Biology – Quantitative Biology – Genomics
Scientific paper
2011-09-29
Biology
Quantitative Biology
Genomics
16 pages, 1 figure
Scientific paper
We address the problem of estimating the mode and strength of directional selection from observed patterns of polymorphism and divergence using a generative probabilistic model. We focus on the case in which selection is to be measured from a large collection of short, dispersed elements of the same kind, such as binding sites for a particular transcription factor. To avoid the confounding effects of demography, our method directly contrasts these elements with putatively neutral flanking sites. The method is similar in spirit to Poisson Random Field methods based on the site-frequency spectrum, but makes a somewhat different set of assumptions, which should make it less sensitive to complex demographic scenarios and to violations of assumptions of independence across sites. We derive a likelihood function and an expectation maximization for inference. We then show that the method performs well on simulated data, and present preliminary results for real data.
Arbiza Leonardo
Gronau Ilan
Siepel Adam
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