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: After determining the estimated insertion position for each individual taxon, insertion positions between taxa were compared. Between 120,214 (M. vivesi) and 143,322 (M. auriculus) unique Ves insertions were identified, excluding M. lucifugus, which sequenced poorly (table 2). When insertions from different taxa were within 100 bp of each other, a majority were within 10 bp of each other (fig. 2). Insertions within this narrow window were assumed to be orthologous for downstream analysis.Fig. 2.—
Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.