Effect of Breeding Structure on Population Genetic Parameters in Drosophila

Gravot, Emmanuelle; Huet, Michèle; Veuille, Michel

doi:10.1534/genetics.166.2.779

Cited by 14 publications

(13 citation statements)

References 53 publications

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“…Furthermore, the out-of-Africa expansion could not have created artifactual evidence of adaptive evolution if, as evidence suggests, non-African populations have a lower N e than do African populations (Andolfatto 2001;; Schö fl and Schlö tterer 2004). That said, the causes of the reduced diversity in non-African populations have been disputed (Hamblin and Veuille 1999;Begun and Whitley 2000;Wall et al 2002;Gravot et al 2004).…”

Section: Discussionmentioning

confidence: 99%

Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila

2006

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When polymorphism and divergence data are available for multiple loci, extended forms of the McDonald-Kreitman test can be used to estimate the average proportion of the amino acid divergence due to adaptive evolution-a statistic denoted a. But such tests are subject to many biases. Most serious is the possibility that high estimates of a reflect demographic changes rather than adaptive substitution. Testing for between-locus variation in a is one possible way of distinguishing between demography and selection. However, such tests have yielded contradictory results, and their efficacy is unclear. Estimates of a from the same model organisms have also varied widely. This study clarifies the reasons for these discrepancies, identifying several method-specific biases in widely used estimators and assessing the power of the methods. As part of this process, a new maximum-likelihood estimator is introduced. This estimator is applied to a newly compiled data set of 115 genes from Drosophila simulans, each with each orthologs from D. melanogaster and D. yakuba. In this way, it is estimated that a % 0:4 6 0:1, a value that does not vary substantially between different loci or over different periods of divergence. The implications of these results are discussed. T HE McDonald-Kreitman test (McDonald andKreitman 1991; Kreitman and Akashi 1995) is an important technique for quantifying the contribution of positive Darwinian selection to molecular evolution. The test compares levels of polymorphism within a species to measures of divergence between species and relies on the assumption that a certain class of mutations can be treated as effectively neutral, a priori. Following McDonald and Kreitman, most studies have focused on protein-coding sequences and used synonymous mutations as their assumed-neutral referent. As such, the tests compare levels of synonymous polymorphism (P s ) and divergence (D s ) with their nonsynonymous (amino acid changing) equivalents (P n and D n ). The focus of many studies has been to estimate the proportion of the nonsynonymous divergence, D n , that was due to adaptive evolution, a statistic that is denoted a.A serious problem with these tests is that levels of polymorphism are typically low in most population samples at most loci, especially if rare variants are excluded, and this means that single-locus estimates of a can be unreliable. To solve this problem, many methods of combining data from multiple loci have been introduced (Fay et al. 2001;Bustamante et al. 2002;Smith and Eyre-Walker 2002;Sawyer et al. 2003;Bierne and Eyre-Walker 2004). Such methods can be used to estimate a, the average value of a across the sampled loci. However, it is now clear that different variants of the test have given different results when applied to data from the same model organism. Consider, for example, published results using polymorphism data from Drosophila simulans. Smith and Eyre-Walker (2002) introduced a heuristic estimator of a that they applied to a data set of 35 loci. Measuring diverg...

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Section: Discussionmentioning

confidence: 99%

Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila

2006

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“…Hale & Singh, 1991;Berry & Kreitman, 1993;Gockel et al, 2001;Sezgin et al, 2004) and gene flow among populations sufficient to preclude population differentiation due to genetic drift (e.g. Kennington et al, 2003;Gravot et al, 2004). Thus, latitudinal clines observed for candidate genes and phenotypes in D. melanogaster have been interpreted as a selective response to climatic heterogeneity (e.g.…”

Section: Introductionmentioning

confidence: 99%

Maintenance of clinal variation for shell colour phenotype in the flat periwinkle Littorina obtusata

Phifer‐Rixey

Heckman

Trussell

et al. 2008

J of Evolutionary Biology

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Clines can signal spatially varying selection and therefore have long been used to investigate the role of environmental heterogeneity in maintaining genetic variation. However, clinal patterns alone are not sufficient to reject neutrality or to establish the mechanism of selection. Indirect, inferential methods can be used to address neutrality and mechanism, but fully understanding the adaptive significance of clinal variation ultimately requires a direct approach. Ecological model systems such as the rocky intertidal provide a useful context for direct experimentation and can serve as a complement to studies in more traditional genetic model systems. In this study, we use indirect and direct approaches to investigate the role of environmental heterogeneity in the maintenance of shell colour polymorphism in the flat periwinkle snail, Littorina obtusata. We document replicated clines in shell colour morph frequencies over thermal gradients at two spatial scales, contrasting with patterns at previously reported microsatellite loci. In addition, experimental results demonstrate that that shell colour has predictable effects on shell temperature and that these differences in temperature, in turn, coincide with patterns of survivorship under episodic thermal stress. Direct manipulation of shell colour revealed that shell colour, and not a correlated character, was the target of selection. Our study provides evidence that spatially varying selection via thermal regime contributes to the maintenance of shell colour phenotype variation in L. obtusata in the sampled areas of the Gulf of Maine.

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“…These studies cover: chromosomal polymorphism of inversions (there is a large number of inversions in the whole karyotype); allozyme polymorphism; lethal genes; mtDNA; nucleotide sequences of nuclear genes and microsatellites (Loukas and Krimbas 1980; Prevosti et al 1989; Ayala et al 1989; Krimbas 1992, 1993; Mestres et al 2005). However, although the genetic structure of populations is still considered a cornerstone in evolutionary biology (Kusakabe et al 2000; Gravot et al 2004; Glémin 2005), we know little on the genetic structure of natural populations of D. subobscura . In general, the theories of population genetics are based on ideal populations.…”

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The genetic structure of Balkan populations of Drosophila subobscura

2007

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Although Drosophila subobscura has been a model organism for European and American population geneticists, little information is available on the genetic structure of its natural populations. In this paper we report the estimates of some population parameters. We have used data from lethal allelism tests in four Balkan populations (Kamariste, Djerdap and Petnica in Serbia and Zanjic in Montenegro). In all populations, lethal genes were found to have a deleterious effect on heterozygotes. The N(e) values varied greatly from 370 (Petnica) to 19413 (Kamariste), depending on the habitat conditions and some environmental factors. Finally, gene flow between the Balkan populations was detected by the estimates of N(m) (from 4.68 in Petnica to 106.2 in Kamariste) and m (from 0.0041 in Djerdap to 0.0126 in Petnica). These results agree with those obtained in a previous study where the frequencies of allelism between populations were greater than predicted by independently arising lethal genes.

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Effect of Breeding Structure on Population Genetic Parameters in Drosophila

Cited by 14 publications

References 53 publications

Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila

Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila

Maintenance of clinal variation for shell colour phenotype in the flat periwinkle Littorina obtusata

The genetic structure of Balkan populations of Drosophila subobscura

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