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Weinberger CS, Vianna JA, Faugeron S, Marquet PA. Inferring the impact of past climate changes and hunting on the South American sea lion. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Constanza S. Weinberger
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente Facultad de Agronomía e Ingeniería Forestal Pontifícia Universidad Católica de Chile Santiago Chile
- Centro Cambio Global UC Pontificia Universidad Católica de Chile Santiago Chile
| | - Sylvain Faugeron
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
- IRL3614 Evolutionary Biology and Ecology of Algae CNRS Sorbonne Université Pontificia Universidad Católica de ChileUniversidad Austral de ChileStation Biologique Roscoff France
| | - Pablo A. Marquet
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
- Centro Cambio Global UC Pontificia Universidad Católica de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
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2
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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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3
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Souza BC, Cruz VP, Almeida TRA, Sales JBL, Rodrigues-Filho LFS, Vianna M, Rotundo MM, Oliveira C, Foresti F. Genetic diversity assessment for the vulnerable migratory cownose ray Rhinoptera bonasus (Myliobatiformes: Rhinopteridae) from the southwestern Atlantic Ocean. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Rhinoptera bonasus is a bento-pelagic and highly migratory species occurring from southern United States to northern Argentina. Due to overfishing effects, R. bonasus is currently at risk, classified by the IUCN Red List as vulnerable. Considering the lack of molecular data available for R. bonasus, this study aimed to describe the genetic variability and population structure of specimens sampled from three Brazilian coast ecoregions (Amazon ecoregion, Pará; Northeastern ecoregion, Pernambuco and Southeastern ecoregion, Rio de Janeiro, São Paulo and Santa Catarina), through five polymorphic microsatellite markers. Here testing the panmixia hypothesis for Brazilian ecoregions and test natal philopathy. A total of 69 analyzed specimens revealed individual and significant genetic differentiation between the sampled locations. Φ ST (0.12), PCA, DAPC and Bayesian analyses of the genetic population structure revealed at least two distinct genetic R. bonasus groupings. IBD tests were significant, indicating a correlation between genetic and geographical distance among populations, which can be explained by reproductive philopatric behavior. Philopatric behavior associated with R. bonasus mobility may influence the differentiation values observed for all loci in the investigated samples.
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Affiliation(s)
- Bruno C. Souza
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil
| | - Vanessa P. Cruz
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil
| | | | | | | | | | | | | | - Fausto Foresti
- Universidade Estadual Paulista Júlio de Mesquita Filho, Brazil
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4
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Nikolic N, Thompson P, de Bruyn M, Macé M, Chevalet C. Evolutionary history of a Scottish harbour seal population. PeerJ 2020; 8:e9167. [PMID: 32728487 PMCID: PMC7357561 DOI: 10.7717/peerj.9167] [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: 01/15/2020] [Accepted: 04/19/2020] [Indexed: 12/02/2022] Open
Abstract
Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area.
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Affiliation(s)
- Natacha Nikolic
- ARBRE (Reunion Island Biodiversity Research Agency), Saint-Leu, La Réunion
- Génétique Physiologie et Systèmes d’Elevage - UMR1388, INRAE, Castanet Tolosan, France
| | - Paul Thompson
- Lighthouse Field Station, Sciences School of Biological Sciences, University of Aberdeen, Cromarty, United Kingdom
| | - Mark de Bruyn
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Matthias Macé
- Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse - UMR 5288, CNRS, Toulouse, France
| | - Claude Chevalet
- Génétique Physiologie et Systèmes d’Elevage - UMR1388, INRAE, Castanet Tolosan, France
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5
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Fietz K, Galatius A, Teilmann J, Dietz R, Frie AK, Klimova A, Palsbøll PJ, Jensen LF, Graves JA, Hoffman JI, Olsen MT. Shift of grey seal subspecies boundaries in response to climate, culling and conservation. Mol Ecol 2017; 25:4097-112. [PMID: 27616353 DOI: 10.1111/mec.13748] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/06/2016] [Accepted: 06/22/2016] [Indexed: 12/01/2022]
Abstract
Identifying the processes that drive changes in the abundance and distribution of natural populations is a central theme in ecology and evolution. Many species of marine mammals have experienced dramatic changes in abundance and distribution due to climatic fluctuations and anthropogenic impacts. However, thanks to conservation efforts, some of these species have shown remarkable population recovery and are now recolonizing their former ranges. Here, we use zooarchaeological, demographic and genetic data to examine processes of colonization, local extinction and recolonization of the two northern European grey seal subspecies inhabiting the Baltic Sea and North Sea. The zooarchaeological and genetic data suggest that the two subspecies diverged shortly after the formation of the Baltic Sea approximately 4200 years bp, probably through a gradual shift to different breeding habitats and phenologies. By comparing genetic data from 19th century pre-extinction material with that from seals currently recolonizing their past range, we observed a marked spatiotemporal shift in subspecies boundaries, with increasing encroachment of North Sea seals on areas previously occupied by the Baltic Sea subspecies. Further, both demographic and genetic data indicate that the two subspecies have begun to overlap geographically and are hybridizing in a narrow contact zone. Our findings provide new insights into the processes of colonization, extinction and recolonization and have important implications for the management of grey seals across northern Europe.
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Affiliation(s)
- Katharina Fietz
- Evolutionary Genomics Section, Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.,Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anders Galatius
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Jonas Teilmann
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | | | - Anastasia Klimova
- Department of Animal Behaviour, University of Bielefeld, PO Box 10 01 31, 33501 Bielefeld, Germany
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lasse F Jensen
- Fisheries and Maritime Museum, Tarphagevej 2, DK-6710 Esbjerg V, Denmark
| | - Jeff A Graves
- Scottish Oceans Institute, School of Biology, University of St Andrews, Fife KY16 9TH, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, PO Box 10 01 31, 33501 Bielefeld, Germany
| | - Morten Tange Olsen
- Evolutionary Genomics Section, Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
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6
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Andersen LW, Jacobsen MW, Lydersen C, Semenova V, Boltunov A, Born EW, Wiig Ø, Kovacs KM. Walruses (Odobenus rosmarus rosmarus) in the Pechora Sea in the context of contemporary population structure of Northeast Atlantic walruses. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx093] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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Gaynor KM, Solomon JW, Siller S, Jessell L, Duffy JE, Rubenstein DR. Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes. Mol Ecol Resour 2017; 17:e160-e173. [PMID: 28776934 DOI: 10.1111/1755-0998.12705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/16/2017] [Accepted: 07/25/2017] [Indexed: 11/28/2022]
Abstract
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.
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Affiliation(s)
- Kaitlyn M Gaynor
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Joseph W Solomon
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Stefanie Siller
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Linnet Jessell
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Institution, Washington, DC, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Ornithology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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8
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Abadía-Cardoso A, Freimer NB, Deiner K, Garza JC. Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris. J Hered 2017; 108:618-627. [PMID: 28821186 PMCID: PMC5892393 DOI: 10.1093/jhered/esx053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species.
