Tree of Life | Miao Sun | 孙苗

JSE: Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Thu, 21 Jul 2022 00:00:00 +0000

Front. Ecol. Evol.: Relative Importance of Ecological, Evolutionary and Anthropogenic Pressures on Extinction Risk in Chinese Angiosperm Genera

Tue, 15 Mar 2022 00:00:00 +0000

Syst. Biol.: The implications of incongruence between gene tree and species tree topologies for divergence time estimation

Tue, 15 Feb 2022 00:00:00 +0000

Noise does not equal bias in assessing the evolutionary history of the angiosperm flora of China: A response to Qian (2019)

Wed, 09 Sep 2020 00:00:00 +0000

Recent accelerated diversification in rosids occurred outside the tropics

Fri, 03 Jul 2020 00:00:00 +0000

Supplementary data and code can be found here.

AJB: Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

Tue, 09 Jun 2020 00:00:00 +0000

MPE: Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae

Sat, 26 Oct 2019 00:00:00 +0000

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.

Research Talk at IBCAS Youth Forum

Wed, 25 Sep 2019 00:00:00 +0000

I had the great honor and was invited by Dr. Zhiduan Chen to visit his lab. We had great conversations and we also discussed to collaborate a few great project in comming futher.

Later on I was invited by Dr. Limin Lu, who hosted a Youth Forum organized by the State Key Laboratory of Systematic and Evolutionary Botany (LSEB) at IBCAS.

I briedly introduced my research works conducted in these 5-year post-doc life in Soltis Lab. I used rosids as an example to illustrate how to build and use large-scale phylogentic trees. Key points are:

Data mining public database (e.g, GenBank and GBIF), and data cleaning for downstream analyses. E.g, recent manuscript in bioRxiv and paper in AJB.
Knowing the potential issues when applying large-scale data for macro-ecology and -evolution. E.g., papers in AJB, Ecology, and another recent manuscript in bioRxiv.
Large-scale trees can be used for [Diversification]. E.g., recent manuscript in bioRxiv and an accepted paper collaborated with Dr. Xue.
Large-scale trees can be used for Phylogentic Diversity (PD)

Relationships matter!!

Please let me know if you have any questions and want to know more details.

Overall, it turned out full house!! More than expected!! ✌️ ✌️

Especially I have met Prof. Jianfeng Mao from Beijing Forestry University. I had great cinversation with him and his students.

Ecology: For common community phylogenetic analyses, go ahead and use synthesis phylogenies

Fri, 21 Jun 2019 00:00:00 +0000

Research Lightning Talks at Florida Museum of Natural History

Fri, 01 Feb 2019 00:00:00 +0000

All my research is phylogeny based. Phylogeny trees are illustrating relationships among organisms. Relationships matter! In my understanding, phylogeny serves as a beautiful platform, which links all the biology data together with an evolutionary background. I’m insterested in phylogeny of angiosperms, particularly rosids.

I briedly introduced three main research interests:

It turned out that people like my talk! ✌️ ✌️

You can download my talk slides here 👈

Teaching Tree of Life

Fri, 04 Jan 2019 00:00:00 +0000

We are all Tree Tenders!

Those outreach activities always make me wondering how could I deliver the knowledge I learned to the public and also make me realized that how important my work is! Tree of life is beautiful metaphor! It perfectly explains how everything in this enormous tree connected and related. If we can educate the public about the biodiversity and conservation, and how our future depends on it! Then so, ultimately more and more people realize it and will initiatively promote saving the Tree of Life! It’s never too big to do something about it! We all play a part for the greater good!

Here are some photos from the workshops I teaching tree of life and outreach activities I show people how the vegetables and fruits on their diner table are related.

Biodiversity and the Earth

Wed, 26 Dec 2018 00:00:00 +0000

Saving the Biodiversity on the Earth = Saving Ourselves

It’s never too big to do something about it! We all play a part for the greater good!

Our world’s heartbeat is its biodiversity! This complex network of all life is responsible for the food we eat, the water we drink and the air we breathe. But we often don’t realize how much even our subtile actions may have huge consequences to the earth’s cultivation or damage. That’s why researchers come together from all over the world to map our biodiversity and call for conservation. We are building a robust family tree for all life on earth as the foundation for its preservation and for the greater good of our own species.
Evolutionary relationship matters! Tree of Life (phylogeny) is able to help us with the discovery of medicines, curing diseases, improving crops, identifying conservation priorities, and even predicting the global response of species to a rapidly changing climate. Our knowledge of phylogeny also can help to increase public understanding of conservation, biodiversity, emphasizing the importance and connectivity of all life. Scientists and the publics, and policy makers need to be partnership togther contributing this great course! See Soltis and Soltis (2019).

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).

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

❄️ 🎅 🌵 🔔 ☃️ 🌲

Evolutionary history of the angiosperm flora of China

Wed, 31 Jan 2018 00:00:00 +0000

I contributed equally to this work.

AJB: Challenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids

Mon, 01 Jan 2018 00:00:00 +0000

JSE: Global versus Chinese perspectives on the phylogeny of the N-fixing clade

Fri, 01 Jul 2016 00:00:00 +0000

JSE: Phylogeny of the Rosidae: A dense taxon sampling analysis

Fri, 01 Jan 2016 00:00:00 +0000

JSE: Tree of life for the genera of Chinese vascular plants

Fri, 01 Jan 2016 00:00:00 +0000

Tree of Life and Its Applications

Wed, 01 Jan 2014 00:00:00 +0000