High DNA Sequence Diversity in Pericentromeric Genes of the Plant <i>Arabidopsis lyrata</i>

Kawabe, Akira; Forrest, Alan; Wright, Stephen I.; Charlesworth, Deborah

doi:10.1534/genetics.107.085282

Cited by 22 publications

(18 citation statements)

References 78 publications

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“…Moreover, the lack of an effect for self-compatibility in our estimates of N e for Arabidopsis may be not surprising as selfcompatibility might evolved relatively recently in Arabidopsis (Bechsgaard et al 2006;Tang et al 2007). Furthermore, both Arabidopsis species have high sequence diversity in pericentromeric regions (Borevitz et al 2007;Kawabe et al 2008) that is not caused by varying mutation rates. Therefore this could be a major determinant of variation in N e in those species and interfere with the effects of the breeding system.…”

Section: Discussionmentioning

confidence: 85%

Quantifying the Variation in the Effective Population Size Within a Genome

2011

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The effective population size (N e ) is one of the most fundamental parameters in population genetics. It is thought to vary across the genome as a consequence of differences in the rate of recombination and the density of selected sites due to the processes of genetic hitchhiking and background selection. Although it is known that there is intragenomic variation in the effective population size in some species, it is not known whether this is widespread or how much variation in the effective population size there is. Here, we test whether the effective population size varies across the genome, between protein-coding genes, in 10 eukaryotic species by considering whether there is significant variation in neutral diversity, taking into account differences in the mutation rate between loci by using the divergence between species. In most species we find significant evidence of variation. We investigate whether the variation in N e is correlated to recombination rate and the density of selected sites in four species, for which these data are available. We find that N e is positively correlated to recombination rate in one species, Drosophila melanogaster, and negatively correlated to a measure of the density of selected sites in two others, humans and Arabidopsis thaliana. However, much of the variation remains unexplained. We use a hierarchical Bayesian analysis to quantify the amount of variation in the effective population size and show that it is quite modest in all species-most genes have an N e that is within a few fold of all other genes. Nonetheless we show that this modest variation in N e is sufficient to cause significant differences in the efficiency of natural selection across the genome, by demonstrating that the ratio of the number of nonsynonymous to synonymous polymorphisms is significantly correlated to synonymous diversity and estimates of N e , even taking into account the obvious nonindependence between these measures.T HE effective population size (N e ) is one of the most fundamental quantities in population genetics, evolutionary biology, and molecular ecology, since it determines the effectiveness of natural selection and the level of neutral genetic diversity that a population contains (Charlesworth 2009). Populations and regions of the genome with small N e tend to have low levels of genetic diversity, to be susceptible to the accumulation of deleterious mutations through genetic drift, and to have potentially low rates of adaptive evolution (Charlesworth 2009).The effective population size is expected to vary across the genome as a consequence of genetic hitchhiking (Smith and Haigh 1974) and background selection (Charlesworth et al. 1993). The action of both positive and negative natural selection, particularly in regions of the genome with low rates of recombination, is expected to reduce the effective population size leading to lower levels of genetic diversity and reduced effectiveness of selection. Hence variation in the rate of recombination and the density of selected sit...

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Section: Discussionmentioning

confidence: 85%

Quantifying the Variation in the Effective Population Size Within a Genome

2011

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“…Roselius et al (2005) found a significant relation between diversity levels and recombination rate in wild tomato species. Nordborg et al (2005) and Kawabe et al (2008) found a negative association between gene density and diversity levels in A. thaliana and A. lyrata, respectively, as did Flowers et al (2012) in rice; given the positive correlation between recombination rate and gene density, this tends to obscure any effect of recombination rate. Positive correlations between recombination rate and putatively neutral diversity have also been reported in budding yeast (Cutter and Moses 2011) and chickens (Rao et al 2011).…”

