An Analysis of Signatures of Selective Sweeps in Natural Populations of the House Mouse

Abstract

Population and locus-specific reduction of variability of polymorphic loci could be an indication of positive selection at a linked site (selective sweep) and therefore point toward genes that have been involved in recent adaptations. Analysis of microsatellite variability offers a way to identify such regions and to ask whether they occur more often than expected by chance. We studied four populations of the house mouse (Mus musculus) to assess the frequency of such signatures of selective sweeps under natural conditions. Three samples represent the subspecies Mus m. dometicus [corrected] and came from Germany, France, and Cameroon. One sample came from Kazakhstan and constitutes a population of the subspecies Mus m. [corrected] musculus. Mitochondrial D-loop sequences from all animals confirm their respective assignments. Approximately 200 microsatellite loci were typed for up to 60 unrelated individuals from each population and evaluated for signs of selective sweeps on the basis of Schlötterer's ln RV and ln RH statistics. Our data suggest that there are slightly more signs of selective sweeps than would have been expected by chance alone in each of the populations and also highlights some of the statistical challenges faced in genome scans for detecting selection. Single-nucleotide polymorphism typing of one sweep signature in the M. m. domesticus populations around the beta-defensin 6 locus confirms a lowered nucleotide diversity in this region and limits the potential sweep region to about 20 kb. However, no amino acid exchange has occurred in the coding region when compared to M. m. musculus. If this sweep signature is due to a recent adaptation, it is expected that a regulatory change would have caused it. Our data provide a framework for conducting a systematic whole genome scan for signatures of selective sweeps in the mouse genome.

Micro-evolutionary divergence patterns of mandible shapes in wild house mouse (Mus musculus) populations

“…This would imply that differences between populations should be driven by positive selection to new environmental conditions. However, neutral accumulation of differences over time would also be a possibility, in particular since there appears to be little gene flow even between populations of the same subspecies [40]. Some of the patterns that we see in our data allow to address this question.…”

“…In the first we used laboratory outbred M. m. domesticus derived from animals trapped in the Massif Central in France [40] and fed them with soft diet versus hard diet. The hard diet animals (17 offspring from four breeding pairs) were fed on normal rodent pellets (Altromin standard diet No.1324).…”

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice

“…The cecal contents of 80 wild-caught mice described by Linnenbrink et al (7) and an additional 10 mice transferred from the Massif Central region of France were separated from cecal tissue and preserved in 4 mL RNALater according to manufacturer's instructions until further processing, as previously described (7). Of the 10 mice from the Massif Central that were transferred to the breeding facility of the Max Planck Institute for Evolutionary Biology, six were housed in individual cages and four were maintained as two breeding pairs to generate offspring to be included in an outbred colony derived from this region (19). The four mice involved in breeding were maintained as pairs (i.e., cohoused) for 1 to 2 mo, but were housed separately for >6 mo before being killed.…”

Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

“…There have been numerous applications of both approaches utilizing data from humans (Payseur et al, 2002;Akey et al, 2004;Hahn et al, 2004;Rockman et al, 2004Rockman et al, , 2005Voight et al, 2006), Drosophila (Harr et al, 2002;Glinka et al, 2003;Kauer et al, 2003;Orengo and Aguade, 2004;Schofl and Schlotterer, 2004;Pool et al, 2006), Mus musculus (Ihle et al, 2006) and Arabidopsis thaliana (Cork and Purugganan, 2005). However, because in most of these cases neither the ecological context in which selection occurred nor the potential selective agent are known (but see Cork and Purugganan, 2005), here we focus on other recent applications.…”