Biology subjects

Glemin, S.

Publications and source records attributed to Glemin, S..

33 records · Page 2Linked to original sources

bioRxiv2020

Phenotypic plasticity, population structure and adaptation in a young weed species with a worldwide distribution

The colonization success of a species depends on phenotypic plasticity, adaptive potential and population structure. Assessing their relative contributions during a colonization process is challenging, and a large-scale experiment had yet to be done. In this study, we attempted to tease apart their effects on the fitness of one of the most common plant on Earth, the shepherds purse (Capsella bursa-pastoris), a self-fertilizing and allopolyploid weed, with a worldwide distribution. The overarching goal is to eventually understand how the shepherds purse extensive distribution range was established so rapidly. To do so, we carried out three common gardens, located in Europe, Asia and North America, and measured several life-history traits on field-collected accessions belonging to three distinct genetic clusters (Middle East, Europe, and Asia). Our experiment showed that (i) the success of C. bursa-pastoris is mainly due to its high degree of phenotypic plasticity; and (ii), genetic cluster effect reflected a classic pattern observed in core vs marginal populations, with the Middle Eastern cluster (putative core population) outperforming the European and Asian clusters. This study therefore revealed, in a model species, different relative contributions of plasticity and adaptation to fitness, depending on the population and the time since colonization occurred.

evolutionary biology↗

bioRxiv2020

The selfing syndrome overshadows other differences when comparing fitness across Capsella species

Self-fertilization has recurrently evolved from outcrossing. Self-fertilization provides an advantage in the short-term as individuals do not require a mate to reproduce, but self-fertilization is also associated with both decreased genetic diversity and accumulation of weakly deleterious mutations, which could, however, be alleviated in polyploid selfers. If pollinators are not limited, individual fitness is thus expected to be higher in outcrossers than in selfers. We measured several life history traits in four Capsella species under two different treatments (disturbed and undisturbed) to assess the effects of mating system and ploidy level on reproductive, vegetative and phenological traits. The experiment was carried out outdoor in Northwest Greece, within the range of the obligate outcrossing species, C. grandiflora, so it could be naturally pollinated and its fitness directly compared to that of its self-fertilizing relatives. Disturbance of the environment did not affect the phenotype in any of the four species. However, for most traits the obligate outcrossing species performed better than all selfing ones. In contrast, polyploidy did not seem to confer an advantage in terms of survival or reproduction compared to diploidy. Finally, plants from Asia and northern Europe had lower performances than accessions from southern Europe and the Middle-East.

evolutionary biology↗

bioRxiv2020

The road to sorghum domestication: evidence from nucleotide diversity and gene expression patterns

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and 9 wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a genetic bottleneck in the domestication history of sorghum, although several genes showed also patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyses revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totalizing 2449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that domestication and improvement do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome during the domestication event and the improvement process. Overall, these analyses pave the way towards the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.

evolutionary biology↗

bioRxiv2019

Evolution of barrier loci at an intermediate stage of speciation with gene flow

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of differentiation; however, the underlying mechanisms are not well understood. We used an integrated approach to investigate evolutionary processes governing genetic differentiation between the hybridizing campions (Silene dioica (L.) Clairv. and S. latifolia Poiret). Demographic modeling indicated that the two species diverged with continuous gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that 5% of the loci evolved without gene flow. Differentiation (FST) and sequence divergence (dXY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection and differentiation was significantly elevated around previously identified QTLs associated with assortative mating. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated suggesting that the interplay of background selection and conserved genomic features is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection drove the evolution of barrier loci played and the genomic landscape of differentiation between the two species, consistent with predictions for speciation in the face of gene flow.

evolutionary biology↗

bioRxiv2019

From drift to draft: How much do beneficial mutations actually contribute to predictions of Ohta’s slightly deleterious model of molecular evolution?

