Neutrality tests based on the distribution of haplotypes under an infinite-site model

Depaulis, Frantz; Veuille, Michel

doi:10.1093/oxfordjournals.molbev.a025905

Cited by 183 publications

(144 citation statements)

References 15 publications

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“…Consistent with the analysis of temporal differentiation, we observed marginally significant haplotypic structures for the Hen1 gene region for post-P North American populations [frequency of major haplotypes = 15, P = 0.042 (Hudson et al 1994) and haplotype heterozygosity = 0.759, P = 0.031 (Depaulis and Veuille 1998)]. This strong haplotypic structure was extended at least 10 kb upstream and downstream of Hen1 (frequency of major haplotypes = 10, P = 0.003 and haplotype heterozygosity = 0.290, P = 0.001).…”

Section: Recent Horizontal Transfer Of the P Element Does Not Have Wisupporting

confidence: 86%

“…We estimated F st according to Weir and Cockerham (1984) and used permutations to determine the P-values (Hudson et al 1992). To further test for unusual haplotypic structures, we used methods based on the frequency of major haplotypes (Hudson et al 1994), the number of haplotypes, and the heterozygosity of haplotypes (Depaulis and Veuille 1998) and used coalescent simulation without recombination to determine the P-values (Hudson 2002). Although these three haplotype-based tests are related conceptually, their power to detect deviations from the same null hypothesis varies with the alternatives and thus is not fully redundant (Depaulis and Veuille 1998).…”

Section: Melanogaster Variation Data Before P-element Invasionsmentioning

confidence: 99%

“…To further test for unusual haplotypic structures, we used methods based on the frequency of major haplotypes (Hudson et al 1994), the number of haplotypes, and the heterozygosity of haplotypes (Depaulis and Veuille 1998) and used coalescent simulation without recombination to determine the P-values (Hudson 2002). Although these three haplotype-based tests are related conceptually, their power to detect deviations from the same null hypothesis varies with the alternatives and thus is not fully redundant (Depaulis and Veuille 1998). It is worth noting that the significance of haplotype tests was based on coalescent simulations without recombination, which is especially conservative, and our observation of strong evidence for a 20-kb haplotypic structure around Hen1 is highly unusual (see Results).…”

Section: Melanogaster Variation Data Before P-element Invasionsmentioning

confidence: 99%

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Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

Lee

Langley

2012

Genetics

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Transposable elements (TEs) are considered to be genomic parasites and their interactions with their hosts have been likened to the coevolution between host and other nongenomic, horizontally transferred pathogens. TE families, however, are vertically inherited as integral segments of the nuclear genome. This transmission strategy has been suggested to weaken the selective benefits of host alleles repressing the transposition of specific TE variants. On the other hand, the elevated rates of TE transposition and high incidences of deleterious mutations observed during the rare cases of horizontal transfers of TE families between species could create at least a transient process analogous to the influence of horizontally transmitted pathogens. Here, we formally address this analogy, using empirical and theoretical analysis to specify the mechanism of how host-TE interactions may drive the evolution of host genes. We found that host TE-interacting genes actually have more pervasive evidence of adaptive evolution than immunity genes that interact with nongenomic pathogens in Drosophila. Yet, both our theoretical modeling and empirical observations comparing Drosophila melanogaster populations before and after the horizontal transfer of P elements, which invaded D. melanogaster early last century, demonstrated that horizontally transferred TEs have only a limited influence on host TE-interacting genes. We propose that the more prevalent and constant interaction with multiple vertically transmitted TE families may instead be the main force driving the fast evolution of TE-interacting genes, which is fundamentally different from the gene-for-gene interaction of host-pathogen coevolution. HOST-PATHOGEN interactions affect the population dynamics and the evolutionary trajectories of both species. In particular, coevolutionary dynamics will affect the pattern of polymorphism and divergence of genes underlying hostparasite interactions either through an arms race (Van Valen 1973;Dawkins and Krebs 1979) or through balancing selection (Haldane 1949;Hughes et al. 1990; Takahata et al. 1992;Hughes and Yeager 1998;Rose et al. 2004). In either case, accelerated rates of protein evolution and/or recurrent adaptive substitutions are expected in genes engaged in these interactions, which has been observed in both immunity genes (Schlenke and Begun 2003;Jiggins and Kim 2007;Sackton et al. 2007;Obbard et al. 2009b) and antivirus siRNA genes (Obbard et al. 2006(Obbard et al. , 2009a(Obbard et al. ,b, 2011 in Drosophila.Transposable elements (TEs) are ubiquitous genomic constituents that increase their copy number (the number of TEs in a host genome) by replicative transposition (copying to new genomic locations). Like Drosophila, most host genomes are occupied by multiple TE families, which are defined by sequence similarity (homology) and by replication and transposition mechanisms. Even though incidences of potentially adaptive individual TE insertions with high population frequencies have been reported (Daborn et al. 20...

