Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.
Bottom Line: Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa.This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi.These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.
Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.Show MeSH
Mentions: On average, each Ves insertion was sequenced to 129.6 × coverage. Although M. auriculus was sequenced 2.5 × (13.6 million read pairs) more frequently than M. simus, the difference in number of Ves insertions identified was less than 17,800 insertions. Assuming these two taxa that diverged approximately 10 Ma (Stadelmann et al. 2007) have similar numbers of Ves insertions, this suggests that a saturation point is reached where more sequencing does not significantly increase the number of unique insertions discovered (fig. 3A). Our results indicate that after approximately 5 million read pairs, most Ves insertion sequences are represented. Additionally, when the number of reads pair is compared with the number of reads per Ves insertion, a strong linear relationship is recovered (R2 = 0.975; fig. 3B).Fig. 3.—
Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.