86 research outputs found
Evolution under strong balancing selection: how many codons determine specificity at the female self-incompatibility gene SRK in Brassicaceae?
<p>Abstract</p> <p>Background</p> <p>Molecular lock-and-key systems are common among reproductive proteins, yet their evolution remains a major puzzle in evolutionary biology. In the Brassicaceae, the genes encoding self-incompatibility have been identified, but technical challenges currently prevent detailed analyses of the molecular interaction between the male and female components. In the present study, we investigate sequence polymorphism in the female specificity determinant <it>SRK </it>of <it>Arabidopsis halleri </it>from throughout Europe. Using a comparative approach based on published <it>SRK </it>sequences in <it>A. lyrata </it>and Brassica, we track the signature of frequency-dependent selection acting on these genes at the codon level. Using simulations, we evaluate power and accuracy of our approach and estimate the proportion of codon sites involved in the molecular interaction.</p> <p>Results</p> <p>We identified several members of the S-gene family, together with 22 putative S-haplotypes. Linkage to the S-locus and the presence of a kinase domain were formally demonstrated for four and six of these haplotypes, respectively, and sequence polymorphism was extremely high. Twenty-five codons showed signs of positive selection in at least one species, and clustered significantly (but not exclusively) within hypervariable regions. We checked that this clustering was not an artifact due to variation in evolution rate at synonymous sites. Simulations revealed that the analysis was highly accurate, thus providing a reliable set of candidates for future functional analyses, but with an overall power not higher than 60 %. Assuming similar power, we infer from our results that about 23% of all codons in the S-domain may actually be involved in recognition. Interestingly, while simulations demonstrated that this comparison remained reliable even at very high levels of divergence, codons identified in Brassica had higher posterior rates of non-synonymous to synonymous substitutions than codons identified in <it>A. halleri or A. lyrata</it>, possibly suggesting more intense selection in Brassica.</p> <p>Conclusion</p> <p>The signature of balancing selection can be identified reliably at the codon level even in cases of very high sequence divergence, provided that a sufficiently large set of sequences are analyzed. Altogether, our results indicate that a large proportion of codons may be involved in recognition and confirm the particular importance of hypervariable regions. The more intense signature of positive selection detected in Brassica suggests that allelic diversification in this genus was very recent, possibly following a recent demographic bottleneck.</p
Dynamique de l'organisation géographique de la diversité génétique chez l'omble de fontaine Salvelinus fontinalis Mitchill : diversité des habitats et des histoires de vie
Bien que difficiles à identifier, bien que variables, les contraintes du paysage déterminent les possibilités de coalescence entre allèles. La structure de la diversité devrait donc à terme refléter la structure du paysage. Comment alors expliquer que dans certains systèmes, la concordance puisse être si faible ? D’une part, les espèces ont une histoire, souvent liée à celle de leur habitat. D’autre part, les espèces ne sont pas idéales, et leurs paramètres démographiques peuvent varier dans le temps et dans l’espace. Ainsi, les taux de migration peuvent varier d’un point à l’autre de l’aire de répartition sous l’effet des forces qui déterminent l’évolution des forces de dispersion. L’omble de fontaine en milieu côtier se prête particulièrement bien à l’étude empirique des écarts simples aux modèles de génétique des populations, parce que les contraintes de l’habitat sont généralement aisémement identifiables, que l’histoire du nord-est de l’Amérique du Nord est connue, et que la dynamique de la forme anadrome, la forme de dispersion de l’espèce en milieu côtier a été abondamment décrite dans le cadre de l’étude des migrations saisonnières. La faible concordance de la structure de la diversité avec la structure d’un habitat lacustre qui contraint pourtant fortement les patrons de migration a révélé la difficulté associé à cette tâche, particulièrement aux grandes échelles spatiales. Une analyse des variations temporelles des patrons d’isolement par la distance le long d’un gradient de colonisation a ensuite révélé qu’une des causes de la faible concordance pouvait être l’évolution toujours en cours des patrons d’organisation de la diversité. De plus, la forme de dispersion de l’espèce semble avoir évolué au cours de la colonisation en fonction de l’intensité du fardeau de consanguinité, générant ainsi des variations