Show simple item record Platt II., Roy N. Faircloth, Brant C. Sullivan, Kevin A.M. Kieran, Troy J. Glenn, Travis C. Vandewege, Michael W. Lee Jr., Thomas E. Baker, Robert J. Stevens, Richard D. Ray, David A. 2017-08-16T16:35:43Z 2017-08-16T16:35:43Z 2017-08-25
dc.identifier doi:10.5061/dryad.5g205
dc.identifier.citation Platt II. RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee Jr. TE, Baker RJ, Stevens RD, Ray DA (2018) Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats. Systematic Biology 67(2): 236-249.
dc.identifier.issn 1063-5157
dc.description The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3,648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
dc.relation.haspart doi:10.5061/dryad.5g205/2
dc.relation.haspart doi:10.5061/dryad.5g205/3
dc.relation.haspart doi:10.5061/dryad.5g205/1
dc.relation.haspart doi:10.5061/dryad.5g205/4
dc.relation.haspart doi:10.5061/dryad.5g205/5
dc.relation.isreferencedby doi:10.1093/sysbio/syx070
dc.subject incomplete lineage sorting
dc.subject summary tree methods
dc.subject concatenation
dc.subject phylogenomics
dc.subject UCE
dc.subject ultraconserved elements
dc.subject reticulation
dc.title Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats
dc.type Article
dwc.ScientificName Vespertilionidae
dc.contributor.correspondingAuthor Platt, Roy
prism.publicationName Systematic Biology
dryad.dansTransferDate 2018-05-31T09:02:02.279+0000
dryad.dansTransferFailed 2018-05-17T07:32:34.514+0000
dryad.dansArchiveDate 2018-05-31T10:04:35.369+0000

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Title Alignments of individual UCE loci
Downloaded 22 times
Description Individual alignments of UCE loci in nexus format. Loci were aligned using MAFFT and trimmed wtih Gblocks.
Download uceLociAlignments.tgz (1.873 Mb)
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Title Individual gene trees from UCE loci
Downloaded 11 times
Description Individual gene trees per UCE locus were generated using RAxML's GTRGAMMA model of nucleotide evolution and fast bootstrapping options (replicates=1,000). Individual trees are in Newick format.
Download uceGeneTrees.tgz (1.366 Mb)
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Title supFile-all_trees_2017-07-01
Downloaded 15 times
Description Final trees from all analyses in nexus format.
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Title assembled_contigs_from_UCEenriched_reads
Downloaded 10 times
Description All loci assembled from baited reads (per taxa). These sequences were then compared in an all-vs-all manner to identify homologous UCE loci among taxa. As a results, there are some contigs that may not be present in the final alignments since they are not UCE loci.
Download assembled_contigs_from_UCEenriched_reads.tgz (33.18 Mb)
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Title Sup Fig 1. Phylogenetic content of UCE loci based on length.
Downloaded 17 times
Description The length of a UCE locus is correlated with the number of phylogenetically informative characters. UCE loci were sorted by length and ten bins of alignments were created so that the shortest loci were combined into one alignment, the next shortest set of loci were combined … etc. Parsimony informative characters made up a minor part of each alignment.
Download supFigure1-informCharacters_2017-07-01.png (20.30 Kb)
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