3987463
doi
10.5061/dryad.ns1rn8pq4
oai:zenodo.org:3987463
user-dryad
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.
Morales-Briones, Diego F.
University of Minnesota
doi:10.1093/sysbio/syaa066
info:eu-repo/semantics/openAccess
Creative Commons Zero v1.0 Universal
https://creativecommons.org/publicdomain/zero/1.0/legalcode
Amaranthaceae
gene tree discordance
species network
<p>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.</p>
<p>- The file 'Supplementa_Methods_and_Materials.tar.gz' contains the supplemental methods, figures and tables referenced in the main text</p>
<p>- The file 'Homologs.tar.gz' contains the 14584 homolog trees:</p>
<p> raw_homologs.tar.gz - trees without any filtering or pruning</p>
<p> final_homologs.tar.gz - trees after, monophyletic and paraphyletic grades of the same species masked, deep paralogs prunned, and spurious tips removed.</p>
<p><br>
- The file 'Analyses_data.tar.gz' contains the data (alignments and individual gene trees) used for each of the dataset:</p>
<p> 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</p>
<p>Funding provided by: University of Minnesota<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100007249</p><p>Funding provided by: University of Michigan<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100007270</p><p>Funding provided by: US National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB 1354048</p><p>Funding provided by: Department of Energy, Office of Science, Genomic Science Program<br>Crossref Funder Registry ID: <br>Award Number: DE-SC0008834</p>
Zenodo
2020-08-28
info:eu-repo/semantics/other
3987462
user-dryad
1654253473.685245
75452513
md5:a382db48510a2f596308c088fe1b4d56
https://zenodo.org/records/3987463/files/Homologs.zip
1618
md5:d2f21fd410c0297f17ac181ce8173f64
https://zenodo.org/records/3987463/files/README.txt
1293159082
md5:acd34b9dba2728f2a9d3a821acc79e14
https://zenodo.org/records/3987463/files/Analyses_data.tar.gz
11144191
md5:2eacc42dd9b1fe1a1011179d0a0dae23
https://zenodo.org/records/3987463/files/Supplemental_Methods_and_Materials.tar.gz
public
10.1093/sysbio/syaa066
Is cited by
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