  Drosophila melanogaster, a small dipteran of African origin, represents one
of the best-studied model organisms. Early work in this system has uniquely
shed light on the basic principles of genetics and resulted in a versatile
collection of genetic tools that allow to uncover mechanistic links between
genotype and phenotype. Moreover, given its world-wide distribution in diverse
habitats and its moderate genome-size, Drosophila has proven very powerful for
population genetics inference and was one of the first eukaryotes whose genome
was fully sequenced. In this book-chapter, we provide a brief historical
overview of research in Drosophila and then focus on recent advances during the
genomic era. After describing different types and sources of genomic data, we
discuss mechanisms of neutral evolution including the demographic history of
Drosophila and the effects of recombination and biased gene conversion. Then,
we review recent advances in detecting genome-wide signals of selection, such
as soft and hard selective sweeps. We further provide a brief introduction to
background selection, selection of non-coding DNA and codon usage and focus on
the role of structural variants, such as transposable elements and chromosomal
inversions, during the adaptive process. Finally, we discuss how genomic data
helps to dissect neutral and adaptive evolutionary mechanisms that shape
genetic and phenotypic variation in natural populations along environmental
gradients. In summary, this book chapter serves as a starting point to
Drosophila population genomics and provides an introduction to the system and
an overview to data sources, important population genetic concepts and recent
advances in the field.
