Parallel Genomic Responses to Ecological Gradients in the Phalaenopsis amabilis Complex

Abstract

There are multiple mechanisms that can underlie parallel adaptation to similar habitats at the genetic level, including de novo mutations, introgression, and shared standing variation. While evidence for each pathway is emerging, few studies have directly examined how demographic processes, range expansion and introgression interact to shape the fate of adaptive alleles. In the Phalaenopsis amabilis complex, we applied a dimensionality reduction approach to identify environmental extremes and link alleles to ecological gradients. By combining gene–environment association analyses with demographic inference and historical gene flow reconstruction, we evaluated whether repeated adaptation arises from de novo convergent mutations or introgression. The candidate SNP set departed strongly from neutral expectations in DMC analyses; standing variation was the best-fitting model, although its separation from migration was modest. We also found heterogeneous allele sharing and historical introgression involving range-margin populations, coinciding with demographic expansion. These findings suggest that standing variation, demographic history, and heterogeneous introgression may jointly contribute to repeated genomic responses across ecological gradients. A limited subset of environmentally associated candidates also overlapped with floral morphology-associated candidates, but the magnitude of overlap was strongly threshold- and denominator-dependent. These overlaps identify hypotheses concerning ecological and floral trait differentiation, but do not establish pleiotropy or a shared causal architecture. This work highlights how parallel adaptation in plants may emerge from the interplay of neutral and adaptive evolutionary mechanisms in recently diverged lineages.