Population genomic differentiation and demographic history across an elevational gradient in an endemic bromeliad of the Atlantic Forest mountains

Montane elevational gradients provide natural laboratories for investigating how environmental heterogeneity, geographic isolation, and historical climatic dynamics shape demographic history, population divergence, and diversification. Topographic complexity and historical climatic oscillations are major drivers of biodiversity patterns in mountain regions worldwide. The Brazilian Atlantic Forest (BAF), a Neotropical biodiversity hotspot characterized by naturally fragmented montane habitats, provides a suitable system for investigating these processes. Here, we used over a thousand SNPs from populations of Pitcairnia flammea Lindl. (Bromeliaceae) distributed across an elevational gradient to investigate patterns of genetic diversity, population structure, and demographic history. Bayesian and coalescent-based analyses revealed strong population structure, with two major genetic groups broadly contrasting higher-elevation populations with low- and mid-elevation populations, although elevation itself was not directly supported as a driver of genetic divergence. Demographic modeling supported early asymmetric gene flow between the two major genetic groups, with higher migration from Group 2 towards Group 1, followed by subsequent isolation. Divergence-time estimates and heterogeneous changes in effective population size further suggest distinct demographic trajectories during the Middle and Late Pleistocene. Together, our results reveal divergent evolutionary trajectories within a single endemic species and suggest that population differentiation across the Atlantic Forest mountains reflects the combined effects of habitat fragmentation, historical connectivity and isolation, genetic drift, and demographic changes potentially associated with Pleistocene climatic oscillations.