Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Morales-Briones, Diego F.; Kadereit, Gudrun; Tefarikis, Delphine T.; Moore, Michael J.; Smith, Stephen A.; Brockington, Samuel F.; Timoneda, Alfonso; Yim, Won C.; Cushman, John C.; Yang, Ya

doi:10.1093/sysbio/syaa066

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Journal Article · Fri Jun 12 00:00:00 EDT 2020 · Systematic Biology

DOI:https://doi.org/10.1093/sysbio/syaa066· OSTI ID:1851159

Morales-Briones, Diego F. ^[1]; Kadereit, Gudrun ^[2]; Tefarikis, Delphine T. ^[2]; Moore, Michael J. ^[3]; Smith, Stephen A. ^[4]; Brockington, Samuel F. ^[5]; Timoneda, Alfonso ^[5]; Yim, Won C. ^[6]; Cushman, John C. ^[6]; Yang, Ya ^[7]

Univ. of Minnesota, Twin Cities, St. Paul, MN (United States); OSTI
Johannes Gutenberg Univ., Mainz (Germany)
Oberlin College, OH (United States)
Univ. of Michigan, Ann Arbor, MI (United States)
Univ. of Cambridge (United Kingdom)
Univ. of Nevada, Reno, NV (United States)
Univ. of Minnesota, Twin Cities, St. Paul, MN (United States)

Gene tree discordance in large genomic data sets 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 data set 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.

View Accepted Manuscript (DOE)

Research Organization:: University of Nevada, Reno, NV (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC); University of Michigan; University of Minnesota

Grant/Contract Number:: SC0008834

OSTI ID:: 1851159

Journal Information:: Systematic Biology, Journal Name: Systematic Biology Journal Issue: 2 Vol. 70; ISSN 1063-5157

Publisher:: Society of Systematic Biologists - Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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First molecular and morphometric data for the genus Allmania (Amaranthaceae), with the description of a new species from India Sindhu, Arya; Iamonico, Duilio; Suresh, Veerankutty Phytotaxa, Vol. 559, Issue 3 https://doi.org/10.11646/phytotaxa.559.3.1	journal	August 2022
Disentangling sources of gene tree discordance in phylogenomic datasets: testing ancient hybridizations in Amaranthaceae s.l. Morales-Briones, Diego F.; Kadereit, Gudrun; Tefarikis, Delphine Dryad https://doi.org/10.5061/dryad.ns1rn8pq4	dataset	January 2020
Additional file 1 of Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family Dong, Wenpan; Li, Enze; Liu, Yanlei figshare https://doi.org/10.6084/m9.figshare.19654525.v1	dataset	January 2022

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59 BASIC BIOLOGICAL SCIENCES
Amaranthaceae
evolutionary biology
gene tree discordance
hybridization
incomplete lineage sorting
phylogenomics
species network
species tree
transcriptomics

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