Data from: What’s in an outgroup? The impact of outgroup choice on the phylogenetic position of Thalattosuchia (Crocodylomorpha) and the origin of Crocodyliformes

Outgroup sampling is a central issue in phylogenetic analysis. However,
good justification is rarely given for outgroup selection in published
analyses. Recent advances in our understanding of archosaur phylogeny
suggest that many previous studies of crocodylomorph and crocodyliform
relationships have rooted trees on outgroup taxa that are only very
distantly related to the ingroup (e.g., Gracilisuchus stipanicicorum), or
might actually belong within the ingroup. Thalattosuchia, a group of
Mesozoic marine crocodylomorphs, has a controversial phylogenetic
position—they are recovered as either the sister group to Crocodyliformes,
in a basal position within Crocodyliformes, or nested high in the
crocodyliform tree. Thalattosuchians lack several crocodyliform
apomorphies, but share several character states with derived long-snouted
forms with a similar ecological habit, suggesting their derived position
may be the result of convergent evolution. Several of these “shared”
characters may result from ambiguously worded character state
definitions—structures that are superficially similar but anatomically
different in detail are identically coded. A new analysis of
crocodylomorphs with increased outgroup sampling recovers Thalattosuchia
as the sister group to Crocodyliformes, distantly related to long-snouted
crocodyliforms. I also demonstrate that expanding the outgroup sampling of
previously published matrices results in the recovery of thalattosuchians
as sister to Crocodyliformes. The exclusion of thalattosuchians from
Crocodyliformes has numerous implications for large-scale evolutionary
trends within the group, including extensive convergence in the evolution
of the secondary palate characteristic of the group. These results
demonstrate the importance of careful outgroup sampling and character
construction, and their profound effect on the position of labile clades.