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Affiliation(s)
- Alicia Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - Nelson B Freimer
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - Kristy Deiner
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
| | - John Carlos Garza
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Carretera Tijuana-Ensenada Km 103, Pedregal Playitas, 22860 Ensenada, BC, Mexico; University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060; Southwest Fisheries Science Center, National Marine Fisheries Service, 110 McAllister Way, Santa Cruz, CA 95060; Center for Neurobehavioral Genetics, University of California, Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095. Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Rd., Ithaca, NY 14850
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9
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de Oliveira LR, Gehara MCM, Fraga LD, Lopes F, Túnez JI, Cassini MH, Majluf P, Cárdenas-Alayza S, Pavés HJ, Crespo EA, García N, Loizaga de Castro R, Hoelzel AR, Sepúlveda M, Olavarría C, Valiati VH, Quiñones R, Pérez-Alvarez MJ, Ott PH, Bonatto SL. Ancient female philopatry, asymmetric male gene flow, and synchronous population expansion support the influence of climatic oscillations on the evolution of South American sea lion (Otaria flavescens). PLoS One 2017; 12:e0179442. [PMID: 28654647 PMCID: PMC5487037 DOI: 10.1371/journal.pone.0179442] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/29/2017] [Indexed: 12/11/2022] Open
Abstract
The South American sea lion (Otaria flavescens) is widely distributed along the southern Atlantic and Pacific coasts of South America with a history of significant commercial exploitation. We aimed to evaluate the population genetic structure and the evolutionary history of South American sea lion along its distribution by analyses of mitochondrial DNA (mtDNA) and 10 nuclear microsatellites loci. We analyzed 147 sequences of mtDNA control region and genotyped 111 individuals of South American sea lion for 10 microsatellite loci, representing six populations (Peru, Northern Chile, Southern Chile, Uruguay (Brazil), Argentina and Falkland (Malvinas) Islands) and covering the entire distribution of the species. The mtDNA phylogeny shows that haplotypes from the two oceans comprise two very divergent clades as observed in previous studies, suggesting a long period (>1 million years) of low inter-oceanic female gene flow. Bayesian analysis of bi-parental genetic diversity supports significant (but less pronounced than mitochondrial) genetic structure between Pacific and Atlantic populations, although also suggested some inter-oceanic gene flow mediated by males. Higher male migration rates were found in the intra-oceanic population comparisons, supporting very high female philopatry in the species. Demographic analyses showed that populations from both oceans went through a large population expansion ~10,000 years ago, suggesting a very similar influence of historical environmental factors, such as the last glacial cycle, on both regions. Our results support the proposition that the Pacific and Atlantic populations of the South American sea lion should be considered distinct evolutionarily significant units, with at least two managements units in each ocean.
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Affiliation(s)
- Larissa Rosa de Oliveira
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Osório, RS, Brazil
- * E-mail:
| | - Marcelo C. M. Gehara
- Herpetology, American Museum of Natural History, New York, NY, United States of America
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lúcia D. Fraga
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fernando Lopes
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Juan Ignacio Túnez
- Grupo GEMA, Departamento de Ciencias Básicas, Universidad Nacional de Luján and CONICET, Luján, Buenos Aires, Argentina
| | - Marcelo H. Cassini
- Grupo GEMA, Departamento de Ciencias Básicas, Universidad Nacional de Luján and CONICET, Luján, Buenos Aires, Argentina
- Laboratorio de Biología del Comportamiento, Instituto de Biología y Medicina Experimental (CONICET), Buenos Aires, Argentina
| | - Patricia Majluf
- Centro para la Sostenibilidad Ambiental / Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Susana Cárdenas-Alayza
- Centro para la Sostenibilidad Ambiental / Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Héctor J. Pavés
- Departamento de Ciencias Básica, Facultad de Ciencias, Universidad Santo Tomas, Osorno, Chile
| | - Enrique Alberto Crespo
- Laboratorio de Mamíferos Marinos, Centro para el Estudio de los Sistemas Marinos (CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - Nestor García
- Laboratorio de Mamíferos Marinos, Centro para el Estudio de los Sistemas Marinos (CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - Rocío Loizaga de Castro
- Laboratorio de Mamíferos Marinos, Centro para el Estudio de los Sistemas Marinos (CENPAT-CONICET), Puerto Madryn, Chubut, Argentina
| | - A. Rus Hoelzel
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Maritza Sepúlveda
- Centro de Investigación y Gestión de los Recursos Naturales, Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Millenium Nucleus of Invasive Salmonids (INVASAL), Concepción, Chile
| | | | - Victor Hugo Valiati
- Laboratório de Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
| | - Renato Quiñones
- Interdisciplinary Center for Aquaculture Research (FONDAP), Universidad de Concepción, Concepción, Chile
| | - Maria Jose Pérez-Alvarez
- Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Paulo Henrique Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Osório, RS, Brazil
- Laboratório de Ecologia e Conservação de Organismos Aquáticos, Universidade Estadual do Rio Grande do Sul, Osório, RS, Brazil
| | - Sandro L. Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil
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10
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Rothstein AP, McLaughlin R, Acevedo-Gutiérrez A, Schwarz D. wisepair: a computer program for individual matching in genetic tracking studies. Mol Ecol Resour 2016; 17:267-277. [PMID: 27488501 DOI: 10.1111/1755-0998.12590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/23/2016] [Accepted: 07/11/2016] [Indexed: 11/29/2022]
Abstract
Individual-based data sets tracking organisms over space and time are fundamental to answering broad questions in ecology and evolution. A 'permanent' genetic tag circumvents a need to invasively mark or tag animals, especially if there are little phenotypic differences among individuals. However, genetic tracking of individuals does not come without its limits; correctly matching genotypes and error rates associated with laboratory work can make it difficult to parse out matched individuals. In addition, defining a sampling design that effectively matches individuals in the wild can be a challenge for researchers. Here, we combine the two objectives of defining sampling design and reducing genotyping error through an efficient Python-based computer-modelling program, wisepair. We describe the methods used to develop the computer program and assess its effectiveness through three empirical data sets, with and without reference genotypes. Our results show that wisepair outperformed similar genotype matching programs using previously published from reference genotype data of diurnal poison frogs (Allobates femoralis) and without-reference (faecal) genotype sample data sets of harbour seals (Phoca vitulina) and Eurasian otters (Lutra lutra). In addition, due to limited sampling effort in the harbour seal data, we present optimal sampling designs for future projects. wisepair allows for minimal sacrifice in the available methods as it incorporates sample rerun error data, allelic pairwise comparisons and probabilistic simulations to determine matching thresholds. Our program is the lone tool available to researchers to define parameters a priori for genetic tracking studies.
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Affiliation(s)
- Andrew P Rothstein
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | - Ryan McLaughlin
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
| | | | - Dietmar Schwarz
- Department of Biology, Western Washington University, Bellingham, WA, 98225, USA
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11
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Dussex N, Robertson BC, Salis AT, Kalinin A, Best H, Gemmell NJ. Low Spatial Genetic Differentiation Associated with Rapid Recolonization in the New Zealand Fur Seal Arctocephalus forsteri. J Hered 2016; 107:581-592. [PMID: 27563072 DOI: 10.1093/jhered/esw056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/15/2016] [Indexed: 11/14/2022] Open
Abstract
Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.
