Late-Miocene vicariance, adaptive divergence and genomic vulnerability across the eastern North America–Mesoamerica disjunction in the Tertiary relict Liquidambar styraciflua

ABSTRACT The temperate floristic disjunction between eastern North America (ENA) and the montane cloud forests of Mesoamerica (MAM) represents a major yet understudied biogeographic pattern. Using whole-genome resequencing, demographic modeling, phylogenomics, and ecological niche analyses of the Tertiary relict Liquidambar styraciflua , we reconstructed the evolutionary processes underlying this disjunction. Analyses of 109 genomes show that ENA and MAM lineages diverged in the late Miocene (∼6.8–6.9 Mya), coinciding with global cooling and contraction of mesic temperate forests. Nuclear genomic evidence supports a vicariant origin, followed by long-term allopatry with limited asymmetric (north-to-south) gene flow. Demographic reconstructions reveal recurrent Pleistocene bottlenecks, especially within the MAM lineage. Phylogenomic analyses resolve population structure within ENA and identify the Central Appalachians as the source of its subsequent eastward range expansion. Ecological niche modeling indicates persistent and increasing climatic divergence between ENA and MAM habitats, whereas genome-wide scans identify 381 positively selected genes in the MAM lineage, many of which are involved in abiotic stress responses and reproductive processes potentially associated with post-fertilization reproductive isolation. Despite these signatures of local adaptation, the MAM lineage exhibits a disproportionately elevated mutational load, consistent with reduced efficacy of purifying selection following long-term isolation and repeated bottlenecks. Morphological differentiation, notably the predominance of three-lobed leaves, together with pronounced genomic and ecological divergence, supports recognition of the MAM lineage as a distinct species, L. macrophylla . Collectively, our results demonstrate that the interplay among historical isolation, environmental adaptation, and demographic processes has shaped divergence across the ENA–MAM disjunction. More broadly, they show that long-term ecological specialization can promote adaptive divergence while simultaneously increasing genomic load and vulnerability to future climate change in relict montane lineages.