10.5061/DRYAD.NS1RN8PQ4
Morales-Briones, Diego F.
0000-0003-1535-5739
University of Minnesota
Kadereit, Gudrun
Johannes Gutenberg University of Mainz
Tefarikis, Delphine
Johannes Gutenberg University of Mainz
Moore, Michael
Oberlin College
Smith, Stephen
University of Michigan-Ann Arbor
Brockington, Samuel
University of Cambridge
Timoneda, Alfonso
University of Cambridge
Yim, Won
University of Nevada Reno
Cushman, John
University of Nevada Reno
Yang, Ya
University of Minnesota
Disentangling sources of gene tree discordance in phylogenomic datasets:
testing ancient hybridizations in Amaranthaceae s.l.
Dryad
dataset
2020
Amaranthaceae
gene tree discordance
species network
University of Minnesota System
https://ror.org/03grvy078
University of Michigan–Ann Arbor
https://ror.org/00jmfr291
National Science Foundation
https://ror.org/021nxhr62
DEB 1354048
Department of Energy, Office of Science, Genomic Science Program
DE-SC0008834
2020-08-16T00:00:00Z
2020-08-16T00:00:00Z
en
https://doi.org/10.1093/sysbio/syaa066
1379757404 bytes
6
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Gene tree discordance in large genomic datasets can be caused by
evolutionary processes such as incomplete lineage sorting and
hybridization, as well as model violation, and errors in data processing,
orthology inference, and gene tree estimation. Species tree methods that
identify and accommodate all sources of conflict are not available, but a
combination of multiple approaches can help tease apart alternative
sources of conflict. Here, using a phylotranscriptomic analysis in
combination with reference genomes, we test a hypothesis of ancient
hybridization events within the plant family Amaranthaceae s.l. that was
previously supported by morphological, ecological, and Sanger-based
molecular data. The dataset included seven genomes and 88 transcriptomes,
17 generated for this study. We examined gene-tree discordance using
coalescent-based species trees and network inference, gene tree
discordance analyses, site pattern tests of introgression, topology tests,
synteny analyses, and simulations. We found that a combination of
processes might have generated the high levels of gene tree discordance in
the backbone of Amaranthaceae s.l. Furthermore, we found evidence that
three consecutive short internal branches produce anomalous trees
contributing to the discordance. Overall, our results suggest that
Amaranthaceae s.l. might be a product of an ancient and rapid lineage
diversification, and remains, and probably will remain, unresolved. This
work highlights the potential problems of identifiability associated with
the sources of gene tree discordance including, in particular,
phylogenetic network methods. Our results also demonstrate the importance
of thoroughly testing for multiple sources of conflict in phylogenomic
analyses, especially in the context of ancient, rapid radiations. We
provide several recommendations for exploring conflicting signals in such
situations.
- The file 'Supplementa_Methods_and_Materials.tar.gz' contains
the supplemental methods, figures and tables referenced in the main text -
The file 'Homologs.tar.gz' contains the 14584 homolog trees:
raw_homologs.tar.gz - trees without any filtering or pruning
final_homologs.tar.gz - trees after, monophyletic and paraphyletic grades
of the same species masked, deep paralogs prunned, and spurious tips
removed. - The file 'Analyses_data.tar.gz' contains the data
(alignments and individual gene trees) used for each of the dataset:
filtered_transcriptomes.tar.gz - 88 filtered transcriptomes
all_13025_orthologs_cln_aln.tar.gz - all the 13025 'monophyletic
outgroup' orthologs 105-taxon.tar.gz - 936 alignments and trees
of the full 105-taxon analyses 41-taxon.tar.gz - 1242 alignments and
trees of the 41-taxon cloudogram 11-taxon-net.tar.gz - 4138 alignments
and trees of the 11-taxon(net) used for network analyses
4-taxon.tar.gz - alignments and trees (between 7,756 and 8,793) for each
of the 10 4-taxon quartets 11-taxon-tree.tar.gz - 5936 alignments and
trees of the 11-taxon(tree) analyses chloroplast.tar.gz - 11-taxon
alignment and tree and 76 individual CDS alignment and trees of the
plastid analyses