Aim: Pleistocene (2.58 Ma – 11.7 ka) climatic fluctuations have shaped intraspecific genetic patterns worldwide; however, their manifestation in many regions remains unknown. In order to determine the impact of Pleistocene climatic fluctuations on the tropical rain forests of western Ecuador, we explored the evolutionary history of the endemic palm Phytelephas aequatorialis.

Location: Western Ecuador, northwestern South America.

Taxon: Phytelephas aequatorialis (Arecaceae).

Methods: 176 nuclear genes were sequenced in 91 individuals for phylogenomic and population structure analyses. The time of divergence between identified genetic lineages was estimated using a coalescent phylogenomic analysis. Paleoecological niche modelling analyses were performed to determine areas of historical climatic suitability since the Last Glacial Maximum (LGM; 22 ka) that potentially acted as forest refugia during the Pleistocene. A Wilcoxon test and Pearson correlations were used to explore how current levels of genetic diversity (Hs) have been shaped by several paleoclimatic and geographic factors.

Results: Phylogenomic and population structure analyses revealed two genetic lineages with a north-south distribution, which diverged 1.14 Ma during the Pleistocene. Two potential Pleistocene refugia were identified in the Pacific coast of Ecuador and in the Andean foothills of southwestern Ecuador, whose distribution agrees with the spatial location of the two lineages. Within the Andean foothills, Hs was lower for the southern lineage than for the northern lineage. Hs significantly increased with decreasing latitude within the whole species distribution.

Main conclusions: Pleistocene climatic fluctuations promoted intraspecific divergence in P. aequatorialis within the rain forests of western Ecuador. The Andean foothills of southwestern Ecuador could be an important spot for rain forest evolution because they potentially remained climatically suitable through the Pleistocene. Lower genetic diversity in the southern lineage, which apparently remained isolated in the Andean foothills during glacial cycles, adds evidence to the presence of a forest refugium in southwestern Ecuador. The geographic pattern in genetic diversity suggests that P. aequatorialis colonized western Ecuador from the north. This study supports the role of Pleistocene climatic fluctuations in promoting intraspecific divergence, and for the first time, we show their impact west of the Andes.

Data for phylogenomic analyses in Phytelephas aequatorialis. One hundred and seventy six genes were sequenced in 91 individuals using the probes from Heyduk et al. (2016). Only the loci with at least 75% of their lenght reconstructed in at least 75% of individuals we retained. In addition, loci with signs of paralogy were removed, leaving 141 usable loci.