10.5061/DRYAD.43T60
Newman, Catherine E.
Louisiana State University of Alexandria
Austin, Christopher C.
Louisiana State University of Alexandria
Data from: Sequence capture and next-generation sequencing of
ultraconserved elements in a large-genome salamander
Dryad
dataset
2016
Plethodon serratus
2016-11-10T15:20:09Z
2016-11-10T15:20:09Z
en
https://doi.org/10.1111/mec.13909
204692620 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Amidst the rapid advancement in next-generation sequencing (NGS)
technology over the last few years, salamanders have been left behind.
Salamanders have enormous genomes – up to 40 times the size of the human
genome – and this poses challenges to generating NGS data sets of quality
and quantity similar to those of other vertebrates. However, optimization
of laboratory protocols is time-consuming and often cost prohibitive, and
continued omission of salamanders from novel phylogeographic research is
detrimental to species facing decline. Here, we use a salamander endemic
to the southeastern US, Plethodon serratus, to test the utility of an
established protocol for sequence capture of ultraconserved elements
(UCEs) in resolving intraspecific phylogeographic relationships and
delimiting cryptic species. Without modifying the standard laboratory
protocol, we generated a data set consisting of over 600 million reads for
85 P. serratus samples. Species delimitation analyses support recognition
of seven species within P. serratus sensu lato, and all phylogenetic
relationships among the seven species are fully resolved under a
coalescent model. Results also corroborate previous data suggesting
non-monophyly of the Ouachita and Louisiana regions. Our results
demonstrate that established UCE protocols can successfully be used in
phylogeographic studies of salamander species, providing a powerful tool
for future research on evolutionary history of amphibians and other
organisms with large genomes.
RAxML-20percent-allConcatenated phylip alignment for RAxML: all samples,
up to 20 percent missing samples per
locusmafft-nexus-80-all.phylipRAxML-60percent-allConcatenated phylip
alignment for RAxML: all samples, up to 40 percent missing samples per
locusmafft-nexus-60-all.phylipRAxML-20percent-1kConcatenated phylip
alignment for RAxML: 1k-samples, up to 20 percent missing samples per
locusmafft-nexus-80-1k.phylipRAxML-40percent-1kConcatenated phylip
alignment for RAxML: 1k-samples, up to 40 percent missing samples per
locusmafft-nexus-60-1k.phylipStarbeast_BPP_informative70Alignments (nexus)
for *Beast and BPP analyses: 70 most informative
lociStarbeast_informative100Alignments (nexus) for *Beast analysis: 100
most informative lociStarbeast_informative50Alignments (nexus) for *Beast
analysis: 50 most informative lociStarbeast_informative20Alignments
(nexus) for *Beast analysis: 20 most informative
lociStarbeast_BPP_random70_1Alignments (nexus) for *Beast and BPP
analyses: 70 random loci, set 1Starbeast_random70_2Alignments (nexus) for
*Beast analysis: 70 random loci, set 2Starbeast_random70_3Alignments
(nexus) for *Beast analysis: 70 random loci, set
3Starbeast_random70_4Alignments (nexus) for *Beast analysis: 70 random
loci, set 4Starbeast_random70_5Alignments (nexus) for *Beast analysis: 70
random loci, set 5Structure_random_allpopsSNP file for Structure analyses.
Population in second column.
Southeastern United States