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

Platt RN, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA - Genome Biol Evol (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.

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Accuracy of estimated Ves insertion sites shared among species. Estimated Ves insertion sites within each species ([A] M. auriculus, [B] M. dominicensis, [C] M. horsfieldii, [D] M. lucifugus, [E] M. occultus, [F] M. simus, [G] M. vivesi) were compared with the six other species examined. For estimated insertion sites that fell within ± 100 bp of each other between species, the distance was calculated. Orthologous insertions are expected to occur at the same position, whereas independent insertions would occur randomly.
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evv099-F2: Accuracy of estimated Ves insertion sites shared among species. Estimated Ves insertion sites within each species ([A] M. auriculus, [B] M. dominicensis, [C] M. horsfieldii, [D] M. lucifugus, [E] M. occultus, [F] M. simus, [G] M. vivesi) were compared with the six other species examined. For estimated insertion sites that fell within ± 100 bp of each other between species, the distance was calculated. Orthologous insertions are expected to occur at the same position, whereas independent insertions would occur randomly.

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.—


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

Platt RN, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA - Genome Biol Evol (2015)

Accuracy of estimated Ves insertion sites shared among species. Estimated Ves insertion sites within each species ([A] M. auriculus, [B] M. dominicensis, [C] M. horsfieldii, [D] M. lucifugus, [E] M. occultus, [F] M. simus, [G] M. vivesi) were compared with the six other species examined. For estimated insertion sites that fell within ± 100 bp of each other between species, the distance was calculated. Orthologous insertions are expected to occur at the same position, whereas independent insertions would occur randomly.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494050&req=5

evv099-F2: Accuracy of estimated Ves insertion sites shared among species. Estimated Ves insertion sites within each species ([A] M. auriculus, [B] M. dominicensis, [C] M. horsfieldii, [D] M. lucifugus, [E] M. occultus, [F] M. simus, [G] M. vivesi) were compared with the six other species examined. For estimated insertion sites that fell within ± 100 bp of each other between species, the distance was calculated. Orthologous insertions are expected to occur at the same position, whereas independent insertions would occur randomly.
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.—

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.

Show MeSH