Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis

Yann Bourgeois*, Robert P. Ruggiero, Joseph D. Manthey, Stéphane Boissinot, Takashi Gojobori

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Gaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Here, we present the first population genomics survey using whole genome resequencing in the green anole (Anolis carolinensis). Anoles have been intensively studied to understand mechanisms underlying adaptation and speciation. The green anole in particular is an important model to study genome evolution. We quantified how demography, recombination, and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anole's populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the interaction between linked selection and recombination is the main contributor to the genomic landscape of differentiation in the anole genome.

Original languageEnglish (US)
Pages (from-to)2009-2022
Number of pages14
JournalGenome biology and evolution
Issue number7
StatePublished - Jul 1 2019

Bibliographical note

Funding Information:
Recombination rates estimated by LDHat in the EF cluster were highly heterogeneous along chromosomes, with stronger recombination rates at the tips and toward centromeres, though they dropped at the immediate vicinity of the latter (fig. 4). This pattern was supported by the Rozas’s ZZ statistic, suggesting stronger LD in the middle of chromosomes arms (supplementary fig. 6, Supplementary Material online). We observed higher relative differentiation (measured by FST) in regions of low recombination (Spearman’s rank correlation test, all P values <2.2⨯10−16; fig. 4 and supplementary fig. 7, Supplementary Material online). The correlation was however opposite for measures of absolute differentiation (dXY), a statistics directly related to diversity and to the average age of alleles across populations (Cruickshank and Hahn 2014). These correlations are consistent with selection reducing heterozygosity in regions of low recombination, and further support the @a@i models of heterogeneous effective population sizes along the genome. These measures of differentiation were strongly correlated when examining all three pairwise comparisons within Florida (fig. 4 and supplementary fig. 8, Supplementary Material online). There was also a positive

Publisher Copyright:
© 2019 The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


  • Anolis carolinensis
  • divergence
  • recombination
  • selection

ASJC Scopus subject areas

  • Medicine(all)


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