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Affiliation(s)
- Nicolas Dussex
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Bruce C Robertson
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Alexander T Salis
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Aleksandr Kalinin
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Hugh Best
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
| | - Neil J Gemmell
- From the Department of Zoology, University of Otago, Dunedin, New Zealand (Dussex, Robertson, and Salis); Allan Wilson Centre, Dunedin, New Zealand (Dussex and Gemmell); Department of Anatomy, University of Otago, PO Box 913, Dunedin 9054, New Zealand (Dussex and Gemmell); School of Biological Sciences, University of Canterbury, Christchurch, New Zealand (Robertson, Kalinin, and Gemmell); and Marine Conservation Unit, Department of Conservation, Wellington, New Zealand (Best)
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12
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Peters L, Humble E, Kröcker N, Fuchs B, Forcada J, Hoffman JI. Born blonde: a recessive loss-of-function mutation in the melanocortin 1 receptor is associated with cream coat coloration in Antarctic fur seals. Ecol Evol 2016; 6:5705-17. [PMID: 27547348 PMCID: PMC4983585 DOI: 10.1002/ece3.2290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 02/03/2023] Open
Abstract
Although the genetic basis of color variation has been extensively studied in humans and domestic animals, the genetic polymorphisms responsible for different color morphs remain to be elucidated in many wild vertebrate species. For example, hypopigmentation has been observed in numerous marine mammal species but the underlying mutations have not been identified. A particularly compelling candidate gene for explaining color polymorphism is the melanocortin 1 receptor (MC1R), which plays a key role in the regulation of pigment production. We therefore used Antarctic fur seals (Arctocephalus gazella) as a highly tractable marine mammal system with which to test for an association between nucleotide variation at the MC1R and melanin‐based coat color phenotypes. By sequencing 70 wild‐type individuals with dark‐colored coats and 26 hypopigmented individuals with cream‐colored coats, we identified a nonsynonymous mutation that results in the substitution of serine with phenylalanine at an evolutionarily highly conserved structural domain. All of the hypopigmented individuals were homozygous for the allele coding for phenylalanine, consistent with a recessive loss‐of‐function allele. In order to test for cryptic population structure, which can generate artefactual associations, and to evaluate whether homozygosity at the MC1R could be indicative of low genome‐wide heterozygosity, we also genotyped all of the individuals at 50 polymorphic microsatellite loci. We were unable to detect any population structure and also found that wild‐type and hypopigmented individuals did not differ significantly in their standardized multilocus heterozygosity. Such a lack of association implies that hypopigmented individuals are unlikely to suffer disproportionately from inbreeding depression, and hence, we have no reason to believe that they are at a selective disadvantage in the wider population.
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Affiliation(s)
- Lucy Peters
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany; College of Medical, Veterinary & Life Sciences University of Glasgow Graham Kerr Building Glasgow G12 8QQ UK
| | - Emily Humble
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany; British Antarctic Survey High Cross, Madingley Road Cambridge CB3 OET UK
| | - Nicole Kröcker
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
| | - Birgit Fuchs
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
| | - Jaume Forcada
- British Antarctic Survey High Cross, Madingley Road Cambridge CB3 OET UK
| | - Joseph I Hoffman
- Department of Animal Behaviour University of Bielefeld Postfach 100131 33501 Bielefeld Germany
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13
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Hoffman JI, Kowalski GJ, Klimova A, Eberhart-Phillips LJ, Staniland IJ, Baylis AMM. Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160291. [PMID: 27493782 PMCID: PMC4968474 DOI: 10.1098/rsos.160291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.
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Affiliation(s)
- J. I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - G. J. Kowalski
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
- Animal Ecology Group, Institute of Biochemistry and Biology, University of Potsdam, Maulbeerallee 1, 14469, Potsdam, Germany
| | - A. Klimova
- Centro de Investigaciones Biológicas del Noroeste Baja California Sur, La Paz, Mexico
| | - L. J. Eberhart-Phillips
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - I. J. Staniland
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - A. M. M. Baylis
- South Atlantic Environmental Research Institute, Stanley FIQQ1ZZ, Falkland Islands
- Falklands Conservation, Stanley FIQQ1ZZ, Falkland Islands
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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14
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Mihnovets AN, Schultz JK, Wultsch C, Littnan CL, Amato G. A novel microsatellite multiplex assay for the endangered Hawaiian monk seal (Neomonachus schauinslandi). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0517-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Genetic Evidence of a Population Bottleneck and Inbreeding in the Endangered New Zealand Sea Lion,Phocarctos hookeri. J Hered 2016; 107:392-402. [DOI: 10.1093/jhered/esw015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
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16
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Tide line versus internal pools: mating system and breeding success of South American sea lion males. Behav Ecol Sociobiol 2015. [DOI: 10.1007/s00265-015-2010-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Chemical fingerprints encode mother-offspring similarity, colony membership, relatedness, and genetic quality in fur seals. Proc Natl Acad Sci U S A 2015; 112:E5005-12. [PMID: 26261311 DOI: 10.1073/pnas.1506076112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical communication underpins virtually all aspects of vertebrate social life, yet remains poorly understood because of its highly complex mechanistic basis. We therefore used chemical fingerprinting of skin swabs and genetic analysis to explore the chemical cues that may underlie mother-offspring recognition in colonially breeding Antarctic fur seals. By sampling mother-offspring pairs from two different colonies, using a variety of statistical approaches and genotyping a large panel of microsatellite loci, we show that colony membership, mother-offspring similarity, heterozygosity, and genetic relatedness are all chemically encoded. Moreover, chemical similarity between mothers and offspring reflects a combination of genetic and environmental influences, the former partly encoded by substances resembling known pheromones. Our findings reveal the diversity of information contained within chemical fingerprints and have implications for understanding mother-offspring communication, kin recognition, and mate choice.
