phyx published

Joseph Brown (postdoc), Joseph Walker (grad student), and myself just published phyx, a command line set of tools for phylogenetics, phylogenomics, and bioinformatics. See the publication here and get the code here.

Greg Stull joins the lab

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.


Postdoc position available! Join the lab!

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