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

    Read more

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.

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.

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/

phylogenetic discussion and IRC

There are a small number of people that are exploring the old school tech way of discussion on the internet (IRC) for phylogenetics. You can find us on #phyloirc using the freenode.net server. You can just click here
Visit the IRC channel

You can also get there here.