spatiales des paramètres démographiques. La diversité génétique est donc clairement une variable dynamique dont la compréhension nécessite la prise en compte de facteurs biogéographiques. Les résultats de cette thèse mettent en évidence des variations spatiales et temporelles des contraintes de l’habitat qui compromettent l’utilisation de plusieurs méthodes d’inférence démographiques courantes. C’est pourquoi une approche strictement comparative est proposée comme alternative possible.The expected concordance between landscape structure and geographic patterns of genetic structure is due to landscape constraints over potential coalescence among alleles. In the long run, a high level of concordance may thus be expected. Why then is concordance sometimes so weak? First, species have a history, such that landscape disturbances can affect geographic patterns of diversity. Second, species are seldom “ideal”, as defined by population genetic models, such that their demographic properties can vary in space and in time. For instance, migration rates can vary within the species’ range because the form of dispersal can evolve. Brook charr populations in coastal areas is an especially useful model system to empirically investigate the consequences of simple departures from population genetic models because landscape constraints can generally be easily identified, because recent disturbances of north-eastern North America have been extensively described, and because the dynamic of anadromy, brook charr’s form of dispersal in coastal areas, has been ecologically characterized in the frame of seasonal migrations between freshwater and saltwater. Although lakes and rivers strongly constraint migration pathways, geographic patterns of diversity in lacustrine populations were only weakly correlated with landscape structure, especially at large geographic scales. Temporal variation of isolation by distance along a colonization gradient then revealed that spatial patterns of genetic diversity were still evolving toward stable equilibrium. The species’ form of dispersal was also evolving along this gradient, according to variation of the inbreeding load. Our results thus revealed some aspects of the dynamics of genetic diversity in natural populations. Understanding its evolution requires that biogeographic considerations be included into the view of genetic variation in space. Because the accuracy of demographic inference methods would be impaired by spatial and temporal variations in habitat constraints, a strictly comparative approach is proposed as an alternative in empirical population genetics studies
Recent and Ancient Signature of Balancing Selection around the S-Locus in Arabidopsis halleri and A. lyrata
Balancing selection can maintain different alleles over long evolutionary times. Beyond this direct effect on the molecular targets of selection, balancing selection is also expected to increase neutral polymorphism in linked genome regions, in inverse proportion to their genetic map distances from the selected sites. The genes controlling plant self-incompatibility are subject to one of the strongest forms of balancing selection, and they show clear signatures of balancing selection. The genome region containing those genes (the S-locus) is generally described as nonrecombining, and the physical size of the region with low recombination has recently been established in a few species. However, the size of the region showing the indirect footprints of selection due to linkage to the S-locus is only roughly known. Here, we improved estimates of this region by surveying synonymous polymorphism and estimating recombination rates at 12 flanking region loci at known physical distances from the S-locus region boundary, in two closely related self-incompatible plants Arabidopsis halleri and A. lyrata. In addition to studying more loci than previous studies and using known physical distances, we simulated an explicit demographic scenario for the divergence between the two species, to evaluate the extent of the genomic region whose diversity departs significantly from neutral expectations. At the closest flanking loci, we detected signatures of both recent and ancient indirect effects of selection on the S-locus flanking genes, finding ancestral polymorphisms shared by both species, as well as an excess of derived mutations private to either species. However, these effects are detected only in a physically small region, suggesting that recombination in the flanking regions is sufficient to quickly break up linkage disequilibrium with the S-locus. Our approach may be useful for distinguishing cases of ancient versus recently evolved balancing selection in other systems
Controlling for genetic identity of varieties, pollen contamination and stigma receptivity is essential to characterize the self-incompatibility system of Olea europaea L.
