Dimensions | Miao Sun | 孙苗

Demonstrating gene tree conflict with Phyparts Piecharts

Sun, 27 Oct 2019 00:00:00 +0000

We have marched into genome era already, especially using biparental inherited nuclear genome data to examine the framework of tree of life established by plastid data. However, not all gene trees tell one same story, even the most homogeneous genes from plastid organelle. Not to mention nuclear genes may have more than one copy, and other potential biological processes (e.g., hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer, etc); also see Sun et al. (2015). Hence, Smith et al. (2015) did a great job in summarizing current situation, and setting examples of visualization of concordance information in animals and plants genomic phylogenies. They also developed an open source java software to do this job — phyparts.

In this post I will use Sassafras 322 gene trees as an example to show you how to use ASTRAL-III to estimate a species tree, and phyparts to summarize the conflict and concordance information of those individual homologous gene regions, and finally using PhyParts PieCharts to visualize the Phyparts Output. These data was generated by Target Enrichment method using Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes under Dimension project. My other relevant workingflow and scripts are available here.

Note: Matt Johnson has a great tutorial of how to run his script using Jupyter Notebook. The interpretation of PieCharts is well explained as well.

My instructions here focus on the overall procedures from gene trees all the way down to the Pie chart. Hopefully, I’m able to integrate all the steps together into one pipeline.

General steps

Here we need to assess how a number of gene trees how they agree with ours pecies tree, and displaying this discordance and agreeent information with satisfying visualization.

1. Building phylogeny, so that we have all gene trees

My data was generated from 353 target enrichment method
I used 322 gene trees from Sassafras samples as example
Note:
- All trees were rooted by either phyx or The Newick Utilities, or DendroPy
- Though ASTRAL is able to take any gene trees rooted or unrooted, however, for downstream Phyparts performance, rooted trees are preferred. Such so all gene trees and species trees are towards to the same root direction (See Matt Johnson’s post).
- As quote in ASTRAL tutorial:
  “Importantly, we will reroot the tree at the correct node, which is always necessary, since the rooting of the ASTRAL trees is arbitrary and meaningless."
Therefore, rooting all the trees (species tree and gene trees) is preferred for Phyparts Piecharts. Sometimes, when you have hundreds of gene trees, however, not all outgroups presented in your gene tree; in these case, I recommend either use pxrr function from phyx, or MAD (root the tree by Minimal Ancestor Deviation); the latter works well with those trees without outgroups at all; for details see my other post here

2. Species tree estimation

Species tree was estimated by ASTRAL-III, and see tutorials here
Note: Collapse gene tree nodes with BS support less than certain value (saying 10%; see cmd below), will help to improve accuracy; sometime increasing the threshold for collapse may yield better results.
There are many ways to do this: phyx or The Newick Utilities
- using The Newick Utilities as example from ASTRAL-III tutorial e.g., nw_ed 1KP-genetrees.tre 'i & b<=10' o > 1KP-genetrees-BS10.tre
ASTRAL CMD:
java -jar astral.5.6.3.jar -i collapse_genetrees.tre -o output_species_tree.tre 2> running.log

3. Statistic information about conflict, concordance, or even gene duplications

You need to run phyparts with instruction on the repo webpage.
Phyparts “conflict” option CMD:
java -jar target/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar -a 1 -v -d gene_trees -m ASTRAL_species_tree -o output_name

Note: run cmd below, you’ll able to see all the Phyparts options (see snapshot below):
java -jar target/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar

4. Mapping these information on species tree

You need PhyParts PieCharts python script and tutorial from Matt Johnson

Note: Please read the tutorial, Python >2.7 and ETE3 with the graphical options need to be installed before run the python script

how to run script:
python3 phypartspiecharts.py species_tree output_name gene_number

Note: output_name must be the same as you names at the phyparts (# 3) step

5. Visualize the gene tree support and conflic statics with Piecharts

the output format of PhyParts PieCharts is in svg, then you need to Inkscape or AI to convert it as pdf. You also can refine the overall layout of that plot.
Note: make sure Python3, ETE3, and X server installed.

As my plot below:

Last updated: Mon Dec 7 2020

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.

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 👈

Dimensions

Fri, 28 Dec 2018 00:00:00 +0000

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).

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