DOI: 10.5061/dryad.p8cz8w9kq
title: Data from: Phylogeny and biogeography of the Amazonian Pachyptera (Bignonieae, Bignoniaceae)

description: 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.
description: This
 file is related to the article “Phylogeny and Biogeography of the
 Amazonian <i>Pachyptera</i> (Bignonieae, Bignoniaceae)”, to be
 published to Systematic Botany, and derived from a part of my master
 dissertation.    Supplementary
 Materials Tables Table S1. Information on the phylogenetic, phylogeographic, and time calibration analyses, partitions, models, and parameters. Table S2. Divergence time estimates and ancestral area reconstructions for <i>Pachyptera </i>conducted with S-DIVA, DEC, and BSSVS. Areas with (/) suggest similar posterior probabilities. Figures Fig. S1.<b> </b>Consensus tree of <i>Pachyptera </i>inferred from the Bayesian analysis of the <i>ndh</i>F (A) and <i>rpl</i>32<i>–trn</i>L<i> </i>(B) datasets. Posterior probability and bootstrap values are shown above branches. The outgroups are shown in grey. Fig. S2.<b> </b>Consensus tree of <i>Pachyptera</i> inferred from the Bayesian analysis of the combined cpDNA dataset (i.e., <i>ndhF</i> and<i> rpl32–trnL</i>). Posterior probability and bootstrap values are shown above branches. The outgroups are shown in grey. Fig. S3. Consensus tree of <i>Pachyptera </i>inferred from the Bayesian analysis of the <i>Pep</i>C<i> </i>dataset. Posterior probability and bootstrap values are shown above branches. The outgroups are shown in grey. Fig. S4. Statistical parsimony network of <i>Pachyptera kerere</i> constructed based on the analysis of the <i>ndh</i>F<i> </i>and <i>rpl</i>32<i>–trn</i>L datasets. Circle sizes are proportional to the frequency of each haplotype. Small empty circles represent mutational steps.