Interploidy gene flow does not prevent adaptive genetic differentiation in sympatric populations of <i>Epidendrum fulgens</i> and <i>E. puniceoluteum</i> (Orchidaceae)

Abstract Polyploids often exhibit ecological divergence from diploid parents, but the relative importance of selection in speciation by polyploidy remains to be tested in most systems. Here we use transcriptome-derived single nucleotide polymorphisms (SNPs) to test whether increased gene flow between the diploid Epidendrum fulgens and tetraploid E. puniceoluteum (Orchidaceae) in sympatry could prevent adaptation to contrasting habitats (sand dunes and swamps, respectively), and to infer genes probably under differential selection. Additionally, we used species distribution data to test for climatic niche divergence between species and a subset of synonymous SNPs to test for past demographic signatures. We found no evidence of introgression in the transcribed portion of their genomes. For the most differentiated loci between species, we annotated biological processes related to replication machineries and also to differential responses to habitat features. We also found that climatic niches slightly diverge due to increased tolerance to lower temperatures and wider amplitude of precipitation in E. fulgens, which probably explains the species’ distinct signatures of past demographic changes. By combining ecological transcriptomics with climatic niche comparisons, we shed light on the potential role of adaptive processes in originating and maintaining plant biodiversity in Neotropical coastal environments.