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      Multi-Locus Phylogeographic and Population Genetic Analysis of Anolis carolinensis: Historical Demography of a Genomic Model Species

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          Abstract

          The green anole ( Anolis carolinensis) has been widely used as an animal model in physiology and neurobiology but has recently emerged as an important genomic model. The recent sequencing of its genome has shed new light on the evolution of vertebrate genomes and on the process that govern species diversification. Surprisingly, the patterns of genetic diversity within natural populations of this widespread and abundant North American lizard remain relatively unknown. In the present study, we use 10 novel nuclear DNA sequence loci ( N = 62 to 152) and one mitochondrial locus ( N = 226) to delimit green anole populations and infer their historical demography. We uncovered four evolutionarily distinct and geographically restricted lineages of green anoles using phylogenetics, Bayesian clustering, and genetic distance methods. Molecular dating indicates that these lineages last shared a common ancestor ∼2 million years ago. Summary statistics and analysis of the frequency distributions of DNA polymorphisms strongly suggest range-wide expansions in population size. Using Bayesian Skyline Plots, we inferred the timing of population size expansions, which differ across lineages, and found evidence for a relatively recent and rapid westward expansion of green anoles across the Gulf Coastal Plain during the mid-Pleistocene. One surprising result is that the distribution of genetic diversity is not consistent with a latitudinal shift caused by climatic oscillations as is observed for many co-distributed taxa. This suggests that the most recent Pleistocene glacial cycles had a limited impact on the geographic distribution of the green anole at the northern limits of its range.

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          Most cited references 43

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          Positional effect of single bulge nucleotide on PNA(peptide nucleic acid)/DNA hybrid stability

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            Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution.

            A mismatch distribution is a tabulation of the number of pairwise differences among all DNA sequences in a sample. In a population that has been stationary for a long time these distributions from nonrecombinant DNA sequences become ragged and erratic, whereas a population that has been growing generates mismatch distributions that are smooth and have a peak. The position of the peak reflects the time of the population growth. The signature of an ancient population expansion is apparent even in the low-resolution mtDNA typings described by Merriwether et al. (1991). The smoothness of the mismatch distribution, an indicator of population expansion, is hardly affected by population structure, whereas mean sequence divergence increases in a pooled sample from highly isolated subpopulations.
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              Genealogical trees, coalescent theory and the analysis of genetic polymorphisms.

              Improvements in genotyping technologies have led to the increased use of genetic polymorphism for inference about population phenomena, such as migration and selection. Such inference presents a challenge, because polymorphism data reflect a unique, complex, non-repeatable evolutionary history. Traditional analysis methods do not take this into account. A stochastic process known as the 'coalescent' presents a coherent statistical framework for analysis of genetic polymorphisms.
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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, USA )
                1932-6203
                2012
                7 June 2012
                : 7
                : 6
                Affiliations
                [1 ]Biology Department, Queens College, City University of New York, Flushing, New York, United States of America
                [2 ]Biology Program: Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, New York, United States of America
                Louisiana State University, United States of America
                Author notes

                Conceived and designed the experiments: MT SB. Performed the experiments: MT GA DG. Analyzed the data: MT. Wrote the paper: MT.

                Article
                PONE-D-12-08805
                10.1371/journal.pone.0038474
                3369884
                22685573
                Tollis 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
                Pages: 14
                Categories
                Research Article
                Biology
                Computational Biology
                Genomics
                Genome Evolution
                Evolutionary Modeling
                Developmental Biology
                Evolutionary Developmental Biology
                Evolutionary Biology
                Evolutionary Processes
                Genetic Drift
                Evolutionary Systematics
                Molecular Systematics
                Phylogenetics
                Organismal Evolution
                Animal Evolution
                Population Genetics
                Effective Population Size
                Gene Flow
                Genetic Polymorphism
                Evolutionary Ecology
                Evolutionary Genetics
                Genomic Evolution
                Genomics
                Genome Evolution
                Model Organisms

                Uncategorized

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