ome Biol. Evol. 13(10) doi:ten.1093/gbe/evab220 Advance Access publication 23 SeptemberEvolutionary History in the Abp Expansion in MusGBEof evidence that Abp features a role in sexual selection between home mouse subspecies (Laukaitis et al. 1997; Talley et al. 2001; B imov et al. 2005). Hwang et al. (1997) observed a a high nonsynonymous/synonymous substitution ratio (dN/dS) in their Abpa (now a27) sequence information from six Mus taxa and proposed that directional selection was a sufficient explanation of their information. They envisioned the possibility of cyclical selection of particular amino acid variants that became advantageous at some stage and they posited that homoplasy occurred in the phylogeny with the Abpa haplotypes that was incongruent using the canonical phylogeny of your genus. Karn and Nachman (1999) applied the HKA test (Hudson et al. 1987) to investigate patterns of DNA sequence variation at a27 within and in between species of mice. Their final results supplied evidence that choice has shaped the evolution of Abpa in Topo II Storage & Stability residence mice and was consistent having a recent adaptive fixation (a selective sweep) at or near Abpa. In addition they calculated the ratio of nonsynonymous substitutions to synonymous substitutions on a per-site basis (Ka/Ks) for the Mus sequences of Hwang et al. (1997). Primarily based on the combined observations of no variation at a27 inside M. m. domesticus and uniformly high Ka/Ks values amongst species, they suggested that good directional choice has acted lately at this locus. Laukaitis et al. (2012) assessed site-specific good selection around the coding sequences of 3 genes, a27, bg26, and bg27, in 5 Mus taxa working with the system CODEML inside the PAML package (Yang 2007). They concluded that no less than two (a27, bg26) of the three genes encoding the subunits of ABP dimers evolved below constructive choice and suggested that the third a single may have also. These choice tests were primarily based around the assumption that the a27 genes in the subspecies of M. musculus are orthologs and therefore that the studied variants were alleles. On the other hand, some genes possess a phylogeny at variance with all the species phylogeny and Karn et al. (2002) recommended that the M. musculus taxa are certainly not monophyletic and its subspecies are outgroups relative to other Palearctic species. Here, we offer evidence that pah and car each appear to possess duplications of modules associated to M27, especially MX and MY in pah; too as M27a (bg27a-a27a) and M26/27b (bg26a27bp) in car (figs. two, 3, and five). These further M27 modules will not be located inside the Palearctic taxa which have their a27 topologies incongruent with that of your species phylogeny (Karn et al. 2002). Such duplications and deletions may also have occurred inside the ancestor with the Palearctics, to ensure that the copies we observe now aren’t necessarily all orthologous. That could N-type calcium channel list present a parsimonious explanation for why the gene phylogeny is incongruent with the species phylogeny. Interestingly, figure 2 shows that clades a26, bg25, and bg26 are also noncongruent with all the species phylogeny. Karn et al. (2002) discussed and discarded an explanation for the incongruent gene and species trees that was based on a hypothetical duplication that made two copies of a27 in an early ancestor(s). In this view, differentsupplementary table S2, Supplementary Material on the internet; see also fig. three). This clade is bigger and much more complicated inside the 3 subspecies of M. musculus and seems to possess been the source of most of the volatility identified when compar
