title: The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards.
abstract: Understanding the process of adaptation during rapid environmental change remains one of the central focal points of evolutionary biology. The recently formed White Sands system of southern New Mexico offers an outstanding example of rapid adaptation, with a variety of species having rapidly evolved blanched forms on the dunes that contrast with their close relatives in the surrounding dark soil habitat. In this study, we focus on two of the White Sands lizard species, Sceloporus cowlesi and Aspidoscelis inornata, for which previous research has linked mutations in the melanocortin-1 receptor gene (Mc1r) to blanched coloration. We sampled populations both on and off the dunes and used a custom sequence capture assay based on probed fosmid libraries to obtain >50 kb of sequence around Mc1r and hundreds of other random genomic locations. We then used model-based statistical inference methods to describe the demographic and adaptive history characterizing the colonization of White Sands. We identified a number of similarities between the two focal species, including strong evidence of selection in the blanched populations in the Mc1r region. We also found important differences between the species, suggesting different colonization times, different genetic architecture underlying the blanched phenotype and different ages of the beneficial alleles. Finally, the beneficial allele is dominant in S. cowlesi and recessive in A. inornata, allowing for a rare empirical test of theoretically expected patterns of selective sweeps under these differing models.
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.|Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Laurent
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.|Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Susanne P
authors.initials: SP
authors.lastname: Pfeifer
authors.affiliation: Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Settles
authors.affiliation: Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.
authors.forename: Samuel S
authors.initials: SS
authors.lastname: Hunter
authors.affiliation: Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.
authors.forename: Kayla M
authors.initials: KM
authors.lastname: Hardwick
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.|Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Louise
authors.initials: L
authors.lastname: Ormond
authors.affiliation: Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.|Institute of Ecology and Evolution, University of Berne, Baltzerstrasse 6, CH-3012, Berne, Switzerland.
authors.forename: Vitor C
authors.initials: VC
authors.lastname: Sousa
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV IBI-SV UPJENSEN, Station 15, CH-1015, Lausanne, Switzerland.|Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Jensen
authors.affiliation: Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.|Department of Environmental Sciences, Policy & Management, Berkeley, CA, 94720, USA.
authors.forename: Erica Bree
authors.initials: EB
authors.lastname: Rosenblum
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000818:Animals; D005075:Biological Evolution; D020451:Contig Mapping; D017753:Ecosystem; D005828:Genetics, Population; D008116:Lizards / Q000145:classification / Q000235:genetics*; D008957:Models, Genetic; D009154:Mutation; D009516:New Mexico; D010858:Pigmentation / Q000235:genetics; D044102:Receptor, Melanocortin, Type 1 / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D044102:Receptor, Melanocortin, Type 1
keywords: adaptation; ecological genetics; molecular evolution; population genetics; reptiles