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.
It has been a bit since our last update but just added a bunch of new papers to the publications page. This includes a first author publication by graduate student Joseph Walker! Congrats!
Here is the list for the year so far
- Smith, S. A. and J. W. Brown. accepted. Constructing a comprehensive seed plant phylogeny.
American Journal of Botany
- Pease J.B., J. W. Brown, J. F. Walker, C. E. Hinchliff, S. A. Smith. in press. Quartet Sampling distinguishes lack of support from conflicting support in the plant tree of life. American Journal of Botany
- Fleischmann, A., J. Schlauer, T. Givnish, and S. A. Smith. In press. Evolution of carnivory in angiosperms. Chapter 3. in forthcoming book on Carnivory in angiosperms.
- Lopez-Nieves, S., Y. Yang, T. Feng, S. A. Smith, S. F. Brockington, and H. A. Maeda. In press. Relaxation of Tyrosine Pathway Regulation Underlies the Evolution of Betalain Pigmentation in Caryophyllales. New Phytologist
- Brown, J. W., N. Wang, and S. A. Smith. 2017. The development of scientific consensus: analyzing conflict and concordance among Avian phylogenies. Molecular Phylogenetics and Evolution https://doi.org/10.1101/123034
- Brown, J. W. and S. A. Smith. 2017. The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates. Systematic Biology https://doi.org/10.1101/113720
- Walker, J., Y. Yang, M. Moore, S. F. Brockington, and S. A. Smith. 2017. Conflict among carnivores: whole transcriptomes unable to resolve the carnivorous clade of Caryophyllales. American Journal of Botany. https://doi.org/10.1101/115741
- Smith, S. A., M. J. Moore, S. F. Brockington, and Y. Yang. 2017. Disparity, Diversity, and Duplications in Caryophyllales. New Phytologist. https://doi.org/10.1101/132878
- Yang, Y., M. J. Moore, S. F. Brockington, J. Mikenas, and S. A. Smith. 2017. Improved transcriptome sampling pinpoints widespread paleopolyploidy events in Caryophyllales New Phytologist. https://doi.org/10.1101/143529
- Brown, J., J. Walker, and S. A. Smith. 2017. phyx: Phylogenetic tools for Unix. Bioinfor- matics. https://doi.org/10.1093/bioinformatics/btx063
- Yang, Y., M. J. Moore, S. F. Brockington, A. Timoneda-Monfort, T. Feng, H. E. Marx, Joseph F. Walker, and S. A. Smith. 2017. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences. https://doi.org/10.1101/ 079582
I decided to move more detailed discussion of issues, topics, papers, and code at evoblackrim.com. Any opinions over there are my own (and therefore, not on the lab page, here).
Right now, there is some information on phyx updates and some cool opentree of life toys.
James Pease and I just published a paper describing the problems that you might find when using BLAST for phylogenomics. The paper is here and published in Briefings in Bioinformatics.
Greg is joining us from the NSF collections postdoc program.
Greg finished up his dissertation in the Solti labs and was awarded an NSF post-doctoral fellowship for “Research Using Biological Collections”. These fellowships are meant to support transformative science that employs biological collections.
The title of Greg’s post-doctoral fellowship is ” Integrating diverse collections data for deep-time distribution modeling in a tropical flowering plant family (Icacinaceae) with an extensive fossil record.” Chris Dick and I serve as the sponsoring scientists.
Below is part of the abstract for Greg NSF Fellowship.
Understanding how species have responded to previous instances of climate change is critical for predicting the impact of future climate change on the distribution of biological diversity. Because the fossil record is highly incomplete, additional tools are necessary to reconstruct historical distributions at different points in the past (e.g., when the earth’s climate was considerably warmer during the early Eocene, ca. 50 Ma). Species distribution modeling (SDM) has emerged as a powerful computational tool for modeling the ecological requirements of species, using the wealth of locality/geographic data available for modern species in natural history collections. SDM has been used extensively to predict possible future distributions as shaped by climate change; the application of SDM for reconstructing distributions in deep time, however, has been underexplored, despite its potential for understanding how climate change has shaped the diversity and distribution of organisms through time. The fellowship research will explore and expand methods of using geographic data from modern species, obtained through online repositories of collections data from around the world (e.g., GBIF, iDigBio), to generate species distribution models of extinct species, allowing for the reconstruction of distribution patterns across broad time scales (e.g., the past 65 Ma). This research will use as a model the pantropical plant family Icacinaceae, which has an extensive fossil record, allowing for the validation of the historical projections and, by extension, the methods used to generate them. In particular, this research will investigate the climatic suitability of major land bridges/rafts for the migration of tropical plants throughout the Cenozoic (65 Ma to present). The will constitute one of the first studies to employ SDM across such a broad time scale, using the fossil record to validate the results. This research will therefore serve as an important proof of concept for this approach, and the novel methodological tools generated will advance future research related to biogeography and climate change.
Happy to add Drew Larson and Lijun Zhao to the lab! Drew is co-advised with Chris Dick in the department.
Joseph Walker, Joseph Brown, and I have been working on tools for the command line for phylogenetics and phylogenomics. We have a good release and logo now. Check it out at github.
Ya Yang has been a member of the lab working on transcriptomics in Caryophyllales and will be moving on to a position at UMinn this fall. Congrats Ya! http://www.yangya.org/
James Pease has been a member of the lab working on the Andes and got a position at Wake Forest. Congrats! https://peaselab.github.io/
Two new postdocs will be joining the lab. More on that in a bit
Post-doctoral position to work on ongoing projects including phylogenetics,
phylogenomics, and evolution. In particular, there are projects involving
work with the Open Tree of Life, phylogenetic dataset construction, large
phylogenetic analyses, phylogenomic analyses involving genomes and
transcriptomes, orthology and homology searching, analysis of differential
gene expression using phylogenies, large comparative analysis, and
evolution of plants.
Qualifications: A PhD, good publication record, and strong background in
phylogenetics. The candidate will preferably have skills in computational
work and computer programming.
Start date: The candidate can start as early as August 2016 (preferable).
Length of position: The position is for one year with review for a second
year and possible extension.
Salary: Commiserate with experience.
To apply: via email, send a CV, statement of research interests, and names
and contact information for three references. Applications and inquiries
should be addressed to Stephen Smith at firstname.lastname@example.org.
Nice article in Scientific American about the OpenTreeOfLife with a figure that was made in the lab.