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18
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Browning HM, Acevedo-Whitehouse K, Gulland FMD, Hall AJ, Finlayson J, Dagleish MP, Billington KJ, Colegrove K, Hammond JA. Evidence for a genetic basis of urogenital carcinoma in the wild California sea lion. Proc Biol Sci 2015; 281:20140240. [PMID: 25339718 PMCID: PMC4213630 DOI: 10.1098/rspb.2014.0240] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Although neoplasia is a major cause of mortality in humans and domestic animals, it has rarely been described in wildlife species. One of the few examples is a highly prevalent urogenital carcinoma in California sea lions (CSLs). Although the aetiology of this carcinoma is clearly multifactorial, inbreeding depression, as estimated using levels of microsatellite multilocus heterozygosity, is identified as predictive for this neoplasia. On further analysis, this relationship appears to be largely driven by one marker, suggesting that a single locus might be associated with the occurrence of this disease in CSLs. In a case–control study, carcinoma was significantly associated with homozygosity at the Pv11 microsatellite locus. Pv11 was mapped to intron 9 of the heparanase 2 gene (HPSE2) locus, a very large gene encoding heparanase 2, which in humans is associated with multiple carcinomas. Correspondingly, immunohistochemical labelling in tissues was present in carcinoma cases within a single homozygous Pv11 genotype. To our knowledge, this is the first report of an individual locus being associated with cancer in any wildlife species. This adds emphasis to the study of HPSE2 in other species, including humans and will guide future studies on this sentinel species that shares much of its diet and environment with humans
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Affiliation(s)
- Helen M Browning
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, UK
| | | | | | - Ailsa J Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, UK
| | - Jeanie Finlayson
- The Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, UK
| | - Mark P Dagleish
- The Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, UK
| | | | - Kathleen Colegrove
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Maywood, IL, USA
| | - John A Hammond
- Pirbright Laboratory, The Pirbright Institute, Surrey, UK
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19
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Fine-scale matrilineal population structure in the Galapagos fur seal and its implications for conservation management. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0725-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Osborne AJ, Pearson J, Chilvers BL, Kennedy MA, Gemmell NJ. Examining the role of components of Slc11a1 (Nramp1) in the susceptibility of New Zealand sea lions (Phocarctos hookeri) to disease. PLoS One 2015; 10:e0122703. [PMID: 25874773 PMCID: PMC4397024 DOI: 10.1371/journal.pone.0122703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/13/2015] [Indexed: 12/20/2022] Open
Abstract
The New Zealand sea lion (NZSL, Phocarctos hookeri) is a Threatened marine mammal with a restricted distribution and a small, declining, population size. The species is susceptible to bacterial pathogens, having suffered three mass mortality events since 1998. Understanding the genetic factors linked to this susceptibility is important in mitigating population decline. The gene solute carrier family 11 member a1 (Slc11a1) plays an important role in mammalian resistance or susceptibility to a wide range of bacterial pathogens. At present, Slc11a1 has not been characterised in many taxa, and despite its known roles in mediating the effects of infectious disease agents, has not been examined as a candidate gene in susceptibility or resistance in any wild population of conservation concern. Here we examine components of Slc11a1 in NZSLs and identify: i) a polymorphic nucleotide in the promoter region; ii) putative shared transcription factor binding motifs between canids and NZSLs; and iii) a conserved polymorphic microsatellite in the first intron of Slc11a1, which together suggest conservation of Slc11a1 gene structure in otariids. At the promoter polymorphism, we demonstrate a shift away from normal allele frequency distributions and an increased likelihood of death from infectious causes with one allelic variant. While this increased likelihood is not statistically significant, lack of significance is potentially due to the complexity of genetic susceptibility to disease in wild populations. Our preliminary data highlight the potential significance of this gene in disease resistance in wild populations; further exploration of Slc11a1 will aid the understanding of susceptibility to infection in mammalian species of conservation significance.
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Affiliation(s)
- Amy J. Osborne
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - John Pearson
- Department of Public Health and General Practice, University of Otago, Christchurch, New Zealand
| | - B. Louise Chilvers
- Marine Species and Threats Team, Department of Conservation, Wellington, New Zealand
| | - Martin A. Kennedy
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Neil J. Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
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Characterisation of a novel panel of polymorphic microsatellite loci for the liver fluke, Fasciola hepatica, using a next generation sequencing approach. INFECTION GENETICS AND EVOLUTION 2015; 32:298-304. [PMID: 25796359 PMCID: PMC4424948 DOI: 10.1016/j.meegid.2015.03.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 02/02/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022]
Abstract
2448 microsatellite loci were identified within 83 Mb of F. hepatica genome sequence data. A panel of 15 polymorphic loci were developed and validated using genomic DNA from 46 parasites. The panel was developed and optimised as a multiplex PCR protocol. All loci could be amplified from several F. hepatica lifecycle stages with the multiplex approach.
The liver fluke, Fasciola hepatica is an economically important pathogen of sheep and cattle and has been described by the WHO as a re-emerging zoonosis. Control is heavily reliant on the use of drugs, particularly triclabendazole and as a result resistance has now emerged. The population structure of F. hepatica is not well known, yet it can impact on host–parasite interactions and parasite control with drugs, particularly regarding the spread of triclabendazole resistance. We have identified 2448 potential microsatellites from 83 Mb of F. hepatica genome sequence using msatfinder. Thirty-five loci were developed and optimised for microsatellite PCR, resulting in a panel of 15 polymorphic loci, with a range of three to 15 alleles. This panel was validated on genomic DNA from 46 adult F. hepatica; 38 liver flukes sourced from a Northwest abattoir, UK and 8 liver flukes from an established isolate (Shrewsbury; Ridgeway Research). Evidence for null alleles was found at four loci (Fh_1, Fh_8, Fh_13 and Fh_14), which showed markedly higher levels of homozygosity than the remaining 11 loci. Of the 38 liver flukes isolated from cattle livers (n = 10) at the abattoir, 37 genotypes were identified. Using a multiplex approach all 15 loci could be amplified from several life cycle stages that typically yield low amounts of DNA, including metacercariae, the infective life cycle stage present on pasture, highlighting the utility of this multiplex microsatellite panel. This study reports the largest panel of microsatellite markers available to date for population studies of F. hepatica and the first multiplex panel of microsatellite markers that can be used for several life cycle stages.
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22
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O'Corry-Crowe G, Gelatt T, Rea L, Bonin C, Rehberg M. Crossing to safety: dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus. Mol Ecol 2014; 23:5415-34. [PMID: 25266462 DOI: 10.1111/mec.12944] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 12/01/2022]
Abstract
Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here, we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n = 1106) and 16 microsatellite loci (n = 588) and show that new Steller sea lion breeding sites did not follow the typical paradigm and were instead colonized by sea lions from both a declining (Endangered) population and an increasing population. Dispersing individuals colonized rookeries in the distributional hiatus between two evolutionarily distinct (Φ¯(st) = 0.222, R¯(st) = 0.053, K = 2) metapopulations recently described as separate subspecies. Hardy-Weinberg, mixed-stock and relatedness analysis revealed levels of interbreeding on the new rookeries that exclude (i) assortative mating among eastern and western forms, and (ii) inbreeding avoidance as primary motivations for dispersal. Positive and negative density dependence is implicated in both cases of individual transfer. Migration distance limits, and conspecific attraction and performance likely influenced the sequence of rookery colonizations. This study demonstrates that resource limitation may trigger an exodus of breeding animals from declining populations, with substantial impacts on distribution and patterns of genetic variation. It also revealed that this event is rare because colonists dispersed across an evolutionary boundary, suggesting that the causative factors behind recent declines are unusual or of larger magnitude than normally occur.
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Affiliation(s)
- Greg O'Corry-Crowe
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 north, Fort Pierce, FL, 34946, USA; Southwest Fisheries Science Center, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
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23
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Franco-Trecu V, Costa P, Schramm Y, Tassino B, Inchausti P. Sex on the rocks: reproductive tactics and breeding success of South American fur seal males. Behav Ecol 2014. [DOI: 10.1093/beheco/aru145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Valtonen M, Palo JU, Aspi J, Ruokonen M, Kunnasranta M, Nyman T. Causes and consequences of fine-scale population structure in a critically endangered freshwater seal. BMC Ecol 2014; 14:22. [PMID: 25005257 PMCID: PMC4106222 DOI: 10.1186/1472-6785-14-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/03/2014] [Indexed: 11/10/2022] Open
Abstract
Background Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland. Results Microsatellite diversity within the subspecies (HE = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST = 0.107) than in maternally inherited mtDNA (FST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females. Conclusions Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.
