Annual Project Report

Fri, 21 Dec 2018 00:00:00 +0000

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

Nextstep:
- 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

Plotting Christmas Tree

Mon, 17 Dec 2018 00:00:00 +0000

I saw a figure of all potential Christmas tree 🎄 at 🐦 Polypompholyx’s Tweet.

It looks strange for my first impression. So I did a quick check from Open Tree. This looks much better!

See code below:

rm(list=ls())
# install.packages("rotl")
# install.packages("ape")
#loading libraries
library("rotl") #for querying open tree database
library("ape") #for tree manipulation
#First I preapred a table for those potential **Christmas Trees** with first column is common names,a nd second column is the scientific names
# then we read in the table as a query list to the Open Tree
query <- read.csv("XsmasTree.csv", header=TRUE, sep=",", stringsAsFactors=FALSE, quote="")
# check what our table look like this
head(query)
# query names and get ottid
species <- tnrs_match_names(names = query$Scientific_name_rept.)
# check results
head(species)
# fix fuzzy match on row 16, then updated it
new_species<- update(species, row_number=16, new_ott_id = 248313)
# checking object
head(new_species)
species <- new_species
species.ottid <- ott_id(species)
# extracting the phylogeny summarized in the Open tree
tree <- tol_induced_subtree(ott_ids=species$ott_id, label_format = "name")
# make it looks good
tree <- ladderize(tree)
plot.phylo(tree, cex=0.8)
# rename the tree tip labels
query[[2]][16] <- "Picea pungens" #remove one extra space
query[[2]] <- gsub(pattern="\\s", "_", query[[2]])
new_label <- paste0(tree$tip.label,"(", query[[1]][match(tree$tip.label, query[[2]])], ")")
new_tree <- tree
new_tree$tip.label <- new_label
#png("The Tree of Christams Tree.png")
#plot(new_tree, cex=0.7)
#dev.off()
#write.tree(new_tree, "renamed_Xsmas_tree.tre")
#plot a prettier tree
plot.phylo(new_tree, edge.color = "dark green", edge.width = 2, tip.color = "red",
label.offset = 0.5, main="The Tree of Christmas Tree", col.main="red")
mtext("---source from Open Tree", col="dark green", 3)

Tree of Xsmas Trees