Data from: The biogeography of deep time phylogenetic reticulation

Most phylogenies are typically represented as purely bifurcating. However,
as genomic data has become more common in phylogenetic studies, it is not
unusual to find reticulation among terminal lineages or among internal
nodes (deep time reticulation; DTR). In these situations, gene flow must
have happened in the same or adjacent geographic areas for these DTRs to
have occurred and therefore biogeographic reconstruction should provide
similar area estimates for parental nodes, provided extinction or
dispersal has not eroded these patterns. We examine the phylogeny of the
widely distributed New World kingsnakes (Lampropeltis), determine if DTR
is present in this group, and estimate the ancestral area for
reticulation. Importantly, we develop a new method that uses coalescent
simulations in a machine learning framework to show conclusively that this
phylogeny is best represented as reticulating at deeper time. Using joint
probabilities of ancestral area reconstructions on the bifurcating
parental lineages from the reticulating node, we show that this
reticulation likely occurred in northwestern Mexico/southwestern US and
subsequently led to the diversification of the Mexican kingsnakes. This
region has been previously identified as an area important for
understanding speciation and secondary contact with gene flow in snakes
and other squamates. This research shows that phylogenetic reticulation is
common, even in well-studied groups, and that the geographic scope of
ancient hybridization is recoverable.