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Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is known as a selective sweep. The fixation of the beneficial allele not only affects sequence diversity at single neutral loci but also the joint allele distribution of several partially linked neutral loci. This distribution can be studied using the ancestral recombination graph for samples of partially linked neutral loci during the selective sweep. To approximate this graph, we extend recent work by Schweinsberg & Durrett 2005 and Etheridge, Pfaffelhuber & Wakolbinger 2006 using a marked Yule tree for the genealogy at a single neutral locus linked to a strongly beneficial one. We focus on joint genealogies at two partially linked neutral loci in the case of large selection coefficients \alpha and recombination rates \rho = O(\alpha/\log\alpha) between loci. Our approach leads to a full description of the genealogy with accuracy of O((\log \alpha)^{-2}) in probability. As an application, we derive the expectation of Lewontin's D as a measure for non-random association of alleles.

Symbionts that distort their host?s sex ratio by favouring the production and survival of females are common in arthropods. Their presence produces intense Fisherian selection to return the sex ratio to parity, typified by the rapid spread of host ?suppressor? loci that restore male survival/development. In this study, we investigated the genomic impact of a selective event of this kind in the butterfly Hypolimnas bolina. Through linkage mapping we first identified a genomic region that was necessary for males to survive Wolbachia-induced killing. We then investigated the genomic impact of the rapid spread of suppression that converted the Samoan population of this butterfly from a 100:1 female-biased sex ratio in 2001, to a 1:1 sex ratio by 2006. Models of this process revealed the potential for a chromosome-wide selective sweep. To measure the impact directly, the pattern of genetic variation before and after the episode of selection was compared. Significant changes in allele frequencies were observed over a 25cM region surrounding the suppressor locus, alongside generation of linkage disequilibrium. The presence of novel allelic variants in 2006 suggests that the suppressor was introduced via immigration rather than through de novo mutation. In addition, further sampling in 2010 indicated that many of the introduced variants were lost or had reduced in frequency since 2006. We hypothesise that this loss may have resulted from a period of purifying selection - removing deleterious material that introgressed during the initial sweep. Our observations of the impact of suppression of sex ratio distorting activity reveal an extraordinarily wide genomic imprint, reflecting its status as one of the strongest selective forces in nature.

This article is from G3: Genes|Genomes|Genetics , volume 4 . Abstract The discovery that genetic pathways can be manipulated to extend lifespan has revolutionized our understanding of aging, yet their function within natural populations remains poorly characterized. In particular, evolutionary theories of aging predict tradeoffs in resource investment toward somatic maintenance vs. reproductive output that should impose strong natural selection on genetic components that influence this balance. To explore such selective pressure at the molecular level, we examine population genetic variation in the insulin-like signaling pathway of the nematode Caenorhabditis remanei. We document a recent global selective sweep on the phosphoinositide-3-kinase pathway regulator, age-1, the first life-extension gene to have been identified. In particular, we find that age-1 has 5−20 times less genetic variation than any other insulin-like signaling pathway components and that evolutionary signatures of selection center on the age-1 locus within its genomic environment. These results demonstrate that critical components of aging-related pathways can be subject to shifting patterns of strong selection, as predicted by theory. This highly polymorphic outcrossing species offers high-resolution, population-level analyses of molecular variation as a complement to functional genetic studies within the self-reproducing C. elegans model system.

This article is from G3: Genes|Genomes|Genetics , volume 4 . Abstract There is a growing interest in investigating the relationship between genes with signatures of natural selection and genes identified in QTL mapping studies using combined population and quantitative genetics approaches. We dissected an X-linked interval of 6.2 Mb, which contains two QTL underlying variation in chill coma recovery time (CCRT) in Drosophila melanogaster from temperate (European) and tropical (African) regions. This resulted in two relatively small regions of 131 kb and 124 kb. The latter one co-localizes with a very strong selective sweep in the European population. We examined the genes within and near the sweep region individually using gene expression analysis and P-element insertion lines. Of the genes overlapping with the sweep, none appears to be related to CCRT. However, we have identified a new candidate gene of CCRT, brinker, which is located just outside the sweep region and is inducible by cold stress. We discuss these results in light of recent population genetics theories on quantitative traits.

