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.

Koalas have undergone a series of sequential founding events on islands in south‐eastern Australia in recent times. Populations in South Australia at the Eyre Peninsula and Mt Lofty Ranges were founded in the 1960s from a colony on Kangaroo Island. The Kangaroo Is. colony was derived from animals introduced to French Island from mainland Victoria over a century ago. In this study, we first use microsatellite markers to quantify levels of genetic variation within the South Australian koala populations and the relatively unperturbed Strzelecki Ranges population from mainland Victoria. This analysis revealed low levels of allelic diversity (1.7 ± 0.2 to 2.7 ± 0.5) and heterozygosity (0.208 ± 0.088 to 0.340 ± 0.110) in the three South Australian koala populations relative to the Strzelecki Ranges population, which has the highest levels of allelic diversity (4.7 ± 1.1) and heterozygosity (0.476 ± 0.122) in Victoria. Second, we measured the incidence of testicular aplasia, a unilateral or bilateral failure in testicular development, in the Eyre Peninsula and Kangaroo Is. populations, and in the ultimate founding population at French Is. Testicular aplasia was present at a frequency of 4.3% in French Is., 12.8% in Kangaroo Is. and 23.9% in the Eyre Peninsula, but was undetectable in the non‐bottlenecked Pilliga State Forest population of New South Wales. The incidence of testicular aplasia correlated positively with effective inbreeding coefficients derived from heterozygosity values (0.13 ± 0.06 in the Pilliga State Forest, 0.57 ± 0.17 in French Is., 0.63 ± 0.12 on Kangaroo Is. and 0.77 ± 0.12 in the Eyre Peninsula), which may indicate inbreeding depression. These findings are of concern when evaluating the long‐term conservation and viability of the South Australian koala populations, which may benefit from genetic augmentation in the future. Finally, unconfirmed reports suggested that animals from other states in Australia were introduced into the Mt Lofty Ranges population. Therefore, we quantified differentiation between the three South Australian populations and the Strzelecki Ranges and French Is. populations, based on microsatellites and mtDNA d‐loop region variation. R‐statistics and Goldstein's delta mu square distance revealed that differentiation at nuclear loci between populations paralleled known recent population history, except for the close relationship between Mt Lofty Ranges and French Is. This suggested a recent contribution to the Mt Lofty Ranges populations of animals derived from the French Is. translocation program. Furthermore, mtDNA d‐loop analysis found no evidence of contributions to the gene pool from animals of New South Wales or Queensland stock, implying that the population was derived exclusively from Victorian stock.

Changes in gene expression are known to occur between closely related species, but it is not yet clear how many of these are due to random fixation of allelic variants or due to adaptive events. In a microarray survey between subspecies of the Mus musculus complex, we identified the mitogen-activated protein-kinase-kinase MKK7 as a candidate for change in gene expression. Quantitative PCR experiments with multiple individuals from each subspecies confirmed a specific and significant up-regulation in the testis of M. m. domesticus. Northern blot analysis shows that this is due to a new transcript that is not found in other tissues, nor in M. m. musculus. A cis-trans test via allele specific expression analysis of the MKK7 gene in F1 hybrids between domesticus and musculus shows that the expression change is mainly caused by a mutation located in cis. Nucleotide diversity was found to be significantly reduced in a window of at least 20 kb around the MKK7 locus in domesticus, indicative of a selective sweep. Because the MKK7 gene is involved in modulating a kinase signalling cascade in a stress response pathway, it seems a plausible target for adaptive differences between subspecies, although the functional role of the new testis-specific transcripts will need to be further studied

Differences in recombination rates along the chromosomes can influence the evolution of neutral loci via hitchhiking effects. Generally, these effects should be stronger in regions of low recombination than in regions of high recombination. Detailed information on physical and genetic maps in the house mouse now allows an assessment of the correlation between neutral variability and recombination rates at given chromosomal regions. We chose 29 microsatellite loci from chromosomal regions which show differences in recombination rates and tested their variability in samples from five wild populations of Mus musculus musculus and M. m. domesticus . Our results provide no evidence for a correlation between microsatellite variability and recombination rates. This suggests that the high average mutation rate of microsatellites in mammals counterbalances the effects of long-range hitchhiking in the mouse genome.

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