we are going to launch a new project insighted by Wang et al., (2018).
-
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
- morphological data
- trait characters
- Medical traits
- molecular data
- GenBank data mining using PhylotaR
- choose gene with most coverage
- sequence length
- distribution data
- GBIF
- iDigBio
- NSII (CVH?)
- Environmental data
-
[] 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
- 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
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