Section: Recombination Rate and Bgsmentioning

confidence: 93%

The Effects of Deleterious Mutations on Evolution at Linked Sites

2012

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The process of evolution at a given site in the genome can be influenced by the action of selection at other sites, especially when these are closely linked to it. Such selection reduces the effective population size experienced by the site in question (the HillRobertson effect), reducing the level of variability and the efficacy of selection. In particular, deleterious variants are continually being produced by mutation and then eliminated by selection at sites throughout the genome. The resulting reduction in variability at linked neutral or nearly neutral sites can be predicted from the theory of background selection, which assumes that deleterious mutations have such large effects that their behavior in the population is effectively deterministic. More weakly selected mutations can accumulate by Muller's ratchet after a shutdown of recombination, as in an evolving Y chromosome. Many functionally significant sites are probably so weakly selected that Hill-Robertson interference undermines the effective strength of selection upon them, when recombination is rare or absent. This leads to large departures from deterministic equilibrium and smaller effects on linked neutral sites than under background selection or Muller's ratchet. Evidence is discussed that is consistent with the action of these processes in shaping genome-wide patterns of variation and evolution. MUTATIONS that increase the fitness of their carriers are, of course, the basis of adaptive evolution. For this reason, the literature on evolutionary genetics is full of studies that document "positive" selection on genetic variants in natural populations-with the advent of data on the resequencing of numerous whole genomes from the same species, we can expect a tidal wave of such examples. But, as was pointed out long ago by geneticists such as TimofeeffRessovsky (1940) and Muller (1949Muller ( , 1950, most mutations that affect the phenotype must be deleterious, because biological machinery has been subject to billions of years of selection to improve its performance. Because the nucleotide sites at which deleterious mutations can arise are numerous and distributed throughout the genome, the constant mutational production of deleterious variants and their elimination by "purifying" selection have major effects on the mean fitness of a population, its level of inbreeding depression, and its genetic variability with respect to fitness components.These properties of populations have important consequences for the evolution of such fundamental features of organisms as sex and genetic recombination, diploidy vs. haploidy, outbreeding vs. inbreeding, mate choice, and aging. Jim Crow, a great admirer of Muller (Crow 2005), has devoted much of his career both to improving our theoretical understanding of the population consequences of deleterious mutations and to documenting their rates of occurrence and their effects on fitness, summed up in several masterly reviews (Crow 1970(Crow , 1993(Crow , 2000Simmons and Crow 1977;Crow and Simmons 1983). T...

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“…In many taxa, there is a positive correlation between intrapopulation diversity and genomically local recombination rates (3). In A. thaliana (16,17) and the outbred A. lyrata (31), there is, unusually, high sequence diversity near centromeres. This has been considered contrary to classical theory as centromeres were assumed to have low CO rates, and thus prone to weak HillRobertson interference reducing diversity (31).…”

Section: Pericentromeric Recombination May Explain Prior Unusual Obsementioning

confidence: 99%

Great majority of recombination events in Arabidopsis are gene conversion events

Yang

Yuan

Wang

et al. 2012

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

105

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The evolutionary importance of meiosis may not solely be associated with allelic shuffling caused by crossing-over but also have to do with its more immediate effects such as gene conversion. Although estimates of the crossing-over rate are often well resolved, the gene conversion rate is much less clear. In Arabidopsis, for example, nextgeneration sequencing approaches suggest that the two rates are about the same, which contrasts with indirect measures, these suggesting an excess of gene conversion. Here, we provide analysis of this problem by sequencing 40 F 2 Arabidopsis plants and their parents. Small gene conversion tracts, with biased gene conversion content, represent over 90% (probably nearer 99%) of all recombination events. The rate of alteration of protein sequence caused by gene conversion is over 600 times that caused by mutation. Finally, our analysis reveals recombination hot spots and unexpectedly high recombination rates near centromeres. This may be responsible for the previously unexplained pattern of high genetic diversity near Arabidopsis centromeres.W hen considering the population genetic impact of recombination, classical theories predominantly concentrate on the impact of allelic shuffling, mediated by crossing-over, and the effect this has on linkage disequilibrium and, in turn, the effect the fate of one allele has on its genomic neighbors (1). However, when programmed double-strand breaks (DSBs) are introduced into chromosomes to initiate meiotic recombination, both crossover (CO) and noncrossover (non-CO) recombination events can occur.

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High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

Cited by 22 publications

References 78 publications

Quantifying the Variation in the Effective Population Size Within a Genome

Quantifying the Variation in the Effective Population Size Within a Genome

The Effects of Deleterious Mutations on Evolution at Linked Sites

Great majority of recombination events in Arabidopsis are gene conversion events

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