Gouqi

we are going to launch a new project insighted by Wang et al., (2018).

Task List

• prepare species list

  • all the recorded names
  • validated by The Plant List (TPL) using Taxonstand @Ruuyu please check file "data/OpenTree_data/species_list/Gouqi_checkname_TPLQery.csv" and "data/Lycium_PL_no_name_TPLQery.csv"
  • Outgroup Mybe we need to select a few species from its closed relatives or tribes inside Solanoideae (e.g, Grabowskia, Nicandreae?)
    • Atropa belladonna
    • Jaborosa integrifolia
    • Nolana arenicola

• [] data mining

1. morphological data
   • trait characters
   • Medical traits
2. molecular data
   • GenBank data mining using PhylotaR
   • choose gene with most coverage
   • sequence length
3. distribution data
   • GBIF
   • iDigBio
   • NSII (CVH?)
4. Environmental data
   • WorldClim?

• [] data cleaning and evaluation

• [] phylogeny and dating

  • adding constraint tree from Miller et al. (2011) [x]
  • updated the phylogeny with Phphlawd data and constraint tree from Miller et al. (2011) and the file path: \results\tree\updated_tree12032018
  • two names were validated by the plant list:
  • Lycium arenicola is the syn of Lycium cinereum
  • Lycium tenue is the syn of Lycium acutifolium

• [] niche modelling species distribution model

• [] wrapping up with a paper @Ruuyu, @Christmas-Wu, @Cactusolo

other stuff

• lists and tables better use ".csv" format put into "data" folder
• references and other Documents put into "reference" folder
• likewise scripts go to "script" foder