Atlantic Forest Origins and Amazon Connections: The Evolutionary History of Adenocalymma

Abstract Background and Aims The Amazon and the Atlantic Forest are the most diverse tropical rainforests globally. They are separated by a “dry diagonal” of mesic forests and savannas. The formation times of these ecoregions and the historical connections between them remain debated, highlighting gaps in our understanding of the continent’s biogeographic history. Here, we used the endemic clade Adenocalymma to further understand the formation and connections of current ecoregions in the Neotropics. Methods We sampled 68 species of Adenocalymma, representing 87% of species diversity, and used nuclear genomic data to infer their phylogeny. To better characterize the evolutionary history of Adenocalymma, we applied supermatrix and species-tree methods, as well as approaches that account for introgression and incomplete lineage sorting (ILS). Divergence times were inferred using a subset of genes. Finally, we applied the resulting phylogenetic hypothesis to infer ancestral ranges and the diversification patterns within the genus. Key Results Adenocalymma was strongly supported as monophyletic in all analyses. Support for internal clades was generally high. ILS and introgression accounted for a minor portion of gene-tree incongruences, suggesting that methodological factors may be relevant. The Atlantic Forest was identified as the ancestral area and main source of lineages for adjacent ecoregions. Vicariance was clearly observed in two instances. Adenocalymma showed a sharp increase in speciation and net diversification rates during the last 5 Ma. Conclusions Our results demonstrate that nuclear genomic data are highly valuable for inferring robust phylogenetic trees and networks in Bignoniaceae. ILS and introgression appear to be less relevant for shaping phylogenetic incongruence. Furthermore, the Amazon Forest may have contributed fewer plant lineages to other ecoregions than previously suggested. Diversification within Adenocalymma showed a pronounced accumulation of lineages during the last 5 Ma, especially in the Atlantic Forest.