Data from: Phylogenomics of elongate-bodied Springtails reveals independent transitions from aboveground to belowground habitats in deep time

Soil has become a major hotspot of biodiversity studies, yet the pattern
and timing of the evolution of soil organisms are poorly known because of
the scarcity of palaeontological data. To overcome this limitation, we
conducted a genome-based macroevolutionary study of an ancient,
diversified, and widespread lineage of soil fauna, the elongate-bodied
springtails (class Collembola, order Entomobryomorpha). To build the first
robust backbone phylogeny of this previously refractory group, we sampled
representatives of major higher taxa (6 out of 8 families, 11 out of 16
subfamilies) of the order with an emphasis on the most problematic
superfamily Tomoceroidea, applied whole-genome sequencing (WGS) methods,
and compared the performance of different combinations of datasets
(universal single-copy orthologues/USCO versus ultraconserved
elements/UCE) and modelling schemes. The fossil-calibrated timetree was
used to reconstruct the evolution of body size, sensory organs, and
pigmentation to establish a time frame of the ecomorphological
divergences. The resultant trees based on different analyses were
congruent in most nodes. Several discordant nodes were carefully evaluated
by considering method fitness, morphological information, and topology
test. The evaluation favoured the well-resolved topology from analyses
using USCO amino acid matrices and complex site-heterogeneous models
(CAT+GTR and LG+PMSF (C60)). The preferred topology supports the
monophyletic superfamily Tomoceroidea as an early-diverging lineage and a
sister relationship between Entomobryoidea and Isotomoidea. The family
Tomoceridae was recovered as monophyletic, while Oncopoduridae was
recovered as paraphyletic, with Harlomillsia as a sister to Tomoceridae
and hence deserving a separate family status as Harlomillsiidae Yu and
Zhang fam. n. Ancestral Entomobryomorpha were reconstructed as
surface-living, supporting independent origins of soil-living groups
across the Palaeozoic–Mesozoic, and highlighting the ancient evolutionary
interaction between aboveground and belowground fauna.