title: Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.
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.
authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.
authors.forename: Roy N
authors.initials: RN
authors.lastname: Platt
authors.affiliation: Bionomics Research & Technology Center, Environmental and Occupational Health Science Institute, Rutgers, The State University of New Jersey.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Human Genetics, University of Utah Health Sciences Center.
authors.forename: David J
authors.initials: DJ
authors.lastname: Witherspoon
authors.affiliation: Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey.
authors.forename: Jinchuan
authors.initials: J
authors.lastname: Xing
authors.affiliation: Department of Evolutionary Biology, Uppsala University, Sweden.
authors.forename: Alexander
authors.initials: A
authors.lastname: Suh
authors.affiliation: Department of Biological Sciences, Texas Tech University.
authors.forename: Megan S
authors.initials: MS
authors.lastname: Keith
authors.affiliation: Department of Human Genetics, University of Utah Health Sciences Center.
authors.forename: Lynn B
authors.initials: LB
authors.lastname: Jorde
authors.affiliation: Department of Natural Resources Management and the Museum of Texas Tech University.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Stevens
authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University david.4.ray@gmail.com.
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
mesh_terms: D000818:Animals; D002685:Chiroptera / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D020086:Short Interspersed Nucleotide Elements
keywords: Dollo parsimony; Myotis lucifugus; phylogenetics; rare genomic events; retrotransposon