Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations.

Drosophila melanogaster spread from sub-Saharan Africa to the rest of the world colonizing new environments. Here, we modeled the joint demography of African (Zimbabwe), European (The Netherlands), and North American (North Carolina) populations using an approximate Bayesian computation (ABC) approach. By testing different models (including scenarios with continuous migration), we found that admixture between Africa and Europe most likely generated the North American population, with an estimated proportion of African ancestry of 15%. We also revisited the demography of the ancestral population (Africa) and found-in contrast to previous work-that a bottleneck fits the history of the population of Zimbabwe better than expansion. Finally, we compared the site-frequency spectrum of the ancestral population to analytical predictions under the estimated bottleneck model. TO date, several studies have confirmed that Drosophila melanogaster originated in sub-Saharan Africa and spread to the rest of the world (Lachaise et al. 1988;David and Capy 1988;Begun and Aquadro 1993; Andolfatto 2001;Stephan and Li 2007). With its cosmopolitan distribution we expect that different populations have evolved and adapted differently to distinct environments, making D. melanogaster a perfect study system for both adaptation and population history. Extensive research has been performed to detect signatures of adaptation at the genome level (Sabeti et al. 2006;Li and Stephan 2006;Zayed and Whitfield 2008). Such detection usually depends on the underlying demographic scenario, since demographic events can leave similar patterns on the genome as adaptive (selective) events (Kim and Stephan 2002;Glinka et al. 2003;Jensen et al. 2005;Nielsen et al. 2005;Pavlidis et al. 2008Pavlidis et al. , 2010a. Therefore, a better understanding of the demography of a population will not only allow us to estimate past and present population sizes and the times of the population size changes but will also decrease the rate of false positives of signatures of adaptation. Here we study the demography of African, European, and North American populations, with an emphasis on the North American population.There is evidence that D. melanogaster colonized North America ,200 years ago (Johnson 1913;Sturtevant 1920;Keller 2007). D. melanogaster (then known as D. ampelophila) was first reported in New York in 1875 by New York State entomologist Lintner (Lintner 1882;Keller 2007). In the year 1879 several articles were published indicating the appearance of D. melanogaster in several parts of eastern North America, including Connecticut and Massachusetts (Johnson 1913). At that time the dipteran fauna was very well described. It is therefore unlikely that entomologists would have overlooked D. melanogaster for long (Keller 2007). Less than 25 years after its introduction, D. melanogaster became the most common dipteran species in North America (Howard 1900). Johnson (1913) suggested that North America could have been colonized from the tropics, since the fir...

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Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps in Anolis lizards and Loriinii parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson’s hypothesis. [evolutionary jump; Lévy process; phenotypic evolution; punctuated equilibrium; quantitative traits.

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