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Affiliation(s)
- Mia Valtonen
- Department of Biology, University of Eastern Finland, Joensuu, Finland.
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Role of the lymnaeid snailPseudosuccinea columellain the transmission of the liver flukeFasciola hepaticain Egypt. J Helminthol 2014; 89:699-706. [PMID: 24865184 DOI: 10.1017/s0022149x14000406] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractExperimental infections of three EgyptianPseudosuccinea columellapopulations with sympatric miracidia ofFasciolasp., coming from cattle- or sheep-collected eggs, were carried out to determine the capacity of this lymnaeid to support larval development of the parasite. Using microsatellite markers, the isolates of Egyptian miracidia were identified asFasciola hepatica. Apart from being independent of snail origin, prevalences ranging from 60.4 to 75.5% in snails infected with five miracidia ofF. hepaticawere significantly higher than values of 30.4 to 42.2% in snails with bi-miracidial infections. The number of metacercariae ranged from 243 to 472 per cercarial-shedding snail and was independent of snail origin, parasite origin and miracidial dose used for infection. IfP. columellawas subjected to two successive bi-miracidial infections withF. hepatica, prevalence of infection was 63.3%, with a mean of 311 metacercariae per snail. These values were clearly greater than those already reported forRadix natalensisinfected with the same parasite and the same protocol. Successful experimental infection ofP. columellawithF. hepaticasuggests that this lymnaeid snail is an important intermediate host for the transmission of fascioliasis in Egypt.
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Olsen MT, Andersen LW, Dietz R, Teilmann J, Härkönen T, Siegismund HR. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units. Mol Ecol 2014; 23:815-31. [DOI: 10.1111/mec.12644] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 12/11/2013] [Accepted: 12/13/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Morten T. Olsen
- Department of Bioscience; Aarhus University; Frederiksborgvej 399 Roskilde DK-4000 Denmark
- Department of Biology; University of Copenhagen; Ole Maaløes Vej 5 Copenhagen N DK-2200 Denmark
- Centre for Geogenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 Copenhagen K 1350 Denmark
| | | | - Rune Dietz
- Department of Bioscience; Aarhus University; Frederiksborgvej 399 Roskilde DK-4000 Denmark
| | - Jonas Teilmann
- Department of Bioscience; Aarhus University; Frederiksborgvej 399 Roskilde DK-4000 Denmark
| | - Tero Härkönen
- Swedish Museum of Natural History; Box 50007 Stockholm S-10405 Sweden
| | - Hans R. Siegismund
- Department of Biology; University of Copenhagen; Ole Maaløes Vej 5 Copenhagen N DK-2200 Denmark
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27
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Bonin CA, Goebel ME, Hoffman JI, Burton RS. High male reproductive success in a low-density Antarctic fur seal (Arctocephalus gazella) breeding colony. Behav Ecol Sociobiol 2014. [DOI: 10.1007/s00265-013-1674-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Bonin CA, Goebel ME, Forcada J, Burton RS, Hoffman JI. Unexpected genetic differentiation between recently recolonized populations of a long-lived and highly vagile marine mammal. Ecol Evol 2013; 3:3701-12. [PMID: 24198934 PMCID: PMC3810869 DOI: 10.1002/ece3.732] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 11/08/2022] Open
Abstract
Many species have been heavily exploited by man leading to local extirpations, yet few studies have attempted to unravel subsequent recolonization histories. This has led to a significant gap in our knowledge of the long-term effects of exploitation on the amount and structure of contemporary genetic variation, with important implications for conservation. The Antarctic fur seal provides an interesting case in point, having been virtually exterminated in the nineteenth century but subsequently staged a dramatic recovery to recolonize much of its original range. Consequently, we evaluated the hypothesis that South Georgia (SG), where a few million seals currently breed, was the main source of immigrants to other locations including Livingston Island (LI), by genotyping 366 individuals from these two populations at 17 microsatellite loci and sequencing a 263 bp fragment of the mitochondrial hypervariable region 1. Contrary to expectations, we found highly significant genetic differences at both types of marker, with 51% of LI individuals carrying haplotypes that were not observed in 246 animals from SG. Moreover, the youngest of three sequentially founded colonies at LI showed greater similarity to SG at mitochondrial DNA than microsatellites, implying temporal and sex-specific variation in recolonization. Our findings emphasize the importance of relict populations and provide insights into the mechanisms by which severely depleted populations can recover while maintaining surprisingly high levels of genetic diversity.
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Affiliation(s)
- Carolina A Bonin
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego 9500 Gilman Dr., La Jolla, California, 92093-0208
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Soulen BK, Cammen K, Schultz TF, Johnston DW. Factors affecting harp seal (Pagophilus groenlandicus) strandings in the Northwest Atlantic. PLoS One 2013; 8:e68779. [PMID: 23874759 PMCID: PMC3714304 DOI: 10.1371/journal.pone.0068779] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 06/06/2013] [Indexed: 12/03/2022] Open
Abstract
The effects of climate change on high latitude regions are becoming increasingly evident, particularly in the rapid decline of sea ice cover in the Arctic. Many high latitude species dependent on sea ice are being forced to adapt to changing habitats. Harp seals (Pagophilus groenlandicus) are an indicator species for changing high-latitude ecosystems. This study analyzed multiple factors including ice cover, demographics, and genetic diversity, which could affect harp seal stranding rates along the eastern coast of the United States. Ice cover assessments were conducted for the month of February in the Gulf of St. Lawrence whelping region from 1991–2010 using remote sensing data, and harp seal stranding data were collected over the same time period. Genetic diversity, which may affect how quickly species can adapt to changing climates, was assessed using ten microsatellite markers to determine mean d2 in a subset of stranded and by-caught (presumably healthy) seals sampled along the northeast U.S. coast. Our study found a strong negative correlation (R2 = 0.49) between ice cover in the Gulf of St. Lawrence and yearling harp seal strandings, but found no relationship between sea ice conditions and adult strandings. Our analysis revealed that male seals stranded more frequently than females during the study period and that this relationship was strongest during light ice years. In contrast, we found no significant difference in mean d2 between stranded and by-caught harp seals. The results demonstrate that sea ice cover and demographic factors have a greater influence on harp seal stranding rates than genetic diversity, with only a little of the variance in mean d2 among stranded seals explained by ice cover. Any changes in these factors could have major implications for harp seals, and these findings should be considered in the development of future management plans for the Arctic that incorporate climate variability.
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Affiliation(s)
- Brianne K Soulen
- Duke University Marine Laboratory, Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, USA.
