Unraveling species diversification and niche separation in Phedimus Kamtschaticus and P. aizoon using RAD-seq data and ecological niche modeling.

Ecological speciation progresses along a continuum, beginning with population divergence and culminating in reproductive isolation. Defining species boundaries becomes particularly challenging when ecological divergence occurs despite morphological similarity, yet precise delineation is essential for biodiversity assessment and conservation. Phedimus aizoon and P. kamtschaticus, two perennial herbs, exemplify this challenge, exhibiting high morphological similarity despite distinct habitat preferences. To investigate their divergence, we genotyped 80 individuals from these two species, along with a reference species, using 5,051 SNPs. Integrating morphometric and phylogenetic analysis and environmental niche modeling, our study provides compelling evidence that ecological factors have driven species divergence in these taxa. While genetic analyses reveal clear differentiation, we also detected instances of gene flow, as indicated by admixture patterns in STRUCTURE, TreeMix, and f₄ statistics. Despite minimal morphological differences, substantial genetic divergence suggests that precipitation and temperature seasonality have played a critical role in their speciation.