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Data from: Sources of gene tree discordance and their implications for systematics and evolution of a megadiverse Australian plant radiation (subtribe Hakeinae, Proteaceae)

Skeels, Alexander1

Published Oct 22, 2024; Updated Dec 20, 2024 on Dryad. https://doi.org/10.5061/dryad.6t1g1jx6b

Data files

Oct 22, 2024 version files 65.76 MB
Dec 20, 2024 version files 65.46 MB

Abstract

Resolving phylogenetic relationships in the presence of conflicting signal across genes is one of the major challenges of the phylogenomic era. Conflicting signals can emerge from biological processes, such as incomplete lineage sorting or introgression, or have technical origins, such as from misaligned sequences. As such, decisions made in the process of estimating species trees may result in alternative tree topologies and large variation in branch support values with important systematic consequences. Here we compare alternative strategies for alignment cleaning, loci filtering, and phylogenetic estimation in 551 taxa in the Proteaceae subtribe Hakeinae, to explore how these methodological choices affect the estimation of relationships. We found that node support values across gene trees were low and gene discordance was high in the Hakeinae, particularly in lineages from the Temperate Forests biome of southeastern Australia. Higher stringency of alignment cleaning tended to decrease node support and filtering desirable loci tended to increase gene concordance. Cleaning, filtering, and phylogenetic estimation method (short-cut coalescent or concatenation) have significant effects of tree topologies with distinct clusters of similar tree topologies detected in tree space. Of note, when using concatenated approaches, the two largest Hakeinae genera, Hakea and Grevillea, were reciprocally monophyletic. However, using coalescent approaches, we regularly found that Hakea was nested within Grevillea. Our results suggest that widespread gene discordance may be the result of rapid radiation and incomplete lineage sorting, demonstrating the importance of assessing the drivers of discordance to understand phylogenetic relationships.