Limits...
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.

Show MeSH
Pairwise distances within populations.A: Tamura-Nei corrected distance within each mitochondrial clade. B: Average p-distance across nine nuclear loci within each STRUCTURAMA-inferred population.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3369884&req=5

pone-0038474-g005: Pairwise distances within populations.A: Tamura-Nei corrected distance within each mitochondrial clade. B: Average p-distance across nine nuclear loci within each STRUCTURAMA-inferred population.

Mentions: Summary statistics that were calculated per locus for each population are featured in Tables S4, S5, S6 and S7; statistics calculated for each collecting locality with the nDNA are featured in Table S8. Averaged across all loci, haplotype diversity is lowest in the Gulf-Atlantic population and highest in the FL populations. Diversity statistics for mtDNA clades and STRUCTURAMA-inferred populations (calculated from the concatenated nDNA dataset) are shown in Table 4. Nucleotide diversity is highest in the Suwannee for both data sets, and lowest in the Gulf-Atlantic and NC for the mtDNA and in the Everglades for the nDNA. Average p-distance is greatest within the Suwannee for the mtDNA (Figure 5A) and averaged across nine nuclear loci (Figure 5B). The greatest p-distance on average from all other populations is highest in the Suwannee for mtDNA and in the Everglades for nDNA; both datasets show the closest genetic distance exists between NC and the Gulf/Atlantic (Table 5).


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)

Pairwise distances within populations.A: Tamura-Nei corrected distance within each mitochondrial clade. B: Average p-distance across nine nuclear loci within each STRUCTURAMA-inferred population.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0038474-g005: Pairwise distances within populations.A: Tamura-Nei corrected distance within each mitochondrial clade. B: Average p-distance across nine nuclear loci within each STRUCTURAMA-inferred population.
Mentions: Summary statistics that were calculated per locus for each population are featured in Tables S4, S5, S6 and S7; statistics calculated for each collecting locality with the nDNA are featured in Table S8. Averaged across all loci, haplotype diversity is lowest in the Gulf-Atlantic population and highest in the FL populations. Diversity statistics for mtDNA clades and STRUCTURAMA-inferred populations (calculated from the concatenated nDNA dataset) are shown in Table 4. Nucleotide diversity is highest in the Suwannee for both data sets, and lowest in the Gulf-Atlantic and NC for the mtDNA and in the Everglades for the nDNA. Average p-distance is greatest within the Suwannee for the mtDNA (Figure 5A) and averaged across nine nuclear loci (Figure 5B). The greatest p-distance on average from all other populations is highest in the Suwannee for mtDNA and in the Everglades for nDNA; both datasets show the closest genetic distance exists between NC and the Gulf/Atlantic (Table 5).

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