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      Genetic Diversity and Local Connectivity in the Mediterranean Red Gorgonian Coral after Mass Mortality Events

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          Abstract

          Estimating the patterns of connectivity in marine taxa with planktonic dispersive stages is a challenging but crucial task because of its conservation implications. The red gorgonian Paramuricea clavata is a habitat forming species, characterized by short larval dispersal and high reproductive output, but low recruitment. In the recent past, the species was impacted by mass mortality events caused by increased water temperatures in summer. In the present study, we used 9 microsatellites to investigate the genetic structure and connectivity in the highly threatened populations from the Ligurian Sea (NW Mediterranean). No evidence for a recent bottleneck neither decreased genetic diversity in sites impacted by mass mortality events were found. Significant IBD pattern and high global F ST confirmed low larval dispersal capability in the red gorgonian. The maximum dispersal distance was estimated at 20–60 km. Larval exchange between sites separated by hundreds of meters and between different depths was detected at each site, supporting the hypothesis that deeper subpopulations unaffected by surface warming peaks may provide larvae for shallower ones, enabling recovery after climatically induced mortality events.

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          Most cited references 19

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          Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power.

          Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (DLR) appeared to be an effective way to predict whether F0 immigrants could be identified for a particular pair of populations using a given set of markers.
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            Detecting immigration by using multilocus genotypes.

            Immigration is an important force shaping the social structure, evolution, and genetics of populations. A statistical method is presented that uses multilocus genotypes to identify individuals who are immigrants, or have recent immigrant ancestry. The method is appropriate for use with allozymes, microsatellites, or restriction fragment length polymorphisms (RFLPs) and assumes linkage equilibrium among loci. Potential applications include studies of dispersal among natural populations of animals and plants, human evolutionary studies, and typing zoo animals of unknown origin (for use in captive breeding programs). The method is illustrated by analyzing RFLP genotypes in samples of humans from Australian, Japanese, New Guinean, and Senegalese populations. The test has power to detect immigrant ancestors, for these data, up to two generations in the past even though the overall differentiation of allele frequencies among populations is low.
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              Reliability of genetic bottleneck tests for detecting recent population declines.

              The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history. © 2012 Blackwell Publishing Ltd.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                16 March 2016
                2016
                : 11
                : 3
                Affiliations
                [1 ]Departamento de Biologia and CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
                [2 ]Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
                [3 ]ENEA, Marine Environment Research Centre, La Spezia, Italy
                [4 ]CCMAR - Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
                University of Padova, ITALY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: SC HQ. Performed the experiments: JP. Analyzed the data: JP. Contributed reagents/materials/analysis tools: HQ. Wrote the paper: JP HQ SC. Contributed to sampling and data analysis: JB. Contributed to data analysis and reviewed the manuscript: ES.

                Article
                PONE-D-15-27239
                10.1371/journal.pone.0150590
                4794161
                26982334
                © 2016 Pilczynska 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.

                Page count
                Figures: 3, Tables: 5, Pages: 16
                Product
                Funding
                JP was supported by a Ph.D. grant from the Erasmus Mundus Marine Ecosystem Health and Conservation (MARES) doctoral program; http://www.mares-eu.org/. This work is a part of the DiverseShores - Testing associations between genetic and community diversity in European rocky shore environments (PTDC/BIA-BIC/114526/2009) research project, funded by the Fundação para a Ciência e Tecnologia (FCT) under the COMPETE program supported by the European Regional Development Fund.
                Categories
                Research Article
                Biology and Life Sciences
                Marine Biology
                Coral Reefs
                Earth Sciences
                Marine and Aquatic Sciences
                Marine Biology
                Coral Reefs
                Earth Sciences
                Marine and Aquatic Sciences
                Reefs
                Coral Reefs
                Earth Sciences
                Marine and Aquatic Sciences
                Reefs
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Biology and Life Sciences
                Genetics
                Heredity
                Heterozygosity
                Biology and Life Sciences
                Developmental Biology
                Metamorphosis
                Larvae
                People and Places
                Demography
                Death Rates
                Biology and Life Sciences
                Population Biology
                Population Metrics
                Death Rates
                Biology and Life Sciences
                Marine Biology
                Marine Conservation
                Earth Sciences
                Marine and Aquatic Sciences
                Marine Biology
                Marine Conservation
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                All relevant data are within the paper and its Supporting Information files.

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