Lab of Stephen A. Smith

01/11/2009
by blackrim
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About

I am Stephen A. Smith, an evolutionary biologist and Assistant Professor at the University of Michigan, Ann Arbor. You can find out more information about the people in the lab here and the projects here. A lot of the research in the lab focuses on plant evolution, detecting and describing large scale patterns of evolution, examining differences in the rate of molecular evolution, and using new data sources like transcriptomes and genomes to address these questions. A great deal of this involves the development of new methods and new computational tools. My faculty page is here.

05/19/2015
by blackrim
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lab field trip

The lab (and others) went to Magee Marsh for a lab fieldtrip to see the migration. Here is a picture

lab2015

Here is the list from Joseph Brown in the lab, including 56 species in total, and 19 warblers (although of the latter, 3 were by ear only, and 4 others were singletons I got on the walk out):

  • Canada Goose
  • Trumpeter Swan
  • Mallard
  • Double-crested Cormorant
  • Great Blue Heron
  • Great Egret
  • Turkey Vulture
  • Bald Eagle
  • Red-tailed Hawk Continue Reading →

04/21/2015
by blackrim
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phylogenomics and Caryophyllales in MBE

We have gotten the first data out from our Caryophyllales grant (together with 1KP data). We discuss gene and genome duplication, rates of molecular evolution and other fun things!

Yang, Y. M.J. Moore, S.F. Brockington, D.E. Soltis, G.K.-S. Wong, E.J. Carpenter, Y. Zhang, L. Chen, Z.-X. Yan, Y.-L. Xie, R.F. Sage, S. Covshoff, J.M. Hibberd, M.N. Nelson, and S.A. Smith. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution.

04/21/2015
by blackrim
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betalains in Caryophyllales accepted at New Phytologist

With the support of the Caryophyllales grant, we have published (Sam Brockington and Ya Yang as co-first authors).

Brockington S.F., Y. Yang, F. Gandia-Herrero, S. Covshoff, J.M. Hibberd, R.F. Sage, G.K.-S. Wong, M.J. Moore and S.A. Smith. Lineage specific gene radiations underly the evolution of novel betalain pigmentation in Caryophyllales. New Phytologist.

02/13/2014
by blackrim
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Phyloseminar notes

Giving the phyloseminar today.
Here are some instructions for the phylo seminar demos
get input files from here
http://blackrim.org/datafiles/phylo_seminar_files2014.tar.gz

get taxonomy from here
http://files.opentreeoflife.org/ott/

git clone https://github.com/OpenTreeOfLife/treemachine.git
git clone https://github.com/OpenTreeOfLife/gcmdr.git
git clone https://blackrim@bitbucket.org/blackrim/avatol_nexsons.git

cd ../treemachine
./mvn_cmdline.sh

#DEMO 1 -- atol trees
cd treemachine
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar justtrees atol/RAxML_bootstrap.WITH_MT_BS100.rr T life atol.db
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar graphml life atol.graphml F atol.db

#DEMO 2 -- tree + taxonomy
cd ../gcmdr
edit config file (the demo one is called stephen_laptop_conf.py)
edit load_taxonomy.py and synth_one_study.py to import your conf file
python load_taxonomy.py
python synth_one_study.py

#DEMO 3 -- birds
cd ../treemachine
bash DEMO_run_birds_example.sh

#DEMO 4
web site here http://files.opentreeoflife.org/