Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot

The interplay of orographic uplift and climatic changes in the Himalaya-Hengduan Mountains region (HHM) have had a key role in speciation and population demography. To gain further insight into these processes, we investigated their effects on Taxus wallichiana by combining molecular phylogeography and species distribution modeling. Molecular data were obtained from 43 populations of T. wallichiana. Nineteen climatic variables were analyzed alongside genetic discontinuities. Species distribution modeling was carried out to predict potential past distribution ranges. Two distinct lineages were identified, which diverged c. 4.2 (2.0-6.5) million years ago (Ma), a timescale that corresponds well with the recent uplift of the Qinghai-Tibet Plateau and subsequent climatic changes of the region. Correlations with climatic variables also suggest that ecological factors may have further reinforced the separation of the two lineages. Both lineages experienced population expansion during the last glaciation. The high genetic divergence, long-term isolation and ecological differentiation suggest a scenario of cryptic speciation in T. wallichiana associated with geological and climatic changes in the HHM. Our findings also challenge the notion of general population 'contraction' during the last glaciation in the HHM.