Data from: Phylogenomics and a new fossil synthesis illuminate the early evolution of palms (Arecaceae)

Tropical rainforests are home to almost half of plant diversity, yet a
shortfall in phylogenetic hypotheses for tropical plants hinders our
understanding of how rainforests have formed and adapted to past global
changes. Phylogenetic and historical biogeographic evidence from key
rainforest lineages, such as palms (Arecaceae), is required to illuminate
the history of these ecosystems. However, our current understanding of the
palm tree of life is based on uneven sampling of plastid and nuclear data.
Moreover, numerous palm genera and palm fossils have been described or
revised over the past decade, casting doubt on palm relationships, ages,
and ancestral ranges inferred in early studies. Here, we infer the
phylogenetic relationships of all 184 palm genera based on data from 1,033
nuclear genes generated using target sequence capture. Our palm
phylogenomic tree is highly resolved and supported. Remaining areas of
ambiguity reflect the complex dynamics of palm evolution, including rapid
diversification events in subfamily Arecoideae and putative cases of
ancient reticulation throughout the family. We undertake a comprehensive
review of the palm fossil record and use a vetted selection of fossils to
estimate divergence times with two Bayesian methods, the first based on
calibration of five nodes using the age of fossils assigned to them, and
the second based on co-estimation of divergence times and phylogenetic
placements of 113 fossils with a Fossilized Birth-Death model. We then use
the distribution ranges of extant and fossil taxa to infer ancestral
ranges. We show that the palm family first diversified in the Early
Cretaceous in regions corresponding to what is now North, Central, and
South America and Oceania, that many tribes and subtribes had originated
by the Late Cretaceous, and that two-thirds of the genera had diverged by
the Oligocene. Fossil-informed analyses provide a more complex picture of
the early biogeography of palms than analyses relying only on the ranges
of extant taxa. Despite uncertainties regarding fossil placement, it is
clear that palms dispersed dozens of times across oceanic gaps, and that
dispersal and extirpation patterns are consistent with an ancient affinity
of palms for megathermal climates. Our dated phylogenomic trees and
curated fossil dataset provide a new foundation for evolutionary studies
on palms, opening the door to deeper research on the rainforest biome in
which they thrive.