Combining plastome and Sanger sequencing data to reconstruct the phylogeny of Martinella Baill. (Bignonieae, Bignoniaceae)

We use a hybrid approach that combines high-throughput sequencing (HTS) data with traditional targeted loci data to infer the phylogeny of Martinella Baill. (Bignonieae, Bignoniaceae), a group of Neotropical lianas. The genus traditionally included three species, but two new species were described recently. We sequenced, assembled, and annotated six complete or nearly complete plastomes representing four of the five known species. In addition, we obtained sequences of the plastid ndhF and rpl32-trnL and the nuclear pepC markers via Sanger sequencing for 15 additional individuals of Martinella, representing all known species and covering their range of geographic distribution. Two outgroups were sampled, leading to a final dataset with 23 individuals. We used these data to assemble five different dataset combinations to evaluate tree topology and support values. Targeted loci data alone led to a poorly resolved topology, while HTS data recovered a fully resolved tree with maximum support in most branches. Combining HTS and Sanger sequencing data maximized taxon and character sampling, leading to a fully resolved tree with moderate support. This tree is considered the most robust and reliable estimate of the phylogeny of Martinella to date and is used as a basis to evaluate the taxonomy of the group. This phylogeny supports the recognition of five taxa, including the previously recognized M. obovata, M. insculpta, and M. insignis, plus the two newly described Amazonian species, M. lanuginosa and M. tomentosa. Our study highlights the importance of in-depth studies of individual lineages, especially in Amazonia, where important sampling lacunae remain.