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

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.