The evolutionary history of Nebraska deer mice: Local adaptation in the face of strong gene flow

Susanne P. Pfeifer, Stefan Laurent, Vitor C. Sousa, Catherine R. Linnen, Matthieu Foll, Laurent Excoffier, Hopi E. Hoekstra, Jeffrey D. Jensen

Research output: Contribution to journalArticlepeer-review

55 Scopus citations


The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from 11 sites along a transect spanning the Sand Hills at 660,000 single nucleotide polymorphisms across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of the Agouti pigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.

Original languageEnglish
Pages (from-to)792-806
Number of pages15
JournalMolecular Biology and Evolution
Issue number4
StatePublished - Apr 1 2018

Bibliographical note

Funding Information:
We thank J. Larson and K. Turner for laboratory assistance; E. Kay, E. Kingsley, and M. Manceau for field assistance; J. Demboski and the Denver Museum of Nature and Science for logistical support; the University of Nebraska-Lincoln for use of facilities and/or permission to collect mice at Cedar Point Biological Station, Gudmundsen Sandhills Laboratory, and Arapaho Prairie; and J. Chupasko for curation assistance. This work was funded by a Swiss National Science Foundation Sinergia grant to L.E., H.E.H., and J.D.J.

Publisher Copyright:
© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


  • adaptation
  • cryptic coloration
  • population genetics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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