Final Report Summary - NEXTGENMOLECOL (Next Generation Molecular Ecology) This project should be seen in the perspective of an overall ambition to merge evolutionary biology and genomics. To this end, we have obtained one of the first draft genome sequences of a non-model organism, that of the collared flycatcher. We have used the most recent DNA sequencing technology to make this accomplishment and we have combined sequencing data with linkage mapping data to generate a genome assembly with unusual sequence coverage and continuity. We have proceeded by sequencing hundreds of individuals of several flycatcher species to learn about genetic differences between species and how this may relate to speciation. We found that the genomic landscape of species divergence is highly heterogeneous and that this heterogeneity is driven by recombination rate variation via linked selection. We have mapped loci underlying several phenotypic characters in flycatchers as well as in zebra finches. In parallel, we have used molecular evolutionary approaches to study adaptation and to learn about the evolutionary forces affecting DNA sequence evolution.