Paper accepted! Genomic inference accurately predicts the timing and severity of a recent bottleneck in a non-model insect population

This week, a paper I co-authored on the demographic history of the butterfly, E. gillettii, was accepted to Molecular Ecology and Evolution.

In this paper, we recover the demographic history of this small population of E. gillettii that was artificially transferred from Wyoming to Colorado. Wyoming and Colorado are neighboring states that are separated by the rocky mountains. In the 1970s, Paul Erlich (in our biology department) noticed that there were several Gilletii butterflies in Wyoming, but none in Colorado. As far as he could discern, the two environments were identical, and therefore, he was puzzled as to why the butterflies existed in one region and not the other. He speculated that it was possibly due to the physical barrier of the rocky mountains. As a test, he transported several Gilettii to Colorado and measured their population size every year.

Rajiv McCoy, the first author of this paper, performed a de novo RNA seq transcriptome assembly of this non-model organism. We then used this data to perform a demographic analysis using the software DaDi, and found that even with very small sample sizes, we are able to accurately recover the demographic history of this butterfly.

Splash! November 2013

I taught a Splash! class at Stanford this weekend with my colleagues Shaila Musharoff and Sandeep Venkataram on “A Brief Introduction on Population Genetics“, geared at students in grades 9-12. This was the fourth time we taught this class together.  In the class, we covered basic concepts from Hardy-Weinberg equilibrium and demonstrated how allele frequencies change as a consequence of various factors such as small population sizes, demographic events, and selection events. We illustrated these concepts using a game, as well as several examples from the literature, videos available online, and, some of my own 23&Me results.

In case you are curious, I am pasting below some links to movies that I think are particularly fun to watch. Thanks to Pleuni Pennings for sharing some of these on her website.

I particularly enjoyed the videos about lactase persistence and about Darwin’s voyage. See the links on Pleuni’s website.
Here are some videos from 23&Me about human out-of-africa history.
This particularly well made video of Wallace by the New York Times sheds light on an important scientist’s career and the scientific process.

Stanford BioCore Explorations Class on Rapid Adaptation

This week, as part of the Stanford Biocore curriculum for undergraduates, I taught a mini course with my lab-mate, Ben Wilson, on rapid adaptation. This course was geared toward first and second year Stanford undergraduate students focusing on key concepts that Ben and I study in our research including the definition of a hard and soft sweep, the relationship between population size and the rate of adaptation, as well as applications in drug resistance in HIV and Drosophila.

Here is the abstract for the course:

Astonishing examples of adaptation by natural selection inspire many of us to study the mysteries of biology, but how do these adaptations get there? Exactly how does HIV evolve resistance to antiretroviral drugs? Or how did humans gain the ability to consume milk from other mammals long after we finish weaning? The process of adaptation—perhaps the most fundamental process of evolution—can be surprisingly complex, so we will use several case examples, candy games, videos, and computer demonstrations to understand how adaptation occurs.