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E-taxonomy of Sino-Himalayan Umbelliferae (Apiaceae): diversity, phylogeny and species modelling through new web-based tools

Final Report Summary - UMBEL (E-taxonomy of Sino-Himalayan Umbelliferae (Apiaceae): diversity, phylogeny and species modelling through new web-based tools)

After two years’ work, the major objectives implemented in UMBEL have been completed. Our research activities and results will bring positive socio-economic impacts to the general public and the scientific research community.

The UMBEL project has developed an integrated methodological framework that combines traditional taxonomy, phylogeny, and cutting edge SDM (species distribution modelling) analysis as part of an integrative framework for taxonomic study, using Sino-Himalayan Umbelliferae as a model group. In addition to our publishable results, the final products will be presented via our website by using the widely implemented online taxonomic tool - Scratchpads. The website will include available taxonomic data of Sino-Himalayan Umbelliferae accessible for general public and research community. The project’s objectives include two aspects: The scientific investigation and technical implementation.

For research aspects, we investigated the evolution of alpine Umbelliferae by using four genera, Acronema, Chamaesium, Sinocarum and Pternopetalum, as model groups.
We carefully examined 7,000+ specimens deposited in twenty-one herbaria in Europe and Asia, including important type material. The efforts include a register of collection records into a local database, morphological investigation, and georeferencing of locality data. The taxonomic investigation of these historical collections resolved taxonomic confusion relevant to our study, such as oversized Acronema, and its confusing generic boundaries with Sinocarum. This taxonomic study was then fundamental to the subsequent phylogenetic and eco-biogeographic analyses. We carried out field investigations in Sichuan, Tibet and Yunnan of China and acquired molecular samples of 118 accessions covering 32 species. We newly sequenced two chloroplasts (matK, rbcL) and two nuclear (ETS, ITS) genes to build a strong phylogenetic framework in combination with data from GenBank. Phylogenetic analyses indicated that Acronema, Chamaesium and Pternopetalum are well-defined monophyletic groups, but Sinocarum is polyphyletic.
Phylogenetic comparative methods provide a promising avenue for testing the long-term predictions of models of ecological opportunity and speciation that should leave a signature in comparative data. Species-level phylogenies, estimated from DNA sequence data, can be associated with a timescale via relaxed molecular clock methods. SDM analyses used georeferenced occurrence data from natural history collections and high-resolution climate data to characterise environmental dimensions of a species’ niche. Comparison of geographical range overlap and asymmetry between sister species is promising in revealing processes involved in geographical modes of speciation. Ancestral state reconstruction of morphological characters helped to build links between transformations of phenotypic traits and evolution of niche shift. These aspects were integrated in novel ways to characterise the history of diversification for the organisms under investigation, and allowed us to make inferences on patterns of diversification in relation to environmental variables, geographical models, and morphological variations on a relative time scale.
We use above mentioned complementary analyses in combination with molecular, phenotypic, ecological and biogeographic data together to investigate evolution and diversification of the four target groups. Our research allowed us to address the need to quantify and compare macroevolutionary change (i.e. speciation or plant diversification) of mountain herbaceous species in response to Quaternary climatic changes, and identify the evolution of eco-phenotypic traits over the group's phylogenetic history.
Our research revealed that the four groups may represent typical adaptive radiation groups diversified successively from mid-Miocene to Pleistocene in Hengduan mountain area. As one of the important conceptual frameworks, an ecological opportunity (EO) hypothesis is pervasive in the explanation of adaptive radiation in our studies and highlighted its importance in addressing diversification of mountain plants in Himalayan and Hengduan mountain areas. Our study also emphasised the importance of Hengduan mountain as a target region in the study evolution and diversity of mountain plants, because of its unique geological, climatic and biodiversity history. The results revealed in our study will provide an important reference for studies of the adaptive evolution of Sino-Himalayan mountain plants, and allow insights into the characteristics of diversification of these plants in dealing with arisen of EO. These aspects haven’t been fully addressed in related studies before our research.
For technical implementation side, we aggregated data from new and existing data sources and integrate third-party SDM analytical tools into the widely-used Scratchpads tool.
With help from Dr Vincent Smith and his informatics team at the NHM, an online knowledge base of Sino-Himalayan Umbelliferae website ( ) was constructed to host taxonomic data from the project. We collected comprehensive taxonomic data related with Sino-Himalayan Umbelliferae, including checklists, morphological descriptions, distribution, voucher specimens and their images, literature. All these data have been organised with a tree-like structure and one-page view in order for easy access. We will continue upload data and information produced from UMBEL project, and make it updated and permanently available for the research community and the general public.
After these works, we are sure UMBEL project will produce positive socio-economic impact. Because the published scientific papers we will highlight some key points previously ignored by scientists, such as testing and using of EO hypothesis in explanation of regions with rich biodiversity. At the same time, our research has been widely disseminated through the established website. For policy makers, they might use this work to understand that why traditional taxonomic studies should not be seen as ‘a dead science’, rather than it will be more active than ever before once it armed with cutting-edge informatic tools. For the general public, they will benefit from access to authoritative academic knowledge online without any access barriers, hence making biodiversity research better understood by the general public.

Project website:
Contact: Lisong Wang: