The recent demographic and adaptive history of Drosophila melanogaster

Abstract

Population genetic analyses of the past two decades confirmed an earlier hypothesis by L Tsacas and D Lachaise that the cosmopolitan species Drosophila melanogaster has an Afrotropical origin, and that it colonized the rest of the world only very recently. Maximum likelihood analyses based on multilocus data suggest that the putative ancestral African population expanded its size about 60 000 years ago (ya). These demographic changes were accompanied by the fixation of numerous beneficial mutations, as revealed by signatures of positive directional selection in the genome (selective sweeps). The estimated rate of adaptive substitution on the X chromosome is in the order of 10 À11 per nucleotide site per generation. Comparable (but not significantly higher) substitution rates are found in derived populations that colonized new habitats outside Africa, such as in a European population that branched off from the African lineage about 16 000 ya. Heredity (2007) 98, 65-68.

Detecting Directional Selection in the Presence of Recent Admixture in African-Americans

“…Thus, if one rejects neutrality, this could be due to a selective sweep, but it could also be due to the fact that the demographic history of the population is not approximated well by the SNM. This is a serious practical concern because many populations of humans, Drosophila, and domesticated species have demographic histories that are far more complex than allowed for by the SNM (Wright et al 2005; Thornton and Andolfatto 2006;Stephan and Li 2007;Gutenkunst et al 2009;Lohmueller et al 2009;Wall et al 2009;vonHoldt et al 2010). One strategy that has been widely employed to deal with the problem of demography is to use a more realistic demographic model to define the critical values of the standard tests of neutrality (Akey et al 2004;Wright et al 2005;Li and Stephan 2006; Thornton and Andolfatto 2006;Nielsen et al 2009).…”

“…The idea that genetic hitchhiking distorts patterns of genetic variation has been used to derive several statistical tests to evaluate whether one can reject the SNM for a particular region of the genome. Many recent studies have applied tests of neutrality to data from humans (reviewed in Nielsen et al 2007), Drosophila (reviewed in Stephan and Li 2007;, and domestic dogs (Pollinger et al 2005;Akey et al 2010;Boyko et al 2010) to locate regions of the genome that have evolved under natural selection. These signatures have been used to detect the footprints of recent selection (reviewed in Nielsen 2005).…”

Inferences of Demography and Selection in an African Population of Drosophila melanogaster

“…Although it is clear that presumably ancestral East African populations (Pool and Aquadro 2006) show strong signals of nonequilibrium demography (for review see Stephan and Li 2007), it has mostly been assumed that many of the observed deviations from neutrality have been driven by population expansion (although see Haddrill et al 2005). As a consequence, the parameter space for characterizing the demographic history of African populations has not been thoroughly explored.…”

“…Many sophisticated methodologies for estimating demographic parameters have been developed, and application of such methods has revealed much about the demographic history of natural populations of D. melanogaster (Haddrill et al 2005;Ometto et al 2005; Thornton and Andolfatto 2006;Stephan and Li 2007;Laurent et al 2011). Although it is clear that presumably ancestral East African populations (Pool and Aquadro 2006) show strong signals of nonequilibrium demography (for review see Stephan and Li 2007), it has mostly been assumed that many of the observed deviations from neutrality have been driven by population expansion (although see Haddrill et al 2005).…”

“…Indeed, to effectively investigate models of natural selection, which are of great general interest in evolutionary biology, one must take into account the underlying demographic history of a population. Consequently, understanding demographic history is integral for making incisive inferences about the genetic adaptation of populations (e.g., Akey et al 2004;Nielsen et al 2009;Lohmueller et al 2011).Many sophisticated methodologies for estimating demographic parameters have been developed, and application of such methods has revealed much about the demographic history of natural populations of D. melanogaster (Haddrill et al 2005;Ometto et al 2005;Thornton and Andolfatto 2006;Stephan and Li 2007;Laurent et al 2011 demography (for review see Stephan and Li 2007), it has mostly been assumed that many of the observed deviations from neutrality have been driven by population expansion (although see Haddrill et al 2005). As a consequence, the parameter space for characterizing the demographic history of African populations has not been thoroughly explored.…”