In this study, we quantified reproductive success of female North Atlantic right whales with a modified de-lifing approach using reproductive history information collected over decades of field observations. We used double-digest restriction site-associated sequencing to sequence approximately 2% of the genome of 105 female North Atlantic right whales and combined genomic inbreeding estimates with individual fecundity values to assess evidence of inbreeding depression. Inbreeding depression could not explain the variance in reproductive success of females, however we present evidence that inbreeding depression may be affecting the viability of inbred fetuses-potentially lowering the reproductive success of the species as a whole. Combined, these results allay some concerns that genetic factors are impacting species survival as genetic diversity is being retained through selection against inbred fetuses. While still far fewer calves are being born each year than expected, the small role of genetics underlying variance in female fecundity suggests that variance may be explained by external factors that can potentially be mitigated through protection measures designed to reduce serious injury and mortality from human activities.
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Affiliation(s)
- Carla A. Crossman
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Philip K. Hamilton
- Anderson Cabot Center for Ocean Life, New England Aquarium, Central Wharf, Boston, Massachusetts, USA
| | - Moira W. Brown
- Canadian Whale Institute, Welshpool, New Brunswick, Canada
| | - Lisa A. Conger
- NOAA Fisheries, Northeast Fisheries Science Center, Woods Hole, MA, USA
| | - R. Clay George
- Georgia Department of Natural Resources, Wildlife Conservation Section, Brunswick, GA, USA
| | - Katharine A. Jackson
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Saint Petersburg, FL, USA
| | - Sonya N. Radvan
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
| | - Timothy R. Frasier
- Biology Department, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3
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3
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Valladares MA, Fabres AA, Sánchez-Rodríguez F, Collado GA, Méndez MA. Population structure and microscale morphological differentiation in a freshwater snail from the Chilean Altiplano. BMC Ecol Evol 2024; 24:5. [PMID: 38184553 PMCID: PMC10770964 DOI: 10.1186/s12862-023-02196-w] [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: 04/20/2023] [Accepted: 12/26/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND The diversity and population genetic structure of many species have been shaped by historical and contemporary climatic changes. For the species of the South American Altiplano, the historical climatic changes are mainly related to the wet events of great magnitude and regional influence that occurred during the Pleistocene climatic oscillations (PCOs). In contrast, contemporary climate changes are associated with events of lesser magnitude and local influence related to intensifications of the South American Summer Monsoon (SASM). Although multiple studies have analyzed the effect of PCOs on the genetic patterns of highland aquatic species, little is known about the impact of contemporary climate changes in recent evolutionary history. Therefore, in this study, we investigated the change in population structure and connectivity using nuclear and mitochondrial markers throughout the distribution range of Heleobia ascotanensis, a freshwater Cochliopidae endemic to the Ascotán Saltpan. In addition, using geometric morphometric analyses, we evaluated the concomitance of genetic divergence and morphological differentiation. RESULTS The mitochondrial sequence analysis results revealed the presence of highly divergent co-distributed and geographically nested haplotypes. This pattern reflects an extension in the distribution of groups that previously would have differentiated allopatrically. These changes in distribution would have covered the entire saltpan and would be associated with the large-scale wet events of the PCOs. On the other hand, the microsatellite results defined five spatially isolated populations, separated primarily by geographic barriers. Contemporary gene flow analyses suggest that post-PCO, climatic events that would have connected all populations did not occur. The morphometric analyses results indicate that there is significant morphological differentiation in the populations that are more isolated and that present the greatest genetic divergence. CONCLUSIONS The contemporary population structure and morphological variation of H. ascotanensis mainly reflect the post-PCO climatic influence. Although both markers exhibit high genetic structuring, the microsatellite and morphology results show the preponderant influence of fragmentation in recent evolutionary history. The contemporary genetic pattern shows that in species that have limited dispersal capabilities, genetic discontinuities can appear rapidly, erasing signs of historical connectivity.
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Affiliation(s)
- Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alejandra A Fabres
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Fernanda Sánchez-Rodríguez
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Gonzalo A Collado
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
- Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Marco A Méndez
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Institute of Ecology and Biodiversity (IEB), Faculty of Sciences, University of Chile, Universidad de Chile, Santiago, Chile.
- Universidad de Magallanes, Puerto Williams, Chile.
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Haugen H, Dervo BK, Østbye K, Heggenes J, Devineau O, Linløkken A. Genetic diversity, gene flow, and landscape resistance in a pond-breeding amphibian in agricultural and natural forested landscapes in Norway. Evol Appl 2024; 17:e13633. [PMID: 38283603 PMCID: PMC10810167 DOI: 10.1111/eva.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/23/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024] Open
Abstract
Genetic diversity is a key part of biodiversity, threatened by human activities that lead to loss of gene flow and reduction of effective population sizes. Gene flow is a result of both landscape connectivity and demographic processes determining the number of dispersing individuals in space and time. Thus, the effect of human impact on processes determining the level of genetic diversity must be interpreted in the context of basic ecological conditions affecting survival and recruitment. When the intensity of human impact and habitat suitability correlate, the effect on genetic diversity and gene flow may be challenging to predict. We compared genetic diversity, gene flow and landscape resistance in two contrasting landscapes in Norway for the pond-breeding amphibian Triturus cristatus: a highly human-impacted, agricultural landscape with ecologically productive habitats, and a forested landscape with less productive habitats and lower levels of human impact. Our results show that genetic diversity was higher and gene flow lower within the forested landscape. Microclimatic moisture conditions and vegetation cover were important determinants of landscape resistance to gene flow within both landscapes. There were indications that landscape resistance was increased by minor roads in the forested landscape, which was not the case for the agricultural landscape, suggesting a higher vulnerability to human interference within the landscape matrix for the populations in less productive habitats. Our findings suggest that the effect of human impact on genetic diversity may not be straightforward but modulated by the ecological conditions underlying local demographic processes. Populations within both landscapes seem to be vulnerable to loss of genetic diversity, but due to different mechanisms. This has implications for the choice of relevant management actions, that is, increasing population stability may be more relevant within an agricultural landscape still permeable for dispersal, while conserving dispersal corridors may be more appropriate in the forested landscape, to avoid isolation and increased genetic drift.
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Affiliation(s)
- Hanne Haugen
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Børre K. Dervo
- Norwegian Institute for Nature Research (NINA)OsloNorway
| | - Kjartan Østbye
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
- Department of BiosciencesCenter for Ecological and Evolutionary Synthesis (CEES)University of OsloOsloNorway
| | - Jan Heggenes
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayUniversity of South‐Eastern NorwayNotoddenNorway
| | - Olivier Devineau
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
| | - Arne Linløkken
- Department of Forestry and Wildlife ManagementInland Norway University of Applied SciencesHamarNorway
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5
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Renoirt M, Angelier F, Cheron M, Brischoux F. What are the contributions of maternal and paternal traits to fecundity and offspring development? A case study in an amphibian species, the spined toad Bufo spinosus. Curr Zool 2023; 69:527-534. [PMID: 37637310 PMCID: PMC10449425 DOI: 10.1093/cz/zoac072] [Citation(s) in RCA: 1] [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: 03/31/2022] [Accepted: 08/25/2022] [Indexed: 08/29/2023] Open
Abstract
Assessing the determinants of reproductive success is critical but often complicated because of complex interactions between parental traits and environmental conditions occurring during several stages of a reproductive event. Here, we used a simplified ecological situation-an amphibian species lacking post-oviposition parental care-and a laboratory approach to investigate the relationships between parental (both maternal and paternal) phenotypes (body size and condition) and reproductive success (fecundity, egg size, embryonic and larval duration, larval and metamorphic morphology). We found significant effects of maternal phenotype on fecundity, hatching success, and tadpole size, as well as on the duration of larval development. Interestingly, and more surprisingly, we also found a potential contribution of the paternal phenotype occurring during early (embryonic development duration) offspring development. Although our study focused on life-history traits such as body size and development duration, additional mechanisms involving physiological costs of development may well mediate the relationships between parental phenotypes and offspring development. Future studies are required to decipher the mechanisms underlying our findings in order to clarify the mechanistic basis of the links between parental phenotypes and offspring development.