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Section: Recent Horizontal Transfer Of the P Element Does Not Have Wisupporting

confidence: 86%

Section: Melanogaster Variation Data Before P-element Invasionsmentioning

confidence: 99%

Section: Melanogaster Variation Data Before P-element Invasionsmentioning

confidence: 99%

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Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

Lee

Langley

2012

Genetics

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“…A maximum-likelihood estimate for the magnitude of the selection coefficient required to cause such a reduction in heterozygosity is 0.022 (3). Evidence for significantly reduced haplotype diversity (for loci spanning Ͼ800 kb), significantly high levels of linkage disequilibrium, and significantly large negative Tajima's D values immediately flanking the region lacking polymorphism (Table 1) all support the selective sweep hypothesis (14)(15)(16).…”

Section: Resultsmentioning

confidence: 69%

Strong selective sweep associated with a transposon insertion inDrosophila simulans

Schlenke

Begun

2004

Proc. Natl. Acad. Sci. U.S.A.

223

190

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We know little about several important properties of beneficial mutations, including their mutational origin, their phenotypic effects (e.g., protein structure changes vs. regulatory changes), and the frequency and rapidity with which they become fixed in a population. One signature of the spread of beneficial mutations is the reduction of heterozygosity at linked sites. Here, we present population genetic data from several loci across chromosome arm 2R in Drosophila simulans. A 100-kb segment from a freely recombining region of this chromosome shows extremely reduced heterozygosity in a California population sample, yet typical levels of divergence between species, suggesting that at least one episode of strong directional selection has occurred in the region. The 5 flanking sequence of one gene in this region, Cyp6g1 (a cytochrome P450), is nearly fixed for a Doc transposable element insertion. Presence of the insertion is correlated with increased transcript abundance of Cyp6g1, a phenotype previously shown to be associated with insecticide resistance in Drosophila melanogaster. Surveys of nucleotide variation in the same genomic region in an African D. simulans population revealed no evidence for a high-frequency Doc element and no evidence for reduced polymorphism. These data are consistent with the notion that the Doc element is a geographically restricted beneficial mutation. Data from D. simulans Cyp6g1 are paralleled in many respects by data from its sister species D. melanogaster.T he spread of beneficial mutations is expected to reduce variation at linked sites, a phenomenon known as genetic hitchhiking (1, 2). All else being equal, the size of the swept region depends on the selection coefficient of the beneficial mutant and the local recombination rate. Theoretical results show that for regions of normal recombination in Drosophila, hitchhiking effects associated with moderately strong selection should result in localized regions of reduced heterozygosity (3). Thus, in principle, the frequency and locations of selective sweeps can be determined by scanning chromosomes for ''valleys'' of reduced variation (4). The paucity of large genomic regions of severely reduced heterozygosity from recombining regions in Drosophila and other organisms (4-7) suggests that novel mutations with large positive selection coefficients are rare, although it does not rule out the evolutionary importance of such mutations.In this study, we document the existence of a 100-kb chromosomal region that has extremely reduced heterozygosity in a Drosophila simulans population sample from California, but not in a sample from Africa, indicating the recent and geographically restricted sweep of a unique, beneficial mutation. Furthermore, we report the unusual observation of an intact transposable element in this region, which occurs at very high frequency in the California, but not Africa, sample. The transposon insertion is associated with increased transcript abundance of the downstream cytochrome P450 gene Cyp6g1. These data are...

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“…Given that in these cases some summary statistics cannot be computed (that is, they include a division by zero), we summarized our data sets by computing the statistic d-the difference between the average number of pairwise nucleotide differences between sequences in the sample (k) and the Watterson's estimator of the population mutation rate y (Tajima 1989), the haplotype diversity (H; Depaulis and Veuille, 1998) and the total number of segregating sites (S) in the sample. These three statistics are expected to be sensitive to changes in the effective population size (N e ), and to correlate with the severity of population size bottlenecks.…”

Section: Population Genetics and Abc-based Analysesmentioning

confidence: 99%

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism

et al. 2014

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The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management. The Atlantic Forest of Brazil, one of the world's richest biodiversity hot spots, is severely damaged by human activities. To formulate an efficient conservation policy, a good understanding of spatial and temporal biodiversity patterns and their underlying evolutionary mechanisms is required. With this aim, we performed a comprehensive phylogeographic study using a low-dispersal organism, the land planarian species Cephaloflexa bergi (Platyhelminthes, Tricladida). Analysing multi-locus DNA sequence variation under the Approximate Bayesian Computation framework, we evaluated two scenarios proposed to explain the diversity of Southern Atlantic Forest (SAF) region. We found that most sampled localities harbour high levels of genetic diversity, with lineages sharing common ancestors that predate the Pleistocene. Remarkably, we detected the molecular hallmark of the isolation-by-distance effect and little evidence of a recent colonization of SAF localities; nevertheless, some populations might result from very recent secondary contacts. We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes had a minor influence in generating present-day diversity. We also demonstrate that land planarians are an advantageous biological model for making phylogeographic and, particularly, fine-scale evolutionary inferences, and propose appropriate conservation policies.

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Neutrality tests based on the distribution of haplotypes under an infinite-site model

Cited by 183 publications

References 15 publications

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

Long-Term and Short-Term Evolutionary Impacts of Transposable Elements onDrosophila

Strong selective sweep associated with a transposon insertion inDrosophila simulans

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism

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