Data from: Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations

Environmental gradients constrain physiological performance and thus
species’ ranges, suggesting that species occurrence in diverse
environments may be associated with local adaptation. Genome-environment
association analyses (GEAA) have become central for studies of local
adaptation, yet they are sensitive to the spatial orientation of
historical range expansions relative to landscape gradients. To test
whether potentially adaptive genotypes occur in varied climates in
wide-ranged species, we implemented GEAA on the basis of genome-wide data
from the anole lizards Anolis ortonii and A. punctatus, which expanded
from Amazonia, presently dominated by warm and wet settings, into the
cooler and less rainy Atlantic Forest. To examine whether local adaptation
has been constrained by population structure and history, we estimated
effective population sizes, divergence times, and gene flow under a
coalescent framework. In both species, divergence between Amazonian and
Atlantic Forest populations dates back to the mid-Pleistocene, with
subsequent gene flow. We recovered eleven candidate genes involved with
metabolism, immunity, development, and cell signaling in A. punctatus, and
found no loci whose frequency is associated with environmental gradients
in A. ortonii. Distinct signatures of adaptation between these species are
not associated with historical constraints or distinct climatic space
occupancies. Similar patterns of spatial structure between selected and
neutral SNPs along the climatic gradient, as supported by patterns of
genetic clustering in A. punctatus, may have led to conservative GEAA
performance. This study illustrates how tests of local adaptation can
benefit from knowledge about species histories to support hypothesis
formulation, sampling design, and landscape gradient characterization.