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Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: historical demography of a genomic model species.

Tollis M, Ausubel G, Ghimire D, Boissinot S - PLoS ONE (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, Queens College, City University of New York, Flushing, New York, United States of America.

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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Mismatch distributions.The frequency distribution of nDNA polymorphisms within STRUCTURAMA-inferred populations calculated with the concatenated dataset in Arlequin. X-axes are in number of differences and Y-axes are in number of observations. Blue diamonds represent the observed data, green triangles and red squares represent upper and lower bounds expected under a model of expansion, respectively. P-values of the raggedness index for each analysis are given. A: Gulf-Atlantic. B: Suwannee. C: Carolinas. D: Everglades.
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pone-0038474-g006: Mismatch distributions.The frequency distribution of nDNA polymorphisms within STRUCTURAMA-inferred populations calculated with the concatenated dataset in Arlequin. X-axes are in number of differences and Y-axes are in number of observations. Blue diamonds represent the observed data, green triangles and red squares represent upper and lower bounds expected under a model of expansion, respectively. P-values of the raggedness index for each analysis are given. A: Gulf-Atlantic. B: Suwannee. C: Carolinas. D: Everglades.

Mentions: Tajima’s D and Fu’s Fs were negative for most loci (Table 1), suggesting violations of neutrality due to population size expansion. Both D and Fs were also negative in all inferred populations (Table 4). The frequencies of pair-wise differences within each population (Figure 6) are consistent with what is expected under a model of population expansion: raggedness indices (R) derived from these mismatch distributions were all non-significant (p-values given in Figure 6). These three indicators (D, Fs, and R) all suggest that population expansion has occurred.


Multi-locus phylogeographic and population genetic analysis of Anolis carolinensis: historical demography of a genomic model species.

Tollis M, Ausubel G, Ghimire D, Boissinot S - PLoS ONE (2012)

Mismatch distributions.The frequency distribution of nDNA polymorphisms within STRUCTURAMA-inferred populations calculated with the concatenated dataset in Arlequin. X-axes are in number of differences and Y-axes are in number of observations. Blue diamonds represent the observed data, green triangles and red squares represent upper and lower bounds expected under a model of expansion, respectively. P-values of the raggedness index for each analysis are given. A: Gulf-Atlantic. B: Suwannee. C: Carolinas. D: Everglades.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369884&req=5

pone-0038474-g006: Mismatch distributions.The frequency distribution of nDNA polymorphisms within STRUCTURAMA-inferred populations calculated with the concatenated dataset in Arlequin. X-axes are in number of differences and Y-axes are in number of observations. Blue diamonds represent the observed data, green triangles and red squares represent upper and lower bounds expected under a model of expansion, respectively. P-values of the raggedness index for each analysis are given. A: Gulf-Atlantic. B: Suwannee. C: Carolinas. D: Everglades.
Mentions: Tajima’s D and Fu’s Fs were negative for most loci (Table 1), suggesting violations of neutrality due to population size expansion. Both D and Fs were also negative in all inferred populations (Table 4). The frequencies of pair-wise differences within each population (Figure 6) are consistent with what is expected under a model of population expansion: raggedness indices (R) derived from these mismatch distributions were all non-significant (p-values given in Figure 6). These three indicators (D, Fs, and R) all suggest that population expansion has occurred.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, Queens College, City University of New York, Flushing, New York, United States of America.

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.

Show MeSH