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

Title: 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 ^[1]

Univ. of Minnesota, Twin Cities, St. Paul, MN (United States)
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)

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.

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

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

Grant/Contract Number:: SC0008834; DEB 1354048

OSTI ID:: 1851159

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

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

Country of Publication:: United States

Language:: English

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Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes Zhao, Tao; Schranz, M. Eric Proceedings of the National Academy of Sciences, Vol. 116, Issue 6 https://doi.org/10.1073/pnas.1801757116	journal	January 2019
Phylogeny of Amaranthaceae and Chenopodiaceae and the Evolution of C ₄ Photosynthesis Kadereit, G.; Borsch, T.; Weising, K. International Journal of Plant Sciences, Vol. 164, Issue 6 https://doi.org/10.1086/378649	journal	November 2003
Differentiating between Hypotheses of Lineage Sorting and Introgression in New Zealand Alpine Cicadas (Maoricicada Dugdale) Buckley, Thomas R.; Cordeiro, Michael; Marshall, David C. Systematic Biology, Vol. 55, Issue 3 https://doi.org/10.1080/10635150600697283	journal	June 2006
Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone Cloutier, Alison; Sackton, Timothy B.; Grayson, Phil Systematic Biology, Vol. 68, Issue 6 https://doi.org/10.1093/sysbio/syz019	journal	April 2019
The Phylogenetic Association Between Salt Tolerance and Heavy Metal Hyperaccumulation in Angiosperms Moray, Camile; Goolsby, Eric W.; Bromham, Lindell Evolutionary Biology, Vol. 43, Issue 1 https://doi.org/10.1007/s11692-015-9355-2	journal	November 2015
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci Rannala, Bruce; Yang, Ziheng Genetics, Vol. 164, Issue 4 https://doi.org/10.1093/genetics/164.4.1645	journal	August 2003
Phylogeny of Polycnemoideae (Amaranthaceae): Implications for biogeography, character evolution and taxonomy Masson, Rüdiger; Kadereit, Gudrun TAXON, Vol. 62, Issue 1 https://doi.org/10.1002/tax.621009	journal	February 2013
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses Lanfear, R.; Calcott, B.; Ho, S. Y. W. Molecular Biology and Evolution, Vol. 29, Issue 6 https://doi.org/10.1093/molbev/mss020	journal	January 2012
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

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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

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59 BASIC BIOLOGICAL SCIENCES
evolutionary biology
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gene tree discordance
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incomplete lineage sorting
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Title: Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

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