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

Citation

Francisco, Jessica; Lohmann, Lúcia (2020), Data from: Phylogeny and biogeography of the Amazonian Pachyptera (Bignonieae, Bignoniaceae), Dryad, Dataset, https://doi.org/10.5061/dryad.p8cz8w9kq

Abstract

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.

Usage Notes

This file is related to the article “Phylogeny and Biogeography of the Amazonian Pachyptera (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 Pachyptera conducted with S-DIVA, DEC, and BSSVS. Areas with (/) suggest similar posterior probabilities.

Figures

Fig. S1. Consensus tree of Pachyptera inferred from the Bayesian analysis of the ndhF (A) and rpl32–trnL (B) datasets. Posterior probability and bootstrap values are shown above branches. The outgroups are shown in grey.

Fig. S2. Consensus tree of Pachyptera inferred from the Bayesian analysis of the combined cpDNA dataset (i.e., ndhF and rpl32–trnL). Posterior probability and bootstrap values are shown above branches. The outgroups are shown in grey.

Fig. S3. Consensus tree of Pachyptera inferred from the Bayesian analysis of the PepC dataset. Posterior probability and bootstrap values are shown above branches. The outgroups are shown in grey.

Fig. S4. Statistical parsimony network of Pachyptera kerere constructed based on the analysis of the ndhF and rpl32–trnL datasets. Circle sizes are proportional to the frequency of each haplotype. Small empty circles represent mutational steps.