10.5061/DRYAD.6P58D0K
Singhal, Sonal
CSU Dominguez Hills
Colston, Timothy
Florida State University
Grundler, Maggie
UC Berkeley
Smith, Stephen
University of Michigan
Costa, Gabriel
Auburn University at Montgomery
Colli, Guarino
Universidade de Brasília
Moritz, Craig
Australian National University
Pyron, Alexander
The George Washington University
Rabosky, Daniel
University of Michigan
Data from: Congruence and conflict in the higher-level phylogenetics of
squamate reptiles: an expanded phylogenomic perspective
Dryad
dataset
2019
anchored hybrid enrichment (AHE)
Snakes
gene tree conflict
ultraconserved elements (UCE)
Lizards
2020-08-25T00:00:00Z
2020-08-25T00:00:00Z
en
93998495 bytes
6
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Genome-scale data have the potential to clarify phylogenetic relationships
across the tree of life, but have also revealed extensive gene tree
conflict. This seeming paradox, whereby larger datasets both increase
statistical confidence and uncover significant discordance, suggests that
understanding sources of conflict is important for accurate reconstruction
of evolutionary history. We explore this paradox in squamate reptiles, the
vertebrate clade comprising lizards, snakes, and amphisbaenians. We
collected an average of 5103 loci for 91 species of squamates that span
higher-level diversity within the clade, which we augmented with publicly
available sequences for an additional 17 taxa. Using a locus-by-locus
approach, we evaluated support for alternative topologies at 17
contentious nodes in the phylogeny. We identified shared properties of
conflicting loci, finding that rate and compositional heterogeneity drives
discordance between gene trees and species tree and that conflicting loci
rarely overlap across contentious nodes. Finally, by comparing our tests
of nodal conflict to previous phylogenomic studies, we confidently resolve
nine of the 17 problematic nodes. We suggest this locus-by-locus and
node-by-node approach can be used to build consensus on which topological
resolutions remain uncertain in phylogenomic studies of other contentious
groups.
Included are: A zipped file of all the trimmed alignments used for tree
inference A zipped file of all the gene trees inferred from these trimmed
alignments trees inferred using RAxML nodes are annotated with SH-like
values Supplementary Information Supplementary Tables & Figures
for Manuscript