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Affiliation(s)
- Matthias Renoirt
- Centre d’Etudes Biologiques de Chizé, CEBC UMR 7372 CNRS-La Rochelle Université, 79360 Villiers en Bois, France
| | - Frédéric Angelier
- Centre d’Etudes Biologiques de Chizé, CEBC UMR 7372 CNRS-La Rochelle Université, 79360 Villiers en Bois, France
| | - Marion Cheron
- Centre d’Etudes Biologiques de Chizé, CEBC UMR 7372 CNRS-La Rochelle Université, 79360 Villiers en Bois, France
| | - François Brischoux
- Centre d’Etudes Biologiques de Chizé, CEBC UMR 7372 CNRS-La Rochelle Université, 79360 Villiers en Bois, France
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6
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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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Hudson DW, McKinley TJ, Benton CH, Delahay R, McDonald RA, Hodgson DJ. Multi-locus homozygosity promotes actuarial senescence in a wild mammal. J Anim Ecol 2023; 92:1881-1892. [PMID: 37427855 DOI: 10.1111/1365-2656.13979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/05/2023] [Indexed: 07/11/2023]
Abstract
Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value. Here we infer associations between multi-locus homozygosity (MLH), sex, disease and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers Meles meles in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis [bTB]). We find important effects of MLH on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later life. Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bTB. These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.
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Affiliation(s)
- Dave W Hudson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | | | - Clare H Benton
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Richard Delahay
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Robbie A McDonald
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Dave J Hodgson
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
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8
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Bererhi B, Duchesne P, Schwartz TS, Ujvari B, Wapstra E, Olsson M. Effect of MHC and inbreeding on disassortative reproduction: A data revisit, extension and inclusion of fertilization in sand lizards. Ecol Evol 2023; 13:e9934. [PMID: 36993149 PMCID: PMC10041550 DOI: 10.1002/ece3.9934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
The harmful effects of close inbreeding have been recognized for centuries and, with the rise of Mendelian genetics, was realized to be an effect of homozygosis. This historical background led to great interest in ways to quantify inbreeding, its depression effects on the phenotype and flow‐on effects on mate choice and other aspects of behavioral ecology. The mechanisms and cues used to avoid inbreeding are varied and include major histocompatibility complex (MHC) molecules and the peptides they transport as predictors of the degree of genetic relatedness. Here, we revisit and complement data from a Swedish population of sand lizards (Lacerta agilis) showing signs of inbreeding depression to assess the effects of genetic relatedness on pair formation in the wild. Parental pairs were less similar at the MHC than expected under random mating but mated at random with respect to microsatellite relatedness. MHC clustered in groups of RFLP bands but no partner preference was observed with respect to partner MHC cluster genotype. Male MHC band patterns were unrelated to their fertilization success in clutches selected for analysis on the basis of showing mixed paternity. Thus, our data suggest that MHC plays a role in pre‐copulatory, but not post‐copulatory partner association, suggesting that MHC is not the driver of fertilization bias and gamete recognition in sand lizards.
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Affiliation(s)
- Badreddine Bererhi
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | | | | | - Beata Ujvari
- School of Life and Environmental Sciences, Centre for Integrative EcologyDeakin UniversityWaurn PondsVictoriaAustralia
| | - Erik Wapstra
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Mats Olsson
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- School of Biological SciencesUniversity of WollongongWollongongNew South WalesAustralia
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9
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Hiillos AL, Rony I, Rueckert S, Knott KE. Coinfection patterns of two marine apicomplexans are not associated with genetic diversity of their polychaete host. J Eukaryot Microbiol 2023; 70:e12932. [PMID: 35711085 PMCID: PMC10084031 DOI: 10.1111/jeu.12932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/21/2022] [Accepted: 05/08/2022] [Indexed: 01/13/2023]
Abstract
Coinfections of two or more parasites within one host are more of a rule than an exception in nature. Interactions between coinfecting parasites can greatly affect their abundance and prevalence. Characteristics of the host, such as genetic diversity, can also affect the infection dynamics of coinfecting parasites. Here, we investigate for the first time the association of coinfection patterns of two marine apicomplexans, Rhytidocystis sp. and Selenidium pygospionis, with the genetic diversity of their host, the polychaete Pygospio elegans, from natural populations. Host genetic diversity was determined with seven microsatellite loci and summarized as allelic richness, inbreeding coefficient, and individual heterozygosity. We detected nonsignificant correlations between infection loads and both individual host heterozygosity and population genetic diversity. Prevalence and infection load of Rhytidocystis sp. were higher than those of S. pygospionis, and both varied spatially. Coinfections were common, and almost all hosts infected by S. pygospionis were also infected by Rhytidocystis sp. Rhytidocystis sp. infection load was significantly higher in dual infections. Our results suggest that factors other than host genetic diversity might be more important in marine apicomplexan infection patterns and experimental approaches would be needed to further determine how interactions between the apicomplexans and their host influence infection.
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Affiliation(s)
- Anna-Lotta Hiillos
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Irin Rony
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Sonja Rueckert
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK.,Centre for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK
| | - K Emily Knott
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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10
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Osborne MJ, Caeiro-Dias G, Turner TF. Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years. Mol Ecol 2023; 32:316-334. [PMID: 36321869 DOI: 10.1111/mec.16760] [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: 04/27/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022]
Abstract
Many long-term genetic monitoring programmes began before next-generation sequencing became widely available. Older programmes can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programmes should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
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11
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Cristescu RH, Strickland K, Schultz AJ, Kruuk LEB, de Villiers D, Frère CH. Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression. Mol Ecol 2022; 31:5455-5467. [PMID: 36043238 PMCID: PMC9826501 DOI: 10.1111/mec.16676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/11/2023]
Abstract
The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and, to date, we know little about the determinants of individual susceptibility to disease. Here, we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95% CI: 0.06-0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.
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Affiliation(s)
- Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
| | - Kasha Strickland
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Anthony J. Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia,Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Loeske E. B. Kruuk
- Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK,Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - Céline H. Frère
- School of Biological SciencesUniversity of QueenslandSt LuciaQueenslandAustralia
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12
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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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13
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Laseca N, Molina A, Ramón M, Valera M, Azcona F, Encina A, Demyda-Peyrás S. Fine-Scale Analysis of Runs of Homozygosity Islands Affecting Fertility in Mares. Front Vet Sci 2022; 9:754028. [PMID: 35252415 PMCID: PMC8891756 DOI: 10.3389/fvets.2022.754028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
The loss of genetic variability in livestock populations bred under strict selection processes is a growing concern, as it may lead to increased inbreeding values and lower fertility, as a consequence of the “inbreeding depression” effect. This is particularly important in horses, where inbreeding levels tend to rise as individuals become more and more closely related. In this study, we evaluated the effect of increased inbreeding levels on mare fertility by combining an SNP-based genomic approach using runs of homozygosity and the estimation of genetic breeding values for reproductive traits in a large population of Pura Raza Española mares. Our results showed a negative correlation between whole-genome homozygosity and fertility estimated breeding values (EBVs) at the genome level (ρ = −0.144). However, the analysis at chromosome level revealed a wide variability, with some chromosomes showing higher correlations than others. Interestingly, the correlation was stronger (−0.241) when we repeated the analysis in a reduced dataset including the 10% most and least fertile individuals, where the latter showed an increase in average inbreeding values (FROH) of around 30%. We also found 41 genomic regions (ROHi, runs of homozygosity islands) where homozygosity increased 100-fold, 13 of which were significantly associated with fertility after cross-validation. These regions encompassed 17 candidate genes previously related to oocyte and embryo development in several species. Overall, we demonstrated the relationship between increased homozygosis at the genomic level and fertility in mares. Our findings may help to deal with the occurrence of inbreeding depression, as well as further our understanding of the mechanisms underlying fertility in mares.
