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
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Mentions: To recreate the phylogenetic relationships of available taxa, we used an unweighted Dollo parsimony analysis. After excluding derived Ves insertions, those present in only one species, 85,028 parsimony-informative characters were retained for analyses. Dollo parsimony resulted in a single most-parsimonious tree (fig. 5; length = 166,575 steps, consistency index = 0.518. rescaled consistency index = 0.166, retention index = 0.321, homoplasy index = 0.4820). Following 10,000 bootstrap replicates, all nodes received strong support.Fig. 5.—
Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.