Projects | Miao Sun | 孙苗

PhyloSynth

Tue, 01 Oct 2019 00:00:00 +0000

We are marching on Phylosynth project! Some primary data, code and results will share here. Our goal is reconstructing a larger-scale plant Tree of Life for all seed plants (Spermatophyta), using methods described in Smith and Brown (2018) and ideas described in Eiserhardt et al. (2018; see below), and integrating the phylogenetic backbone from the Plant and Fungal Trees of Life Project (PAFTOL) and robust taxonomy database from World Checklist of Selected Plant Families (WCSP). We endeavor to push the boundary of the knowledge of Tree of Life, keeping this tree portable and dynamically updated, providing knowledge of the plant tree of life to science community and the public education.

Pipeline Schema from Eiserhardt et al. (2018)

Some key feactures:

Flexible
Easy for other pipelines to integrate
Dynamically updated
Establish a schedule for running this pipeline at regular intervals, producing up-to-date trees. For this, we need to decide an initial frequency for generating trees. This frequency can later be adjusted based on download statistics and user feedback.
Portable for different audiences
Establish one or more outlet(s) for PhyloSynth trees. This needs to take into consideration where different audiences would be looking for trees, and ensure (for scientific audiences) that there is a citable paper.
High quality
- Build module that maps NCBI taxonomy to a widely accepted botanical taxonomy. This should in the first place be the WCSP/”names backbone” at Kew, but we need to consider the fact that other lists are in circulation.
- Build a module that filters NCBI data automatically according to certain rules. This could be a simple decision tree based on metadata, or a more complex machine learning approach.
- Build a module that evaluates resulting trees automatically using a set of statistics. This could include, among other things, monophyly statistics for higher ranks from the taxonomy used (genera and families in the case of WCSP).
- Establish a procedure for manual quality control by taxon experts. This would need to include a procedure for storing decisions/annotations and avoiding duplication of effort.
- Establish a procedure for user feedback. This would need to include a procedure for storing decisions/annotations and avoiding duplication of effort.

Dimensions

Fri, 28 Dec 2018 00:00:00 +0000

Tree of Life

Thu, 20 Dec 2018 00:00:00 +0000

“Dealing with conservation is about dealing with people, not about dealing with animails (and plants)" — Sarah Hauck

Tree of Life — A map of the relationships between all life on earth — A metaphor for the importance and connectivity of all species — Aiming to increase public understanding of conservation and biodiversity. The knowledge of Tree of Life has many practical applications which will benifit ourselves.

Under this big project, I have mainly involved fowllowing two subset projects as primary researcher:

Rosid Phylogeny and Diversification We recently used 5-locus, 19,740-taxon supermatrix to investigate the sampling bias of rosid in GenBank, and how sampling differences may influence the phylogeny and downstream diversification analyses (See rosids Project);
The Tree of Life: China project ( Chen et al., 2016) We build a tree of life for the plants of China (~30,000 flowering plant species), uncovering a distinct regional pattern in biodiversity. Eastern China is a floral “museum” with a rich array of ancient lineages and distant relatives while the western provinces are an evolutionary “cradle” for newer and more closely related species. More detail see Lu et al. (2018).

Rosid Phylogeny and Diversification

Mon, 10 Dec 2018 00:00:00 +0000

We recently used large biodiversity datasets representing the state of the art in rosids to explore (1) phylogenetic and dating uncertainties, and sampling bias persisted in major flowering plant clades, and (2) the impacts of incomplete sampling schemes on different diversification methods; (3) with deep understand of our data and methods, we then further explored the association betweed rosid diversification and tropicality, and both historical and present-day temperature.

As more molecular data, species distribution data, and other ecological data available, we’ll continously work on developing climatic layers over time that can trace the expansion of strong seasonality, and especially areas with seasonal freezing temperatures. These layers, when coupled with more fine-grained, modeled past and present species distribution information would provide a strong basis for more explicit testing of current pattern with more mechanism-focused hypothesis.

Taxonomy

Mon, 10 Dec 2018 00:00:00 +0000

Under this project, mainly two parts related to my Master work:

Taxonomic revision of Elaeagus L. (Elaeagnaceae) in China
Combined knowledges from field observations and comprehensive study on more than 7000 specimens from 20 herbaria, I have recognised of 36 species, one subspecies and five varieties in mainland China. 13 species names and three variety names are regarded as new synonyms. See more details in Sun et al. (2010)
Validation and lectotypification for all type specimens deposited in PE

A type is a really important object in taxonomy; it can be a particular specimen (in some cases a diagram, or a group of specimens) of an organism to which the scientific name of that organism is formally attached. Based on detailed study of 20,000 cited type specimens housed at China National Herbarium (PE) in litertures, we selected ca. 8,000 type specimens according to the updated International Code of Botanical Nomenclature. Our research was published as a book of Types Specimens in China National Herbarium (PE) (2015) with 15 volumes in total, and I’m the Coauthor of Vols. 6, 7, and 10. This book include type specimens from moss, ferns, and seed plants belong to 217 families, 1,174 genera, 6,627 species, 67 subspecies, 1,149 varities, and 126 forms; composed of 4,583 Holotypes, 2,372 Isotypes, 395 Lectotypes, 9 Isolectotypes, 3 Neotypes, 3 Isoepitypes, 34 Syntypes, 100 Isosyntypes, 293 Paratypes, 178 Isoparatypes. It was called as Masterpiece for research and study plants in China, and professional reference book for botanists, taxonomists, and systematists. All the type specimens were digitalized as high-resoluton images and its protologues referrences. Detailed information was recorded in databased. It perhaps be the most comprehensive collection of types specimens in the world. More information can be found from the publisher and China Daily.
This project was supported by Plant Specimen Digitisation and Chinese Virtual Herbarium Establishment.

15 Volums of Types Specimens in China National Herbarium (PE)