open7siBervillé et al. express concern about the existence of the diallelic self-incompatibility (DSI) system in Olea europaea, mainly because our model does not account for results from previous studies from their group that claimed to have documented asymmetry of the incompatibility response in reciprocal crosses. In this answer to their comment, we present original results based on reciprocal stigma tests that contradict conclusions from these studies. We show that, in our hands, not a single case of asymmetry was confirmed, endorsing that symmetry of incompatibility reactions seems to be the rule in Olive. We discuss three important aspects that were not taken into account in the studies cited in their comments and that can explain the discrepancy: (i) the vast uncertainty around the actual genetic identity of vernacular varieties, (ii) the risk of massive contamination associated with the pollination protocols that they used and (iii) the importance of checking for stigma receptivity in controlled crosses. These studies were thus poorly genetically controlled, and we stand by our original conclusion that Olive tree exhibits DSI.openSaumitou-Laprade, Pierre; Vernet, Philippe; Vekemans, Xavier; Castric, Vincent; Barcaccia, Gianni; Khadari, Bouchaib; Baldoni, LucianaSaumitou-Laprade, Pierre; Vernet, Philippe; Vekemans, Xavier; Castric, Vincent; Barcaccia, Gianni; Khadari, Bouchaib; Baldoni, Lucian
Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection
Recently diverged species typically have incomplete reproductive barriers, allowing introgression of genetic material from one species into the genomic background of the other. The role of natural selection in preventing or promoting introgression remains contentious. Because of genomic co-adaptation, some chromosomal fragments are expected to be selected against in the new background and resist introgression. In contrast, natural selection should favor introgression for alleles at genes evolving under multi-allelic balancing selection, such as the MHC in vertebrates, disease resistance, or self-incompatibility genes in plants. Here, we test the prediction that negative, frequency-dependent selection on alleles at the multi-allelic gene controlling pistil self-incompatibility specificity in two closely related species, Arabidopsis halleri and A. lyrata, caused introgression at this locus at a higher rate than the genomic background. Polymorphism at this gene is largely shared, and we have identified 18 pairs of S-alleles that are only slightly divergent between the two species. For these pairs of S-alleles, divergence at four-fold degenerate sites (K = 0.0193) is about four times lower than the genomic background (K = 0.0743). We demonstrate that this difference cannot be explained by differences in effective population size between the two types of loci. Rather, our data are most consistent with a five-fold increase of introgression rates for S-alleles as compared to the genomic background, making this study the first documented example of adaptive introgression facilitated by balancing selection. We suggest that this process plays an important role in the maintenance of high allelic diversity and divergence at the S-locus in flowering plant families. Because genes under balancing selection are expected to be among the last to stop introgressing, their comparison in closely related species provides a lower-bound estimate of the time since the species stopped forming fertile hybrids, thereby complementing the average portrait of divergence between species provided by genomic data
Bulk pollen sequencing reveals rapid evolution of segregation distortion in the male germline of Arabidopsis hybrids
International audienceGenes that do not segregate in heterozygotes at Mendelian ratios are a potentially important evolutionary force in natural populations. Although the impacts of segregation distortion are widely appreciated, we have little quantitative understanding about how often these loci arise and fix within lineages. Here, we develop a statistical approach for detecting segregation distorting genes from the comprehensive comparison of whole genome sequence data obtained from bulk gamete versus somatic tissues. Our approach enables estimation of map positions and confidence intervals, and quantification of effect sizes of segregation distorters. We apply our method to the pollen of two interspecific F1 hybrids of Arabidopsis lyrata and A. halleri and we identify three loci across eight chromosomes showing significant evidence of segregation distortion in both pollen samples. Based on this, we estimate that novel segregation distortion elements evolve and achieve high frequencies within lineages at a rate of approximately one per 244,000 years. Furthermore, we estimate that haploid-acting segregation distortion may contribute between 10% and 30% of reduced pollen viability in F1 individuals. Our results indicate haploid acting factors evolve rapidly and dramatically influence segregation in F1 hybrid individuals
Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes
International audienceBackground: Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results: Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion: Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion
Cosmopolitan distribution of phlD-containing dicotyledonous crop-associated biocontrol pseudomonads of worldwide origin
Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis
Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus) in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae
Does Speciation between Arabidopsis halleri and Arabidopsis lyrata Coincide with Major Changes in a Molecular Target of Adaptation?
Ever since Darwin proposed natural selection as the driving force for the origin of species, the role of adaptive processes in speciation has remained controversial. In particular, a largely unsolved issue is whether key divergent ecological adaptations are associated with speciation events or evolve secondarily within sister species after the split. The plant Arabidopsis halleri is one of the few species able to colonize soils highly enriched in zinc and cadmium. Recent advances in the molecular genetics of adaptation show that the physiology of this derived ecological trait involves copy number expansions of the AhHMA4 gene, for which orthologs are found in single copy in the closely related A. lyrata and the outgroup A. thaliana. To gain insight into the speciation process, we ask whether adaptive molecular changes at this candidate gene were contemporary with important stages of the speciation process. We first inferred the scenario and timescale of speciation by comparing patterns of variation across the genomic backgrounds of A. halleri and A. lyrata. Then, we estimated the timing of the first duplication of AhHMA4 in A. halleri. Our analysis suggests that the historical split between the two species closely coincides with major changes in this molecular target of adaptation in the A. halleri lineage. These results clearly indicate that these changes evolved in A. halleri well before industrial activities fostered the spread of Zn- and Cd-polluted areas, and suggest that adaptive processes related to heavy-metal homeostasis played a major role in the speciation process
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