Aim: Ecological differentiation of closely related species has attracted wide attention to explore its evolutionary significance in speciation. In particular, the prevalence of ecological speciation of sister species driven by Quaternary climate changes is debated. Here, we used two parapatric sister species, Roscoea humeana and R. cautleoides, to test whether ecological speciation was associated with Quaternary climate changes in these taxa.  

Location: Hengduan-Mountain Region (HMR), south-west of China. 

Methods: Nuclear ribosomal (ITS) and chloroplast DNA (cpDNA: psbA–trnH and trnL–trnF) were sequenced from 200 individuals. Gene genealogies were reconstructed using network, Bayesian inference and maximum likelihood methods. Interspecific divergence times were estimated with an isolation with migration model. Suitable habitats for each species were estimated with ecological niche modelling using Maxent and BIOCLIM. Niche overlap and niche divergence were tested using Schoener’s D and Warren’s I. Principal components analysis (PCA), multivariate analysis of variance (MANOVA) and discriminant function analysis (DFA) were also used to test ecological differentiation.  

Results: Gene genealogies indicated that the low-elevational species R. cautleoides was derived from the high-elevational species R. humeana. Divergence among species occurred during the middle to late Quaternary (0.01–1.48 Ma). The species distribution and phylogeographical pattern were inconsistent with a geographical barrier. Niche models and statistical analyses showed significant ecological differentiation. 

Main conclusions: Divergence between R. humeana and R. cautleoides was recent and coincident with Quaternary climate cycles. Ecological niche differentiation within Quaternary refugia may have promoted speciation.