Geogenomics of montane palms points to Miocene–Pliocene Andean segmentation related to strike-slip tectonics

Aim: In geographically and ecologically heterogeneous landscapes, such as tropical mountains, widely distributed species may be informative proxies for studying landscape and climatic evolution. We explore historical vicariant and dispersal processes that may have determined the genetic structure and variation of a palm species complex living in cloud forests. We hypothesize that the genomic groupings reflect uplift-based isolation by vicariance, divergence via dispersal events driven by faulted montane segments or recent divergence due to climate fluctuations. Location: Colombian Andes. Taxon: Geonoma undata–G. orbignyana species complex (Arecaceae). Methods: We sampled 195 individuals of the species complex plus the outgroup (G. interrupta) across the three cordilleras of Colombia, the Colombian Massif and the Sierra Nevada de Santa Marta. We used target capture sequencing to generate a dataset of 12,750 quality-filtered genome-wide SNPs. We conducted phylogenetic, multivariate and population genomics and structure analyses to infer demographical history. Results: We found four genetically distinct groups within the species complex. The geographical distributions of the genetic groups, and their inferred phylogenetic and population divergence are consistent with a history of colonization of mountain segments that were disconnected until the late Pliocene. These breaks coincide with the distribution of Pliocene strike-slip faulting events. Main conclusions: The faulting and resultant topographic disruption of the northernmost Andean cordillera prior to the onset of the Pleistocene is implied by the presence of phylogeographic breaks in areas that are topographically continuous today. These cordilleras were formed by connecting segments that were previously uplifted but historically detached in areas where dense fault systems occur. Large-scale strike-slip faulting can generate topographic gaps, features that likely caused the divergence by dispersal with gene flow of the Geonoma undata–G. orbignyana complex.