New genomic resources and the historical demography of the Tourmaline Sunangel (Trochilidae, Heliangelus exortis) in the Colombian Andes.

Abstract

Understanding the demographic history of tropical montane species offers insights into how climate-driven habitat dynamics shape genetic diversity and population structure. The Tourmaline Sunangel (Heliangelus exortis), a hummingbird endemic to the Northern Andes of Colombia and Ecuador, inhabits high-elevation ecosystems that were repeatedly impacted by Pleistocene glacial-interglacial cycles. To enable genomic and evolutionary studies in this system, we generated a high-quality, chromosome-level reference genome using PacBio HiFi long reads and Hi-C scaffolding. The resulting 1.05 Gb assembly has contig and scaffold N50s of 8.4 mb and 73.9 mb, respectively, with >94% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Using this reference, we analyzed whole-genome resequencing data from 10 individuals collected at a single locality in the Eastern Andes of Colombia and reconstructed demographic history with pairwise sequentially Markovian coalescent models. Our results indicate a pronounced population expansion between ~1 Mya and ~300 kya, likely driven by increased habitat connectivity during glacial periods when highland vegetation was displaced downslope, followed by a decline likely associated with interglacial fragmentation. These trends broadly align with paleoecological records, suggesting that populations of forest-associated species such as H. exortis responded to Pleistocene climatic oscillations, though demographic patterns did not strictly mirror known glacial-interglacial dynamics. This work establishes a foundation for future genomic studies in Andean birds and highlights the potential of combining genomic and paleoecological data to unravel how biodiversity responds to environmental change.