My co-authors, Pleuni Pennings, Zoe Assaf, Alison Feder, and Ben WIlson, and I recently wrote a review on: The population genetics of drug resistance evolution in natural populations of viral, bacterial, and eukaryotic pathogens. Our review will be coming out in Molecular Ecology.
I posted my latest paper with Dmitri Petrov on BioRxiv on the Elevation of linkage disequilibrium above neutral expectations in ancestral and derived populations of Drosophila melanogaster. In this paper, we show that signatures of elevated LD and haplotype homozygosity are common in multiple populations of D. melanogaster and that signatures of partial soft sweeps are generic to multiple populations. We welcome any feedback or questions about the paper.
I had the opportunity to present my latest paper draft on long range linkage disequilibrium in D. melanogaster at the SMBE 2015 meeting held in Vienna Austria. In this paper, Dmitri Petrov and I show that levels of LD both at short and long distances are elevated above neutral expectations in both Raleigh and Zambian populations of D. melanogaster. Furthermore, we find that levels of haplotype homozygosity are also elevated in both populations. Examination of the haplotype frequency spectra in the two populations reveals that signatures of soft sweeps are common in both populations, suggesting that soft sweeps are generic to multiple populations of Drosophila.
Here is a picture that Alex Cagan drew of me and my talk!
I’m really pleased to share that my paper with Noah Rosenberg on the mathematical properties of H12 and H2/H1 is now published in Theoretical Population Biology. In this paper we introduce a normalization for the H2/H1 statistic as a function of H12 and show that the two statistics must be used in conjunction with each other to be able to differentiate hard and soft sweeps.
I am very grateful to have received the SMBE Young Investigator Travel Award for my oral presentation in Vienna this July on Long-range linkage disequilibrium in multiple natural populations of D. melanogaster.
Our paper on detecting hard and soft sweeps in D. melanogaster population genomic data from North America is finally published in PLoS Genetics!
Check it out here.
On Friday, November 14, I will be giving a talk to the Stanford Genetics department about a paper I am writing on pervasive long-range linkage disequilibrium (LD) in natural populations of D. melanogaster. LD is a measure of the amount of correlation between pairs of polymorphisms in the data, also known in statistics at R^2. The expectation is that polymorphisms far apart from one another should have low amounts of LD because recombination and mutation events should break up any structure in the genome. However, I show that there actually is a very high amount of LD even at long ranges where neutral expectations suggest there should be little to no LD. I suggest that a plausible explanation for the genome-wide elevation in LD is repeatable selective events in the Drosophila genome.
SelectionHapStats is a repository of Python scripts written to identify natural selection events in the genome and R scripts written to visualize the signatures of selective sites. The python code provided calculates haplotype homozygosity statistics H12 and H2/H1 in a genome-wide scan, as well as identified H12 peaks in genomic data. The R code provided visualizes the haplotype frequency spectra for the top peaks in the data and the genome-wide scan of H12.
This code presented in this repository is based on the arXived paper, Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps (http://arxiv.org/abs/1303.0906).
Check out my blog post for further description on the project and examples of visual output from the code!
URL: https://github.com/ngarud/SelectionHapStats
Here is a video of me giving at talk at the Bay Area Population Genetics meeting at Stanford University in January 2013 on my project on the detection of hard and soft selective sweeps.
I have been awarded a fellowship from the Stanford Center for Human Genomics to support my PhD studies for the upcoming Fall and Winter quarters.