Elena Conti

Trait loss has been documented across broad phylogenetic scales and dissected genetically within species, but how the genetic basis of loss varies among lineages and over evolutionary time remains poorly understood. Heterostyly, a floral polymorphism, represents an ideal case study, as it has been lost repeatedly across angiosperms. In Primula , heterostyly is controlled by the S -locus supergene, and loss-of-function mutations in CYP ᵀ cause transitions to homostyly. We investigated the critically endangered Primula boveana , whose floral morphology is debated, in the diploid, self-compatible P. sect. Sphondylia . We quantified herkogamy dynamics during anthesis, performed controlled pollination experiments, assembled a chromosome-scale genome, compared S -locus structure and gene expression with heterostylous relatives, and reconstructed phylogenetic relationships within the section. Our results revealed that P. boveana is homostylous, with a disrupted CYPᵀ . Herkogamy declines during anthesis, resulting in early anther-stigma contact, autonomous selfing, and reproductive assurance. Thus, unlike other homostylous Primula species, these developmental changes do not represent a delayed selfing strategy. These findings link developmental changes in herkogamy with autonomous selfing and support CYPᵀ inactivation as the genetic basis of long homostyly in P. boveana . The extensive degeneration of CYPᵀ suggests that prolonged relaxed selection promotes progressive degeneration of non-functional S -genes following heterostyly loss.

Evolution reflects a balance between innovation and constraint, often repurposing existing components in new contexts. Convergent evolution exemplifies this interplay, with similar traits evolving independently in different species, yet the genomic mechanisms enabling this repeatability remain poorly understood. Here, by analyzing 10 chromosome-scale genome assemblies, including seven newly generated, we found that the S -locus supergene (a cluster of tightly linked genes controlling a floral dimorphism called distyly) arose independently multiple times within the primrose family, Darwin’s iconic system for studying distyly. In each case, the same gene was independently duplicated and co-opted. However, the resulting genomic architectures differed, ranging from hemizygous (present on one chromosome copy) to heterozygous (on both copies), challenging the prevailing view that hemizygosity is intrinsic to S -loci and suggesting alternative evolutionary routes to distyly supergene formation. By uncovering multiple mechanisms for supergene origins, our work shows how convergent evolution can produce similar phenotypes by reusing the same genetic building blocks while exploring distinct genomic configurations.

Evolution reflects a balance between innovation and constraint, often repurposing existing components in new contexts. Convergent evolution exemplifies this interplay, with similar traits evolving independently in different species, yet the genomic mechanisms enabling such repeatability remain poorly understood. Here, by analyzing ten chromosome-scale genome assemblies, including seven newly generated, we discovered that the S-locus supergene (a cluster of tightly linked genes controlling a floral dimorphism called distyly) arose independently multiple times within the primrose family, Darwin's iconic system for studying distyly. In each case, the same gene was independently duplicated and co-opted, yet the resulting genomic architectures differed, ranging from hemizygous (present on one chromosome copy) to heterozygous (on both copies). These diverse architectures shaped supergene evolution differently, with genetic degeneration occurring only in the heterozygous case. By uncovering multiple mechanisms for supergene origins, our work shows how convergent evolution can produce similar phenotypes by reusing the same genetic building blocks while exploring distinct genomic configurations.

Transitions from outcrossing to selfing and from diploidy to polyploidy often co-occur in plants, likely because the ability to produce selfed seed increases the likelihood of newly formed polyploids to become established. An ideal system to study these transitions is Primula, where the shift from diploid, outcrossing progenitors to polyploid, selfing descendants co-occurred repeatedly and the genetic basis of the mating-system shift is known. In Primula, outcrossing is enforced in distylous, typically diploid species characterized by florally heteromorphic, self-incompatible individuals, whereas selfing is enabled in homostylous, typically polyploid species, characterized by florally homomorphic populations of self-compatible plants. Distyly is controlled by the S-locus supergene. Small loss-of-function mutations in the S-locus CYPT gene, which controls style length and female self-incompatibility, are associated with loss of heterostyly in diploid, ancestrally heterostylous Primula species. However, CYPT and the S-locus have never been investigated in inter-specific shifts from distylous, diploid species to homostylous, polyploid species. By analyzing the first assembled genome of a homostylous, polyploid species (Primula grandis) in a comparative framework, we discovered two, nearly identical S-locus alleles in the same subgenome, consistent with the hypothesis that the species originated from a cross between a homostylous, diploid pollen donor and a long-styled, diploid pollen recipient. Conformant to theoretical predictions, the macroevolutionary loss of distyly coincided with considerable degeneration of CYPT, including multiple mutations and exon loss, while other S-locus genes remained largely unaffected. This study advances knowledge on the macroevolutionary dynamics of supergenes and genomes in shifts between breeding systems and ploidy levels.