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30
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Hoffman JI, Dasmahapatra KK, Nichols HJ. PERMANENT GENETIC RESOURCES: Ten novel polymorphic dinucleotide microsatellite loci cloned from the Antarctic fur seal Arctocephalus gazella. Mol Ecol Resour 2013; 8:459-61. [PMID: 21585821 DOI: 10.1111/j.1471-8286.2007.01993.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ten new dinucleotide microsatellite loci were isolated from the Antarctic fur seal Arctocephalus gazella. These markers should prove useful for studying the reproductive ecology of Antarctic fur seals and other related pinniped species.
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Affiliation(s)
- Joseph I Hoffman
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK, 4 Stephenson Way, Galton Laboratory, Department of Biology, University College London, London NW1 2HE, UK
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31
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Design and implementation of degenerate microsatellite primers for the mammalian clade. PLoS One 2011; 6:e29582. [PMID: 22216321 PMCID: PMC3246486 DOI: 10.1371/journal.pone.0029582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 12/01/2011] [Indexed: 11/19/2022] Open
Abstract
Microsatellites are popular genetic markers in molecular ecology, genetic mapping and forensics. Unfortunately, despite recent advances, the isolation of de novo polymorphic microsatellite loci often requires expensive and intensive groundwork. Primers developed for a focal species are commonly tested in a related, non-focal species of interest for the amplification of orthologous polymorphic loci; when successful, this approach significantly reduces cost and time of microsatellite development. However, transferability of polymorphic microsatellite loci decreases rapidly with increasing evolutionary distance, and this approach has shown its limits. Whole genome sequences represent an under-exploited resource to develop cross-species primers for microsatellites. Here we describe a three-step method that combines a novel in silico pipeline that we use to (1) identify conserved microsatellite loci from a multiple genome alignments, (2) design degenerate primer pairs, with (3) a simple PCR protocol used to implement these primers across species. Using this approach we developed a set of primers for the mammalian clade. We found 126,306 human microsatellites conserved in mammalian aligned sequences, and isolated 5,596 loci using criteria based on wide conservation. From a random subset of ~1000 dinucleotide repeats, we designed degenerate primer pairs for 19 loci, of which five produced polymorphic fragments in up to 18 mammalian species, including the distinctly related marsupials and monotremes, groups that diverged from other mammals 120-160 million years ago. Using our method, many more cross-clade microsatellite loci can be harvested from the currently available genomic data, and this ability is set to improve exponentially as further genomes are sequenced.
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Hoffman JI, Grant SM, Forcada J, Phillips CD. Bayesian inference of a historical bottleneck in a heavily exploited marine mammal. Mol Ecol 2011; 20:3989-4008. [PMID: 21895820 DOI: 10.1111/j.1365-294x.2011.05248.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and Approximate Bayesian Computation, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important problems in conservation and evolutionary biology.
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Affiliation(s)
- J I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany.
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33
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Dar Y, Amer S, Courtioux B, Dreyfuss G. Microsatellite analysis of Fasciola spp. in Egypt. Parasitol Res 2011; 109:1741-4. [PMID: 21744021 DOI: 10.1007/s00436-011-2520-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/22/2011] [Indexed: 11/25/2022]
Abstract
Recently, the topic of diversity in Fasciola population in Egypt is controversial. The present study was performed to study the genetic diversity of isolated flukes based on microsatellites markers. Fasciola worms were collected from different hosts and geographical locations in Egypt. Control samples of Fasciola hepatica from France as well as Fasciola gigantica from Cameroon were included in the study. Collected flukes were identified morphologically and subjected for analysis using four microsatellite markers. Results of microsatellite profile (FM1 and FM2) proved that both species of Fasciola are distributed in Egypt irrespective of geographical location and host. Nevertheless, the microsatellite profile of some analyzed loci (FM2 and FM3) proved that Egyptian flukes showed more alleles compared to the reference ones. Differences of microsatellite profile in Egyptian isolates than that of corresponding reference samples indicate the remarkable diversity of these isolates. The present results highlighted the utility of microsatellite profile to discriminate between Fasciola species and to elucidate the diversity within the species. To our knowledge, this is the first time to study microsatellite polymorphism in Fasciola populations in Egypt.
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Affiliation(s)
- Yasser Dar
- Zoology Department, Faculty of Sciences, Tanta University, Tanta, Egypt
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34
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Schultz JK, Baker JD, Toonen RJ, Harting AL, Bowen BW. Range-wide genetic connectivity of the Hawaiian monk seal and implications for translocation. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2011; 25:124-132. [PMID: 21166713 DOI: 10.1111/j.1523-1739.2010.01615.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Hawaiian monk seal (Monachus schauinslandi) is one of the most critically endangered marine mammals. Less than 1200 individuals remain, and the species is declining at a rate of approximately 4% per year as a result of juvenile starvation, shark predation, and entanglement in marine debris. Some of these problems may be alleviated by translocation; however, if island breeding aggregates are effectively isolated subpopulations, moving individuals may disrupt local adaptations. In these circumstances, managers must balance the pragmatic need of increasing survival with theoretical concerns about genetic viability. To assess range-wide population structure of the Hawaiian monk seal, we examined an unprecedented, near-complete genetic inventory of the species (n =1897 seals, sampled over 14 years) at 18 microsatellite loci. Genetic variation was not spatially partitioned ((w) =-0.03, p = 1.0), and a Bayesian clustering method provided evidence of one panmictic population (K =1). Pairwise F(ST) comparisons (among 7 island aggregates over 14 annual cohorts) did not reveal temporally stable, spatial reproductive isolation. Our results coupled with long-term tag-resight data confirm seal movement and gene flow throughout the Hawaiian Archipelago. Thus, human-mediated translocation of seals among locations is not likely to result in genetic incompatibilities.
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Affiliation(s)
- Jennifer K Schultz
- Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii, Kaneohe, HI 96744, U.S.A.
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ANDERSEN LISELOTTEW, LYDERSEN CHRISTIAN, FRIE ANNEK, ROSING-ASVID AQQALU, HAUKSSON ERLINGUR, KOVACS KITM. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina). Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2010.01577.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Osborne AJ, Brauning R, Schultz JK, Kennedy MA, Slate J, Gemmell NJ. Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora. Mol Ecol Resour 2010; 11:503-13. [PMID: 21481208 DOI: 10.1111/j.1755-0998.2010.02962.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding genetic variation responsible for phenotypic differences in natural populations is significantly hampered by a lack of genomic data for many species. Levels of variation can, however, be estimated using microsatellite markers, which may be useful for relating individual fitness to genetic diversity. Prior studies have demonstrated correlations between heterozygosity and individual fitness in some species. These correlations are sometimes driven by a subset of markers, and it is unclear whether this is because those markers best reflect genome-wide heterozygosity, or whether they are linked to fitness-related genes. Differentiating between these scenarios is hindered when the genomic location of markers is unknown. Here, we develop a predicted genomic map of pinniped microsatellite loci based on conservation of primary sequence and genomic location between dog, cat and giant panda. We mapped 210 of 260 (81%) microsatellites from pinnipeds to locations in dog, cat and giant panda genomes. Based on the demonstrable synteny between the genomes of closely related taxa within the Carnivora, we use these data to identify those microsatellites with the greatest chance of cross-species amplification success and demonstrate successful amplification of 21 of 26 loci for cat, dog and two seal species. We also demonstrate the potential to identify candidate genes that may underpin the functional relationship with individual fitness. Overall, we show that this approach provides a rapid and robust method to elucidate genome organisation for nonmodel organisms and have established a resource that facilitates further genetic research on pinnipeds that also has wider applicability to other carnivores.
