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Title: Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora}
Article:
Abstract:
The extent that both positive and negative selection vary across different portions of plant genomes remains poorly understood. Here, we sequence whole genomes of 13 Capsella grandiflora individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that selection is strong in coding regions, but weak in most noncoding regions, with the exception of 5′ and 3′ untranslated regions( UTRs). However, estimates of selection on noncoding regions conserved across the Brassicaceae family show strong signals of selection. Additionally, we see reductions in neutral diversity around functional substitutions in both coding and conserved noncoding regions, indicating recent selective sweeps at these sites. Finally, using expression data from leaf tissue we show that genes that are more highly expressed experience stronger negative selection but comparable levels of positive selection to lowly expressed genes. Overall, we observe widespread positive and negative selection in coding and regulatory regions, but our results also suggest that both positive and negative selection on plant noncoding sequence are considerably rarer than in animal genomes.
Introduction:
Determining the amount of positive and negative selection and how it varies across the genome has wide-ranging implications for understanding genome function and the maintenance of genetic variation[1]. Current evidence suggests that both positive and negative selection are common in coding and some noncoding sequences in several model systems[2]–[8]. However our understanding of genome-wide selection in plants remains relatively limited[6], particularly in noncoding regions. One key question concerns the extent to which both positive and negative selection act in noncoding regions of the genome compared with coding regions[2],[5]–[8]. For example, it has been suggested that the majority of adaptive evolution may occur in noncoding regulatory regions, where new mutations may have fewer deleterious pleiotropic effects[9],[10] but see[11]. Halligan and colleagues[8] showed that there have been many more adaptive substitutions in noncoding DNA than in coding regions in house mice, although adaptive substitutions in coding regions may experience stronger positive selection. Moreover, studies in Drosophila species and vertebrates have found that, although noncoding regions as a whole are generally less conserved than coding regions, there is more functional noncoding sequence than constrained coding sequence by a considerable margin[2],[12]. Comparing these results to noncoding selection across plant genomes is of particular interest because it has been hypothesized that in plants, regulatory evolution may occur more often through gene duplication than cis-regulatory change[13], possibly leading to lower levels of functional constraint and positive selection on plant noncoding DNA. Consistent with this prediction, Haudry and colleagues[14] recently compared the genomes of nine Brassicaceae species, and showed that approximately one quarter of the conserved sites in the Arabidopsis thaliana genome were in noncoding regions, a much smaller fraction than found to date in studies of vertebrates and Drosophila. However, the strength of selection on these noncoding sites, the extent of species-specific selection in noncoding regions, and the extent of positive selection in noncoding regions compared with coding regions have not been quantified. While the strength of selection is expected to vary between coding and noncoding sequence, it also varies between genes. Gene expression level is one of the major determinants of rates of nonsynonymous evolution in coding regions in many species[15]–[17], including plants[18]–[21]. Variation in the strength of selection on genes could reflect differences in the relative importance of gene products for organism fitness, or it may simply relate to inherent properties of expression[22]. For example, deleterious mutations that cause misfolding or mis-interaction have more opportunity to interfere with cellular function when they occur in high expression genes[23]–[25]. Regardless of the underlying selective mechanisms, the negative correlation between expression level and nonsynonymous divergence could reflect relaxed purifying selection in lowly expressed genes, increased positive selection in lowly expressed genes, or both. Here, we use population genomics to quantify the strength of both positive and negative selection inside and outside of coding regions and within highly and lowly expressed genes in a species-wide sample of 13 outbred Capsella grandiflora individuals. C. grandiflora is an obligately outcrossing member of the Brassicaceae family with a large effective population size( Ne∼600, 000) and relatively low population structure[26],[27]. We estimate the strength of negative selection by fitting polymorphism data to a model of the distribution of negative fitness effects of mutations. We then quantify the contribution of positive selection to divergence in C. grandiflora using two complementary approaches: an extension of the McDonald-Kreitman test[28] and an analysis of neutral variation linked to lineage-specific fixed substitutions[29]. Our results demonstrate that both positive and negative selection are pervasive in coding regions, 5′ and 3′ untranslated regions( UTRs), and constrained noncoding regions of the C. grandiflora genome, but also that a large proportion of noncoding DNA may evolve neutrally. In addition, we find stronger negative selection in high expression genes compared to low expression genes, suggesting that differences in negative selection drive differences in rates of molecular evolution.
