10.5061/DRYAD.4VT08
Leaché, Adam D.
University of Washington
Chavez, Andreas S.
University of Washington
Jones, Leonard N.
University of Washington
Grummer, Jared A.
University of Washington
Gottscho, Andrew D.
San Diego State University
Linkem, Charles W.
University of Washington
Data from: Phylogenomics of phrynosomatid lizards: conflicting signals
from sequence capture versus restriction site associated DNA sequencing
Dryad
dataset
2015
Holbrookia
Coalescence
Uta
Urosaurus
ultraconserved element
Cophosaurus
Uma
Phrynosoma
Callisaurus
UCE
Phrynosomatidae
Petrosaurus
Sceloporus
2015-02-10T15:39:18Z
2015-02-10T15:39:18Z
en
https://doi.org/10.1093/gbe/evv026
4828337 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Sequence capture and restriction site associated DNA sequencing (RADseq)
are popular methods for obtaining large numbers of loci for phylogenetic
analysis. These methods are typically used to collect data at different
evolutionary timescales; sequence capture is primarily used for obtaining
conserved loci, whereas RADseq is designed for discovering single
nucleotide polymorphisms (SNPs) suitable for population genetic or
phylogeographic analyses. Phylogenetic questions that span both “recent”
and “deep” timescales could benefit from either type of data, but studies
that directly compare the two approaches are lacking. We compared
phylogenies estimated from sequence capture and double digest RADseq
(ddRADseq) data for North American phrynosomatid lizards, a species-rich
and diverse group containing nine genera that began diversifying
approximately 55 million years ago. Sequence capture resulted in 584 loci
that provided a consistent and strong phylogeny using concatenation and
species tree inference. However, the phylogeny estimated from the ddRADseq
data was sensitive to the bioinformatics steps used for determining
homology, detecting paralogs, and filtering missing data. The topological
conflicts among the SNP trees were not restricted to any particular
timescale, but instead were associated with short internal branches.
Species tree analysis of the largest SNP assembly, which also included the
most missing data, supported a topology that matched the sequence capture
tree. This preferred phylogeny provides strong support for the paraphyly
of the earless lizard genera Holbrookia and Cophosaurus, suggesting that
the earless morphology either evolved twice, or that it evolved once and
was subsequently lost in Callisaurus.
mtDNA alignmentNexus formatted file containing the partial (fragmented)
mtDNA genome data.mtDNA.nexddRADseq dataCompressed folder containing all
of the ddRADseq data assemblies in phylip format. Each *.phy file contains
one concatenated alignment of the ddRADseq data. The folders are organized
at three levels: 1) homology filter (80 or 90 or 95), 2) paralog filter (1
or 3), 3) minimum individuals (3, 4, 5, 6, 7, 8, 9, or
10).SNPdata_drayd.zipSequence capture data (all 584 captured loci)Sequence
capture loci in nexus file format. Files are named according to locus
name. Also includes a concatenated matrix of the 584
loci.nexus.zipSequence capture data (471 complete loci)A subset of the
sequence capture loci that were captured for all species included in the
study. The files are in nexus file format. Files are named according to
locus name. Also included is a concatenated matrix of the 471
loci.nexus_471complete_loci.zip