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Affiliation(s)
- Nora Laseca
- Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Molina
- Laboratorio de Diagnóstico Genético Veterinario, Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Manuel Ramón
- Cersyra de Valdepeñas, Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal Castilla La Mancha, Tomelloso, Spain
| | - Mercedes Valera
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
| | - Florencia Azcona
- IGEVET (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | - Ana Encina
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniería Agronómica, Universidad de Sevilla, Sevilla, Spain
- Asociación Nacional de Criadores de Caballos de Pura Raza Española, Sevilla, Spain
| | - Sebastián Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET LA PLATA), La Plata, Argentina
- *Correspondence: Sebastián Demyda-Peyrás
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14
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Richardson J, Smiseth PT. A behavioral ecology perspective on inbreeding and inbreeding depression. ADVANCES IN THE STUDY OF BEHAVIOR 2022. [DOI: 10.1016/bs.asb.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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Schultz AJ, Strickland K, Cristescu RH, Hanger J, de Villiers D, Frère CH. Testing the effectiveness of genetic monitoring using genetic non-invasive sampling. Ecol Evol 2022; 12:e8459. [PMID: 35127011 PMCID: PMC8794716 DOI: 10.1002/ece3.8459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/26/2021] [Accepted: 11/26/2021] [Indexed: 01/07/2023] Open
Abstract
Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling (gNIS) as a cost-effective population-wide genetic monitoring approach. gNIS has, however, known limitations which may impact the accuracy of downstream genetic analyses. Here, using high-quality single nucleotide polymorphism (SNP) data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures. We found that gNIS at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled. We show that gNIS at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.
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Affiliation(s)
- Anthony James Schultz
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Icelandic Museum of Natural History (Náttúruminjasafn Íslands)ReykjavikIceland
| | - Kasha Strickland
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- Department of Aquaculture and Fish BiologyHólar UniversityHólarIceland
| | - Romane H. Cristescu
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
| | | | | | - Céline H. Frère
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQldAustralia
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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16
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TARANG MITEK, KUMAR PUSHPENDRA, KUMAR AMIT, SAINI BL, KAUSHAL SHOBHANA, SACHAN SHWETA, CHAUHAN ANUJ, PRAKASH JAI, BHUSHAN BHARAT. Genetic characterization of F0 outbred and F1 inbred Swiss albino mice using microsatellite markers and their performance evaluation. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v91i3.114144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Swiss albino mice have been widely utilized in various biological researches worldwide. Phenotypic and fitness related traits of F0 and F1 inbred mice were estimated on 918 and 707 individual offsprings, respectively. The influence of fixed effects (litter size and sex) on birth weight (BW), weaning weight (WW) and adult body weight (ABW) in both the generations were found to be statistically significant. Genetic characterization of F0 outbred and the F1 inbred strain of Swiss albino mice were evaluated by using 10 microsatellites markers. The results indicated that total number of alleles per locus ranged from 3 (D2Mit61, D3Mit55, D8Mit14, D9Mit27, D10Mit180, D11Mit167) to 4 (D1Mit15, D2Mit51, D5Mit18, D7Mit323) in F0 and F1 inbred population, with a mean value of 3.4 indicating polymorphism in all 10 loci. The mean of effective number of alleles was 2.935 and 2.733 in F0 and F1 population, respectively. Estimates of the FIS ranged from 0.139 (D10Mit180) to 0.999 (D9Mit27); and from 0.109 (D3Mit55) to 0.679 (D2Mit51) in F0 and F1 inbred population, respectively. The estimated mean markerbased FIS was 0.294 and 0.372 in F0 and F1 populations, respectively. The mean values of observed heterozygosity (Ho) and expected heterozygosity (He) were 0.460 and 0.654, respectively for F0 and 0.390 and 0.627, respectively for F1 inbred mice population. Slight reduction in heterozygosity and 7.8% increase in inbreeding coefficient were observed in F1 inbred in comparison to F0 population. The results suggested that genome wide microsatellite genotyping might be more useful for accurate measuring and reliable estimation of population genetic parameters and inbreeding coefficient.
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17
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Gutiérrez J, Seguel M, Saenz‐Agudelo P, Acosta‐Jamett G, Verdugo C. Genetic diversity and kinship relationships in one of the largest South American fur seal (
Arctocephalus australis
) populations of the Pacific Ocean. Ecol Evol 2021. [DOI: 10.1002/ece3.7683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Josefina Gutiérrez
- Instituto de Patología Animal Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
- Programa de Investigación Aplicada a la Fauna Silvestre Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
| | - Mauricio Seguel
- Department of Pathobiology Ontario Veterinary College University of Guelph ON Canada
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y Evolutivas Facultad de Ciencias Universidad Austral de Chile Valdivia Chile
| | - Gerardo Acosta‐Jamett
- Programa de Investigación Aplicada a la Fauna Silvestre Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
- Instituto de Medicina Preventiva Veterinaria Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
| | - Claudio Verdugo
- Instituto de Patología Animal Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
- Programa de Investigación Aplicada a la Fauna Silvestre Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
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18
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DeWoody JA, Harder AM, Mathur S, Willoughby JR. The long-standing significance of genetic diversity in conservation. Mol Ecol 2021; 30:4147-4154. [PMID: 34191374 DOI: 10.1111/mec.16051] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/20/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
Since allozymes were first used to assess genetic diversity in the 1960s and 1970s, biologists have attempted to characterize gene pools and conserve the diversity observed in domestic crops, livestock, zoos and (more recently) natural populations. Recently, some authors have claimed that the importance of genetic diversity in conservation biology has been greatly overstated. Here, we argue that a voluminous literature indicates otherwise. We address four main points made by detractors of genetic diversity's role in conservation by using published literature to firmly establish that genetic diversity is intimately tied to evolutionary fitness, and that the associated demographic consequences are of paramount importance to many conservation efforts. We think that responsible management in the Anthropocene should, whenever possible, include the conservation of ecosystems, communities, populations and individuals, and their underlying genetic diversity.
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Affiliation(s)
- J Andrew DeWoody
- Department of Forestry and Natural Resources, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Avril M Harder
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, USA
| | - Samarth Mathur
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Janna R Willoughby
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama, USA
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19
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How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq. BMC Genom Data 2021; 22:22. [PMID: 34182923 PMCID: PMC8237422 DOI: 10.1186/s12863-021-00974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
Background Fitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers. Results Estimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations. Conclusions The results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00974-3.