The widespread loss and fragmentation of habitats have caused significant declines in biodiversity. Among plants, animal-pollinated species are particularly threatened because of the negative effects of these factors on pollinators. Heterostyly is a unique reproductive system defined by two or three floral morphs having a distinct position of anthers and style. The spatial separation of reproductive organs, accompanied by a self-incompatibility system, restricts self-pollination and favours pollinator-mediated pollen transfer between different morphs. In this review, we synthesize knowledge about the effects of loss in the area and connectivity of habitats, and related reduction in population size on heterostylous plants. We conducted a literature search to obtain an overview of studies investigating the short- and long-term consequences of the decreased area and connectivity of habitats as well as plant population size for heterostylous species. To quantify the relationship between plant population size and morph ratio bias, we applied a meta-analytical approach. First, the meta-analysis showed that reductions in population size can significantly disrupt the optimal morph ratio, leading to fewer compatible mates and lower reproductive output. Second, the literature review highlights the negative consequences of biased morph ratios for population viability and genetic diversity of heterostylous plants. Finally, heterostylous species may adapt to the loss of pollination by shifting their mating system to homostyly and selfing. This review demonstrates that habitat loss and fragmentation have various consequences for heterostylous plants, e.g. reduced population size, morph ratio bias, and disruption of pollination. With ongoing environmental changes, there are still important knowledge gaps that need to be addressed more systematically. These include the long-term impact of skewed morph frequencies on population viability, the selective forces driving variation in anther-stigma separation and intra-morph compatibility, the role of habitat loss and connectivity, and related reduction in pollinator abundance and diversity in the selection for homostyly.

Despite the evolutionary importance of supergenes, their properties in polyploids remain unexplored. Polyploid genomes are expected to undergo chromosomal rearrangements and gene losses over time, potentially affecting supergene architecture. The iconic distyly supergene ( S -locus), controlling a floral heteromorphism with two self-incompatible morphs, has been well-documented in diploids, but remains unknown in polyploids. Primula , the classic model for distyly since Darwin, is ancestrally diploid and distylous, yet polyploid, homostylous species with a single, self-compatible floral morph evolved repeatedly. The intraspecific loss of distyly is associated with small loss-of-function mutations in the S -locus CYP ^T gene controlling style length and female self-incompatibility. Over longer timescales, relaxed selection on CYP ^T should generate greater accumulation of larger mutations, including exon and gene loss. By analyzing the first assembled genome of an allotetraploid, homostylous species ( Primula grandis ) in a comparative framework, we discovered two, nearly identical S -locus alleles in the same subgenome, suggesting it originated via inter-specific hybridization between a homostylous and a distylous progenitor. Conformant to predictions from theory, the macroevolutionary loss of distyly coincided with considerable degeneration of CYP ^T , while other S -locus genes remained largely unaffected, suggesting the shift to homostyly preceded and facilitated polyploid establishment. At the whole-genome level, we found minimal subgenome dominance — as expected, given the inferred recent origin of P. grandis — and highly reduced genetic diversity, congruently with its narrow distribution and self-compatibility. This study provides the first comparison of a supergene across ploidy levels and reproductive systems, contributing new knowledge on the previously unknown fate of supergenes in polyploids. SIGNIFICANCE: This study advances knowledge on genome evolution by elucidating how supergenes (clusters of tightly linked genes) evolve across species with different sets of chromosomes and reproductive systems. By analyzing the newly assembled genome of the polyploid, self-compatible Primula grandis in a broad framework, we provide the first comparison of the distyly supergene between diploid outcrossers and polyploid self-fertilizers. We discovered one pair of identical supergene alleles in the same subgenome, rather than one pair per subgenome, revealing the species originated via a cross between a self-compatible and a self-incompatible progenitor. Conformant to theory, the gene controlling female self-incompatibility and style length ( CYP ^T ) was considerably degenerated, because of relaxed selection over time, with the rest of the supergene largely unaffected.

Genetic diversity is heterogeneously distributed among populations of the same species, due to the joint effects of multiple demographic processes, including range contractions and expansions, and mating systems shifts. Here, we ask how both processes shape genomic diversity in space and time in the classical Primula vulgaris model. This perennial herb originated in the Caucasus region and was hypothesized to have expanded westward following glacial retreat in the Quaternary. Moreover, this species is a long-standing model for mating system transitions, exemplified by shifts from heterostyly to homostyly. Leveraging a high-quality reference genome of the closely related Primula veris and whole-genome resequencing data from both heterostylous and homostylous individuals from populations encompassing a wide distribution of P. vulgaris, we reconstructed the demographic history of P. vulgaris. Results are compatible with the previously proposed hypothesis of range expansion from the Caucasus region approximately 79,000 years ago and suggest later shifts to homostyly following rather than preceding postglacial colonization of England. Furthermore, in accordance with population genetic theoretical predictions, both processes are associated with reduced genetic diversity, increased linkage disequilibrium, and reduced efficacy of purifying selection. A novel result concerns the contrasting effects of range expansion versus shift to homostyly on transposable elements, for the former, process is associated with changes in transposable element genomic content, while the latter is not. Jointly, our results elucidate how the interactions among range expansion, transitions to selfing, and Quaternary climatic oscillations shape plant evolution.

