Biology subjects

Le veve, A.

Publications and source records attributed to Le veve, A..

3 recordsLinked to original sources

bioRxiv2024

The effect of parental conflict in imprinting genes in A. lyrata.

Genomic imprinting is a form of gene regulation leading to the unequal expression of maternal and paternal alleles. The main hypothesis invoked to explain the evolution of imprinted genes is the kinship theory, which posits a conflict between parental genomes over resource allocation in progeny. According to this theory, such conflicts select for parent-of-origin-dependent expression of genes involved in resource allocation. How such conflicts translate into signatures of selection at coding or regulatory sequences remains model-dependent and is not explicitly predicted by the kinship theory. However, most studies addressing selection in imprinted genes in flowering plants, particularly those based on population-genomic or phylogenetic analyses, have focused on self-fertilizing species, where conflicts over resource allocation are predicted to be weak. Consequently, the impact of the kinship theory on the evolution of imprinted genes remains largely unexplored in systems where parental conflict is expected to be strong. Furthermore, potential coevolution between antagonistically acting imprinted genes, as proposed in extensions of parental conflict models, has not yet been tested empirically. Using combined phylogenetic and population genomic approaches, we investigated signatures of selection on imprinted genes across the Brassicaceae family and in autogamous and allogamous populations of Arabidopsis lyrata, and searched for evidence of coevolution among imprinted genes. We found that endosperm-expressed genes exhibited signals of balancing selection across Brassicaceae and within allogamous populations, consistent with models of unresolved intralocus conflict. These population-level signals varied with the mating system, in line with expectations that parental conflict is reduced under self-fertilization. Moreover, phylogenetic analyses indicated signatures of purifying (negative) selection acting on imprinted genes. However, the population-level signatures of selection were independent of the mating system and showed limited concordance with kinship predictions, possibly due to stronger selection acting on expression than on coding sequences. Finally, we identified coevolution between imprinted genes, although not at specific sites, suggesting that interactions beyond protein sequence may contribute to this process.

evolutionary biology↗

bioRxiv2024

DNA methylation shows footprints of altitude selection in the clonal plant species Fragaria vesca

O_LIClimate change threatens plant species, potentially pushing them beyond their adaptive capacities. DNA methylation and other epigenetic modifications may enable rapid adaptation to environmental changes by generating locally adapted phenotypes. These phenotypic changes can be inherited across generations and may become targets of natural selection. However, direct evidence for selection on epialleles remains scarce. Addressing this gap is crucial, as population survival may heavily rely on DNA methylation, especially in clonal plants with limited genetic diversity. C_LIO_LIWe employed population genomics approaches to investigate altitude-driven selection on epigenetic sites in clonal offspring of natural woodland strawberry (Fragaria vesca) populations. These offspring were grown in a common garden and derived from seven populations spanning an altitudinal range. C_LIO_LIOur genomic, epigenomic, and transcriptomic analyses identified epialleles in clones exhibiting signs of selection related to altitude. These loci overlapped with genes involved in the O-methyltransferase activity, potentially aiding altitude adaptation through enhanced secondary metabolite production. Interestingly, these epialleles were mostly independent of genetic variation, suggesting they may have arisen stochastically or in response to environmental variation. C_LIO_LIThese findings suggest that heritable epigenetic variation could help clonal species quickly adapt to environmental challenges as those related to varying altitudes and/or temperatures. C_LI

evolutionary biology↗

bioRxiv2023

The genetic architecture of the load linked to dominant and recessive self-incompatibility alleles in Arabidopsis halleri and A. lyrata

The long-term balancing selection acting on mating-types or sex determining genes is expected to lead to the accumulation of deleterious mutations in the tightly linked chromosomal segments that are locally "sheltered" from purifying selection. However, the factors determining the extent of this accumulation are poorly understood. Here, we took advantage of variations in the intensity of balancing selection along a dominance hierarchy formed by alleles at the sporophytic self-incompatibility system of the Brassicaceae to compare the pace at which linked deleterious mutations accumulate among them. We first experimentally measured the phenotypic manifestation of the linked load at three different levels of the dominance hierarchy. We then sequenced and phased polymorphisms in the chromosomal regions linked to 126 distinct copies of S-alleles in two populations of Arabidopsis halleri and three populations of A. lyrata. We find that linkage to the S-locus locally distorts phylogenies over about 10-30kb along the chromosome. The more intense balancing selection on dominant S-alleles results in greater fixation of linked deleterious mutations, while recessive S-alleles accumulate more linked deleterious mutations that are segregating. Hence, the structure rather than the overall magnitude of the linked genetic load differs between dominant and recessive S-alleles. Our results have consequences for the long-term evolution of new S-alleles, the evolution of dominance modifiers between them, and raise the question of why the non-recombining regions of some sex and mating type chromosomes expand over evolutionary times while others, such as that the S-locus of the Brassicaceae, remain restricted to small chromosomal regions.

evolutionary biology↗