Biology subjects

Gode, C.

Publications and source records attributed to Gode, C..

10 recordsLinked to original sources

bioRxiv2026

The structure and evolution of sex chromosomes in an androdioecious species with two mating types.

Though flowering plants are ancestrally hermaphroditic, some species have evolved sexual specialization and are now composed of individuals expressing just one of their two reproductive functions (either male or female) together with co-sexual individuals. Androdioecy, the co-existence of males with hermaphrodites, is rare across the living world, but unusually common in species of the Oleaceae plant family. The mediterranean shrub Phillyrea angustifolia has a simple mendelian XY sex-determination system for androdioecy, but the underlying molecular determinants and the evolutionary history of the X and Y chromosomes remain unknown. The ability of males to by-pass the self-incompatibility phenotype expressed in hermaphrodites is essential to explain their high frequency in natural populations, but how the loci governing sex and self-incompatibility epistatically interact also remains unknown. To address these questions, we obtained full haplotype-resolved de novo chromosomal assemblies of P. angustifolia and its sister species P. latifolia. The sex-determining region in P. angustifolia spanned a fifth of chromosome 12, and was strikingly larger and more rearranged than that in P. latifolia. The male-specific region contains two putative sex-determining genes, ANDY1 and ANDY2, a tandem encoding two flowering-related transcription factors that arose by translocation followed by duplication of an autosomal gene before the two species diverged. Strikingly, this sex-determining region also contains a recent duplicate of the pollen allergen gene Ole-e1, which shows the strongest differential expression between the two self-incompatibility groups of hermaphrodites, hence establishing a direct molecular link between sex and self-incompatibility. Overall, our results provide novel insight on sex determination and the evolution of sex chromosomes in a plant lineage where the separation between sexes is still incomplete, and offer a possible mechanistic basis for the strong epistatic interaction between the sex and self-incompatibility determinants, with direct implication for how sex-ratios are established in nature.

evolutionary biology↗

bioRxiv2026

Local genetic neighbourhoods but resilient gene flow across anthropogenic landscapes in the red campion (Silene dioica)

Background and AimsIn the plant kingdom, gene flow occurs through pollen and seed dispersal, shaping both within-population spatial genetic structure and among-population genetic differentiation. Anthropogenic land-use change can affect levels of gene flow by reducing pollinator abundance and altering pollen and seed dispersal pathways. Yet, how environmental features shape gene flow events in common herbaceous plants - a fundamental building block of many ecosystems - remains poorly understood. We address this gap by investigating how environmental context influences population genetic structure at regional and local scales in the red campion (Silene dioica). MethodsBy sampling 1,005 individuals from 29 populations across habitats ranging from semi-natural to strongly human-altered, we assessed whether population size and landscape composition influenced within-population genetic diversity and population genetic differentiation. At the local scale, we examined whether landscape composition affected fine-scale spatial genetic structure and pollen dispersal distances in a subset of six populations representing the two extremes of an anthropogenic gradient. Key ResultsNo effect of either demographic or landscape factors was found on levels of genetic diversity. We detected moderate levels of genetic differentiation among populations that matched an isolation-by-distance pattern, with high levels of population admixture, while landscape composition did not explain variation in population genetic differentiation. At the local scale, five of the six studied populations exhibited significant spatial genetic structuring, indicating distinct neighbourhoods at spatial scales less than 10 m. Paternity analyses based on 4,800 offspring further revealed predominantly short-distance pollen dispersal together with substantial immigration from external sources. Neither fine-scale genetic structure nor pollen dispersal distances differed between habitat types. ConclusionsAltogether, our results demonstrate a multimodal pattern of gene flow and a remarkable resilience of this common herbaceous species to anthropogenic habitat change, as substantial genetic connectivity is maintained despite insect-mediated pollen dispersal and gravity-driven seed dispersal.

plant biology↗

bioRxiv2026

Male-biased sexual selection persists across contrasting habitats in a dioecious plant

In most angiosperms, pollinators mediate access to sexual partners, making attractive floral traits key targets of sexual selection. Theory predicts stronger selection through the male function, due to greater dependence of male reproductive success on mate acquisition. However, habitat degradation may alter plant-pollinator interactions and disrupt sex-specific selection. In particular, reduced pollinator density may increase the dependency of female reproductive success on mate acquisition and strengthen selection on floral traits in both sexes. We tested this hypothesis in the dioecious species Silene dioica by measuring pollinator visitation, pollination service, and phenotypic selection on floral traits in both sexes across six populations located in either forest or anthropogenic habitats. Despite lower visitation in anthropogenic sites, pollination service was comparable between habitats with consistent selection on fertility-related traits in females. In contrast, we found stronger selection on a male trait likely promoting efficient pollen transfer in anthropogenic habitats, indicating a sex-specific response to land use change. Finally, male--but not female--reproductive success increased with the number of sexual partners in both habitats, supporting stronger sexual selection in males. More broadly, our results emphasize the need for a sex-specific perspective on floral trait evolution and demonstrate the persistence of male-biased sexual selection under environmental change.