Research on supergenes, non‐recombining genomic regions housing tightly linked genes that control complex phenotypes, has recently gained prominence in genomics. Heterostyly, a floral heteromorphism promoting outcrossing in several angiosperm families, is controlled by the S‐locus supergene. The S‐locus has been studied primarily in closely related Primula species and, more recently, in other groups that independently evolved heterostyly. However, it remains unknown whether genetic architecture and composition of the S‐locus are maintained among species that share a common origin of heterostyly and subsequently diverged across larger time scales. To address this research gap, we present a chromosome‐scale genome assembly of Primula edelbergii, a species that shares the same origin of heterostyly with Primula veris (whose S‐locus has been characterized) but diverged from it 18 million years ago. Comparative genomic analyses between these two species allowed us to show, for the first time, that the S‐locus can ‘jump’ (i.e. translocate) between chromosomes maintaining its function in controlling heterostyly. Additionally, we found that four S‐locus genes were conserved but reshuffled within the supergene, seemingly without affecting their expression, thus we could not detect changes explaining the lack of self‐incompatibility in P. edelbergii. Furthermore, we confirmed that the S‐locus is not undergoing genetic degeneration. Finally, we investigated P. edelbergii evolutionary history within Ericales in terms of whole genome duplications and transposable element accumulation. In summary, our work provides a valuable resource for comparative analyses aimed at investigating the genetics of heterostyly and the pivotal role of supergenes in shaping the evolution of complex phenotypes.

Uniparental reproduction is advantageous when lack of mates limits outcrossing opportunities in plants. Baker’s law predicts an enrichment of uniparental reproduction in habitats colonized via long-distance dispersal, such as volcanic islands. To test it, we analyzed reproductive traits at multiple hierarchical levels and compared seed-set after selfing and crossing experiments in both island and mainland populations of Limonium lobatum, a widespread species that Baker assumed to be self-incompatible because it had been described as pollen-stigma dimorphic, i.e., characterized by floral morphs differing in pollen-surface morphology and stigma-papillae shape that are typically self-incompatible. We discovered new types and combinations of pollen and stigma traits hitherto unknown in the literature on pollen-stigma dimorphism and a lack of correspondence between such combinations and pollen compatibility. Contrary to previous reports, we conclude that Limonium lobatum comprises both self-compatible and self-incompatible plants characterized by both known and previously undescribed combinations of reproductive traits. Most importantly, plants with novel combinations are overrepresented on islands, selfed seed-set is higher in islands than the mainland, and insular plants with novel pollen-stigma trait-combinations disproportionally contribute to uniparental reproduction on islands. Our results thus support Baker’s law, connecting research on reproductive and island biology.

Distyly, a floral dimorphism that promotes outcrossing, is controlled by a hemizygous genomic region known as the S‐locus. Disruptions of genes within the S‐locus are responsible for the loss of distyly and the emergence of homostyly, a floral monomorphism that favors selfing. Using whole‐genome resequencing data of distylous and homostylous individuals from populations of Primula vulgaris and leveraging high‐quality reference genomes of Primula we tested, for the first time, predictions about the evolutionary consequences of transitions to selfing on S‐genes. Our results reveal a previously undetected structural rearrangement in CYPᵀ associated with the shift to homostyly and confirm previously reported, homostyle‐specific, loss‐of‐function mutations in the exons of the S‐gene CYPᵀ. We also discovered that the promoter and intronic regions of CYPᵀ in distylous and homostylous individuals are conserved, suggesting that down‐regulation of CYPᵀ via mutations in its promoter and intronic regions is not a cause of the shift to homostyly. Furthermore, we found that hemizygosity is associated with reduced genetic diversity in S‐genes compared with their paralogs outside the S‐locus. Additionally, the shift to homostyly lowers genetic diversity in both the S‐genes and their paralogs, as expected in primarily selfing plants. Finally, we tested, for the first time, long‐standing theoretical models of changes in S‐locus genotypes during early stages of the transition to homostyly, supporting the assumption that two copies of the S‐locus might reduce homostyle fitness.