Data from: Phylogenomic analyses reveal novel relationships among snake families

Snakes are a diverse and important group of vertebrates. However,
relationships among the major groups of snakes have remained highly
uncertain, with recent studies hypothesizing very different (and typically
weakly supported) relationships. Here, we address family-level snake
relationships with new phylogenomic data from 3,776 nuclear loci from
ultraconserved elements (1.34 million aligned base pairs, 52% missing data
overall) sampled from 29 snake species that together represent almost all
families, a dataset ∼100 times larger than used in previous studies. We
found relatively strong support from species-tree analyses (NJst) for most
relationships, including three largely novel clades: (1) a clade uniting
the boas, pythons and their relatives, (2) a clade placing cylindrophiids
and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round
Island boas) with pythonids and their relatives (xenopeltids and
loxocemids). Relationships among families of advanced snakes
(caenophidians) were also strongly supported. The results show the
potential for phylogenomic analyses to resolve difficult groups, but also
show a surprising sensitivity of the analyses to the inclusion or
exclusion of outgroups.