DOI: 10.5061/dryad.ns1rn8pq4
title: Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l.

description: 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.
description: - 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. <br> - 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<br>   
  all_13025_orthologs_cln_aln.tar.gz - all the 13025 'monophyletic
 outgroup' orthologs<br>     105-taxon.tar.gz - 936 alignments
 and trees of the full 105-taxon analyses<br>     41-taxon.tar.gz -
 1242 alignments and trees of the 41-taxon cloudogram<br>   
  11-taxon-net.tar.gz - 4138 alignments and trees of the 11-taxon(net) used
 for network analyses<br>     4-taxon.tar.gz - alignments and trees
 (between 7,756 and 8,793) for each of the 10 4-taxon quartets<br>   
  11-taxon-tree.tar.gz - 5936 alignments and trees of the 11-taxon(tree)
 analyses<br>     chloroplast.tar.gz - 11-taxon alignment and tree
 and 76 individual CDS alignment and trees of the plastid
 analyses