# Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis

## TL;DR

Researchers developed a method to identify SINE insertions in bat species, enabling phylogenetic analysis even without complete genome sequences.

## Contribution

Extended the ME-Scan method to identify Ves SINE insertions in nonmodel bat species without reference genomes.

## Key findings

- Identified 120,000–143,000 Ves SINE insertions in six Myotis species using a reference genome.
- Created a presence–absence matrix for ~796,000 insertions and used Dollo parsimony to infer phylogeny.
- Results align with mitochondrial phylogenies, except for M. vivesi placement.

## Abstract

Identification of retrotransposon insertions in nonmodel taxa can be technically challenging and costly. This has inhibited progress in understanding retrotransposon insertion dynamics outside of a few well-studied species. To address this problem, we have extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis. We identified between 120,000 and 143,000 SINE insertions in six taxa lacking a draft genome by comparing to the M. lucifugus reference genome. On average, each Ves insertion was sequenced to 129.6 × coverage. When mapped back to the M. lucifugus reference genome, all insertions were confidently assigned within a 10-bp window. Polymorphic Ves insertions were identified in each taxon based on their mapped locations. Using cross-species comparisons and the identified insertion positions, a presence–absence matrix was created for approximately 796,000 insertions. 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.