Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species

The Primula edelbergii S-locus is an example of a jumping supergene

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.

Island plants with newly discovered reproductive traits have higher capacity for uniparental reproduction, supporting Baker's law

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.

Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum

Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.

Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly

Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures and can involve parallel evolution within related lineages. Adaptive evolution of morphological traits is often assumed to evolve faster than nonadaptive features of the genomic selfing syndrome. We investigated phenotypic and genomic changes associated with transitions from distyly to homostyly in the Primula oreodoxa complex. We determined whether the transition to selfing occurred more than once and investigated stages in the evolution of morphological and genomic selfing syndromes using 22 floral traits and both nuclear and plastid genomic data from 25 populations. Two independent transitions were detected representing an earlier and a more recently derived selfing lineage. The older lineage exhibited classic features of the morphological and genomic selfing syndrome. Although features of both selfing syndromes were less developed in the younger selfing lineage, they exhibited parallel development with the older selfing lineage. This finding contrasts with the prediction that some genomic changes should lag behind adaptive changes to morphological traits. Our findings highlight the value of comparative studies on the timing and extent of transitions from outcrossing to selfing between related lineages for investigating the tempo of morphological and molecular evolution.

Heterostyly

Scharman and Lenhard introduce heterostyly, a phenomenon where individuals in a plant population produce flowers with more than one morphologically distinct form.

Floral morph variation mediated by clonal growth and pollinator functional groups of Limonium otolepis in a heterostylous fragmented population

Abstract. Heterostyly, a genetic style polymorphism, is linked to symmetric pollen transfer, vital for its maintenance. Clonal growth typically impacts sexual reproduction by influencing pollen transfer. However, the floral morph variation remains poorly understood under the combined effects of pollinators and clonal growth in heterostyly characterized by negative frequency-dependent selection and disassortative mating. We estimated morph ratios, ramets per genet and heterostylous syndrome and quantified legitimate pollen transfer via clonal growth, pollinators and reciprocal herkogamy between floral morphs in Limonium otolepis, a fragmented population composed of five subpopulations in the desert environment of northwestern China, with small flower and large floral morph variation. All subpopulations but one exhibited pollen-stigma morphology dimorphism. The compatibility between mating types with different pollen-stigma morphologies remained consistent regardless of reciprocal herkogamy. Biased ratios and ramets per genet of the two mating types with distinct pollen-stigma morphologies caused asymmetric pollen flow and varying fruit sets in all subpopulations. Short-tongued insects were the primary pollinators due to small flower sizes. However, pollen-feeding Syrphidae sp. triggered asymmetry in pollen flow between high and low sex organs, with short-styled morphs having lower stigma pollen depositions and greater variation. Clonal growth amplified this variation by reducing intermorph pollen transfer. All in all, pollinators and clonal growth jointly drive floral morph variation. H-morphs with the same stigma-anther position and self-incompatibility, which mitigate the disadvantages of sunken low sex organs with differing from the classical homostyly, might arise from long- and short-styled morphs through a 'relaxed selection'. This study is the first to uncover the occurrence of the H-morph and its associated influencing factors in a distylous plant featuring clonal growth, small flowers and a fragmented population.

Inheritance of distyly and homostyly in self-incompatible Primula forbesii

The evolutionary transition from self-incompatible distyly to self-compatible homostyly frequently occurs in heterostylous taxa. Although the inheritance of distyly and homostyly has been deeply studied, our understanding on modifications of the classical simple Mendelian model is still lacking. Primula forbesii, a biennial herb native to southwest China, is a typical distylous species, but after about 20 years of cultivation with open pollination, self-compatible homostyly appeared, providing ideal material for the study of the inheritance of distyly and homostyly. In this study, exogenous homobrassinolide was used to break the heteromorphic incompatibility of P. forbesii. Furthermore, we performed artificial pollination and open-pollination experiments to observe the distribution of floral morphs in progeny produced by different crosses. The viability of seeds from self-pollination was always the lowest among all crosses, and the homozygous S-morph plants (S/S) occurred in artificial pollination experiments but may experience viability selection. The distyly of P. forbesii is governed by a single S-locus, with S-morph dominant hemizygotes (S/-) and L-morph recessive homozygotes (-/-). Homostylous plants have a genotype similar to L-morph plants, and homostyly may be caused by one or more unlinked modifier genes outside the S-locus. Open pollinations confirm that autonomous self-pollination occurs frequently in L-morphs and homostylous plants. This study deepens the understanding of the inheritance of distyly and details a case of homostyly that likely originated from one or more modifier genes.

Primrose homostyles: A classic case of possible balancing selection revisited

In this issue of Molecular Ecology, Mora-Carrera et al. (2022) revisit a case of the loss of an outcrossing system in primroses, which has been studied as an example of balancing selection in the wild since the 1940s. Molecular variants in the gene involved in the mutant self-fertile phenotype, which is now known, help towards understanding this textbook example of breakdown of an outcrossing system. However, as often happens, new information also raises further questions.

Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot

Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.

Genomic insights into inter- and intraspecific mating system shifts in Primulina

The mating system shift from outcrossing to selfing is one of the most frequent evolutionary trends in flowering plants. However, the genomic consequences of this shift remain poorly understood. Specifically, the relative importance of the demographic and genetic processes causing changes in genetic variation and selection efficacy associated with the evolution of selfing is unclear. Here we sequenced the genomes of two Primulina species with contrasting mating systems: P. eburnea (outcrossing) versus P. tabacum (outcrossing, mixed-mating and selfing populations). Whole-genome resequencing data were used to investigate the genomic consequences of mating system shifts within and between species. We found that highly selfing populations of P. tabacum display loss of genetic diversity, increased deleterious mutations, higher genomic burden and fewer adaptive substitutions. However, compared with outcrossing populations, mixed-mating populations did not display loss of genetic diversity and accumulation of genetic load. We find no evidence of population bottlenecks associated with the shift to selfing, which suggests that the genetic effects of selfing on N_e and possibly linked selection, rather than demographic history, are the primary drivers of diversity reduction in highly selfing populations. Our results highlight the importance of distinguishing the relative contribution of mating system and demography on the genomic consequences associated with mating system evolution in plants.