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      Long‐term demographic decline and late glacial divergence in a Californian paleoendemic: Sequoiadendron giganteum (giant sequoia)

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          Abstract

          Mediterranean ecosystems comprise a high proportion of endemic taxa whose response to climate change will depend on their evolutionary origins. In the California flora, relatively little attention has been given to the evolutionary history of paleoendemics from a molecular perspective, yet they number among some of the world's most iconic plant species. Here, we address questions of demographic change in Sequoiadendron giganteum (giant sequoia) that is restricted to a narrow belt of groves in the Sierra Nevada Mountains. We ask whether the current distribution is a result of northward colonization since the last glacial maximum ( LGM), restriction of a broader range in the recent past ( LGM) or independent colonizations in the deeper past. Genetic diversity at eleven microsatellite loci decreased with increasing latitude, but partial regressions suggested this was a function of smaller population sizes in the north. Disjunct populations north of the Kings River were divergent from those south of the Kings River that formed a single cluster in Bayesian assignment tests. Demographic inferences supported a demographic contraction just prior to the LGM as the most likely scenario for the current disjunct range of the species. This contraction appeared to be superimposed upon a long‐term decline in giant sequoia over the last 2 million years, associated with increasing aridity due to the Mediterranean climate. Overall, low genetic diversity, together with competition in an environment to which giant sequoia is likely already poorly adapted, will pose major constraints on its success in the face of increasing aridity.

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          Isolation by distance, web service

          Background The population genetic pattern known as "isolation by distance" results from spatially limited gene flow and is a commonly observed phenomenon in natural populations. However, few software programs exist for estimating the degree of isolation by distance among populations, and they tend not to be user-friendly. Results We have created Isolation by Distance Web Service (IBDWS) a user-friendly web interface for determining patterns of isolation by distance. Using this site, population geneticists can perform a variety of powerful statistical tests including Mantel tests, Reduced Major Axis (RMA) regression analysis, as well as calculate F ST between all pairs of populations and perform basic summary statistics (e.g., heterozygosity). All statistical results, including publication-quality scatter plots in Postscript format, are returned rapidly to the user and can be easily downloaded. Conclusion IBDWS population genetics analysis software is hosted at and documentation is available at . The source code has been made available on Source Forge at .
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            Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

            Summary: Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC. Availability: The software DIY ABC is freely available at http://www.montpellier.inra.fr/CBGP/diyabc. Contact: j.cornuet@imperial.ac.uk Supplementary information: Supplementary data are also available at http://www.montpellier.inra.fr/CBGP/diyabc
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              Estimation of pairwise relatedness with molecular markers.

              Applications of quantitative genetics and conservation genetics often require measures of pairwise relationships between individuals, which, in the absence of known pedigree structure, can be estimated only by use of molecular markers. Here we introduce methods for the joint estimation of the two-gene and four-gene coefficients of relationship from data on codominant molecular markers in randomly mating populations. In a comparison with other published estimators of pairwise relatedness, we find these new "regression" estimators to be computationally simpler and to yield similar or lower sampling variances, particularly when many loci are used or when loci are hypervariable. Two examples are given in which the new estimators are applied to natural populations, one that reveals isolation-by-distance in an annual plant and the other that suggests a genetic basis for a coat color polymorphism in bears.
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                Author and article information

                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                12 April 2016
                May 2016
                : 6
                : 10 ( doiID: 10.1002/ece3.2016.6.issue-10 )
                : 3342-3355
                Affiliations
                [ 1 ] Department of Environmental Science Policy and ManagementUniversity of California Berkeley California 94720
                Author notes
                [*] [* ] Correspondence

                Richard S. Dodd, Department of Environmental Science Policy and Management, University of California, Berkeley, CA 94720.

                Tel: (1) 510 643 1635;

                Fax: (1) 510 643 5438;

                E‐mail: dodd@ 123456berkeley.edu

                Article
                ECE32122
                10.1002/ece3.2122
                4870217
                27252835
                444dd339-7693-4cfd-8036-86f08124a60d
                © 2016 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 11 November 2015
                : 14 March 2016
                : 21 March 2016
                Page count
                Pages: 14
                Funding
                Funded by: Save the Redwoods League – USA
                Award ID: 070
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece32122
                May 2016
                Converter:WILEY_ML3GV2_TO_NLMPMC version:4.8.9 mode:remove_FC converted:17.05.2016

                Evolutionary Biology
                demographic change,genetic structure,giant sequoia,pleistocene,population decline,sierra nevada

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