The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

Abstract

By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on background matching, a particular facet of crypsis that involves the ability of an organism to conceal itself through matching its color to the surrounding environment. While interesting in and of itself, the study of this phenotype has also provided fruitful population genetic insights into the interplay of strong positive selection with other evolutionary processes. Specifically, and predicated upon the findings of previous candidate gene association studies, a primary focus of this recent literature involves the realization that the inference of selection from DNA sequence data first requires a robust model of population demography in order to identify genomic regions which do not conform to neutral expectations. Moreover, these demographic estimates provide crucial information about the origin and timing of the onset of selective pressures associated with, for example, the colonization of a novel environment. Furthermore, such inference has revealed crypsis to be a particularly useful phenotype for investigating the interplay of migration and selection-with examples of gene flow constraining rates of adaptation, or alternatively providing the genetic variants that may ultimately sweep through the population. Here, we evaluate the underlying evidence, review the strengths and weaknesses of the many population genetic methodologies used in these studies, and discuss how these insights have aided our general understanding of the evolutionary process.

Fig. 1

Overview of the focal study systems: a Chaetodipus intermedius, b Peromyscus polionotus, c Peromyscus maniculatus, d Sceloporus cowlesi, e Aspidoscelis inornata, and f Lepus americanus. Each panel depicts the estimated demographic model and the major findings to-date in understanding the genes underlying crypsis. See bottom of each panel for further details. Animal photos from: a Nachman et al. , b the U.S. Fish and Wildlife Service (P. polionotus - light) and the U.S. National Park Service (P. polionotus - dark), both released in to the public domain, c C. Linnen, d, e Laurent et al. , f Karl Friedrich Herhold (L. americanus–light) released under the CC BY 3.0 license, and Walter Siegmund (L. americanus–dark) released under the CC BY-SA 3.0 license

Fig. 2

Workflow for identifying beneficial loci. From the top: population sampling is followed by wet-lab procedures, bioinformatic pipelines, and post-assembly analyses. Examples adjacent to black arrows indicate some of the more popular tools of analysis