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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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Bayesian Skyline Plots (BSPs).BSPs represent population size changes over time, inferred with mtDNA and an assumed mutation rate of 1.3% per million years. The X-axes are time in millions of years. Y-axes are mean effective population size in millions of individuals divided by generation time (for Anolis we assume a generation time of one year) on a log scale. Shaded areas encompass 95% highest posterior density (HPD). A: Suwannee. B: Everglades. C: Gulf/Atlantic. D: North Carolina. E: Tennessee.
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pone-0038474-g007: Bayesian Skyline Plots (BSPs).BSPs represent population size changes over time, inferred with mtDNA and an assumed mutation rate of 1.3% per million years. The X-axes are time in millions of years. Y-axes are mean effective population size in millions of individuals divided by generation time (for Anolis we assume a generation time of one year) on a log scale. Shaded areas encompass 95% highest posterior density (HPD). A: Suwannee. B: Everglades. C: Gulf/Atlantic. D: North Carolina. E: Tennessee.

Mentions: The BSPs indicate that the Suwannee and Everglades clades both experienced expansions ∼500–700Kya (Figure 7A and B, respectively), while the Gulf-Atlantic clade experienced a more dramatic and recent expansion ∼250Kya (Figure 7C). In contrast, the NC and TN populations have remained relatively stable during the last 150–200Ky (Figure 7D and E, respectively). Multi-locus EBSPs from the Suwannee and Everglades show highest posterior probabilities for single past population size expansions. The timing of these expansions is consistent with the single-locus BSPs (lower-bound estimates for both are between ∼0.5–1Mya) (Figure 8). Effective population size estimates from all skyline plots are given in Table 6.


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)

Bayesian Skyline Plots (BSPs).BSPs represent population size changes over time, inferred with mtDNA and an assumed mutation rate of 1.3% per million years. The X-axes are time in millions of years. Y-axes are mean effective population size in millions of individuals divided by generation time (for Anolis we assume a generation time of one year) on a log scale. Shaded areas encompass 95% highest posterior density (HPD). A: Suwannee. B: Everglades. C: Gulf/Atlantic. D: North Carolina. E: Tennessee.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0038474-g007: Bayesian Skyline Plots (BSPs).BSPs represent population size changes over time, inferred with mtDNA and an assumed mutation rate of 1.3% per million years. The X-axes are time in millions of years. Y-axes are mean effective population size in millions of individuals divided by generation time (for Anolis we assume a generation time of one year) on a log scale. Shaded areas encompass 95% highest posterior density (HPD). A: Suwannee. B: Everglades. C: Gulf/Atlantic. D: North Carolina. E: Tennessee.
Mentions: The BSPs indicate that the Suwannee and Everglades clades both experienced expansions ∼500–700Kya (Figure 7A and B, respectively), while the Gulf-Atlantic clade experienced a more dramatic and recent expansion ∼250Kya (Figure 7C). In contrast, the NC and TN populations have remained relatively stable during the last 150–200Ky (Figure 7D and E, respectively). Multi-locus EBSPs from the Suwannee and Everglades show highest posterior probabilities for single past population size expansions. The timing of these expansions is consistent with the single-locus BSPs (lower-bound estimates for both are between ∼0.5–1Mya) (Figure 8). Effective population size estimates from all skyline plots are given in Table 6.

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