Lab of Stephen A. Smith at UMich

More updates coming

2022-12-12T16:25:32+00:00

I have been really bad at keeping these pages up to date over the last couple of yearse (COVID and all). But we are updating all the pages here over the next few days! It has already started with the people page but publications and projects will also be updating shortly.

Ericales position

2019-08-01T16:25:32+00:00

I am pleased to announce that the lab is advertising for a postdoctoral position related to the phylogenomics and evolution of the Ericales plant clade. The position has funding for two years. We are looking to have someone start by the beginning of the year 2020 if possible though there is some flexibility.

Our project, working with the University of Florida, is to collect, sequence, and analyze hundreds of transcriptomes of Ericales along with thousands of targeted capture sequences (we will assist UoF with this). Once these are collected we are interested in answering questions about the evolution of the group between temperate and tropical areas and how morphological evolution intersects with these movements. Position duties include managing the sequencing of transcriptomes and the analysis once the data come back. There will be opportunities to train undergrads and grads as well as direct involvement in project planning. There are also opportunities to help develop, plan, and teach a bilingual workshop on phylogenetics and genomics.

Qualifications include a PhD in biological sciences, preferably with a focus on ecology and on organismal and evolutionary biology. In addition, expertise in laboratory work, organization and analysis of diverse datatypes, and interests in large scale questions regarding the evolution of flowering plants.

The Smith lab is a diverse bunch of folks that range in interests from plant evolution to computational biology. There are great opportunities for interaction and collaboration for those interested. The University of Michigan also has great resources for professional development.

If you are interested or have any questions, please send your CV and information for references (eebsmith@umich.edu).

Review of applications will begin immediately.

The University of Michigan is an equal opportunity employer.

PyPHLAWD published

2018-09-18T16:25:32+00:00

Dr. Joe Walker (recent grad from the lab) and I have published our program PyPHLAWD in Methods in Ecology and Evolution. Check it out here! You can check out PyPHLAWD here.

Joe Walker defends

2018-06-28T16:25:32+00:00

Dr. Joe Walker successfully defended his dissertation today! Joe Walker is the first Smith lab graduate student to finish. And he did it in a cool 4 years with all chapters published or in review. Congrats Joe!!

PyPHLAWD site up

2018-05-10T16:25:32+00:00

PyPHLAWD website has been put up and updated! You can find it here. There are several examples of runs. More updates will follow!

A couple new papers: plant tree of life and quartet sampling

2018-01-14T16:25:32+00:00

A couple of our papers just came out in the Tree of Life special edition of AJB. Pease et al. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life looks at different ways to examine support in a phylogeny using a bunch of green plant examples. Smith and Brown Constructing a broadly inclusive seed plant phylogeny uses OpenTreeOfLife and GenBank to make a big dated seed plant phylogeny.

Postdocs moving on to new positions

2017-12-14T21:05:32+00:00

Congrats to Simon and Joseph who are moving on to a research position (Joseph) and a new phylogenetic startup phylagen.com (Simon). It was awesome to have you here at Michigan and good luck!

A number of new publications!

2017-09-20T21:05:32+00:00

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