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      Low mtDNA diversity in a highly differentiated population of spinner dolphins ( Stenella longirostris) from the Fernando de Noronha Archipelago, Brazil

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          Abstract

          Spinner dolphins ( Stenella longirostris, Gray 1828) are widely distributed in tropical waters around the world. Although they occur in large, pelagic groups in the Eastern Tropical Pacific, elsewhere in the Pacific they are found in small and genetically isolated populations associated with islands. This species is considered to be “Least Concern” (LC) by the World Conservation Union (IUCN). To assess genetic diversity and population structure of an island-associated population in the South Atlantic Ocean we surveyed 162 spinner dolphins throughout the Fernando de Noronha Archipelago of the northeast coast of Brazil using ten microsatellite loci and sequencing a 413-bp section of the mitochondrial DNA (mtDNA) control region. Eleven mtDNA haplotypes were identified and haplotype diversity ( h) and nucleotide diversity ( π) were 0.3747 and 0.0060, respectively. Median-Joining Network revealed the presence of two very divergent haplotypes and F-statistics indicated some heterogeneity between two sampling years. All microsatellite loci were polymorphic ( H o : 0.767; H e : 0,764) but, revealed no detectable substructure. We also compared the mtDNA haplotypes from Noronha to 159 haplotypes representing 893 individuals from 14 locations worldwide. We found that the two common haplotypes from the Fernando de Noronha Archipelago were absent in all other populations. These comparisons showed that Noronha spinner dolphins are likely more differentiated than other island populations, suggesting that they form societies with strong site fidelity mediated by females.

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          Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.

          We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population that has been growing in size exponentially for a long time. We show that, in a population of constant size, the sample distribution of pairwise differences will typically deviate substantially from the geometric distribution expected, because the history of coalescent events in a single sample of genes imposes a substantial correlation on pairwise differences. Consequently, a goodness-of-fit test of observed pairwise differences to the geometric distribution, which assumes that each pairwise comparison is independent, is not a valid test of the hypothesis that the genes were sampled from a panmictic population of constant size. In an exponentially growing population in which the product of the current population size and the growth rate is substantially larger than one, our analytical and simulation results show that most coalescent events occur relatively early and in a restricted range of times. Hence, the "gene tree" will be nearly a "star phylogeny" and the distribution of pairwise differences will be nearly a Poisson distribution. In that case, it is possible to estimate r, the population growth rate, if the mutation rate, mu, and current population size, N0, are assumed known. The estimate of r is the solution to ri/mu = ln(N0r) - gamma, where i is the average pairwise difference and gamma approximately 0.577 is Euler's constant.
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            Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution

            Genetic methods are routinely used to estimate contemporary effective population size (N e) in natural populations, but the vast majority of applications have used only the temporal (two-sample) method. We use simulated data to evaluate how highly polymorphic molecular markers affect precision and bias in the single-sample method based on linkage disequilibrium (LD). Results of this study are as follows: (1) Low-frequency alleles upwardly bias , but a simple rule can reduce bias to
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              Microsatellite markers for the study of cetacean populations.

              Microsatellites are one of the most important classes of nuclear genetic markers and offer many advantages for the study of marine mammals. Here we describe the isolation and characterization of 12 cetacean microsatellites which are then tested across 30 different cetacean species. For around half the species tested, five or more polymorphic loci were identified. Since many species were represented by only one or two specimens, this figure is likely to underestimate the usefulness of these markers. No relationship was found between microsatellite repeat length and proportion of species which gave polymorphic products.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: ConceptualizationRole: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                7 April 2020
                2020
                : 15
                : 4
                : e0230660
                Affiliations
                [1 ] Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, Espírito Santo, Brazil
                [2 ] Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Fernando de Noronha, Pernambuco, Brazil
                [3 ] Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória, Espírito Santo, Brazil
                [4 ] Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil
                [5 ] Instituto de Biociências, Departamento de Genética, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, São Paulo, Brazil
                [6 ] Instituto de Biociências, Campus do Litoral Paulista, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São Vicente, São Paulo, Brazil
                [7 ] Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, Oregon, United States of America
                [8 ] Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo (UFES), São Mateus, Espírito Santo, Brazil
                Universidad de los Andes, COLOMBIA
                Author notes

                Competing Interests: Petrobrás (Petrobras Socioenvironmental Program), Aqualie Institute, Chevron Brasil Upstream Frade Ltda and BG Group support the sampling expeditions at the Fernando de Noronha Archipelago. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

                Author information
                http://orcid.org/0000-0003-1594-8294
                http://orcid.org/0000-0001-7987-5800
                Article
                PONE-D-19-15246
                10.1371/journal.pone.0230660
                7138316
                32255776
                64b8e52e-bf8c-4572-bcbb-c50ee94faaca
                © 2020 Faria et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 June 2019
                : 5 March 2020
                Page count
                Figures: 5, Tables: 4, Pages: 18
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100002322, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior;
                Award ID: 001
                Award Recipient :
                Funded by: Fundação Estadual de Amparo à Pesquisa do Estado do Espírito Santo (BR)
                Award Recipient :
                This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001, to DMF, and in part by the Fundação de Amparo à Pesquisa e Inovação do Espírito Santo (FAPES) to DMF. Petrobrás Ambiental (Petrobras Environmental), Aqualie Institute, Chevron Brasil Upstream Frade Ltda and BG Group support the sampling expeditions at the Fernando de Noronha Archipelago. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Marine Mammals
                Dolphins
                Biology and Life Sciences
                Marine Biology
                Marine Mammals
                Dolphins
                Earth Sciences
                Marine and Aquatic Sciences
                Marine Biology
                Marine Mammals
                Dolphins
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Mapping
                Haplotypes
                Biology and Life Sciences
                Biogeography
                Phylogeography
                Ecology and Environmental Sciences
                Biogeography
                Phylogeography
                Earth Sciences
                Geography
                Biogeography
                Phylogeography
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
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                Genetics
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                Population Biology
                Population Genetics
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                Genetics
                DNA
                Forms of DNA
                Mitochondrial DNA
                Biology and life sciences
                Biochemistry
                Nucleic acids
                DNA
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                Mitochondrial DNA
                Earth Sciences
                Geomorphology
                Topography
                Landforms
                Islands
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
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                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Biology and Life Sciences
                Genetics
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                Microsatellite Loci
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