These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.
This work investigated the patterns of genetic variation along a recombining chromosome by constructing ancestral recombination graphs that are modified to incorporate the effect of genetic hitchhiking, and proposed a statistical method to test the significance of a local reduction of variation and a skew of the frequency spectrum caused by a hitchhiker event.
Features of the organization of repetitive sequences in eukaryotic genomes, and their distribution in natural populations, reflect the evolutionary forces acting on selfish DNA.
A maximum likelihood method that allows us to infer demographic changes and detect recent positive selection in populations of varying size from DNA polymorphism data found that the African population expanded about 60,000 y ago and that the European population split off from the African lineage about 15,800 y ago, thereby suffering a severe population size bottleneck.
The Hitchhiking effect on the site frequency spectrum, as measured by Tajima's D and several other statistics, is investigated using a computer simulation model based on the coalescent process and recurrent hitchhiking events to demonstrate that under the simple hitchh hiking model the expected value of Tajima’s D is large and negative, indicating a skew toward rare variants.
This study uses a multi-locus scan of X-linked DNA sequence variation in a putatively ancestral African and a derived European population to investigate the relative effects of demographic and selection forces in Drosophila melanogaster, and shows the advantages of a genomic approach (over a locus-specific analysis) in disentangling demographic and selective forces.
Strong effects of the sampling scheme on Tajima's D and Fu and Li's D statistics are demonstrated, particularly under specieswide (range) expansions, which suggests that validating the assumption of panmixia is crucial if robust demographic inferences are to be made from local or pooled samples.
This work modeled the joint demography of African, European, and North American populations using an approximate Bayesian computation (ABC) approach and found that admixture between Africa and Europe most likely generated the North American population.
The characteristic parameter of this steady-state model is alpha v, the product of selection intensity and the frequency of beneficial mutations v, and it is demonstrated that the steady- state model describes the hitchhiking process adequately, unless the recombination rate is very low.