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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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Neighbor-joining tree derived from pairwise FST of green anole subpopulations.Colors indicate the mitochondrial clade to which individuals in the subpopulation belong: Gulf/Atlantic (green), NC (yellow), Suwannee (blue) and Everglades (magenta).
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pone-0038474-g004: Neighbor-joining tree derived from pairwise FST of green anole subpopulations.Colors indicate the mitochondrial clade to which individuals in the subpopulation belong: Gulf/Atlantic (green), NC (yellow), Suwannee (blue) and Everglades (magenta).

Mentions: Despite these minor differences, the AMOVA partitioned the same amount of variation in the nDNA genetic data when grouped by mtDNA clade and by STRUCTURAMA-inferred group (35%, see Table 2). Therefore, both mtDNA and nDNA recover very similar geographic patterns. In both hierarchical AMOVA setups, the least amount of genetic variation existed between subpopulations within groups. This is expected if relatively little gene flow is occurring. FST values between STRUCTURAMA-inferred populations are all significant (Table 3), suggesting strong population structure with limited gene flow between adjacent clusters. The greatest differentiation exists between the Everglades and all other populations. The NJ tree derived from the pairwise FST distance matrix (Figure 4) recovered a pattern that is largely consistent with the cluster and phylogenetic analyses, including long branch lengths separating subpopulations from NC and SC, Southern FL, and those whose members are in the Gulf-Atlantic STRUCTURAMA-inferred group and mtDNA clade. The subpopulations whose members were assigned to the Suwannee clade/population fall in slightly disparate regions of the NJ tree, close the mid-point and with short branch lengths.


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)

Neighbor-joining tree derived from pairwise FST of green anole subpopulations.Colors indicate the mitochondrial clade to which individuals in the subpopulation belong: Gulf/Atlantic (green), NC (yellow), Suwannee (blue) and Everglades (magenta).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0038474-g004: Neighbor-joining tree derived from pairwise FST of green anole subpopulations.Colors indicate the mitochondrial clade to which individuals in the subpopulation belong: Gulf/Atlantic (green), NC (yellow), Suwannee (blue) and Everglades (magenta).
Mentions: Despite these minor differences, the AMOVA partitioned the same amount of variation in the nDNA genetic data when grouped by mtDNA clade and by STRUCTURAMA-inferred group (35%, see Table 2). Therefore, both mtDNA and nDNA recover very similar geographic patterns. In both hierarchical AMOVA setups, the least amount of genetic variation existed between subpopulations within groups. This is expected if relatively little gene flow is occurring. FST values between STRUCTURAMA-inferred populations are all significant (Table 3), suggesting strong population structure with limited gene flow between adjacent clusters. The greatest differentiation exists between the Everglades and all other populations. The NJ tree derived from the pairwise FST distance matrix (Figure 4) recovered a pattern that is largely consistent with the cluster and phylogenetic analyses, including long branch lengths separating subpopulations from NC and SC, Southern FL, and those whose members are in the Gulf-Atlantic STRUCTURAMA-inferred group and mtDNA clade. The subpopulations whose members were assigned to the Suwannee clade/population fall in slightly disparate regions of the NJ tree, close the mid-point and with short branch lengths.

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