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20
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Rönkä N, Pakanen VM, Pauliny A, Thomson RL, Nuotio K, Pehlak H, Thorup O, Lehikoinen P, Rönkä A, Blomqvist D, Koivula K, Kvist L. Genetic differentiation in an endangered and strongly philopatric, migrant shorebird. BMC Ecol Evol 2021; 21:125. [PMID: 34147062 PMCID: PMC8214799 DOI: 10.1186/s12862-021-01855-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background Populations living in fragmented habitats may suffer from loss of genetic variation and reduced between-patch dispersal, which are processes that can result in genetic differentiation. This occurs frequently in species with reduced mobility, whereas genetic differentiation is less common among mobile species such as migratory birds. The high dispersal capacity in the latter species usually allows for gene flow even in fragmented landscapes. However, strongly philopatric behaviour can reinforce relative isolation and the degree of genetic differentiation. The Southern Dunlin (Calidris alpina schinzii) is a philopatric, long-distance migratory shorebird and shows reduced dispersal between isolated breeding patches. The endangered population of the Southern Dunlin breeding at the Baltic Sea has suffered from habitat deterioration and fragmentation of coastal meadows. We sampled DNA across the entire population and used 12 polymorphic microsatellite loci to examine whether the environmental changes have resulted in genetic structuring and loss of variation. Results We found a pattern of isolation-by-distance across the whole Baltic population and genetic differentiation between local populations, even within the southern Baltic. Observed heterozygosity was lower than expected throughout the range and internal relatedness values were positive indicating inbreeding. Conclusions Our results provide long-term, empirical evidence for the theoretically expected links between habitat fragmentation, population subdivision, and gene flow. They also demonstrate a rare case of genetic differentiation between populations of a long-distance migratory species. The Baltic Southern Dunlin differs from many related shorebird species that show near panmixia, reflecting its philopatric life history and the reduced connectivity of its breeding patches. The results have important implications as they suggest that reduced connectivity of breeding habitats can threaten even long-distance migrants if they show strong philopatry during breeding. The Baltic Southern Dunlin warrants urgent conservation efforts that increase functional connectivity and gene flow between breeding areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01855-0.
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Affiliation(s)
- Nelli Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Veli-Matti Pakanen
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland.,Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Angela Pauliny
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Robert L Thomson
- Section of Ecology, Department of Biology, University of Turku, 20014, Turku, Finland.,Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kimmo Nuotio
- Environmental Agency, Valtakatu 11, 28100, Pori, Finland
| | - Hannes Pehlak
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia.,OÜ Xenus, Koguva, 94724, Muhu Island, Saare, Estonia
| | - Ole Thorup
- , V. Vedsted Byvej 32, Vester Vedsted, 6760, Ribe, Denmark
| | - Petteri Lehikoinen
- The Helsinki Lab of Ornithology, Finnish Museum of Natural History, University of Helsinki, 00014, Helsinki, Finland
| | - Antti Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Donald Blomqvist
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden.
| | - Kari Koivula
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
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21
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Dominguez JC, Calero-Riestra M, Olea PP, Malo JE, Burridge CP, Proft K, Illanas S, Viñuela J, García JT. Lack of detectable genetic isolation in the cyclic rodent Microtus arvalis despite large landscape fragmentation owing to transportation infrastructures. Sci Rep 2021; 11:12534. [PMID: 34131199 PMCID: PMC8206325 DOI: 10.1038/s41598-021-91824-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023] Open
Abstract
Although roads are widely seen as dispersal barriers, their genetic consequences for animals that experience large fluctuations in population density are poorly documented. We developed a spatially paired experimental design to assess the genetic impacts of roads on cyclic voles (Microtus arvalis) during a high-density phase in North-Western Spain. We compared genetic patterns from 15 paired plots bisected by three different barrier types, using linear mixed models and computing effect sizes to assess the importance of each type, and the influence of road features like width or the age of the infrastructure. Evidence of effects by roads on genetic diversity and differentiation were lacking. We speculate that the recurrent (each 3-5 generations) episodes of massive dispersal associated with population density peaks can homogenize populations and mitigate the possible genetic impact of landscape fragmentation by roads. This study highlights the importance of developing spatially replicated experimental designs that allow us to consider the large natural spatial variation in genetic parameters. More generally, these results contribute to our understanding of the not well explored effects of habitat fragmentation on dispersal in species showing "boom-bust" dynamics.
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Affiliation(s)
- Julio C Dominguez
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain.
| | - María Calero-Riestra
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Pedro P Olea
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Darwin 2, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049, Madrid, Spain
| | - Juan E Malo
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/Darwin 2, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, C. Darwin 2, 28049, Madrid, Spain
| | - Christopher P Burridge
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Kirstin Proft
- Discipline of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Sonia Illanas
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Javier Viñuela
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
| | - Jesús T García
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo, 12, 13071, Ciudad Real, Spain
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22
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Genomics for conservation: a case study of behavioral genes in the Tasmanian devil. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01354-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Sin SYW, Hoover BA, Nevitt GA, Edwards SV. Demographic History, Not Mating System, Explains Signatures of Inbreeding and Inbreeding Depression in a Large Outbred Population. Am Nat 2021; 197:658-676. [PMID: 33989142 DOI: 10.1086/714079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractInbreeding depression is often found in small, inbred populations, but whether it can be detected in and have evolutionary consequences for large, wide-ranging populations is poorly known. Here, we investigate the possibility of inbreeding in a large population to determine whether mild levels of inbreeding can still have genetic and phenotypic consequences and how genomically widespread these effects can be. We apply genome-wide methods to investigate whether individual and parental heterozygosity is related to morphological, growth, or life-history traits in a pelagic seabird, Leach's storm-petrel (Oceanodroma leucorhoa). Examining 560 individuals as part of a multiyear study, we found a substantial effect of maternal heterozygosity on chick traits: chicks from less heterozygous (relatively inbred) mothers were significantly smaller than chicks from more heterozygous (noninbred) mothers. We show that these heterozygosity-fitness correlations were due to general genome-wide effects and demonstrate a correlation between heterozygosity and inbreeding, suggesting inbreeding depression. We used population genetic models to further show that the variance in inbreeding was probably due to past demographic events rather than the current mating system and ongoing mate choice. Our findings demonstrate that inbreeding depression can be observed in large populations and illustrate how the integration of genomic techniques and fieldwork can elucidate its underlying causes.
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24
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Cheron M, Angelier F, Ribout C, Brischoux F. Clutch quality is related to embryonic development duration, hatchling body size and telomere length in the spined toad (Bufo spinosus). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Abstract
Reproductive success is often related to parental quality, a parameter expressed through various traits, such as site selection, mate selection and energetic investment in the eggs or progeny. Owing to the complex interactions between environmental and parental characteristics occurring at various stages of the reproductive event, it is often complicated to tease apart the relative contributions of these different factors to reproductive success. Study systems where these complex interactions are simplified (e.g. absence of parental care) can help us to understand how metrics of parental quality (e.g. gamete and egg quality) influence reproductive success. Using such a study system in a common garden experiment, we investigated the relationships between clutch hatching success (a proxy of clutch quality) and offspring quality in an amphibian species lacking post-oviposition parental care. We found a relationship between clutch quality and embryonic development duration and hatchling phenotype. We found that hatchling telomere length was linked to hatching success. These results suggest that clutch quality is linked to early life traits in larval amphibians and that deciphering the influence of parental traits on the patterns we detected is a promising avenue of research.