Since its inception in 1973 the slightly deleterious model of molecular evolution, aka the Nearly Neutral Theory of molecular evolution, remains a central model to explain the main patterns of DNA polymorphism in natural populations. This is not to say that the quantitative fit to data is perfect. In a recent study CO_SCPLOWASTELLANOC_SCPLOW et al. (2018) used polymorphism data from D. melanogaster to test whether, as predicted by the Nearly Neutral Theory, the proportion of effectively neutral mutations depends on the effective population size (Ne). They showed that a nearly neutral model simply scaling with Ne variation across the genome could not explain alone the data but that consideration of linked positive selection improves the fit between observations and predictions. In the present article we extended their work in two main directions. First, we confirmed the observed pattern on a set of 59 species, including high quality genomic data from 11 animal and plant species with different mating systems and effective population sizes, hence a priori different levels of linked selection. Second, for the 11 species with high quality genomic data we also estimated the full Distribution of Fitness Effects (DFE) of mutations, and not solely the DFE of deleterious mutations. Both Ne and beneficial mutations contributed to the relationship between the proportion of effectively neutral mutations and local Ne across the genome. In conclusion, the predictions of the slightly deleterious model of molecular evolution hold well for species with small Ne. But for species with large Ne the fit is improved by incorporating linked positive selection to the model.

evolutionary biology↗

bioRxiv2019

Ecological strategy and genetic load in the shepherd's purse (Capsella bursa-pastoris) from the core and the limit of its natural range.

Species range expansion is a complex process whose outcome depends on the interplay of demographic, environmental and genetic factors. In plants, self-fertilizing species that do not require a mate to reproduce usually show higher invasive ability. However, this comes at a cost as both selfing and bottlenecks occurring during colonization lead to an increase in deleterious mutations accumulation (genetic load). Although they are theoretically clearly spelled out, the relationships between genomic and phenotypic characteristics of expanding populations have hitherto rarely been characterized. In the present study we analyzed how different accessions of the shepherds purse, C. bursa-pastoris, coming from the front of colonization or from the core of the natural range performed under increasing density of competitors. We first showed that, as expected, accessions from the front of colonization performed the worst for most life history traits compared with accessions from core populations. Second, competitor density had a negative impact on both vegetative growth and reproductive output in term of fruits production for all accessions. However, somewhat unexpectedly given their higher genetic load and their lower absolute performance, accessions from the front of colonization were less affected by competition than accessions from the core of the species range. This could be due to phenotypic tradeoffs and a shift in phenology that allow the accessions from the front of colonization to avoid competition. These results are discussed in terms of ecological strategies of expanding populations.

evolutionary biology↗

bioRxiv2018

Estimating the fitness effect of deleterious mutations during the two phases of the life cycle: a new method applied to the root-rot fungus Heterobasidion parviporum

Many eukaryote species including taxa such as fungi or algae have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance, a measure that accounts for these two effects, should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum, a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.\n\nArticle summary for Issue HighlightsMany eukaryote species including taxa such as fungi or algae spend a large portion of their life cycle as haploids and as diploids. Clergeot, Rode et al. derive a statistical model to test whether deleterious mutations have stronger effects in homozygous diploids than in haploids, whether they are partially recessive in heterozygous diploids and whether diploids have higher fitness than haploids on average. As an illustration, they use their model to study growth rate and the ability to degrade wood in the root-rot fungus Heterobasidion parviporum. Their model should help gaining further insights into the evolution of haploid-diploid life cycles.

evolutionary biology↗

bioRxiv2018

Towards the new normal: Transcriptomic and genomic changes in the two subgenomes of a 100,000 years old allopolyploid, Capsella bursa-pastoris

Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to become more similar and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allote-traploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora. Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers suggests that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load.

evolutionary biology↗

bioRxiv2018

Dioecy in plants: an evolutionary dead end? Insights from a population genomics study in the Silene genus

About 15,000 angiosperm species ([~]6%) have separate sexes, a phenomenon known as dioecy. Early work reported a lower species richness in dioecious compared to non-dioecious sister clades, which was taken to suggest that dioecy might be an evolutionary dead end. More recently, phylogenetic analyses using different methodologies have challenged this conclusion. Here, we used a population genomics approach to look for evidence of evolutionary handicaps of dioecy in the Silene genus at the molecular level. We obtained RNA-seq data of individuals from several populations in 13 closely related species with different breeding systems: seven dioecious, three hermaphroditic and three gynodioecious species. We show that dioecy is associated with increased genetic diversity and a higher selection efficacy both against deleterious and for beneficial mutations while controlling for differences in population size. We conclude that, in the Silene genus, dioecious species bear no sign of mutational burden or upcoming extinction. On the contrary, dioecious species harbor a higher potential for adaptation than their non-dioecious relatives. Our results do not support the evolutionary dead end hypothesis and re-open the question why dioecy is rare in angiosperms.\n\nSignificance statementDioecy (=separate sexes) is much rarer in flowering plants compared to animals and other organisms. The \"dead-end hypothesis\" states that dioecious plant populations might experience evolutionary handicaps such as low seed dispersal (as only 50% of the individuals, the females, contribute), which might cause high genetic drift, low adaptation and ultimately extinction. Here we tested this hypothesis by focusing on the genus Silene and by comparing the population genetics of 13 dioecious and non-dioecious species. We found that dioecious Silene species exhibit lower genetic drift and more adaptation compared to their non-dioecious relatives. Our results thus reject the dead-end hypothesis and re-open the question of why dioecy is rare in flowering plants.

