Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats

Platt II. RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee Jr. TE, Baker RJ, Stevens RD, Ray DA

Date Published: August 16, 2017

DOI: https://doi.org/10.5061/dryad.5g205

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Title Alignments of individual UCE loci
Downloaded 6 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 3 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 5 times
Description Final trees from all analyses in nexus format.
Download supFile-all_trees_2017-07-01.nexus (569.7 Kb)
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Title assembled_contigs_from_UCEenriched_reads
Downloaded 6 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 7 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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When using this data, please cite the original publication:

Platt II. RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee Jr. TE, Baker RJ, Stevens RD, Ray DA (2017) Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syx070

Additionally, please cite the Dryad data package:

Platt II. RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee Jr. TE, Baker RJ, Stevens RD, Ray DA (2017) Data from: Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis bats. Dryad Digital Repository. https://doi.org/10.5061/dryad.5g205
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