RT Journal Article
SR Electronic
T1 Disentangling Sources of Gene Tree Discordance in Phylotranscriptomic Datasets: A Case Study from Amaranthaceae s.l.
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 794370
DO 10.1101/794370
A1 Diego F. Morales-Briones
A1 Gudrun Kadereit
A1 Delphine T. Tefarikis
A1 Michael J. Moore
A1 Stephen A. Smith
A1 Samuel F. Brockington
A1 Alfonso Timoneda
A1 Won C. Yim
A1 John C. Cushman
A1 Ya Yang
YR 2019
UL http://biorxiv.org/content/early/2019/10/07/794370.abstract
AB Phylogenomic datasets have become common and fundamental to understanding the phylogenetic relationships of recalcitrant groups across the Tree of Life. At the same time, working with large genomic or transcriptomic datasets requires special attention to the processes that generate gene tree discordance, such as data processing and orthology inference, incomplete lineage sorting, hybridization, model violation, and uninformative gene trees. Methods to estimate species trees from phylogenomic datasets while accounting for all sources of conflict are not available, but a combination of multiple approaches can be a powerful tool to tease apart alternative sources of conflict. Here using a phylotranscriptomic analysis in combination with reference genomes, we explore sources of gene tree discordance in the backbone phylogeny of the plant family Amaranthaceae s.l. The dataset was analyzed using multiple phylogenetic approaches, including coalescent-based species trees and network inference, gene tree discordance analyses, site pattern test of introgression, topology test, synteny analyses, and simulations. We found that a combination of processes might have acted, simultaneously and/or cumulatively, to generate the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, other analytical shortcomings like uninformative genes as well as misspecification of the model of molecular evolution seem to contribute to tree discordance signal in this family. Despite the comprehensive phylogenomic dataset and detailed analyses presented here, no single source can confidently be pointed out to account for the strong signal of gene tree discordance, suggesting that the backbone of Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains —and probably will remain— unresolved even with genome-scale data. Our work highlights the need to test for multiple sources of conflict in phylogenomic analyses and provide a set of recommendations moving forward in disentangling ancient and rapid diversification.