Data from: The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics

Opiliones are iconic arachnids with a Palaeozoic origin and a diversity
that reflects ancient biogeographic patterns dating back at least to the
times of Pangea. Owing to interest in harvestman diversity, evolution and
biogeography, their relationships have been thoroughly studied using
morphology and PCR-based Sanger approaches to infer their systematic
relationships. More recently, two studies utilized transcriptomics-based
phylogenomics to explore their basal relationships and diversification,
but sampling was limiting for understanding deep evolutionary patterns, as
they lacked good taxon representation at the family level. Here, we
analysed a set of the 14 existing transcriptomes with 40 additional ones
generated for this study, representing approximately 80% of the extant
familial diversity in Opiliones. Our phylogenetic analyses, including a
set of data matrices with different gene occupancy and evolutionary rates,
and using a multitude of methods correcting for a diversity of factors
affecting phylogenomic data matrices, provide a robust and stable
Opiliones tree of life, where most families and higher taxa are precisely
placed. Our dating analyses using alternative calibration points, methods
and analytical parameters provide well-resolved old divergences,
consistent with ancient regionalization in Pangea in some groups, and
Pangean vicariance in others. The integration of state-of-the-art
molecular techniques and analyses, together with the broadest taxonomic
sampling to date presented in a phylogenomic study of harvestmen, provide
new insights into harvestmen interrelationships, as well as an overview of
the general biogeographic patterns of this ancient arthropod group.