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Affiliation(s)
- Marion Cheron
- Centre d’Etudes Biologiques de Chizé, CEBC-CNRS UMR 7372, 79360 Villiers en Bois,France
| | - Frédéric Angelier
- Centre d’Etudes Biologiques de Chizé, CEBC-CNRS UMR 7372, 79360 Villiers en Bois,France
| | - Cécile Ribout
- Centre d’Etudes Biologiques de Chizé, CEBC-CNRS UMR 7372, 79360 Villiers en Bois,France
| | - François Brischoux
- Centre d’Etudes Biologiques de Chizé, CEBC-CNRS UMR 7372, 79360 Villiers en Bois,France
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Fan Q, E M, Wei Y, Sun W, Wang H. Mate Choice in Double-Breeding Female Great Tits ( Parus Major): Good Males or Compatible Males. Animals (Basel) 2021; 11:ani11010140. [PMID: 33440643 PMCID: PMC7826884 DOI: 10.3390/ani11010140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Double breeding is a common reproductive strategy among temperate passerines to increase annual fecundity. To produce two clutches in the same breeding season and to ensure offspring quality, choosing a good mate is important for females. Uncovering the method used in social mate choice for genetic benefits adopted by double-breeding females would provide a better understanding of the life history and rules of female choice. In the present study, we tested the effects of the date of the first egg of the first brood and of female quality on double breeding, and good genes and genetic compatibility hypotheses on mate choice for double breeding female great tits (Parus major) in a population breeding inside nest boxes of Zuojia Natural Reserve in northeast China. The date of the first egg of the first brood did not affect initiation of a second brood, and female individual heterozygosity slightly influenced initiation of a second breeding. Female great tits choose males with both compatible genes and good genes in double-breeding mating. Double-breeding females prefer males with large breast stripes, high heterozygosity, and lower relatedness. The number of offspring of the first clutch did not affect the pairing status of male great tits in double breeding. The genetic quality of offspring from double-breeding pairs was higher than that of those from single-breeding pairs (higher heterozygosity and lower individual F). Abstract Producing two broods within the same season may be a good strategy by which short-lived species can maximize reproductive success. To produce two clutches in the same breeding season and to ensure offspring quality, choosing a good mate is important for females. Previous studies on double breeding focused on the associated influencing factors, and few studies examined how females choose social mates. Good genes and genetic compatibility are the two main hypotheses of the genetic benefit that females obtain from choosing mates. Uncovering the method used in mate choice for genetic benefits adopted by double-breeding females would provide a better understanding of the life history and rules of female choice. The great tit is an optionally double-breeding species in temperate-latitude populations. Here, we used a dataset for a Chinese population monitored between 2014 and 2016 to test two hypotheses on double-breeding female mate choice. A total of 30.1% of the breeding pairs initiated second breeding attempts, always remating with the same mate. The date of the first egg of the first brood did not affect initiation of a second brood, and female individual heterozygosity slightly influenced initiation of a second breeding. Female great tits choose males with both compatible genes and good genes in double-breeding mating. Double-breeding females prefer males with large breast stripes, high heterozygosity, and lower relatedness, while tarsus length, repertoire size, and individual F are not the main factors considered by females when selecting males for double breeding. The number of offspring of the first clutch did not affect the pairing status of male great tits in double breeding. The genetic quality of offspring from double-breeding pairs was higher than that of those from single-breeding pairs (higher heterozygosity and lower individual F). Taken together, our results showed that double breeding female great tits adopt multiple methods for genetic benefits to choose mates.
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Affiliation(s)
- Qianxi Fan
- Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics, School of Life Sciences, Northeast Normal University, Renmin Street 5268, Changchun 130024, China; (Q.F.); (M.E); (Y.W.)
- Key Laboratory for Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Renmin Street 5268, Changchun 130024, China
| | - Mingju E
- Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics, School of Life Sciences, Northeast Normal University, Renmin Street 5268, Changchun 130024, China; (Q.F.); (M.E); (Y.W.)
- School of Life Sciences, Changchun Normal University, 677 Changjibei Road, Changchun 130032, China
| | - Yusheng Wei
- Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics, School of Life Sciences, Northeast Normal University, Renmin Street 5268, Changchun 130024, China; (Q.F.); (M.E); (Y.W.)
| | - Wei Sun
- Key Laboratory for Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Renmin Street 5268, Changchun 130024, China
- Correspondence: (W.S.); (H.W.)
| | - Haitao Wang
- Jilin Engineering Laboratory for Avian Ecology and Conservation Genetics, School of Life Sciences, Northeast Normal University, Renmin Street 5268, Changchun 130024, China; (Q.F.); (M.E); (Y.W.)
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, School of Life Sciences, Northeast Normal University, Renmin Street 5268, Changchun 130024, China
- Correspondence: (W.S.); (H.W.)
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Leftwich PT, Spurgin LG, Harvey-Samuel T, Thomas CJE, Paladino LC, Edgington MP, Alphey L. Genetic pest management and the background genetics of release strains. Philos Trans R Soc Lond B Biol Sci 2020; 376:20190805. [PMID: 33357053 DOI: 10.1098/rstb.2019.0805] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Genetic pest management (GPM) methods involve releasing modified versions of a pest species to mate with wild pests in the target area. Proposed for a wide range of applications in public health, agriculture and conservation, most progress has been made with pest insects. Offspring of the released modified insects and wild pests carry the modification-which might be transgenes, artificially introduced Wolbachia or genetic damage from radiation, for example-but they also carry a complete haploid genome from their laboratory-reared parent, as well as one from their wild parent. Unless these F1 hybrids are completely unable to reproduce, further mating will lead to introgression of DNA sequences from the release strain into the wild population. We discuss issues around strain selection and the potential consequences of such introgression. We conclude that such introgression is probably harmless in almost all circumstances, and could, in theory, provide specific additional benefits to the release programme. We outline population monitoring approaches that could be used, going forward, to determine how background genetics may affect GPM. This article is part of the theme issue 'Novel control strategies for mosquito-borne diseases'.
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Affiliation(s)
- Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK
| | | | | | | | | | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright GU24 0NF, UK
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Sams AJ, Ford B, Gardner A, Boyko AR. Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations. Evol Appl 2020; 13:2555-2565. [PMID: 33294008 PMCID: PMC7691451 DOI: 10.1111/eva.13038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 11/30/2022] Open
Abstract
In many ways, dogs are an ideal model for the study of genetic erosion and population recovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning of the 1800s, when modern breeding practices came into fashion. As such, inbreeding in domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression. Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panels are also used in some cases to choose mating pairs to produce litters with low levels of inbreeding. However, the long-term impact of such practices has not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genome to examine the impact of using limited marker panels to guide pairwise mating decisions on genome-wide population-level genetic diversity. Our results suggest that in unmanaged populations, where breeding decisions are made at the pairwise-rather than population-level, such panels can lead to accelerated loss of genetic diversity at genome regions unlinked to panel markers, compared to random mating. These results demonstrate the importance of genome-wide genetic panels for managing and conserving genetic diversity in dogs and other companion animals.
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Affiliation(s)
| | - Brett Ford
- Embark Veterinary, IncorporatedBostonMAUSA
| | | | - Adam R. Boyko
- Embark Veterinary, IncorporatedBostonMAUSA
- Department of Biomedical SciencesCollege of Veterinary MedicineCornell UniversityIthacaNYUSA
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Pei 裴一凡 Y, Forstmeier W, Wang 王代平 D, Martin K, Rutkowska J, Kempenaers B. Proximate Causes of Infertility and Embryo Mortality in Captive Zebra Finches. Am Nat 2020; 196:577-596. [PMID: 33064590 DOI: 10.1086/710956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSome species show high rates of reproductive failure, which is puzzling because natural selection works against such failure in every generation. Hatching failure is common in both captive and wild zebra finches (Taeniopygia guttata), yet little is known about its proximate causes. Here we analyze data on reproductive performance (the fate of >23,000 eggs) based on up to 14 years of breeding of four captive zebra finch populations. We find that virtually all aspects of reproductive performance are negatively affected by inbreeding (mean r=-0.117); by an early-starting, age-related decline (mean r=-0.132); and by poor early-life nutrition (mean r=-0.058). However, these effects together explain only about 3% of the variance in infertility, offspring mortality, fecundity, and fitness. In contrast, individual repeatability of different fitness components varied between 15% and 50%. As expected, we found relatively low heritability in fitness components (median: 7% of phenotypic variation and 29% of individually repeatable variation). Yet some of the heritable variation in fitness appears to be maintained by antagonistic pleiotropy (negative genetic correlations) between male fitness traits and female and offspring fitness traits. The large amount of unexplained variation suggests a potentially important role of local dominance and epistasis, including the possibility of segregating genetic incompatibilities.
