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: To verify the presence of Ves insertions identified by Ves reads, 42 loci were amplified in all seven taxa (fig. 4). Filled sites are expected to be approximately 200 bp larger than empty sites. Of the loci tested, 32 of 42 amplified in five or more samples, and 30 of the 32 primer pairs produced amplicons of predicted sizes confirming the expected insertion genotype. After verifying the increase in band size that is expected from a Ves insertion, loci were sequenced using internal Ves primers to confirm the approximately 200 bp insertion was indeed a Ves. For each locus, either one or two taxa were selected for sequencing to verify the presence of the Ves insertion as well as the expected flanking DNA sequence. In each case, the Ves sequence was found as expected.Fig. 4.—
Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.