Discussion:
In this study, we took advantage of the two detectable signatures expected to remain after recurrent classic selective sweeps from new mutations: 1) an excess of replacement substitutions relative to expectations based on polymorphism, and 2) reduced neutral diversity near fixed differences. Our findings strongly suggest that positive selection has been common in coding regions, UTRs and conserved noncoding regions in C. grandiflora and that classic selective sweeps contribute significantly to divergence in these regions. To our knowledge, this is the first time that the signature of recurrent selective sweeps has been observed in a non-Drosophila species, despite being tested in other species[8],[47]. Our ability to detect the signature of recurrent sweeps may be because C. grandiflora has relatively low linkage disequilibrium, increasing power. However, many positively selected alleles may not follow the trajectory of a classic selective sweep. Soft sweeps— adaptation from an allele previously maintained in the population by mutation-selection-drift balance or the simultaneous fixation of multiple independently derived mutations at the same allele— may still increase the replacement to silent divergence ratio, but are expected to have a smaller effect on linked neutral diversity[48]–[50]. We expect that soft sweeps will also be common in C. grandiflora because of its large Ne[50],[51]. In addition, adaptation in genes that contribute to polygenic traits is often expected to occur without fixation of new mutations[52], and this will be missed by both of our tests for positive selection. These considerations suggest that both measures of positive selection are conservative and may miss many instances of positive selection acting in the genome. Our conclusions about the prevalence of selective sweeps in C. grandiflora may seem to conflict with our observation that diversity and Tajima's D are slightly higher at 4-fold degenerate sites than intergenic sites, since frequent sweeps in coding regions should reduce diversity more strongly in sites near and within genes. There are two likely contributors to this discrepancy. First, recurrent sweeps may in fact reduce average diversity in 4-fold degenerate sites and, by using these sites to set neutral expectations, we are underestimating the strength of purifying selection in intergenic regions. Second, because recombination rates are relatively high, and intergenic regions near coding regions relatively small in Capsella, the average impact of linked selection may be similar at 4-fold degenerate sites and intergenic sequences. Highly expressed genes diverge less than genes with low expression in many species[15]–[17],[19],[24],[53]–[55]. This pattern could be due to stronger positive selection in low expression genes or stronger negative selection in high expression genes, or both. Our results suggest that variation in divergence rates between high and low expression genes is largely due to increased negative selection in high expression genes compared to low expression genes. This result is consistent with previous studies that have suggested that new nonsynonymous mutations that cause protein mis-folding or mis-interaction will have stronger deleterious effects in high expression genes than low expression genes and that new mutations that cause mRNA mis-folding are under stronger negative selection in high expression genes than low expression genes[23]–[25]. In addition, our results agree with a similar study in Medicago truncatula that found stronger purifying selection in genes that were expressed than in genes that were not expressed[20].
Selection affects patterns of genomic variation , but it is unclear how much the effects of selection vary across plant genomes , particularly in noncoding regions . To determine the strength and extent of selective signatures across the genome , we sequenced and analyzed genomes from 13 Capsella grandiflora individuals . Because C . grandiflora has experienced a large , stable effective population size , we expect that selection signatures will not be overly distorted by demographic effects . Our analysis shows that positive and negative selection acting on new mutations have broadly shaped patterns of genomic diversity in coding regions but not in most noncoding regions . However , when we focus only on noncoding regions that show evidence of constraint across species , we see evidence for strong positive and negative selection . In addition , we find that genes with high expression experience stronger negative selection than genes with low expression , but the extent of positive selection appears to be equivalent across expression categories .