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...

Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.

Southeast Asian populations of the fruit fly Drosophila melanogaster differ from ancestral African and derived European populations by several morphological characteristics. It has been argued that this morphological differentiation could be the result of an early colonization of Southeast Asia that predated the migration of D. melanogaster to Europe after the last glacial period (around 10,000 years ago). To investigate the colonization process of Southeast Asia, we collected nucleotide polymorphism data for more than 200 X-linked fragments and 50 autosomal loci from a population of Malaysia. We analyzed this new single nucleotide polymorphism data set jointly with already existing data from an African and a European population by employing an Approximate Bayesian Computation approach. By contrasting different demographic models of these three populations, we do not find any evidence for an early divergence between the African and the Asian populations. Rather, we show that Asian and European populations of D. melanogaster share a non-African most recent common ancestor that existed about 2,500 years ago.

Seed and egg dormancy is a prevalent life-history trait in plants and invertebrates whose storage effect buffers against environmental variability, modulates species extinction in fragmented habitats, and increases genetic variation. Experimental evidence for reliable differences in dormancy over evolutionary scales (e.g., differences in seed banks between sister species) is scarce because complex ecological experiments in the field are needed to measure them. To cope with these difficulties, we developed an approximate Bayesian computation (ABC) framework that integrates ecological information on population census sizes in the priors of the parameters, along with a coalescent model accounting simultaneously for seed banks and spatial genetic structuring of populations. We collected SNP data at seven nuclear loci (over 300 SNPs) using a combination of three spatial sampling schemes: population, pooled, and species-wide samples. We provide evidence for the existence of a seed bank in two wild tomato species (Solanum chilense and Solanum peruvianum) found in western South America. Although accounting for uncertainties in ecological data, we infer for each species (i) the past demography and (ii) ecological parameters, such as the germination rate, migration rates, and minimum number of demes in the metapopulation. The inferred difference in germination rate between the two species may reflect divergent seed dormancy adaptations, in agreement with previous population genetic analyses and the ecology of these two sister species: Seeds spend, on average, a shorter time in the soil in the specialist species (S. chilense) than in the generalist species (S. peruvianum).Bayesian analysis | bet-hedging | coalescent theory T he effective size of a population or species (N e ) defines its evolutionary potential because it determines the rate at which adaptive substitutions appear and get fixed (1), as well as the vulnerability to loss of genetic diversity by genetic drift. A fundamental question in plant evolutionary biology, and of practical relevance for conservation biology, is to understand how the census size of a population above ground (N cs ) is affected by ecological disturbances and how this process, in turn, affects the N e (2). Habitat loss and fragmentation attributable to human activities are indeed acute problems for conservation of spatially structured populations because they reduce deme sizes (N e and N cs ) and gene flow among demes. The genetic diversity, reflected by the N e , of many plant (and invertebrate) species, can be seen as an iceberg. The tip of the iceberg is composed of individuals observable above ground (N cs ), whereas the major part of the diversity is accounted for by among-population differences (3, 4) and seed banks (5-8).Most, if not all, plant and animal species exist as spatially structured populations (metapopulations) with many demes linked by migration, which may be subjected to extinction/ recolonization (9). Depending on extinction/recolonization rates and the type of group fo...

Self-fertilization is hypothesized to be an evolutionary dead end because reversion to outcrossing can rarely happen, and selfing lineages are thought to rapidly become extinct because of limited potential for adaptation and/or accumulation of deleterious mutations. We tested these two assumptions by combining morphological characters and molecular-evolution analyses in a tribe of hermaphroditic grasses (Triticeae). First, we determined the mating system of the 19 studied species. Then, we sequenced 27 protein-coding loci and compared base composition and substitution patterns between selfers and outcrossers. We found that the evolution of the mating system is best described by a model including outcrossing-to-selfing transitions only. At the molecular level, we showed that regions of low recombination exhibit signatures of relaxed selection. However, we did not detect any evidence of accumulation of nonsynonymous substitutions in selfers compared to outcrossers. Additionally, we tested for the potential deleterious effects of GC-biased gene conversion in outcrossing species. We found that recombination and not the mating system affected substitution patterns and base composition. We suggest that, in Triticeae, although recombination patterns have remained stable, selfing lineages are of recent origin and inbreeding may have persisted for insufficient time for differences between the two mating systems to evolve. K E Y W O R D S :Biased gene conversion, effective population size, mating system, protein evolution, recombination, selection efficiency, substitution rate.