Data from: Phylogeny and biogeography of the Amazonian Pachyptera (Bignonieae, Bignoniaceae)

The Amazon houses a large proportion of the overall biodiversity currently
found on Earth. Despite that, our knowledge of Amazonian biodiversity is
still limited. In this study, we reconstruct the phylogeny of Pachyptera
(Bignoniaceae), a genus of neotropical lianas, centered in the Amazon. We
then use this phylogenetic framework to re-evaluate species limits and
study the biogeographic history of the genus. We sampled three molecular
markers (i.e., ndhF , rpl32-trnL , and PepC ) and 51 individuals
representing the breadth of morphological variation and geographic
distribution of all species recognized in the genus. We used this
information to reconstruct phylogenetic relationships among individuals of
Pachyptera using Bayesian and Maximum Likelihood approaches. The resulting
molecular phylogeny was used as a basis to test species limits within the
P. kerere species complex using a cpDNA coalescent approach (GMYC). GMYC
identified five potential species within the P. kerere species complex
that were subsequently evaluated in the light of morphology. Morphological
data supported the recognition of four of the five potential species
suggested by GMYC, all of which were also supported by a multispecies
coalescent model in a Bayesian framework (BEAST). The phylogeny of
Pachyptera was time-calibrated using BEAST and used to reconstruct the
biogeographical history of the genus using the DEC model implemented in
RASP. We identified historically important migration pathways using our
comprehensive cpDNA dataset and a Bayesian stochastic search variable
selection (BSSVS) framework. Our results indicate that the genus
originated in lowland Amazonia during the Middle Eocene, and subsequently
occupied Central America and the Andes. Most of the diversification of
Pachyptera occurred in the Miocene, a period of intense perturbations in
South America.