Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus)

Copy–number variants (CNVs) may play an important role in early adaptations, potentially facilitating rapid divergence of populations. We describe an approach to study this question by investigating CNVs present in natural populations of mice in the early stages of divergence and their involvement in selective sweeps. We have analyzed individuals from two recently diverged natural populations of the house mouse (Mus musculus domesticus) from Germany and France using custom, high–density, comparative genome hybridization arrays (CGH) that covered almost 164 Mb and 2444 genes. One thousand eight hundred and sixty one of those genes we previously identified as differentially expressed between these populations, while the expression of the remaining genes was invariant. In total, we identified 1868 CNVs across all 10 samples, 200 bp to 600 kb in size and affecting 424 genic regions. Roughly two thirds of all CNVs found were deletions. We found no enrichment of CNVs among the differentially expressed genes between the populations compared to the invariant ones, nor any meaningful correlation between CNVs and gene expression changes. Among the CNV genes, we found cellular component gene ontology categories of the synapse overrepresented among all the 2444 genes tested. To investigate potential adaptive significance of the CNV regions, we selected six that showed large differences in frequency of CNVs between the two populations and analyzed variation in at least two microsatellites surrounding the loci in a sample of 46 unrelated animals from the same populations collected in field trappings. We identified two loci with large differences in microsatellite heterozygosity (Sfi1 and Glo1/Dnahc8 regions) and one locus with low variation across the populations (Cmah), thus suggesting that these genomic regions might have recently undergone selective sweeps. Interestingly, the Glo1 CNV has previously been implicated in anxiety–like behavior in mice, suggesting a differential evolution of a behavioral trai

Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini)

Ullrich B, Reinhold K, Niehuis O, Misof B. Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini). JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH. 2010;48(3):219-228.We inferred secondary structure models of the internal transcribed spacers (ITS) 1 and 2 of bush crickets using a combined comparative and thermodynamic approach. The inferred secondary structure models were used to account for interdependency of interacting nucleotides in a phylogenetic analysis of the bush cricket genus Poecilimon. Our analysis indicates that the two previously reported conformational structures (i.e., hairpin and ring) of ITS2 are likely to fold in bush crickets as well and that both predicted structures are similar to those proposed for other eukaryotes. Comparing predicted ITS1 secondary structure models proved to be difficult because of substantial variation in their nucleotide sequence length. Our study revealed that the phylogenetic signal of ITS1 and ITS2 is largely congruent with that preserved in the mitochondrial genes 16S rRNA, tRNA-Val and 12S rRNA. The phylogenetic signal in both the nuclear and the mitochondrial genome question the monophyly of the genus Poecilimon: species of the genera Poecilimonella, Parapoecilimon, Polysarcus and Phonochorion consistently cluster within Poecilimon