Harvard PhD candidate Philip Lai recently used an Anolis distichus specimen to practice his X-Ray Micro-Computed Tomography (aka microCT) wizardry. The technology takes many X-Ray images of a subject from varying angles then relies on powerful software to reconstruct a three dimensional representation based on the reflectance or transmission of X-Rays through different tissue types (bone in this case). The results are quite impressive and provide a really unique view of a species that I have spend countless hours studying. Now that I have a 3D shapefile I’m working on getting a baseball sized skull 3D printed.
Just a quick note that I have posted (my first!) two R packages to GitHub. The first (POPBAMTools) is a set of functions to organize, annotate and analyze data from the population genomic software POPBAM, written by my co-advisor Dan Garrigan. The second package, AFLPTools, performs error rate calculation of AFLP data to assist in the selection of appropriate locus and phenotype thresholds.
install.packages("devtools") devtools::install_github("geneva/AFLPTools") devtools::install_github("geneva/POPBAMTools")
The hard work of others has made publishing R packages on GitHub embarrassingly easy. I largely followed a tutorial by Hilary Parker. This approach uses the aforementioned devtools package and roxygen2 to make the creation of documentation a snap. Another extremely helpful resource is an in-progress book all about R packages by Hadley Wickham, that he has posted in its current state online.
A few years ago the Glor lab wrote a series of posts on Anole Annals about the evolution of our lizard room at the University of Rochester. The room has since moved to the University of Kansas and continues to be successful using many of the same methods. Today Jonathan Losos collected our efforts into a single convenient post. For anyone interested PDFs of some of our lizard room methods can also be found here under the Protocols tab.
The folks in the Glor lab have been doing a lot of AFLP work recently and using structure to analyze these data. To identify K (the number of genotypic clusters in a sample in individuals) we have been using a hierarchical approach proposed by Coulon and colleagues. We’ve largely been happy with this method, but it requires that you run a lot of analyses to fully evaluate a dataset. I wrote a few small shell scripts to somewhat automate the process of running jobs using the University of Rochester Center for Integrated Research Computing’s BlueHive Cluster. The scripts and details on running them can be found after the jump…
It has been a good year in my research life. I have been lucky to be involved in some fun projects that hit the presses in 2012. Over the next few weeks I will post a brief summary of each, in the order they were published. Links to access each paper can be found on the publications page.
Earlier this year, Yoel Stuart and colleagues (myself included) published a report on the expanding distribution of the introduced Cuban Green anole (Anolis porcatus) in the Dominican Republic. Previously this species was restricted to the Santo Domingo metropolis, including the airport. Recently a Harvard group led by Yoel, and Miguel Landestoy independently discovered two new populations, both to the east and west of Santo Domingo. In the paper, we present our findings on these two new populations, suggest explanations for the ability of A. porcatus to spread to these sites, and make suggestion about managing further spread.
I just heard from Jonathan Losos that I’m in a video playing at the Boston Museum of Science. Here is the backstory…
Before starting my PhD research on anoles, I studied New Caledonian geckos with Todd Jackman and Aaron Bauer at Villanova University. I continued that research while I worked at the Academy of Natural Sciences of Philadelphia. I was approached by our exhibits staff to serve as a scientific advisor for a traveling museum exhibit on geckos that was being developed by Clyde Peeling’s Reptileland.
For the exhibit, Geckos | Tails to Toepads, I filmed a small vignette where I describe morphological and molecular systematic techniques. Visitors use a touchscreen to interact with me while they try to determine if an imaginary sample represents a new gecko species. It was a fun experience, although I learned that acting does not come naturally to me. If you happen by the museum, let me know if anyone is visiting the kiosk and whether it seems well received.
I’m slowly working my way to making this a fully functional site. I’ve added my publication list, a (to be expanded) research summary, and an area to make data publicly available. I’ll keep at it, next up are PDFs for the pubs page. Also in the works is a digital bookshelf of my personal library, and a CV section.