Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Premise of the Study— The Caryophyllales contains ~12,500 species and is
known for its cosmopolitan distribution, convergence of trait evolution,
and extreme adaptations. Some relationships within the Caryophyllales,
like those of many large plant clades, remain unclear and phylogenetic
studies often recover alternative hypotheses. We explore the utility of
broad and dense transcriptome sampling across the order for resolving
evolutionary relationships in Caryophyllales. Methods— We generated 84
transcriptomes and combined these with 224 publicly available
transcriptomes to perform a phylogenomic analysis of Caryophyllales. To
overcome the computational challenge of ortholog detection in such a large
data set, we developed an approach for clustering gene families that
allowed us to analyze >300 transcriptomes and genomes. We then
inferred the species relationships using multiple methods and performed
gene tree conflict analyses. Key Results— Our phylogenetic analyses
resolved many clades with strong support, but also showed significant
gene-tree discordance. This discordance is a common feature of
phylogenomic studies but also represents an opportunity to understand
processes that have structured phylogenies. We also found taxon sampling
influences species-tree inference, highlighting the importance of more
focused studies with additional taxon sampling. Conclusions—
Transcriptomes are useful both for species tree inference and for
uncovering evolutionary complexity within lineages. Through analyses of
gene-tree conflict and multiple methods of species tree inference, we
demonstrate that phylogenomic data can provide unparalleled insight into
the evolutionary history of Caryophyllales. We also discuss a method for
overcoming computational challenges associated with homolog clustering in
large datasets.