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.
We just published a new paper in BMC Evolutionary Biology looking at first steps in characterizing conflict, concordance, and gene duplications in phylogenomic datasets. See it here.
There are some new members of the lab. Julia Oliviera is with us from Michael Moore at Oberlin and is working here in the lab on gene duplication over the summer. James Pease joined the lab as a postdoc working with Chris Dick and myself on Andean plants and transcriptomics. Welcome!
The lab (and others) went to Magee Marsh for a lab fieldtrip to see the migration. Here is a picture
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
- Double-crested Cormorant
- Great Blue Heron
- Great Egret
- Turkey Vulture
- Bald Eagle
- Red-tailed Hawk
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.
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.
We posted a bioarxiv version of our OpenTree paper that is in review here. Fun!
There is code that implements most of what we go over here.
Ya Yang and Smith published a paper in MBE on orthology methods and phylogenomics. Check it here.
Cody and Stephen published a paper on the limitations of public data to construct large phylogenetic trees. Check it out here.