Our research focuses on understanding the evolutionary forces that have shaped genetic differences between individuals, populations, and closely related species. A unifying principal of our work is the blending together of modeling and data analysis.

The role of geography in adaptation.
Many of our simple population genetics models of adaptation, and its effects on linked sites, ignore the complications of population structure. Given the ability to generate large population genomic datasets there is now a pressing need to address this shortfall in order to understand the geography of adaptation. Our work in this area has included trying to understand geographic patterns of adaptation (Coop et al 2009, Pickrell et al 2009), developing new methods to identify loci potentially involved in local adaptation (Coop et al. 2010) and developing theory of the process of adaptation (Ralph and Coop 2010).

The impact of Natural Selection on linked polymorphism
While selection clearly shapes much of the phenotypic diversity within and between species, its role in molecular diversity and divergence has been long been debated. A dominant hypothesis for many years was that much of molecular diversity is neutral (or very weakly deleterious), with levels of diversity representing a balance between mutation and genetic drift. However, this view is slowly crumbled in light of evidence in many species that a large percentage substitutions being driven by selection and that even at putative neutral sites levels of genetic diversity are likely shaped by the effect of selection at linked sites. A major component of our work is modeling the effect of selection on linked polymorphism both to identify specific novel targets of selection (Spencer and Coop 2004, Coop and Griffiths 2004) and to understand more generally the role of selection in shaping genome-wide patterns of polymorphism (Pritchard et al 2010).

The causes and consequence of variation in recombination rates.
In humans and many other organisms, recombination plays a central role in ensuring the segregation of chromosomes during meiosis, and in generating novel combinations of alleles for natural selection to act upon. Surprisingly recombination rates are highly variable within and between species. On a fine-scale, in many species, recombination events are tightly localized to recombination hotspots, which are often polymorphic between individuals and evolve rapidly between species. As yet, we understand relatively little about the evolutionary forces underlying this variation. We have made a number of contributions to characterizing patterns of recombination (Coop et al 2008), understanding its genetic basis (Coop et al 2008, Baudat et al 2010, Fedel-Alon et al 2011), modeling its evolution (Coop and Myers 2007, Brandvain and Coop 2010), and evaluating the consequences for molecular evolution (Bullaughey et al 2008).

The inference of Demographic history from population genetic data.
All individuals with a species are related to each other to varying degrees. In small samples of individuals at most loci are genetically related to each over tens or hundreds of thousands of generations ago. This allows us to learn about demographic patterns (e.g. migration and population size changes) over vast epochs of history. We work to develop novel tools to exploit patterns of polymorphism to learn about this history (Davison et al 2009, Noonan et al 2006)