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Phenotype data, genotype input files, and scripts related to adaptation in wild house mice from Western North America

Citation

Ferris, Kathleen et al. (2021), Phenotype data, genotype input files, and scripts related to adaptation in wild house mice from Western North America, Dryad, Dataset, https://doi.org/10.5061/dryad.sxksn0324

Abstract

Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America.  Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change.  We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight.  We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.

Methods

Genotype and phenotype data was collected for 50 house mice (Mus musculus domesticus) from 5 populations across 21 degrees of latitude between Tucson, AZ, USA and Edmonton, AB, CAN. Whole exomes were sequenced for each individual and phenotypic data such as bodyweight, length, coat coloar brightness etc was taken. In addition we raised individuals from the Tucson and Edmonton populations for >5 generations in the lab and then measured body weight and behavioral phenotypes such as nest building in a common environment to test for genetic differences in these traits. Exome wide selection analysis was performed using the program LFMM and a genome wide associatoin analysis on body weight was performed using the program GEMMA.

Usage Notes

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