Phylogeny and Biogeography of the Amazonian Pachyptera (Bignonieae, Bignoniaceae)

Abstract

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 that is 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. The phylogeny of Pachyptera was time-calibrated and used to reconstruct the biogeographical history of the genus. 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.

Phylogeny and morphological evolution of the Neotropical genus Cuspidaria (Bignonieae, Bignoniaceae): Combining high‐throughput sequencing and targeted loci data

“…As reported in previous phylogenetic studies, sequences derived from the ndhF , rpl32‐trnL , and PepC markers alone are useful for reconstructing lower‐level phylogenetic relationships in Bignonieae (Lohmann, 2006; Fonseca & Lohmann, 2015; Medeiros & Lohmann, 2015; Kaehler & al., 2019; Francisco & Lohmann, 2020). Despite that, these markers do not provide sufficient characters to reconstruct deep relationships within the tribe (Fig.…”

“…-We selected two chloroplast DNA markers (ndhF, rpl32-trnL) and one nuclear intron marker (PepC) for our targeted Sanger sequencing. These same markers were used in earlier studies of Bignonieae (e.g., Lohmann, 2006;Kaehler & al., 2012Kaehler & al., , 2019Fonseca & Lohmann, 2015;Medeiros & Lohmann, 2015;Francisco & Lohmann, 2020;Calió & al., 2022), and were shown to provide sufficient characters to reconstruct major relationships within individual clades. Chloroplast marker amplification followed Lohmann (2006), including adjustments suggested by Zuntini & al.…”

“…L.G.Lohmann (Kaehler & al., 2019), Pachyptera DC. (Francisco & Lohmann, 2020), Lundia DC. (Kaehler & al., 2012), and Tynanthus Miers (Medeiros & Lohmann, 2015).…”

Phylogenetic placement of enigmatic Astianthus (Bignoniaceae) based on molecular data, wood and bark anatomy

“…For each accession, we amplified portions of the ndhF and rbcL genes and the trnL-F spacer. These three regions from the plastid genome have been useful to estimate phylogenetic relationships within the Bignoniaceae at the tribal (Olmstead et al 2009), generic (Lohmann 2006), and species (e.g., Fonseca & Lohmann 2015, Carvalho-Francisco & Lohmann 2020) levels. We sequenced the ndhF marker in two pieces, using the PCR primer pairs 5F-1318R and 972F-3R described in an earlier study (Olmstead & Sweere 1994).…”

“…In the past decades our knowledge of phylogenetic relationships within members of the Bignoniaceae has improved substantially thanks of phylogenetic reconstructions based on molecular data to the entire family (Spangler & Olmstead 1999, Olmstead et al 2009, its main tribes (Zjhra et al 2004, Lohmann 2006, Grose & Olmstead 2007a, Li 2008, Callmander et al 2016, Ragsac et al 2019, or key genera (Kaehler et al 2012, 2019, Fonseca & Lohmann 2015, Medeiros & Lohmann 2015, Fonseca & Lohmann 2018, Thode et al 2019, Carvalho-Francisco & Lohmann 2020). These phylogenetic reconstructions formed the basis for a series of new taxonomic treatments for the family (Grose & Olmstead 2007b, Lohmann & Taylor 2014.…”