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Zapata D, Rivera-Gutierrez HF, Parra JL, Gonzalez-Quevedo C. Low adaptive and neutral genetic diversity in the endangered Antioquia wren (Thryophilus sernai). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01313-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Jowers MJ, Queirós J, Resende Pinto R, Ali AH, Mutinda M, Angelone S, Alves PC, Godinho R. Genetic diversity in natural range remnants of the critically endangered hirola antelope. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is pivotal to gain an understanding of diversity and differentiation within its range before designing future translocation plans to increase the genetic diversity of the ex situ population. For that purpose, we assessed 55 individuals collected across five localities in eastern Kenya, covering its entire natural range. We used the complete mitochondrial DNA control region and microsatellite genotyping to estimate genetic diversity and differentiation across its range. Nuclear genetic diversity was moderate in comparison to other endangered African antelopes, with no signals of inbreeding. However, the mitochondrial data showed low nucleotide diversity, few haplotypes and low haplotypic differentiation. Overall, the inferred low degree of genetic differentiation and population structure suggests a single population of hirola across the natural range. An overall stable population size was inferred over the recent history of the species, although signals of a recent genetic bottleneck were found. Our results show hope for ongoing conservation management programmes and that there is a future for the hirola in Kenya.
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Affiliation(s)
- Michael Joseph Jowers
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - João Queirós
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Rui Resende Pinto
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
| | - Abdullahi H Ali
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
- National Museums of Kenya, Nairobi, Kenya
- Hirola Conservation Programme, Garissa, Kenya
| | - Mathew Mutinda
- Department of Veterinary and Capture Services, Kenya Wildlife Service, Nairobi, Kenya
| | - Samer Angelone
- Institute of Evolutionary Biology and Environmental Studies (IEU), University of Zurich, Zurich, Switzerland
| | - Paulo Célio Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, University of Johannesburg, South Africa
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Love Stowell SM, Gagne RB, McWhirter D, Edwards W, Ernest HB. Bighorn Sheep Genetic Structure in Wyoming Reflects Geography and Management. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sierra M. Love Stowell
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Roderick B. Gagne
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Doug McWhirter
- Wyoming Game and Fish DepartmentJackson Regional Office 420 N Cache St Jackson WY 830001 USA
| | - William Edwards
- Wyoming Game and Fish DepartmentWildlife Health Laboratory 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Holly B. Ernest
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
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Genetic impacts of conservation management actions in a critically endangered parrot species. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01292-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Schultz AJ, Cristescu RH, Hanger J, Loader J, de Villiers D, Frère CH. Inbreeding and disease avoidance in a free-ranging koala population. Mol Ecol 2020; 29:2416-2430. [PMID: 32470998 DOI: 10.1111/mec.15488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 05/11/2020] [Indexed: 11/30/2022]
Abstract
Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex-biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free-ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free-ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C. pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.
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Affiliation(s)
- Anthony J Schultz
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Romane H Cristescu
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Jon Hanger
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | - Jo Loader
- Endeavour Veterinary Ecology Pty Ltd, Toorbul, QLD, Australia
| | | | - Celine H Frère
- Global Change Ecology Research Group, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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Gooley RM, Hogg CJ, Fox S, Pemberton D, Belov K, Grueber CE. Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils. PeerJ 2020; 8:e9220. [PMID: 32587794 PMCID: PMC7304431 DOI: 10.7717/peerj.9220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/28/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species' range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. METHODS We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. RESULTS Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the "Wild Devil Recovery Program", which is currently augmenting small, isolated populations.
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Affiliation(s)
- Rebecca M. Gooley
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Samantha Fox
- Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
- Toledo Zoo, Toledo, OH, United States of America
| | - David Pemberton
- Save the Tasmanian Devil Program, Hobart, Tasmania, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Catherine E. Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- San Diego Zoo Global, San Diego, CA, United States of America
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Latorre-Cardenas MC, Gutiérrez-Rodríguez C, Rico Y. Estimating genetic and demographic parameters relevant for the conservation of the Neotropical otter, Lontra longicaudis, in Mexico. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
Endangered species face a huge array of challenges, including the negative consequences of individuals having to breed with close genetic relatives. But just how costly is inbreeding in small populations? New research from an endangered bird species suggests that considering inbreeding could be crucial for conservation programmes.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, NR4 7TJ, UK.
| | - Matthew J G Gage
- School of Biological Sciences, University of East Anglia, NR4 7TJ, UK
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Ayala-Burbano PA, Galetti Junior PM, Wormell D, Pissinatti A, Marques MC, de Freitas PD. Studbook and molecular analyses for the endangered black-lion-tamarin; an integrative approach for assessing genetic diversity and driving management in captivity. Sci Rep 2020; 10:6781. [PMID: 32321949 PMCID: PMC7176676 DOI: 10.1038/s41598-020-63542-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/10/2020] [Indexed: 11/09/2022] Open
Abstract
Breeding strategies based on molecular markers have been adopted by ex-situ conservation programs to assess alternative parameters for the genetic diversity estimates. In this work we evaluated molecular and studbook data for captive populations of black-lion-tamarin (BLT), an endangered primate endemic to Brazil's Atlantic Forest. Pedigree analyses were performed using BLT studbook information collected from 1973 to 2018. We analyzed the whole captive population since its foundation; the current captive population (CCP); and all extant BLTs in the Brazilian captive population (BCP), separately. Microsatellite analyses were implemented on the BCP individuals from the eighth generation (BCP-F8) only to avoid generation overlap. The expected heterozygosity for BCP-F8, using molecular, data was 0.45, and the initial expected heterozygosity was 0.69. Kinship parameters showed high genetic relationships in both pedigree and molecular analyses. The genealogy-based endogamy evidenced a high inbreeding coefficient, while the molecular analyses suggested a non-inbreeding signature. The Mate Suitability Index showed detrimental values for the majority of potential pairs in the CCP. Nevertheless, some individuals evidenced high individual heterozygosity and allele representation, demonstrating good potential to be used as breeders. Thus, we propose the use of molecular data as a complementary parameter to evaluate mating-pairs and to aid management decision-making.
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Affiliation(s)
| | | | - Dominic Wormell
- Durrell Wildlife Conservation Trust, Trinity, Jersey, England
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Antaky CC, Conklin EE, Toonen RJ, Knapp IS, Price MR. Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago. PeerJ 2020; 8:e8463. [PMID: 32071808 PMCID: PMC7007978 DOI: 10.7717/peerj.8463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/26/2019] [Indexed: 11/20/2022] Open
Abstract
Seabirds in the order of Procellariiformes have one of the highest proportions of threatened species of any avian order. Species undergoing recovery may be predicted to have a genetic signature of a bottleneck, low genetic diversity, or higher rates of inbreeding. The Hawaiian Band-rumped Storm Petrel ('Akē'akē; Hydrobates castro), a long-lived philopatric seabird, suffered massive population declines resulting in its listing under the Endangered Species Act in 2016 as federally Endangered. We used high-throughput sequencing to assess patterns of genetic diversity and potential for inbreeding in remaining populations in the Hawaiian Islands. We compared a total of 24 individuals, including both historical and modern samples, collected from breeding colonies or downed individuals found on the islands of Kaua'i, O'ahu, Maui, and the Big Island of Hawai'i. Genetic analyses revealed little differentiation between breeding colonies on Kaua'i and the Big Island colonies. Although small sample sizes limit inferences regarding other island colonies, downed individuals from O'ahu and Maui did not assign to known breeding colonies, suggesting the existence of an additional distinct breeding population. The maintenance of genetic diversity in future generations is an important consideration for conservation management. This study provides a baseline of population structure for the remaining nesting colonies that could inform potential translocations of the Endangered H. castro.
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Affiliation(s)
- Carmen C. Antaky
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
| | - Emily E. Conklin
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Ingrid S.S. Knapp
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, USA
| | - Melissa R. Price
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
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Offspring sired by subordinate red deer males under controlled conditions: did some females prefer not to mate with the alpha male? Acta Ethol 2020. [DOI: 10.1007/s10211-020-00336-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Moss JB, Gerber GP, Welch ME. Heterozygosity-Fitness Correlations Reveal Inbreeding Depression in Neonatal Body Size in a Critically Endangered Rock Iguana. J Hered 2019; 110:818-829. [PMID: 31617903 DOI: 10.1093/jhered/esz060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/09/2019] [Indexed: 01/16/2023] Open
Abstract
Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.