A selective sweep describes the reduction of diversity due to strong positive selection. If the mutation rate to a selectively beneficial allele is sufficiently high, Pennings and Hermisson (2006a) have shown, that it becomes likely, that a selective sweep is caused by several individuals. Such an event is called a soft sweep and the complementary event of a single origin of the beneficial allele, the classical case, a hard sweep. We give analytical expressions for the linkage disequilibrium (LD) between two neutral loci linked to the selected locus, depending on the recurrent mutation to the beneficial allele, measured by $D$ and $\hat{\sigma_D^2}$, a quantity introduced by Ohta and Kimura (1969), and conclude that the LD-pattern of a soft sweep differs substantially from that of a hard sweep due to haplotype structure. We compare our results with simulations.

This article is from BMB reports , volume 46 . Abstract Although there have been many studies of native Korean cattle, Hanwoo, there have been no selective sweep studies in these animals. This study was performed to characterize genetic variation and identify selective signatures. We sequencedthe genomes of 12 cattle, and identified 15125420 SNPs, 1768114 INDELs, and 3445 CNVs. The SNPs, INDELs, and CNVs were similarly distributed throughout the genome, and highly variable regions were shown to contain the BoLA family and GPR180, which are related to adaptive immunity. We also identified the domestication footprints of the Hanwoo population by searching for selective sweep signatures, which revealed the RCN2 gene related to BPV resistance. The results of this study may contribute to genetic improvement of the Hanwoo population in Korea. [BMB Reports 2013; 46(7):346-351]

This article is from BMB reports , volume 46 . Abstract Although there have been many studies of native Korean cattle, Hanwoo, there have been no selective sweep studies in these animals. This study was performed to characterize genetic variation and identify selective signatures. We sequencedthe genomes of 12 cattle, and identified 15125420 SNPs, 1768114 INDELs, and 3445 CNVs. The SNPs, INDELs, and CNVs were similarly distributed throughout the genome, and highly variable regions were shown to contain the BoLA family and GPR180, which are related to adaptive immunity. We also identified the domestication footprints of the Hanwoo population by searching for selective sweep signatures, which revealed the RCN2 gene related to BPV resistance. The results of this study may contribute to genetic improvement of the Hanwoo population in Korea. [BMB Reports 2013; 46(7):346-351]

When a beneficial mutation occurs in a population, the new, favored allele may spread to the entire population. This process is known as a selective sweep. Suppose we sample $n$ individuals at the end of a selective sweep. If we focus on a site on the chromosome that is close to the location of the beneficial mutation, then many of the lineages will likely be descended from the individual that had the beneficial mutation, while others will be descended from a different individual because of recombination between the two sites. We introduce two approximations for the effect of a selective sweep. The first one is simple but not very accurate: flip $n$ independent coins with probability $p$ of heads and say that the lineages whose coins come up heads are those that are descended from the individual with the beneficial mutation. A second approximation, which is related to Kingman's paintbox construction, replaces the coin flips by integer-valued random variables and leads to very accurate results.

We study the impact of a hard selective sweep on the genealogy of partially linked neutral loci in the vicinity of the positively selected allele. We consider a sexual population of stochastically varying size and, focusing on two neighboring loci, derive an approximate formula for the neutral genealogy of a sample of individuals taken at the end of the sweep. Individuals are characterized by ecological parameters depending on their genetic type and governing their growth rate and interactions with other individuals (competition). As a consequence, the "fitness" of an individual depends on the population state and is not an intrinsic characteristic of individuals. We provide a deep insight into the dynamics of the mutant and wild type populations during the different stages of a selective sweep.