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 (SI). 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 SI and/or anther height could underlie homostyly and self-compatibility (SC) 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.

Development of microsatellite markers for sister species Linum suffruticosum and Linum tenuifolium in their overlapping ranges.

BACKGROUND: Microsatellite markers were developed for distylous Linum suffruticosum and tested in the monomorphic sister species Linum tenuifolium. These species are perennial herbs endemic to the western and northwestern Mediterranean, respectively, with a partially overlapping distribution area. METHODS AND RESULTS: We developed 12 microsatellite markers for L. suffruticosum using next generation sequencing, and assessed their polymorphism and genetic diversity in 152 individuals from seven natural populations. The markers displayed high polymorphism, with two to 16 alleles per locus and population, and average observed and expected heterozygosities of 0.833 and 0.692, respectively. All loci amplified successfully in the sister species L. tenuifolium, and 150 individuals from seven populations were also screened. The polymorphism exhibited was high, with two to ten alleles per locus and population, and average observed and expected heterozygosities of 0.77 and 0.62, respectively. CONCLUSIONS: The microsatellite markers identified in L. suffruticosum and tested in L. tenuifolium are a powerful tool to facilitate future investigations of the population genetics, mating patterns and hybridization between both Linum species in their contact zone.

Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.

Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.

Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.

Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.

Genetic basis and timing of a major mating system shift in Capsella.

A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.

Evolutionary origin of the latitudinal diversity gradient in liverworts.

A latitudinal diversity gradient towards the tropics appears as one most recurrent patterns in ecology, but the mechanisms underlying this pattern remain an area of controversy. In angiosperms, the tropical conservatism hypothesis proposes that most groups originated in the tropics and are adapted to a tropical climatic regime, and that relatively few species have evolved physiological adaptations to cold, dry or unpredictable climates. This mechanism is, however, unlikely to apply across land plants, and in particular, to liverworts, a group of about 7500 species, whose ability to withstand cold much better than their tracheophyte counterparts is at odds with the tropical conservatism hypothesis. Molecular dating, diversification rate analyses and ancestral area reconstructions were employed to explore the evolutionary mechanisms that account for the latitudinal diversity gradient in liverworts. As opposed to angiosperms, tropical liverwort genera are not older than their extra-tropical counterparts (median stem age of tropical and extra-tropical liverwort genera of 24.35 ±â€¯39.65 Ma and 39.57 ±â€¯49.07 Ma, respectively), weakening the 'time for speciation hypothesis'. Models of ancestral area reconstructions with equal migration rates between tropical and extra-tropical regions outperformed models with asymmetrical migration rates in either direction. The symmetry and intensity of migrations between tropical and extra-tropical regions suggested by the lack of resolution in ancestral area reconstructions towards the deepest nodes are at odds with the tropical niche conservatism hypothesis. In turn, tropical genera exhibited significantly higher net diversification rates than extra-tropical ones, suggesting that the observed latitudinal diversity gradient results from either higher extinction rates in extra-tropical lineages or higher speciation rates in the tropics. We discuss a series of experiments to help deciphering the underlying evolutionary mechanisms.

Early burst in body size evolution is uncoupled from species diversification in diving beetles (Dytiscidae).

Changes in morphology are often thought to be linked to changes in species diversification, which is expected to leave a signal of early burst (EB) in phenotypic traits. However, such signal is rarely recovered in empirical phylogenies, even for groups with well-known adaptive radiation. Using a comprehensive phylogenetic approach in Dytiscidae, which harbours ~4,300 species with as much as 50-fold variation in body size among them, we ask whether pattern of species diversification correlates with morphological evolution. Additionally, we test whether the large variation in body size is linked to habitat preference and whether the latter influences species turnover. We found, in sharp contrast to most animal groups, that Dytiscidae body size evolution follows an early-burst model with subsequent high phylogenetic conservatism. However, we found no evidence for associated shifts in species diversification, which point to an uncoupled evolution of morphology and species diversification. We recovered the ancestral habitat of Dytiscidae as lentic (standing water), with many transitions to lotic habitat (running water) that are concomitant to a decrease in body size. Finally, we found no evidence for difference in net diversification rates between habitats nor difference in turnover in lentic and lotic species. This result, together with recent findings in dragonflies, contrasts with some theoretical expectations of the habitat stability hypothesis. Thus, a thorough reassessment of the impact of dispersal, gene flow and range size on the speciation process is needed to fully encompass the evolutionary consequences of the lentic-lotic divide for freshwater fauna.

High migration rates shape the postglacial history of amphi-Atlantic bryophytes.

Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework.

Increased diversification rates follow shifts to bisexuality in liverworts.

Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism.

Modeling species distributions from heterogeneous data for the biogeographic regionalization of the European bryophyte flora.

The definition of biogeographic regions provides a fundamental framework for a range of basic and applied questions in biogeography, evolutionary biology, systematics and conservation. Previous research suggested that environmental forcing results in highly congruent regionalization patterns across taxa, but that the size and number of regions depends on the dispersal ability of the taxa considered. We produced a biogeographic regionalization of European bryophytes and hypothesized that (1) regions defined for bryophytes would differ from those defined for other taxa due to the highly specific eco-physiology of the group and (2) their high dispersal ability would result in the resolution of few, large regions. Species distributions were recorded using 10,000 km2 MGRS pixels. Because of the lack of data across large portions of the area, species distribution models employing macroclimatic variables as predictors were used to determine the potential composition of empty pixels. K-means clustering analyses of the pixels based on their potential species composition were employed to define biogeographic regions. The optimal number of regions was determined by v-fold cross-validation and Moran's I statistic. The spatial congruence of the regions identified from their potential bryophyte assemblages with large-scale vegetation patterns is at odds with our primary hypothesis. This reinforces the notion that post-glacial migration patterns might have been much more similar in bryophytes and vascular plants than previously thought. The substantially lower optimal number of clusters and the absence of nested patterns within the main biogeographic regions, as compared to identical analyses in vascular plants, support our second hypothesis. The modelling approach implemented here is, however, based on many assumptions that are discussed but can only be tested when additional data on species distributions become available, highlighting the substantial importance of developing integrated mapping projects for all taxa in key biogeographically areas of Europe, and the Mediterranean peninsulas in particular.

How do temperate bryophytes face the challenge of a changing environment? Lessons from the past and predictions for the future.

Bryophytes are a group of early land plants, whose specific ecophysiological and biological features, including poikilohydry, sensitivity to moderately high temperature and high dispersal ability, make them ideal candidates for investigating the impact of climate changes. Employing a combined approach of species distribution modelling (SDM) and molecular phylogeography in the temperate moss Homalothecium sericeum, we explore the significance of the Mediterranean refugia, contrasting the southern and northern refugia hypotheses, determine the extent to which recolonization of previously glaciated areas has been facilitated by the high dispersal ability of the species and make predictions on the extent to which it will be impacted by ongoing climate change. The Mediterranean areas exhibit the highest nucleotidic diversities and host a mixture of ancestral, endemic and more recently derived haplotypes. Extra-Mediterranean areas exhibit low genetic diversities and Euro-Siberian populations display a significant signal of expansion that is identified to be of Euro-Siberian origin, pointing to the northern refugia hypothesis. The SDMs predict a global net increase in range size owing to ongoing climate change, but substantial range reductions in southern areas. Presence of a significant phylogeographical signal at different spatial scales suggests, however, that dispersal limitations might constitute, as opposed to the traditional view of spore-producing plants as efficient dispersers, a constraint for migration. This casts doubts about the ability of the species to face the massive extinctions predicted in the southern areas, threatening their status of reservoir of genetic diversity.