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Affiliation(s)
- Jeanette B Moss
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
| | - Glenn P Gerber
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Mark E Welch
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
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Chattopadhyay B, Garg KM, Soo YJ, Low GW, Frechette JL, Rheindt FE. Conservation genomics in the fight to help the recovery of the critically endangered Siamese crocodile Crocodylus siamensis. Mol Ecol 2019; 28:936-950. [PMID: 30659682 DOI: 10.1111/mec.15023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/03/2018] [Indexed: 12/13/2022]
Abstract
Endangered species are often characterized by low genetic diversity and it is imperative for conservation efforts to incorporate the knowledge obtained from genetic studies for effective management. However, despite the promise of technological advances in sequencing, application of genome-wide data to endangered populations remains uncommon. In the present study we pursued a holistic conservation-genomic approach to inform a field-based management programme of a Critically Endangered species, the Siamese crocodile Crocodylus siamensis. Using thousands of single nucleotide polymorphisms from throughout the genome, we revealed signals of introgression from two other crocodile species within our sample of both wild and captive-bred Siamese crocodiles from Cambodia. Our genetic screening of the Siamese crocodiles resulted in the subsequent re-introduction of 12 individuals into the wild as well as the selection of four individuals for captive breeding programmes. Comparison of intraspecific genetic diversity revealed an alarmingly low contemporary effective population size in the wild (<50) with evidence of a recent bottleneck around Tonle Sap Lake. We also projected a probable future extinction in the wild (within fewer than five generations) in this population in the absence of re-introduction efforts. However, an increase in the number of potential breeders through re-introductions, including the one resulting from this project, could counter this trend. Our results have been implemented in ongoing re-introduction and captive breeding programmes, with major implications for the conservation management of Siamese crocodiles, and provide a blueprint for the rescue effort of other "terminally ill" populations of critically endangered species.
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Affiliation(s)
- Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yun Jing Soo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Gabriel W Low
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Gkafas GA, Hatziioannou M, Malandrakis EE, Tsigenopoulos CS, Karapanagiotidis IT, Mente E, Vafidis D, Exadactylos A. Heterozygosity fitness correlations and generation interval of the Norway lobster in the Aegean Sea, eastern Mediterranean. ACTA ACUST UNITED AC 2019; 26:14. [PMID: 31728339 PMCID: PMC6842237 DOI: 10.1186/s40709-019-0103-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/18/2019] [Indexed: 11/10/2022]
Abstract
Background Comprehensively detailed information on population dynamics for benthic species is crucial since potential admixture of individuals could shift the genetic subdivision and age structure during a full breeding period. The apparent genetic impact of the potential recruitment strategy of Norway lobster Nephrops norvegicus is still under research. For this reason the present study was focused on genetic variation of the species over a given continuous year period in a semi-enclosed gulf of the Aegean Sea. Results Analyses revealed that the relative smaller size class in females and the apparent faster growth of males may represent a key-role differential strategy for the two sexes, whereas females tend to mature slower. Heterozygosity fitness correlations (HFCs) showed substantially significant associations suggesting that inbreeding depression for females and outbreeding depression for males are the proximate fitness mechanisms, respectively. Conclusions Nephrops norvegicus uniformal genetic composition (background of high gene flow), could be attributed to potential population recolonization, due to a hypothesized passive larval movement from deeper waters, which may suggest that some offspring of local residents and potential male non-breeders from other regions admixture randomly.
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Affiliation(s)
- Georgios A Gkafas
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Marianthi Hatziioannou
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Emmanouil E Malandrakis
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Costas S Tsigenopoulos
- 2Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, Heraklion, Crete Greece
| | - Ioannis T Karapanagiotidis
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Elena Mente
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Dimitrios Vafidis
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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González P, Dettleff P, Valenzuela C, Estrada JM, Valdés JA, Meneses C, Molina A. Evaluating the genetic structure of wild and commercial red cusk-eel (Genypterus chilensis) populations through the development of novel microsatellite markers from a reference transcriptome. Mol Biol Rep 2019; 46:5875-5882. [PMID: 31598817 DOI: 10.1007/s11033-019-05021-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/03/2019] [Indexed: 11/30/2022]
Abstract
The red cusk-eel (Genypterus chilensis) is a native Chilean species with a high-value market, with the potential to diversify Chilean aquaculture. The objective of this study was to develop a set of microsatellite markers, estimate genetic parameters, determine population differentiation, and identify the population structure of wild and commercial populations of G. chilensis. We discovered 6427 microsatellites markers from RNA-seq data, of which 54.9%, 20.2% and 16.8% were di-, tri-, and tetranucleotides, respectively. We used 12 of these markers to genotype two sets of broodstock, one group from commercial fish, and one group from wild fish from the Coquimbo Region of G. chilensis. We estimate the genetic parameters of the markers, selecting ten polymorphic markers (PIC > 0.5). We observed differences in the inbreeding coefficient among populations, with high values of inbreeding in one broodstock set and lower values in the other groups. The evaluation of population differentiation using Fst showed small (0.0195) to large (0.1888) genetic differentiation between the groups. The structure analysis showed that commercial and wild groups were formed by three clusters, without relevant evidence of admixture process, suggesting that groups evaluated in this study are formed of at least three subpopulations of G. chilensis, which could be explained by the low or lack of migration suggested for this species. This is the first study that identifies a high number of molecular markers in G. chilensis, providing relevant information of the genetic structure of commercial and wild population of this species.
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Affiliation(s)
- Pamela González
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Phillip Dettleff
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Cristián Valenzuela
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Juan Manuel Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Juan Antonio Valdés
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Alfredo Molina
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 440, Santiago, Chile.
- Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile.
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Çilingir FG, Seah A, Horne BD, Som S, Bickford DP, Rheindt FE. Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin. Ecol Evol 2019; 9:9500-9510. [PMID: 31534671 PMCID: PMC6745661 DOI: 10.1002/ece3.5434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/04/2019] [Accepted: 06/11/2019] [Indexed: 11/14/2022] Open
Abstract
The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD-seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006-2012 and identify high-value breeders instrumental for ex-situ management of the contemporary genetic stock of the species.
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Affiliation(s)
- F. Gözde Çilingir
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Adeline Seah
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Wildlife Conservation Society, Bronx ZooBronxNew YorkUSA
| | - Brian D. Horne
- Wildlife Conservation Society, Bronx ZooBronxNew YorkUSA
| | - Sitha Som
- Wildlife Conservation SocietyPhnom PenhCambodia
| | - David P. Bickford
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Present address:
Department of BiologyUniversity of La VerneLa VerneCaliforniaUSA
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
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Arct A, Drobniak SM, Mellinger S, Gustafsson L, Cichoń M. Parental genetic similarity and offspring performance in blue tits in relation to brood size manipulation. Ecol Evol 2019; 9:10085-10091. [PMID: 31624539 PMCID: PMC6787802 DOI: 10.1002/ece3.5367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/15/2019] [Accepted: 05/19/2019] [Indexed: 11/11/2022] Open
Abstract
In birds, as in many other taxa, higher genetic similarity of mates has long been known to reduce offspring fitness. To date, the majority of avian studies have focused on examination whether the genetic similarity of social mates predicts hatching success. Yet, increased genetic similarity of mates may also reduce offspring fitness during later life stages, including the nestling period and beyond. Here, we investigated whether parental genetic similarity influences offspring performance using data from free-living blue tits (Cyanistes caeruleus) collected across three breeding seasons. Additionally, we tested whether brood size manipulation affects the magnitude and direction of the relationship between genetic similarity of mates and offspring performance. Sixteen microsatellite markers were used to measure genetic similarity between biological parents. We found that the genetic similarity of parents negatively affects offspring immune response and this effect was independent of the experimental brood size manipulation.
