Originally published as Genetics Published Articles Ahead of Print on June 18, 2008.

Genetics, Vol. 179, 1713-1720, July 2008, Copyright © 2008
doi:10.1534/genetics.108.086835

Detecting Local Adaptation Using the Joint Sampling of Polymorphism Data in the Parental and Derived Populations

Hideki Innan*,1 and Yuseob Kim{dagger}

* Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan and {dagger} The School of Life Sciences and the Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287

1 Corresponding author: Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan.
E-mail: innan_hideki{at}soken.ac.jp

When a local colonization in a new niche occurs, the new derived population should be subject to different selective pressures from that in the original parental population; consequently it is likely that many loci will be subject to directional selection. In such a quick adaptation event through environmental changes, it is reasonable to consider that selection utilizes genetic variations accumulated in the precolonization phase. This mode of selection from standing variation would play an important role in the evolution of new species. Here, we developed a coalescent-based simulation algorithm to generate patterns of DNA polymorphism in both parental and derived populations. Our simulations demonstrate that selection causes a drastic change in the pattern of polymorphism in the derived population, but not in the parental population. Therefore, for detecting the signature of local adaptation in polymorphism data, it is important to evaluate the data from both parental and derived populations simultaneously.