Angiosperms353 data for the epidendroid orchid base

Parasites present fascinating examples of evolutionary modification that
simultaneously pose challenges for systematics. This is exemplified by
fully mycoheterotrophic orchids, which are completely dependent on fungi,
constituting nearly half of all mycoheterotrophic plant species. A large
concentration of mycoheterotrophic lineages is found among the eight
tribes comprising the base of the megadiverse orchid subfamily
Epidendroideae, here referred to as the early diverging Epidendroideae
(EDE). To date, relationships among the EDE have been problematic.
Previous analyses have suffered from sparse taxon sampling, weak support
from limited loci, or long-branch attraction in plastid-based analyses. We
conducted the most comprehensive nuclear phylogenomic analysis of the EDE
to date, using Angiosperms353 loci, coalescent analyses, and deep
exploration of support, conflict, saturation, and introgression. Our study
is the first to include phylogenomic sampling from all eight EDE tribes,
with 22 of 26 EDE genera represented. We took a novel approach, selecting
best-fit mixture model configurations at the individual locus level, which
provided significantly better fit overall and required fewer parameters
than all other models, with implications for clades characterized by
lineage-specific rate heterogeneity. We recovered strong support for
monophyly of all EDE tribes except for Neottieae, which were inferred to
be paraphyletic. Information content was generally rich for deep
relationships among the EDE tribes, but overall support was weak. We found
evidence of saturation and putative introgression, with two inferred
reticulation events. We conclude that short internal branches associated
with rapid diversification, incomplete lineage sorting, and putative
introgression resulted in low concordant signal among EDE tribes,
underscoring the continued difficulty in resolving their relationships.
Nonetheless, we provide the first strongly supported phylogenetic
hypothesis for the five genera of Gastrodieae, representing the largest
known diversification of fully mycoheterotrophic plants. We discuss our
findings considering recent phylogenomic studies, taxonomy, morphology,
and biogeographic implications.