evolutionary biology↗

bioRxiv2018

Local adaptation and maladaptation during the worldwide range expansion of a self-fertilizing plant

Species having experienced rapid range expansion represent unique opportunities to evaluate the dynamics of adaptation during colonization of new environments. We investigated the consequences of range expansion on local adaptation of a successful worldwide colonizer, the shepherds purse Capsella bursa-pastoris. This species is an annual weed that originated recently in Eurasia and has now broadly colonized both temperate and subtropical areas. We assessed the performance, genetic diversity, and phenology of field-collected accessions belonging to three distinct genetic clusters of decreasing age (Middle East, Europe and Asia) in three common gardens in Europe, Asia and North America. To understand the genetic basis of local adaptation in this species, we also tested for correlation between SNP allele frequencies and environmental factors in Europe and Asia. Overall, we showed that patterns of local adaptation depended on population history: some older populations were weakly adapted to local conditions while those closer to the front of the colonization wave, far from the origin of the species, were maladapted whatever the common gardens. Altogether, our results have important consequences for the understanding of the evolution and adaptation of self-fertilizing plant during range expansion.

evolutionary biology↗

bioRxiv2018

Pervasive hybridizations in the history of wheat relatives

Bread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor of Aegilops mutica (T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.

evolutionary biology↗

bioRxiv2017

Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)

Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species and how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cg) and the other one from the selfing and genetically depauperate Capsella orientalis (Co). For each subgenome, we assessed its relationship with the diploid relatives, temporal change of effective population size Ne, signatures of positive and negative selection, and gene expression patterns. Introgression between C. bursa-pastoris and its diploid relatives was widespread and the two subgenomes were impacted differentially depending on geographic region. In all three regions, Ne of the two subgenomes decreased gradually and the Co subgenome accumulated more deleterious changes than Cg. Selective sweeps were more common on the Cg subgenome in Europe and the Middle East, and on the Co subgenome in Asia. In contrast, differences in expression were limited with the Cg subgenome slightly more expressed than Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy and were differentially affected by introgression and selection.

evolutionary biology↗

bioRxiv2017

Competitive ability of a tetraploid selfing species (Capsella bursa-pastoris) across its expansion range and comparison with its sister species

Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy in Grimes Competitive-Stress-tolerant-Ruderal (CSR) classification of ecological strategies. Consequently, selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. Although suggested by meta-analyses, these predictions have not been directly tested yet. We compared the competitive ability of four Capsella species differing by their mating system and ploidy level. We found that the two diploid selfing species (C. rubella and C. orientalis) were more sensitive to competition than the diploid outcrosser (C. grandiflora), and that the tetraploid selfer (C. bursa-pastoris) was intermediate. Within C. bursa-pastoris, we also found that sensitivity to competition increased in parallel to range expansion. These results highlight the possible roles of ecological context and ploidy in the evolutionary trajectories of selfing species.

evolutionary biology↗

bioRxiv2017

Codon usage bias in animals: disentangling the effects of natural selection, effective population size and GC-biased gene conversion

Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. Codon usage bias in animals has only been studied in a handful of model organisms so far, and can be affected by confounding, non-adaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data we analysed the relationship between codon usage, gene expression, allele frequency distribution and recombination rate in 31 non-model species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analysing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons are generally preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT{leftrightarrow}GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

evolutionary biology↗

bioRxiv2016

Evolutionary forces affecting synonymous variations in plant genomes

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic datasets based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

evolutionary biology↗