A single locus analysis of divergence with gene-flow under the Isolation with Migration model was therefore conducted.
Due to the small within population sample size (n = 5), we expect our single locus estimates of divergence (i.e. the π xy and FST outlier scans described above) to have relatively modest statistical power.
Samples of DNA sequences were obtained for seven nuclear loci and a mitochondrial locus in order to conduct a multi-locus analysis of divergence and gene flow between two closely related and hybridizing species of hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis.
In the SlpA locus, the majority of divergence is present within this gene, but there was an absence of the predicted calcium-binding gene CD_27970 in CD630.
Searches for loci of high divergence against the genetic background of the focal taxa will help to identify regions under selection, which have played a role in adaptation and speciation.> -wrap-foot> > -wrap-foot> > -wrap-foot> Total number of SNPs within each species is marked in bold.
Contributions of individual loci to measures of divergence and polymorphism for all sites are shown in Table 2. Two estimates of θs are shown: an estimate based on average pairwise nucleotide diversity, θ̂π [21], and Watterson's estimator, θ̂W, which is based on the number of polymorphic sites [22].
Our secondary goal was to evaluate the scope of neutral vs. adaptive differentiation in sockeye salmon as revealed by locus-specific estimates of divergence.
Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses.
Accordingly, we concluded an Aethionema-specific loss of this locus after divergence from the Arabidopsis lineage, creating measurable differences in GS chemotype among Arabidopsis and Aethionema.
Our phylogenetic analysis clearly shows duplication of the MYH14/miR-499 locus after the divergence of spotted gar, indicating that the teleostei-specific WGD provided present-day MYH14/miR-499 paralogs in teleost fish.
Further, when these data were trimmed and/or topological constraints were enforced, divergence estimates increased further, indicating instability in this locus as an estimator of divergence time.
