Showing papers on "Genetic hitchhiking published in 2002"

Detecting a local signature of genetic hitchhiking along a recombining chromosome.

Abstract: The theory of genetic hitchhiking predicts that the level of genetic variation is greatly reduced at the site of strong directional selection and increases as the recombinational distance from the site of selection increases. This characteristic pattern can be used to detect recent directional selection on the basis of DNA polymorphism data. However, the large variance of nucleotide diversity in samples of moderate size imposes difficulties in detecting such patterns. We 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. A statistical method is proposed to test the significance of a local reduction of variation and a skew of the frequency spectrum caused by a hitchhiking event. This method also allows us to estimate the strength and the location of directional selection from DNA sequence data.

The signature of positive selection at randomly chosen loci.

Abstract: In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequency alleles drift to fixation and no longer contribute to polymorphism, while linkage disequilibrium is broken down by recombination. As a result, loci chosen without independent evidence of recent selection are not expected to exhibit either of these features, even if they have been affected by numerous sweeps in their genealogical history. How then can we explain the patterns in the data? One possibility is population structure, with unequal sampling from different subpopulations. Alternatively, positive selection may not operate as is commonly modeled. In particular, the rate of fixation of advantageous mutations may have increased in the recent past.

Testing models of selection and demography in Drosophila simulans.

Abstract: We analyze patterns of nucleotide variability at 15 X-linked loci and 14 autosomal loci from a North American population of Drosophila simulans. We show that there is significantly more linkage disequilibrium on the X chromosome than on chromosome arm 3R and much more linkage disequilibrium on both chromosomes than expected from estimates of recombination rates, mutation rates, and levels of diversity. To explore what types of evolutionary models might explain this observation, we examine a model of recurrent, nonoverlapping selective sweeps and a model of a recent drastic bottleneck (e.g., founder event) in the demographic history of North American populations of D. simulans. The simple sweep model is not consistent with the observed patterns of linkage disequilibrium nor with the observed frequencies of segregating mutations. Under a restricted range of parameter values, a simple bottleneck model is consistent with multiple facets of the data. While our results do not exclude some influence of selection on X vs. autosome variability levels, they suggest that demography alone may account for patterns of linkage disequilibrium and the frequency spectrum of segregating mutations in this population of D. simulans.

Mapping a Cave Fish Genome: Polygenic Systems and Regressive Evolution

Abstract: We used random amplified polymorphic DNA (RAPD) fingerprinting to generate anonymous DNA markers in the fish Astyanax mexicanus, a species with both surface and cave populations. Surface individuals are eyed and pigmented; troglobitic forms are blind and depigmented. We hybridized surface fish and Pachon population cave fish and produced a RAPD genomic map 1064 cM in length (about half the total length of the genome) that was used to screen for quantitative trait loci (QTL) for troglomorphic traits. Three QTL for reduced eye size, two for decreased numbers of melanophores, two for condition factor, and the locus for the unifactorial trait, albinism, were mapped. These factors account for an average of 46% of the variance in these traits in the backcross. The results are the first direct demonstration that troglomorphic changes in this population are multifactorial. Two closely linked pairs of QTL were found. Each consisted of a regressive and a constructive trait QTL. These close linkages are unlikely to have occurred by chance (P <.05 for each) and suggest that troglomorphic evolution might be facilitated by pleiotropy or by genetic hitchhiking.

The effects of multilocus balancing selection on neutral variability.

Abstract: We studied the effect of multilocus balancing selection on neutral nucleotide variability at linked sites by simulating a model where diallelic polymorphisms are maintained at an arbitrary number of selected loci by means of symmetric overdominance. Different combinations of alleles define different genetic backgrounds that subdivide the population and strongly affect variability. Several multilocus fitness regimes with different degrees of epistasis and gametic disequilibrium are allowed. Analytical results based on a multilocus extension of the structured coalescent predict that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. Our simulation results show that although variability increases with the number of genetic backgrounds that are maintained in the population, it is reduced by random fluctuations in the frequencies of those backgrounds and does not reach high levels even in very large populations. We also show that previous results on balancing selection in single-locus systems do not extend to the multilocus scenario in a straightforward way. Different patterns of linkage disequilibrium and of the frequency spectrum of neutral mutations are expected under different degrees of epistasis. Interestingly, the power to detect balancing selection using deviations from a neutral distribution of allele frequencies seems to be diminished under the fitness regime that leads to the largest increase of variability over the neutral case. This and other results are discussed in the light of data from the Mhc.

