Simons Institute for the Theory of Computing

I attended the Simons Institute workshop titled Computation-Intensive Probabilistic and Statistical Methods for Large-Scale Population Genomics. There was a great lineup of speakers and some opportunities to meet colleagues!

Talk at the Biomedical Computation at Stanford Conference (BCATS)

Today I gave a talk on my work on detecting hard and soft sweeps in Drosophila at BCATS. I presented new work inferring the softness of the sweeps in Drosophila, showing that sweeps on average have an adaptive theta compatible with the number of sweeping haplotypes to be around 12.8. The talk was well received, and I appreciate all the questions and comments from the audience.

Recent selective sweeps in Drosophila were abundant and primarily soft

We recently rewrote our paper on identifying soft selective sweeps in Drosophila and posted version 2 on the ArXiv. In this new version, we (i) focus much more on the possibility of complex demographic scenarios generating detected signatures, (ii) carry out extensive ABC computations to estimate the likeliest adaptive theta for all of our peaks, and (iii) investigate the power of our statistics to detect sweeps of varying “softness” either due to varying adaptive theta values or because the sweeping allele starts at varying initial frequency. In the end, our conclusions remain the same: that recent selective sweeps in Drosophila were abundant and primarily soft.

Please feel free to check out version 2 and send us your comments!

CEHG symposium

Today I had the opportunity to attend the Stanford CEHG symposium and presented a poster on my work on soft sweeps. It was great to learn some new ideas and meet researchers interested in scanning for soft sweeps in various genomes!

Blog post about our E. gillettii paper

Our paper (McCoy et al. 2013) was recently featured in a blog post on the CEHG (Computational, Evolutionary and Human Genomics at Stanford) website, and was cross posted on The Molecular Ecologist.

Seminar at Penn State University

Today I had the opportunity to present my work at a special seminar at Penn State University’s department of biology, hosted by Professor Steven Schaeffer.

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.