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      Phylogeography and Demographic History of Chinese Black-Spotted Frog Populations ( Pelophylax nigromaculata): Evidence for Independent Refugia Expansion and Secondary Contact

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      1 , 1 , 1 , 1 ,
      BMC Evolutionary Biology
      BioMed Central

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          Abstract

          Background

          Pleistocene glaciations had considerable impact on phylogeographic patterns within and among closely related species of many vertebrates. Compared to Europe and North America, research on the phylogeography of vertebrates in East Asia, particularly in China, remains limited. The black-spotted frog ( Pelophylax nigromaculata) is a widespread species in East Asia. The wide distribution of this species in China makes it an ideal model for the study of palaeoclimatic effects on vertebrates in East Asia. Our previous studies of P. nigromaculata revealed significant subdivisions between the northeast China populations and populations in other regions of the mainland. In the present study, we aim to see whether the deepest splits among lineages and perhaps subsequent genealogical divisions are temporally consistent with a Pleistocene origin and whether clade geographic distributions, with insight into expansion patterns, are similarly spatially consistent with this model.

          Results

          Using 1143 nucleotides of the mitochondrial cytochrome b gene from 262 individuals sampled from 28 localities, two main clades (clade A and clade B) differing by c. 7.72% sequence divergence were defined from parsimony analyses. The corresponding timing of lineage divergence, 0.92 Mya, indicates a most likely Pleistocene split. The A clade is further subdivided into two sub-clades, A1 and A2 with 1.22% sequence divergence. Nested clade phylogeographical and population demographic analyses suggested that the current distribution of this frog species was the result of range expansion from two independent refugia during the last interglacial period. We discovered a population within which haplotype lineages A and B of P. nigromaculata coexist in the Dongliao area of China by nucleotide sequences, PCR-RFLP and ISSR (inter simple sequence repeat) patterns. The ISSR result in particular supported divergence between the mitochondrial clades A and B and implied introgressive gene flow between the two divergent lineages.

          Conclusion

          Nested clade phylogeographical and population demographic analyses indicate that the current distribution of P. nigromaculata is the result of range expansion from two independent refugia during the last interglacial period in late Pleistocene. One refugium was in east China and the lower elevations of south-western plateau. The distribution of the other mitochondrial clade is consistent with the presence of a refugium in the Korean Peninsula. The gene flow as detected by ISSR markers suggests a range expansion of the two refugia and a secondary contact between the two highly divergent lineages in the Dongliao (DL) area of northeast China.

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          Most cited references49

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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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            Some genetic consequences of ice ages, and their role in divergence and speciation

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              Deglacial sea-level record from Tahiti corals and the timing of global meltwater discharge

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                Author and article information

                Journal
                BMC Evol Biol
                BMC Evolutionary Biology
                BioMed Central
                1471-2148
                2008
                24 January 2008
                : 8
                : 21
                Affiliations
                [1 ]Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
                Article
                1471-2148-8-21
                10.1186/1471-2148-8-21
                2262875
                18215328
                7b42cebf-e1c7-46d8-b8b8-05a85237de9f
                Copyright © 2008 Zhang 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
                : 6 August 2007
                : 24 January 2008
                Categories
                Research Article

                Evolutionary Biology
                Evolutionary Biology

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