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Affiliation(s)
- Amy J Osborne
- Department of Anatomy and Structural Biology, Centre for Reproduction and Genomics, University of Otago, Dunedin, New Zealand.
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37
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Genome-Wide Loss of Diversity in the Critically Endangered Hawaiian Monk Seal. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2060863] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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38
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Dickerson BR, Ream RR, Vignieri SN, Bentzen P. Population structure as revealed by mtDNA and microsatellites in northern fur seals, Callorhinus ursinus, throughout their range. PLoS One 2010; 5:e10671. [PMID: 20498854 PMCID: PMC2871788 DOI: 10.1371/journal.pone.0010671] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 04/07/2010] [Indexed: 11/20/2022] Open
Abstract
Background The northern fur seal (Callorhinus ursinus; NFS) is a widely distributed pinniped that has been shown to exhibit a high degree of philopatry to islands, breeding areas on an island, and even to specific segments of breeding areas. This level of philopatry could conceivably lead to highly genetically divergent populations. However, northern fur seals have the potential for dispersal across large distances and have experienced repeated rapid population expansions following glacial retreat and the more recent cessation of intensive harvest pressure. Methodology/Principal Findings Using microsatellite and mitochondrial loci, we examined population structure in NFS throughout their range. We found only weak population genetic structure among breeding islands including significant FST and ΦST values between eastern and western Pacific islands. Conclusions We conclude that insufficient time since rapid population expansion events (both post glacial and following the cessation of intense harvest pressure) mixed with low levels of contemporary migration have resulted in an absence of genetic structure across the entire northern fur seal range.
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Affiliation(s)
- Bobette R Dickerson
- National Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, Seattle, Washington, United States of America.
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39
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Hoffman JI, Forcada J, Amos W. Exploring the mechanisms underlying a heterozygosity-fitness correlation for canine size in the Antarctic fur seal Arctocephalus gazella. ACTA ACUST UNITED AC 2010; 101:539-52. [PMID: 20457623 DOI: 10.1093/jhered/esq046] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Although heterozygosity-fitness correlations (HFCs) are widely reported in the literature, most studies use too few markers to allow the proximate mechanisms to be convincingly resolved. Two competing hypotheses have been proposed: the general effect hypothesis, in which marker heterozygosity correlates with genome-wide heterozygosity and hence the inbreeding coefficient f, and the local effect hypothesis, in which one or more of the markers by chance exhibit associative overdominance. To explore the relative contributions of general and local effects in a free-ranging marine mammal population, we revisited a strong HFC found using 9 microsatellite loci for canine tooth size in 84 male Antarctic fur seals Arctocephalus gazella (Hoffman JI, Hanson N, Forcada J, Trathan PN, Amos W. 2010. Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in the Antarctic fur seal Arctocephalus gazella. J Hered.). Increasing the number of markers to 76, we find that heterozygosity is uncorrelated across loci, indicating that inbred individuals are rare or absent. Similarly, while the HFC based on overall heterozygosity is lost, stochastic simulations indicate that when an HFC is due to inbreeding depression, increasing marker number invariably strengthens the HFC. Together these observations argue strongly that the original HFC was not due to inbreeding depression. In contrast, a subset of markers show individually significant effects, and these are nonrandomly distributed across the marker panel, being preferentially associated with markers cloned from other species. Using basic alignment search tool searches, we were able to locate 94% of loci to unique locations in the dog genome, but the local genes are functionally diverse, and the majority cannot be linked directly to growth. Our results suggest that inbreeding depression contributes little if at all to the relationship between heterozygosity and tooth size but that instead the primary mechanism involves associative overdominance. These findings contribute to a growing body of evidence suggesting that general effects are likely to be uncommon in natural populations.
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Affiliation(s)
- Joseph I Hoffman
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
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40
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Hoffman JI, Hanson N, Forcada J, Trathan PN, Amos W. Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in Antarctic fur seals Arctocephalus gazella. J Hered 2010; 101:527-38. [PMID: 20457622 DOI: 10.1093/jhered/esq045] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most studies of heterozygosity-fitness correlations (HFCs) in natural populations relate to fitness traits expressed early in life, whereas traits that are often more difficult to measure such as longevity and adult body size remain elusive. Teeth provide a window on an individual's life history, allowing the reliable estimation of both age and body size. Consequently, we collected paired upper canine teeth and tissue samples from 84 adult male Antarctic fur seals Arctocephalus gazella that died of natural causes at Bird Island, South Georgia. Tooth size is a good predictor of skull and body size both within and across taxa, and we similarly find a strong relationship with skull size in our species. In turn, tooth size is itself predicted strongly by genetic heterozygosity estimated using 9 microsatellites. With only 9 loci, the exact mechanisms involved remain unclear, although the observed pattern appears largely attributable to a small subset of loci, suggesting that associative overdominance rather than inbreeding depression provides the proximate mechanism. In addition, locating these markers in the dog genome reveals proximity to genes involved with fat metabolism and growth. Our study illustrates how canine teeth, and potentially other structures such as tympano-periotic bone, waxy inner earplugs, or otoliths, may be used to explore links between genetic variation and important life-history traits in free-ranging vertebrate populations.
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Affiliation(s)
- Joseph I Hoffman
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
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41
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Silva RW, de Freitas TRO, Sbalqueiro IJ. Evaluation of genetic variability in the collared peccary Pecari tajacu and the white-lipped peccary Tayassu pecari by microsatellite markers. Genet Mol Biol 2010; 33:62-7. [PMID: 21637606 PMCID: PMC3036067 DOI: 10.1590/s1415-47572010005000002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 07/01/2009] [Indexed: 11/26/2022] Open
Abstract
In this study, the microsatellite technique was used to evaluate the genetic variability in populations of collared and white-lipped peccaries kept in captivity. Six primers developed for domestic pigs were used and amplified in both species. They revealed the presence of five polymorphic loci and one monomorphic locus. The polymorphic loci included 4 of the 16 alleles in collared peccaries, and 3 of the 10 alleles in the white-lipped peccaries. Polymorphic information content (PIC) in both species and all the loci was highly informative. The probability of paternity exclusion (PEC), if one of the parents is known, was almost as high in white-lipped peccaries (95.53%) as in the collared (99,48%). The Fst values for collared (0.042) and white-lipped (0.1387) peccaries showed that both populations are not structured. The Fis values for all loci, except ACTG2 in white-lipped peccaries (-0.0275) and in both species (0.1985 to 0.9284 in collared peccaries and 0.3621 to 0.4754 in the white-lipped), revealed a high level of homozygosis, probably caused by inbreeding. Data on heterologous amplification and genetic variability in collared and white-lipped peccaries are presented for the first time.
