1) Speciation and evolutionary history of Taxus wallichiana

The interplay of orographic uplift and climatic changes in the Himalaya-Hengduan Mountains region (HHM) is believed to have played 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 its potential distribution ranges. Two distinct lineages were identified, which diverged about 4.2 (2.0-6.5) Ma, a timescale corresponds well with the recent uplift of the Qinghai-Tibet Plateau and subsequent climate 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 ecological speciation in T. wallichiana associated with geology and climate changes, and illustrate the diversification and evolutionary mechanisms through the interaction with geological, climatic and ecological processes in the HHM. Our findings also challenge the notion of general population “contraction” during the last glaciation in the HHM.　(Liu et al. 2013 New Phytologist)

2) Hybridization origion of Rhododendron species

Rhododendron ×duclouxii is morphologically intermediate between Rhododendron spiciferum and Rhododendron spinuliferum, and was suspected to be a natural hybrid between these species. In this study, the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F regions of 34 accessions of R. ×duclouxii and its putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology demonstrated that R. ×duclouxii represents a natural hybrid between R. spiciferum and R. spinuliferum. It also implies that the hybridization between R. spiciferum and R. spinuliferum is bidirectional, and that populations of R. ×duclouxii represent hybrid swarms from backcrossing or selfing of F1 plants. The study is important for understanding the speciation processes in the genus since it demonstrates for the first time the existence of a natural homoploid hybrid in Rhododendron subgenus Rhododendron. (Yan et al. 2013 Journal of Systematics and Evolution)

3) DNA barcoding and cryptic species discovery of Taxus 

The taxonomy of Eurasian yew species is very controversial due to the morphological similarity. We evaluated the utility of five candidate plant DNA barcoding regions [rbcL, matK, trnH-psbA,trnL-F and internal transcribed spacer (ITS)] in Eurasian yews. Forty-seven accessions were analysed, representing all taxa treated in current floristic works and covering most of the distribution range of Taxus in Eurasia. As single loci, trnL-F and ITS showed the highest species discriminatory power, each resolving 11 of 11 lineages (= barcode taxa). Species discrimination using matK, trnH-psbA and rbcL individually was lower, with matK resolving 8 of 10, trnH-psbA 7 of 11 and rbcL 5 of 11 successfully sequenced lineages. The proposed CBOL core barcode (rbcL + matK) resolved 8 of 11 lineages. Combining loci generally increased the robustness (measured by clade support) of the barcoding discrimination. Based on overall performance, trnL-F and ITS, separately or combined, are proposed as barcode for Eurasian Taxus. DNA barcoding discriminated recognized taxa of Eurasian Taxus, namely T. baccata, T. cuspidata, T. fuana and T. sumatrana, and identified seven lineages among the T. wallichiana group, some with distinct geographical distributions and morphologies, and potentially representing new species. Using the proposed DNA barcode, a technical system can be established to rapidly and reliably identify Taxus species in Eurasia for conservation protection and for monitoring illegal trade. (Liu et al. 2011 Molecular Ecology Resources)

4) Delimitate Yews along the Hindu Kush-Himalaya and Adjacent Regions

To clarify the total number of species and their exact distribution ranges of Taxus in the Hindu Kush-Himalaya (HKH) and adjacent regions, we explored the use of comprehensive sets of morphological, molecular and climatic data to answer these questions. A total of 743 samples from 46 populations of wild yew and 47 representative herbarium specimens were analyzed. Principle component analyses on 27 morphological characters and 15 bioclimatic variables plus altitude and maximum parsimony analysis on molecular ITS and trnL-F sequences indicated the existence of three distinct species occurring in different ecological (climatic) niche and altitudinal gradients along the HKH and adjacent regions. Taxus contorta from eastern Afghanistan to the eastern end of Central Nepal, Taxus wallichiana from the western end of Central Nepal to Northwest China, and Taxus mairei in Nepal, Bhutan, Northeast India, Myanmar and South Vietnam. The most intriguing findings of our study were the clear separation of the distributions of the yews in the HKH and adjacent regions and the first report of T. mairei in this region, a species that has previously been considered to be endemic to the South of China. The present study has found that the three yew species are genetically distinct and can be identified easily using the combination of a few morphological characters. (Poudel et al. 2012 PloS ONE)

5) Phylogeographical history of Taxus in China and North Vietnam

To investigate the phylogeographic history and population structure affected by Quaternary glaciation cycles of an endangered species Taxus wallichiana, a total of 1,235 individuals from 50 populations from China and North Vietnam were analyzed. A total of 19 different haplotypes were distinguished, which showed high level of population differentiation and a strong phylogeographic pattern. Strong landscape effects were observed in the Hengduan and Dabashan mountains, where steep mountains and valleys might have been natural dispersal barriers. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggested the existence of several localized refugia during the last glaciation from which the present-day distribution may be derived. The pattern of haplotype distribution across China and North Vietnam corresponded well with the current taxonomic classification of the three intraspecific varieties of T. wallichiana. (Gao et al. 2007, Molecular Ecology)