evolutionary biology↗

bioRxiv2025

Floral display size does not affect the distribution of paternal diversity in Silene dioica

Premise of the studyPaternal diversity and its distribution within maternal plants is governed by various factors, including frequency of pollinator visits, patterns of pollinator movement and pollen carryover. Floral display size may have opposite effects on fruit and plant-level paternal diversity, because plants with large displays should receive more pollinator visits but also more sequential probes per visit. MethodsTo investigate the effect of floral display size on the distribution of paternal diversity in Silene dioica, we genotyped and assigned paternity for 1320 seeds sampled in several fruits per plant in control and manipulated females, whose flower number was artificially increased. We estimated within-fruit paternal diversity and sire profile dissimilarity among fruits and compared these metrics between control and manipulated plants. We then studied pollen carryover using controlled pollinator visits and pollen counts. Key resultsMost fruits were multiply sired, but we found no effect of flower supplementation on within-fruit paternal diversity. Sire profiles were more similar between fruits located on the same than on different females, but sire profile similarity was not higher within manipulated than within control plants. The pollen deposition curve was steep, with an increasing carryover fraction throughout the visitation sequence. ConclusionsOur results suggest that the effect of floral display size on pollinator foraging behaviour is too weak to affect paternal diversity and its distribution in S. dioica, or that other processes, such as limited pollen carryover and spatially restricted pollen dispersal, blur the effect of pollinator visit frequency and movements on sire profiles.

plant biology↗

bioRxiv2024

Contrasting patterns of spatial genetic structure in endangered southern damselfly (Coenagrion mercuriale) populations facing habitat fragmentation and urbanisation.

AimHuman-induced environmental changes result in habitat loss and fragmentation, impacting wildlife population genetic structure and evolution. Urbanised and geographically peripheral areas often represent unfavourable environments, reducing connectivity among populations and causing higher population genetic differentiation and lower intra-population genetic diversity. We examined how geographic peripherality and anthropogenic pressures affect genetic diversity and genetic differentiation in the protected southern damselfly (Coenagrion mercuriale, Odonata), which has low dispersal capabilities and specific habitat requirements and whose populations are declining. LocationWe studied two areas: one in semi-natural habitats at the periphery of the species geographic range (northern France) and the other more central to the species range, in an urbanised area surrounding the city of Strasbourg (Alsace, eastern France). MethodsWe genotyped 2743 individuals from 128 populations using eleven microsatellite loci. We analysed the spatial distribution of neutral genetic diversity (allelic richness, heterozygosity, levels of inbreeding, genetic relatedness), the extent of genetic differentiation, and population affiliations (sPCA analyses) within the two areas. We also examined fine-scale patterns of gene flow in the urbanised area of Alsace by investigating patterns of isolation by distance and estimating effective migration surfaces (EEMS method). ResultsNorthern peripheral populations showed lower levels of genetic diversity and higher levels of genetic differentiation than central Alsacian populations. Although located in anthropised habitats, geographically central Alsacian populations showed high levels of gene flow, with dispersal events mainly occurring overland and not restricted to watercourses. However, the highly urbanised city of Strasbourg negatively impacted nearby populations by reducing levels of genetic diversity and increasing population genetic differentiation. Main conclusionsThese results showed the need for management action by restoring breeding sites and creating migratory corridors for peripheral southern damselfly populations. However, our results also highlighted the resilience of southern damselfly in central range populations facing strong urbanisation pressures.

evolutionary biology↗

bioRxiv2024

Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study.

Genomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a genome reference. Here we describe a methodology for identifying and genotyping thousands of SNP loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of freshwater stream quality classified as near-threatened, with locally declining populations. We used a hybrid approach combining reduced representation sequencing and target enrichment. First, we identified putative SNP loci using ddRADseq and de novo assembly. Then, single primer enrichment technology targeted 6,000 of these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, and aberrant FIS values. We provide recommendations to address such issues. After multiple filtering, we retained 2,092 SNPs. We used them to characterise rear-edge populations of the southern damselfly in Northern France, a region where populations are sparsely distributed. Previous surveys utilising microsatellite markers allowed comparison of genetic diversity and differentiation estimates. Consistent with prior findings, genetic diversity estimates were similar across the studied populations that showed no sign of inbreeding. SNP markers exhibited greater resolution in detecting fine-scaled genetic structure, identifying two putative hybrids in adjacent populations, a feat unattainable with microsatellite loci. Altogether, this study highlighted the ongoing challenge of large-scale SNP genotyping using target sequencing techniques in non-model species to set conservation guidelines. Nonetheless, these new markers showed greater statistical power in identifying conservation units and offered the promise of greater precision in the identification of admixture events or the estimation of key population parameters such as effective population size.

evolutionary biology↗

bioRxiv2023

The diallelic self-incompatibility system in Oleaceae is controlled by a hemizygous genomic region expressing a gibberellin pathway gene