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Han JB, Sun FY, Gao XG, He CB, Wang PL, Ma ZQ, Wang ZH. Low Microsatellite Variation in Spotted Seal (Phoca largha) Shows a Decrease in Population Size in the Liaodong Gulf Colony. ANN ZOOL FENN 2010. [DOI: 10.5735/086.047.0102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Buschiazzo E, Gemmell NJ. Conservation of human microsatellites across 450 million years of evolution. Genome Biol Evol 2010; 2:153-65. [PMID: 20333231 PMCID: PMC2839350 DOI: 10.1093/gbe/evq007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2010] [Indexed: 11/21/2022] Open
Abstract
The sequencing and comparison of vertebrate genomes have enabled the
identification of widely conserved genomic elements. Chief among these are genes
and cis-regulatory regions, which are often under selective
constraints that promote their retention in related organisms. The conservation
of elements that either lack function or whose functions are yet to be ascribed
has been relatively little investigated. In particular, microsatellites, a class
of highly polymorphic repetitive sequences considered by most to be neutrally
evolving junk DNA that is too labile to be maintained in distant species, have
not been comprehensively studied in a comparative genomic framework. Here, we
used the UCSC alignment of the human genome against those of 11 mammalian and
five nonmammalian vertebrates to identify and examine the extent of conservation
of human microsatellites in vertebrate genomes. Out of 696,016 microsatellites
found in human sequences, 85.39% were conserved in at least one other species,
whereas 28.65% and 5.98% were found in at least one and three nonprimate
species, respectively. An exponential decline of microsatellite conservation
with increasing evolutionary time, a comparable distribution of conserved versus
nonconserved microsatellites in the human genome, and a positive correlation
between microsatellite conservation and overall sequence conservation, all
suggest that most microsatellites are only maintained in genomes by chance,
although exceptionally conserved human microsatellites were also found in
distant mammals and other vertebrates. Our findings provide the first
comprehensive survey of microsatellite conservation across deep evolutionary
timescales, in this case 450 Myr of vertebrate evolution, and provide new tools
for the identification of functional conserved microsatellites, the development
of cross-species microsatellite markers and the study of microsatellite
evolution above the species level.
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Affiliation(s)
- Emmanuel Buschiazzo
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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44
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Lancaster ML, Arnould JPY, Kirkwood R. Genetic status of an endemic marine mammal, the Australian fur seal, following historical harvesting. Anim Conserv 2009. [DOI: 10.1111/j.1469-1795.2009.00325.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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45
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History and fate of a small isolated population of Weddell seals at White Island, Antarctica. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9856-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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46
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Vanpé C, Buschiazzo E, Abdelkrim J, Morrow G, Nicol SC, Gemmell NJ. Development of microsatellite markers for the short-beaked echidna using three different approaches. AUST J ZOOL 2009. [DOI: 10.1071/zo09033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We used three different methods, size-selected genomic library, cross-species amplification of a mammal-wide set of conserved microsatellites and genomic sequencing, to develop a panel of 43 microsatellite loci for the short-beaked echidna (Tachyglossus aculeatus). These loci were screened against 13 individuals from three different regions (Tasmania, Kangaroo Island, Perth region), spanning the breadth of the range of the short-beaked echidna. Nine of the 43 tested loci amplified reliably, generated clear peaks on the electropherogram and were polymorphic, with the number of alleles per locus ranging from two to eight (mean = 3.78) in the individuals tested. Polymorphic information content ranged from 0.16 to 0.78, and expected heterozygosity ranged from 0.19 to 0.84. One of the nine microsatellites showed a heterozygote deficit, suggesting a high probability of null alleles. The genomic sequencing approach using data derived from the Roche FLX platform is likely to provide the most promising method to develop echidna microsatellites. The microsatellite markers developed here will be useful tools to study population genetic structure, gene flow, kinship and parentage in Tachyglossus sp. and potentially also in endangered Zaglossus species.
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47
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Caudron AK, Negro SS, Fowler M, Boren L, Poncin P, Robertson BC, Gemmell NJ. Alternative mating tactics in the New Zealand fur seal (Arctocephalus forsteri): when non-territorial males are successful too. AUST J ZOOL 2009. [DOI: 10.1071/zo09024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In polygynous mammals, the status of many males does not allow them to have a high social rank and theory predicts selection for alternative mating tactics. Alternative tactics were suggested to explain discrepancies between mating and paternity successes in several pinniped species. However, information on alternative tactics in fur seals is limited. Here, we focus on the polygynous New Zealand fur seal, Arctocephalus forsteri, predicting that competition for females is likely to cause a diversification of male mating tactics and that non-territorial tactics can yield reproductive success. We describe the behaviour of 38 males in a medium to large colony. Paternity success was assessed using CERVUS and PASOS, from a pool of 82 pups sampled at the study site and at neighbouring breeding areas. To see whether size is correlated with mating tactic, the length of 17 males was estimated using photogrammetry. Cluster analysis identified three male behavioural profiles: one corresponding to large territorial males and two illustrating alternative tactics employed by smaller non-territorial males. Of the 13 pups born at the study site that were assigned a father, eight were sired by three territorial males and five were sired by non-territorial males. Our study highlights that holding a territory is not a necessary condition for reproductive success in all otariids.
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48
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Schultz JK, Baker JD, Toonen RJ, Bowen BW. Extremely low genetic diversity in the endangered Hawaiian monk seal (Monachus schauinslandi). J Hered 2008; 100:25-33. [PMID: 18815116 DOI: 10.1093/jhered/esn077] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hunted to near extinction in the late 19th century, the endangered and endemic Hawaiian monk seal (Monachus schauinslandi) exhibits low variation at all molecular markers tested to date. Here we confirm extreme paucity of genetic diversity, finding polymorphisms at only 8 of 154 microsatellite loci tested (143 novel species-specific loci, 10 loci from Antarctic seals, and 1 previously characterized locus). This screening revealed unprecedentedly low levels of allelic diversity and heterozygosity (A = 1.1, H(e) = 0.026). Subsequent analyses of 2409 Hawaiian monk seals at the 8 polymorphic loci provide evidence for a bottleneck (P = 0.002), but simulations indicate low genetic diversity (H(e) < 0.09) prior to recorded human influence. There is little indication of contemporary inbreeding (F(IS) = 0.018) or population structure (K = 1 population). Minimal genetic variation did not prevent partial recovery by the late 1950s and may not be driving the current population decline to approximately 1200 seals. Nonetheless, genotyping nearly every individual living during the past 25 years sets a new benchmark for low genetic diversity in an endangered species.
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Affiliation(s)
- Jennifer K Schultz
- Department of Zoology and Hawaii Institute of Marine Biology, University of Hawaii, PO Box 1346, Kaneohe, HI 96744, USA.
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49
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Hoffman JI. A panel of new microsatellite loci for genetic studies of antarctic fur seals and other otariids. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9669-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Rijks JM, Hoffman JI, Kuiken T, Osterhaus ADME, Amos W. Heterozygosity and lungworm burden in harbour seals (Phoca vitulina). Heredity (Edinb) 2008; 100:587-93. [PMID: 18398424 DOI: 10.1038/hdy.2008.18] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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