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

Abstract

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 eleven sites along a transect spanning the Sand Hills at 660,000 SNPs across the genome.

Parallel evolution of gene classes, but not genes: Evidence from Hawai'ian honeycreeper populations exposed to avian malaria

“…Our results suggest that the early stage of adaptation to novel strong selection such as introduced malaria may occur via changes in multiple genes that each confers tolerance, only some of which are common across populations. Similar patterns have been found in experimental evolution studies (Elena & Lenski, ; Notley‐McRobb & Ferenci, , ) and in natural populations (Pfeifer et al., ). Parallel evolution is less common when multiple traits confer the same phenotypic function (Thompson et al., ); it is likely that over time, some of these changes will replace others as a result of gene flow (Caprio & Tabashnik, ) and variation in fitness of particular mutations in different environments and genetic backgrounds.…”

“…We still lack a complete understanding of when molecular adaptation should be parallel versus divergent, although some patterns are beginning to emerge (Rosenblum, Parent, & Brandt, ). For phenotypes with multiple physiological or molecular mechanisms, such as tolerance to a pathogen, there are likely multiple genomic solutions that confer adaptation (Pfeifer et al., ). In such cases, the first variant to appear in a population should rapidly increase in frequency, independent of the alleles in other populations, leading to differences among populations in the genomic basis of convergent phenotypes.…”

Recent population genomic insights into the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations

“…As such, the cryptic coloration literature may serve as an informative roadmap outlining the avenues of future research. In that literature, genome-wide polymorphism data from light (derived-state) and dark (ancestral-state) mouse populations were next utilized to fit a demographic history including population size change, structure, and migration, and simulation was used to assess the fit of the model to the data and to characterize sweep-detection performance under the relevant demographic history (Pfeifer et al 2018). Utilizing this model as the appropriate null distribution for characterizing the expected performance of summary statistics under neutrality compared to selection, well-supported candidate loci were identified.…”

Local and regional scale habitat heterogeneity contribute to genetic adaptation in a commercially important marine mollusc (Haliotis rubra) from southeastern Australia

“…Studies of this nature ideally require sampling regimes that allow genetic variation to be contrasted among conspecific populations distributed across defined environmental gradients (Frichot, Schoville, Bouchard, & Francois, ). Most have been carried out in terrestrial systems where habitat heterogeneity is relatively easy to measure and is often well described, with many demonstrating evidence of selection resulting from environmental variation at various spatial scales (Buehler et al, ; Jordan, Hoffmann, Dillon, & Prober, ; Pfeifer et al, ; Termignoni‐Garcia et al, ). In contrast, information on the heterogeneity of marine habitats, particularly benthic habitats, is limited for many coastlines, hindering effective sampling to test for adaptive genetic diversity within marine species.…”