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      Genetic connectivity between land and sea: the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea

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          Abstract

          Introduction

          We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces.

          Results

          Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set.

          Conclusions

          We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.

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          Most cited references28

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          A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.

          We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.
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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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              A simulated annealing approach to define the genetic structure of populations.

              We present a new approach for defining groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by-product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims to maximize the proportion of total genetic variance due to differences between groups of populations (spatial analysis of molecular variance; samova). Monte Carlo simulations were used to study the performance of our approach and, for comparison, the behaviour of the Monmonier algorithm, a procedure commonly used to identify zones of sharp genetic changes in a geographical area. Simulations showed that the samova algorithm indeed finds maximally differentiated groups, which do not always correspond to the simulated group structure in the presence of isolation by distance, especially when data from a single locus are available. In this case, the Monmonier algorithm seems slightly better at finding predefined genetic barriers, but can often lead to the definition of groups of populations not differentiated genetically. The samova algorithm was then applied to a set of European roe deer populations examined for their mitochondrial DNA (mtDNA) HVRI diversity. The inferred genetic structure seemed to confirm the hypothesis that some Italian populations were recently reintroduced from a Balkanic stock, as well as the differentiation of groups of populations possibly due to the postglacial recolonization of Europe or the action of a specific barrier to gene flow.
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                Author and article information

                Journal
                Front Zool
                Front. Zool
                Frontiers in Zoology
                BioMed Central
                1742-9994
                2013
                25 April 2013
                : 10
                : 21
                Affiliations
                [1 ]Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, D–14476, Germany
                [2 ]Department of Biology and Biotechnology “Charles Darwin”, University of Rome “Sapienza”, Viale dell’ Università 32, Rome, 00185, Italy
                Article
                1742-9994-10-21
                10.1186/1742-9994-10-21
                3640956
                23618554
                ed707ad3-def7-4aed-8ddb-f4737447f44a
                Copyright ©2013 Pavesi et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 21 November 2012
                : 3 April 2013
                Categories
                Research

                Animal science & Zoology
                orchestia montagui,talitrids,mediterranean sea,phylogeography,mitochondrial dna,microsatellites,allozymes,approximate bayesian computation

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