Gene Density and Human Nucleotide Polymorphism

Abstract: Population genetics theory indicates that natural selection will affect levels and patterns of genetic variation at closely linked loci. Background selection (Charlesworth, Morgan, and Charlesworth 1993) proposes that the removal of recurrent deleterious mutations and associated neutral variants will cause a reduction of nucleotide variation in low-recombination regions. The strength of background selection depends on the deleterious mutation rate, the magnitude of selection and dominance, and the recombination rate. Genetic hitchhiking (Maynard Smith and Haigh 1974), the fixation of advantageous alleles and the associated fixation of linked neutral alleles, can also decrease nucleotide diversity in low-recombination regions. The extent of genetic hitchhiking depends on the strength of selection and the rate of recombination. Therefore, under both background selection and genetic hitchhiking, theory predicts that genomic regions that rarely recombine may be subject to reductions in nucleotide diversity. Furthermore, if the rate of deleterious mutation or selective sweeps (or both) is sufficiently high, background selection (Hudson and Kaplan 1995) and genetic hitchhiking (Wiehe and Stephan 1993) models predict an overall positive correlation between nucleotide polymorphism and recombination rate. Empirical investigations of nucleotide variation support these predictions. In Drosophila melanogaster, regions of the genome with little recombination show reduced heterozygosity (Aguade, Miyashita, and Langley 1989; Begun and Aquadro 1991; Berry, Ajioka, and Kreitman 1991). Furthermore, there is evidence that nucleotide variation and recombination rate are positively correlated in several taxa, including fruit flies (Begun and Aquadro 1992), house mice (Nachman 1997), goatgrasses (Dvorak, Luo, and Yang 1998), sea beets (Kraft et al. 1998), tomatoes (Stephan and Langley 1998), humans (Nachman et al. 1998; Przeworski, Hudson, and Di Rienzo 2000; Nachman 2001), and maize (Tenaillon et al. 2001). The combination of theoretical and empirical results indicates that selection acting at linked sites is likely to be a major force shaping genomic patterns of nucleotide variation. The documented relationship between nucleotide variation and recombination rate raises the question of whether other measurable variables can explain additional variation in nucleotide polymorphism in the context of selection at linked sites. We predict that the effects of selection at linked sites will depend on local

Genetic niche‐hiking: an alternative explanation for the evolution of flammability

Abstract: In fire-prone ecosystems, many plants possess traits that enhance their relative flammability and ecologists have suggested increased flammability could result from natural selection. To date, theoretical models addressing the evolution of flammable characteristics assume that flammable plants realize some direct fitness advantage. In this paper, we explore the idea that enhanced flammability can increase in frequency in a population without any direct fitness benefit to the flammable type. In our model, flammability evolves due to an association between an allele that promotes flammability and alleles at unlinked loci that give high fitness. In analogy to genetic hitchhiking, in which a deleterious allele can invade due to a genetic linkage, we call this process “genetic niche-hiking,” because the association results from localized niche construction. Specifically, flammable plants sacrifice themselves and their neighbors to produce local fire-cleared gaps (the constructed niche) in which their offspring are able to continually track an ever-changing environment. Niche-hiking requires that mating, dispersal and niche construction all occur locally (i.e. the population is spatially structured), such that offspring are likely to experience the niches their parents construct. Using a spatially-explicit lattice-based simulation, we find that increased flammability can evolve despite the “self-killing” cost of such a trait. Genetic niche-hiking may also be applicable to the evolution of other traits in spatially structured ecological systems such as plant disease susceptibility and forest tree characteristics that influence gap production.

Genomic Effects of Nucleotide Substitutions in Drosophila simulans

Abstract: Selective fixation of beneficial mutations reduces levels of linked, neutral variation. The magnitude of this "hitchhiking effect" is determined by the strength of selection and the recombination rate between selected and neutral sites. Thus, depending on the values of these parameters and the frequency with which directional selection occurs, the genomic scale over which directional selection reduces levels of linked variation may vary widely. Here we present a permutation-based analysis of nucleotide polymorphisms and fixations in Drosophila simulans. We show evidence of pervasive small-scale hitchhiking effects in this lineage. Furthermore, our results reveal that different types of fixations are associated with different levels of linked variation.