Sexual reproduction in flowering plants is commonly controlled by self-incompatibility (SI) systems that are either homomorphic (and typically governed by large numbers of distinct allelic specificities), or heteromorphic (and then typically governed by only two allelic specificities). The SI system of the Oleaceae family is a striking exception to this rule and represents an evolutionary conundrum, with the long-term maintenance of only two allelic specificities, but often in the complete absence of morphological differentiation between them. To elucidate the genomic architecture and molecular bases of this highly unusual SI system, we obtained chromosome-scale genome assemblies of Phillyrea angustifolia individuals belonging to the two SI specificities and connected them to a genetic map. Comparison of the S-locus region revealed a segregating 543-kb indel specific to one of the two specificities, suggesting a hemizygous genetic architecture. Only one of the predicted genes in this indel is conserved with the olive tree Olea europaea, where we also confirmed the existence of a segregating hemizygous indel. We demonstrated full association between presence/absence of this gene and the SI groups phenotypically assessed across six distantly related Oleaceae species. This gene is predicted to be involved in catabolism of the Gibberellic Acid (GA) hormone, and experimental manipulation of GA levels in developing buds modified the male and female SI responses in an S-allele-specific manner. Thus, our results provide a unique example of a reproductive system where a single conserved gibberellin-related gene in a 500-700kb hemizygous indel underlies the long-term maintenance of two groups of reproductive compatibility.

evolutionary biology↗

bioRxiv2021

Genetic mapping of sex and self-incompatibility determinants in the androdioecious plant Phillyrea angustifolia

AO_SCPLOWBSTRACTC_SCPLOWThe diversity of mating and sexual systems in angiosperms is spectacular, but the factors driving their evolution remain poorly understood. In plants of the Oleaceae family, an unusual self-incompatibility (SI) system has been discovered recently, whereby only two distinct homomorphic SI specificities segregate stably. To understand the role of this peculiar SI system in preventing or promoting the diversity of sexual phenotypes observed across the family, an essential first step is to characterize the genetic architecture of these two traits. Here, we developed a high-density genetic map of the androdioecious shrub P. angustifolia based on a F1 cross between a hermaphrodite and a male parent with distinct SI genotypes. Using a double restriction-site associated digestion (ddRAD) sequencing approach, we obtained reliable genotypes for 196 offspring and their two parents at 10,388 markers. The resulting map comprises 23 linkage groups totaling 1,855.13 cM on the sex-averaged map. We found strong signals of association for the sex and SI phenotypes, that were each associated with a unique set of markers on linkage group 12 and 18 respectively, demonstrating inheritance of these traits as single, independent, mendelian factors. The P. angustifolia linkage map shows robust synteny to the olive tree genome overall. Two of the six markers strictly associated with SI in P. angustifolia have strong similarity with a recently identified 741kb chromosomal region fully linked to the SI phenotype on chromosome 18 of the olive tree genome, providing strong cross-validation support. The SI locus stands out as being markedly rearranged, while the sex locus has remained relatively more collinear between the two species. This P. angustifolia linkage map will be a useful resource to investigate the various ways by which the sex and SI determination systems have co-evolved in the broader phylogenetic context of the Oleaceae family.

evolutionary biology↗

bioRxiv2020

Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system in Ligustrum vulgare (Oleaceae)

The breakdown of self-incompatibility (SI) in angiosperms is one of the most commonly observed evolutionary transitions. While multiple examples of SI breakdown have been documented in natural populations, there is strikingly little evidence of stable within-population polymorphism with both inbreeding (self-compatible) and outcrossing (self-incompatible) individuals. This absence of mating system polymorphism corroborates theoretical expectations that predict that in/outbreeding polymorphism is possible only under very restricted conditions. However, theory also predicts that a diallelic sporophytic SI system facilitates the maintenance of such polymorphism. We tested this prediction by studying the mating system of Ligustrum vulgare L., an entomophilous hermaphroditic species of the Oleaceae family. Using stigma tests with controlled pollination and paternity assignment of open-pollinated progenies, we confirmed the existence of two self-incompatibility groups in this species. We also demonstrated the existence of self-compatible individuals in different populations of Western Europe arising from a mutation affecting the expression of the pollen component of SI. We then estimated the selfing rate in a garden experiment. Our results finally show that the observed low frequency of self-compatible individuals in natural populations is compatible with theoretical predictions only if inbreeding depression is very high.

evolutionary biology↗

bioRxiv2020

Congruent population genetic structures and divergence histories in anther-smut fungi and their host plants Silene italica and the S. nutans species complex

The study of population genetic structure congruence between hosts and pathogens gives important insights into their shared phylogeographic and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (Microbotryum genus) and of their host plants, the Silene nutans species complex, and the morphologically and genetically close S. italica, which can be found in sympatry. Phylogeographic population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic SNPs. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with the one previously inferred for the host plant and likely occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of host-pathogen individual pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies are still scarce.

evolutionary biology↗