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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: 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.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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Phylogeny of Myotis based on Ves insertions. Dollo parsimony analyses of the Ves insertion data produced a single most parsimonious tree. Insertion data were coded as either present (1) or absent (0). Due to the failure of the M. lucifugus sequencing libraries, insertions of this species were coded as either present (1) or missing (?). Bootstrap percentages from 10,000 replicates are shown above the branches. Biogeographic distributions are designated by colored branches (blue, neotropical; red, nearctic). As the ancestral state of each Ves insertion is assumed to be its absence, a putative ancestral taxon was created where all insertions were coded as absent.
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evv099-F5: Phylogeny of Myotis based on Ves insertions. Dollo parsimony analyses of the Ves insertion data produced a single most parsimonious tree. Insertion data were coded as either present (1) or absent (0). Due to the failure of the M. lucifugus sequencing libraries, insertions of this species were coded as either present (1) or missing (?). Bootstrap percentages from 10,000 replicates are shown above the branches. Biogeographic distributions are designated by colored branches (blue, neotropical; red, nearctic). As the ancestral state of each Ves insertion is assumed to be its absence, a putative ancestral taxon was created where all insertions were coded as absent.

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.—


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)

Phylogeny of Myotis based on Ves insertions. Dollo parsimony analyses of the Ves insertion data produced a single most parsimonious tree. Insertion data were coded as either present (1) or absent (0). Due to the failure of the M. lucifugus sequencing libraries, insertions of this species were coded as either present (1) or missing (?). Bootstrap percentages from 10,000 replicates are shown above the branches. Biogeographic distributions are designated by colored branches (blue, neotropical; red, nearctic). As the ancestral state of each Ves insertion is assumed to be its absence, a putative ancestral taxon was created where all insertions were coded as absent.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv099-F5: Phylogeny of Myotis based on Ves insertions. Dollo parsimony analyses of the Ves insertion data produced a single most parsimonious tree. Insertion data were coded as either present (1) or absent (0). Due to the failure of the M. lucifugus sequencing libraries, insertions of this species were coded as either present (1) or missing (?). Bootstrap percentages from 10,000 replicates are shown above the branches. Biogeographic distributions are designated by colored branches (blue, neotropical; red, nearctic). As the ancestral state of each Ves insertion is assumed to be its absence, a putative ancestral taxon was created where all insertions were coded as absent.
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.—

Bottom Line: 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.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
Related in: MedlinePlus