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Affiliation(s)
- Aneta Arct
- Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | | | | | - Lars Gustafsson
- Department of Animal Ecology/Ecology and Genetics, Evolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Mariusz Cichoń
- Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
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47
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Inconsistent inbreeding effects during lizard ontogeny. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Schunter C, Pascual M, Raventos N, Garriga J, Garza JC, Bartumeus F, Macpherson E. A novel integrative approach elucidates fine-scale dispersal patchiness in marine populations. Sci Rep 2019; 9:10796. [PMID: 31346216 PMCID: PMC6658486 DOI: 10.1038/s41598-019-47200-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/12/2019] [Indexed: 11/24/2022] Open
Abstract
Dispersal is one of the main determining factors of population structure. In the marine habitat, well-connected populations with large numbers of reproducing individuals are common but even so population structure can exist on a small-scale. Variation in dispersal patterns between populations or over time is often associated to geographic distance or changing oceanographic barriers. Consequently, detecting structure and variation in dispersal on a fine-scale within marine populations still remains a challenge. Here we propose and use a novel approach of combining a clustering model, early-life history trait information from fish otoliths, spatial coordinates and genetic markers to detect very fine-scale dispersal patterns. We collected 1573 individuals (946 adults and 627 juveniles) of the black-faced blenny across a small-scale (2 km) coastline as well as at a larger-scale area (<50 kms). A total of 178 single nucleotide polymorphism markers were used to evaluate relatedness patterns within this well-connected population. In our clustering models we categorized SHORT-range dispersers to be potential local recruits based on their high relatedness within and low relatedness towards other spatial clusters. Local retention and/or dispersal of this potential local recruitment varied across the 2 km coastline with higher frequency of SHORT-range dispersers towards the southwest of the area for adults. An inverse pattern was found for juveniles, showing an increase of SHORT-range dispersers towards the northeast. As we rule out selective movement and mortality from one year to the next, this pattern reveals a complex but not full genetic mixing, and variability in coastal circulation is most likely the main driver of this fine-scale chaotic genetic patchiness within this otherwise homogeneous population. When focusing on the patterns within one recruitment season, we found large differences in temperatures (from approx. 17 °C to 25 °C) as well as pelagic larval duration (PLD) for juveniles from the beginning of the season and the end of the season. We were able to detect fine-scale differences in LONG-range juvenile dispersers, representing distant migrants, depending on whether they were born at the beginning of the season with a longer PLD, or at the end of the reproductive season. The ability to detect such fine-scale dispersal patchiness will aid in our understanding of the underlying mechanisms of population structuring and chaotic patchiness in a wide range of species even with high potential dispersal abilities.
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Affiliation(s)
- C Schunter
- Swire Institute of Marine Science, The University of Hong Kong, Pokfulam, Hong Kong SAR.
| | - M Pascual
- Dept. Genètica, Microbiologia i Estadística - IRBio, Universitat Barcelona, Diagonal 643, 08028, Barcelona, Spain
| | - N Raventos
- Laboratorio de Analisis de Estructurad Biologicas de Crecimiento (CEAB-CSIC), Car. Acc. Cala St. Francesc 14, Blanes, 17300, Girona, Spain
| | - J Garriga
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Car. Acc. Cala St. Francesc 14, Blanes, 17300, Girona, Spain
| | - J C Garza
- Southwest Fisheries Science Center, National Marine Fisheries Service and University of California, 110 McAllister Way, Santa Cruz, 95060, USA
| | - F Bartumeus
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Car. Acc. Cala St. Francesc 14, Blanes, 17300, Girona, Spain.,Centre de Recerca Ecològica i Aplicacions Forestals (CREAF), E08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - E Macpherson
- Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Car. Acc. Cala St. Francesc 14, Blanes, 17300, Girona, Spain
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Asem A, Eimanifar A, van Stappen G, Sun SC. The impact of one-decade ecological disturbance on genetic changes: a study on the brine shrimp Artemia urmiana from Urmia Lake, Iran. PeerJ 2019; 7:e7190. [PMID: 31304060 PMCID: PMC6611446 DOI: 10.7717/peerj.7190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/24/2019] [Indexed: 11/20/2022] Open
Abstract
Urmia Lake, the largest natural habitat of the brine shrimp Artemia urmiana, has progressively desiccated over the last two decades, resulting in a loss of 80% of its surface area and producing thousands of hectares of arid salty land. This ecological crisis has seriously affected the lake’s native biodiversity. Artemia urmiana has lost more than 90% of its population during the decade from 1994 (rainy period) to 2004 (drought period) due to salinity increasing to saturation levels (∼300 g/l). We studied the influence of this ecological crisis on the genetic diversity of A. urmiana in Urmia Lake, based on one cyst collections in 1994 and 2004. AMOVA analysis on ISSR data demonstrated a 21% genetic variation and there was a 5.5% reduction of polymorphic loci between samples. PCoA showed that 77.42% and 68.75% of specimens clustered separately in 1994 and 2004, respectively. Our analyses of four marker genes revealed different genetic diversity patterns with a decrease of diversity at ITS1 and an increase for Na+/K+ ATPase. There was no notable difference in genetic variation detected for COI and 16S genes between the two periods. However, they represented distinctly different haplotypes. ITS1 and COI followed a population expansion model, whereas Na+/K+ ATPase and 16S were under demographic equilibrium without selective pressure in the 1994 samples. Neutrality tests confirmed the excess of rare historical and recent mutations present in COI and ITS1 in both samples. It is evident that a short-term ecological disturbance has impacted the genetic diversity and structure of A. urmiana.
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Affiliation(s)
- Alireza Asem
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.,College of Life Sciences and Ecology, Hainan Tropical Ocean University, Sanya, China
| | | | - Gilbert van Stappen
- Laboratory of Aquaculture and Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Shi-Chun Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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50
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Han QH, Sun RN, Yang HQ, Wang ZW, Wan QH, Fang SG. MHC class I diversity predicts non-random mating in Chinese alligators (Alligator sinensis). Heredity (Edinb) 2019; 122:809-818. [PMID: 30670843 PMCID: PMC6781117 DOI: 10.1038/s41437-018-0177-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/26/2018] [Accepted: 11/28/2018] [Indexed: 11/08/2022] Open
Abstract
The major histocompatibility complex (MHC) has several important roles in kin recognition, pathogen resistance and mate selection. Research in fish, birds and mammals has suggested that individuals optimise MHC diversity, and therefore offspring fitness, when choosing mates. In reptiles, however, it is unclear whether female mate choice is based on genome-wide genetic characteristics such as microsatellite DNA loci, particular functional-trait loci (e.g., MHC) or both, and MHC's effects on mate choice remain relatively understudied. Herein, we used 13 microsatellite loci and two MHC class I loci to investigate female mate choice of Chinese alligators (Alligator sinensis) in the semi-natural condition. We also determined correlations between the MHC genotype of breeding males and male reproductive success. We found that MHC-heterozygous males harbour a greater reproductive success, which probably is the reason that these males are more preferred by the females than MHC-homozygous males. Furthermore, the MHC class I amino-acid distance and functional distance of true mating pairs were higher compared with those of randomly sampled pairs. Analysis of microsatellites revealed that, despite mate choice, females did not completely avoid inbreeding. These findings are the first evidence of MHC-associated mate choice in Chinese alligators, suggesting that females may adopt different mating strategies after assessing the MHC characteristics of potential mates.
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Affiliation(s)
- Qun-Hua Han
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ru-Na Sun
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hai-Qiong Yang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhen-Wei Wang
- Changxing Chinese Alligator Nature Reserve, Changxing, 313100, China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sheng-Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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