March 19th, Eyal Elyashiv: Building a population genetic map of the effects of linked selection, with application to Drosophila melanogaster

About Eyal

Eyal Elyashiv, Columbia University

Eyal Elyashiv, Columbia University

Eyal is PhD candidate at the Hebrew University of Jerusalem and a visiting student at Columbia University, working under the supervision of Prof. Guy Sella.

Talk: Building a population genetic map of the effects of linked selection, with application to Drosophila melanogaster

Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of such “linked selection” on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and gaining insight into the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a site is polymorphic given local annotations and substitution patterns. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a population genetic map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from ~190 lines in Drosophila melanogaster and show that it reliably predicts diversity levels at the 1Mb scale, as well as helps interpret finer diversity patterns around substitutions in proteins and UTRs. The method outperforms existing ones and allows one to distinguish the contribution of sweeps from other modes of linked selection and to obtain robust estimates of sweep parameters, in particular providing strong evidence for sweeps in UTRs. More generally, our findings indicate that linked selection has had a pronounced effect in reducing diversity levels and increasing their variance in D. melanogaster, and suggest that other modes of selection (e.g. partial and soft sweeps) contribute substantially to these effects. Our approach presents the advantages of being flexible in the species to which it can be applied, the modes of selection that it can consider and in its ability to readily incorporate ever-improving functional annotations and genetic maps.

Seminar details

Wednesday March 19th, 2014
1:00 PM Lunch (sign up below)
1:15 PM Seminar
Location: Clark Center S360
If you would like to speak with Eyal, contact Jonathan Pritchard (pritch@stanford.edu)

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