Annual Project Report

1. Prepare Target Enrichment DNA samples for genera phylogeny

Coordinating with Mark and Hanyang, prepared ca. 500 DNA Samples, and submitted Rapid Genomics for Target Enrichment sequencing

- Evaluating, cleanning, and assembling the sequence data
- Reconstructing phylogeny for each genus sampled, and then a big combined tree
- Correlated with other data collected

2. Community phylogeny

Using opentree_pytoys, I have reconstructed community phylogenies for 11 sites (5 Chinese sites, 3,694 species in total, and 6 US sites, 1,663 species intotal), individually and combinedly.

  • Name validation from Open tree
  • Resultant topolgy checking
  • Faith’s phylogenetic diversity (PD~SES~) value is caculated
  • Making a database to tracking all the changed names

Ongoing and nextstep:

  • Phylogenetic diversity

    • Advanced PD measurement, then compare between USA and Chinese sites:
      M(P), ^q^E(P), MP(D), VP(D), NRI, NTI
    • Reveal the whole pattern and/or exploring the cause to the differences (biotic and abiotic factors)
  • Functional traits

    • Assembling some traits data from Tao Zhang (plants) and Teng Yang (soil/fungi) to correlated my community phylogenies
      Using soil-oriented data, Tang et al. (2018) has found that plant phylogeny has a positive association with dissimilarities of fungal community;
      I want to testify if the association is still true with plant-oriented data
    • Functional-traits measurement:
      M(T), ^q^E(T), ^q^E(T*)

3. helped to processed Soil DNA samples

Working with Mark, we helped to dry 20 plates (96 x 20 = 1,920) soil DNA samples from Triplett’s lab, then send back to Goegina.

Next step:
Shipping to China (Dr. Chu) after holiday, and awaiting for DNA sequencing

4. Miscellaneous

  • Participated in Asia-Evo conference with psoter exhibition
  • Collaborated with Dr. Teng Yang and Dr. Haiyang Chu, recontructing phylogeny for disjuct woody species in China to investigate tree–fungus associations. This work was published:
    Yang T, Tedersoo L, Soltis PS, Soltis DE, Gilbert JA, Sun M, Shi Y, Wang HF, Li YT, Zhang J, Chen ZD, Lin HY, Zhao YP, Fu CX, Chu HY. (2018) Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China. The ISME Journal. doi: 10.1038/s41396-018-0303-x
  • Helped Anthony translated 19,712 specimen records of disjuct species from China
  • Continuously served as the main contacting/communicating point among the Soltis', Lichstein’s, Jenny’s, and Chinese labs for primary tasks related to material collecting, extraction, evaluation, and DNA sample preparation
Miao Sun | 孙苗
Miao Sun | 孙苗
Postdoctoral Scientist

My research interests are reconstructing a large scale phylogeny to explore the diversity patterns in angiosperms across space and time using big biological data and biological comparative methods.