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Abstract
Adaptation can occur with or without genome‐wide differentiation. If adaptive loci are linked to traits involved in reproductive isolation, genome‐wide divergence is likely, and speciation is possible. However, adaptation can also lead to phenotypic differentiation without genome‐wide divergence if levels of ongoing gene flow are high. Here, we use the replicated occurrence of melanism in lava flow lizards to assess the relationship between local adaptation and genome‐wide differentiation. We compare patterns of phenotypic and genomic divergence among lava flow and nonlava populations for three lizard species and three lava flows in the Chihuahuan Desert. We find that local phenotypic adaptation (melanism) is not typically accompanied by genome‐wide differentiation. Specifically, lava populations do not generally exhibit greater divergence from nonlava populations than expected by geography alone, regardless of whether the lava formation is 5,000 or 760,000 years old. We also infer that gene flow between lava and nonlava populations is ongoing in all lava populations surveyed. Recent work in the isolation by environment and ecological speciation literature suggests that environmentally driven genome‐wide differentiation is common in nature. However, local adaptation may often simply be local adaptation rather than an early stage of ecological speciation.
Highlights
Given that environmental differences can lead to genetic differ‐ entiation among populations—and even speciation—it is crucial to understand the effects of geography and ecology on genomic differentiation
We demonstrated that genome‐wide differentiation does not ac‐ company local adaptation in three species of lava flow lizards in the Chihuahua Desert
Consistent with previous literature (Lewis, 1949, 1951), we found that C. collaris and S. cowlesi from the Carrizozo Lava Flow (CZLF) (~5,200 years old) and U. ornatus from the Aden Afton Lava Flow (~106,000 years old) were melanistic, indicating strong phenotypic divergence from nonlava flow populations
Summary
Given that environmental differences can lead to genetic differ‐ entiation among populations—and even speciation—it is crucial to understand the effects of geography and ecology on genomic differentiation. Melanism appears to be heritable and associated with environmental variation in many reptile species, it is not clear whether local adaptation in coloration is expected to lead to genome‐ wide differentiation. Color variation in reptiles can have consequences for both natural and sexual selection as many lizard species use visual cues including coloration for mate choice (Hardwick, Robertson, & Rosenblum, 2013; Robertson & Rosenblum, 2009). In this case, local adaptation could lead to genome‐wide divergence and reproductive isolation. Our sampling approach leveraged population trios (where we compared each focal lava flow population with two nearby nonlava flow populations) to disentan‐ gle the effects of IBD and IBE
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