Breeding system of diploid sexuals within the Ranunculus auricomus complex and its role in a geographical parthenogenesis scenario

Phylogenomics of Southern European Taxa in the Ranunculus auricomus Species Complex: The Apple Doesn't Fall Far from the Tree

The taxonomic status of many Southern European taxa of the Ranunculus auricomus complex remains uncertain despite this region's proximity to the native ranges of the sexual progenitor species of the complex. We investigated whether additional sexual progenitor species are present in the Mediterranean region. Utilizing target enrichment of 736 single-copy nuclear gene regions and flow cytometry, we analyzed phylogenomic relationships, the ploidy level, and the reproductive mode in representatives of 16 populations in Southern Europe, with additional sequence data from herbarium collections. Additionally, phased sequence assemblies from suspected nothotaxa were mapped to previously described sexual progenitor species in order to determine hybrid ancestry. We found the majority of Mediterranean taxa to be tetraploid, with hybrid populations propagating primarily via apomixis. Phylogenomic analysis revealed that except for the progenitor species, the Mediterranean taxa are often polyphyletic. Most apomictic taxa showed evidence of mixed heritage from progenitor species, with certain progenitor genotypes having mapped more to the populations from adjacent geographical regions. Geographical trends were found in phylogenetic distance, roughly following an east-to-west longitudinal demarcation of the complex, with apomicts extending to the southern margins. Additionally, we observed post-hybridization divergence between the western and eastern populations of nothotaxa in Southern Europe. Our results support a classification of apomictic populations as nothotaxa, as previously suggested for Central Europe.

Population size affected by environmental variability impacts genetics, traits, and plant performance in Trifolium montanum L

Population size, genetic diversity, and performance have fundamental importance for ecology, evolution, and nature conservation of plant species. Despite well-studied relationships among environmental, genetic, and intraspecific trait variation (ITV), the influence of population size on these aspects is less understood. To assess the sources of population size variation, but also its impact on genetic, functional trait, and performance aspects, we conducted detailed population size estimations, assessed 23 abiotic and biotic environmental habitat factors, performed population genetic analyses using nine microsatellite markers, and recorded nine functional traits based on 260 Trifolium montanum individuals from 13 semi-dry grassland locations of Central Europe. Modern statistical analyses based on a multivariate framework (path analysis) with preselected linear regression models revealed that the variation of abiotic factors (in contrast to factors per se) almost completely, significantly explained fluctuations in population size (R 2 = .93). In general, abiotic habitat variation (heterogeneity) was not affected by habitat area. Population size significantly explained genetic diversity (N A: R 2 = .42, H o: R 2 = .67, H e: R 2 = .43, and I: R 2 = .59), inbreeding (F IS: R 2 = .35), and differentiation (G ST: R 2 = .20). We also found that iFDCV (ITV) was significantly explained by abiotic habitat heterogeneity, and to a lesser extent by genetic diversity H e (R 2 = .81). Nevertheless, habitat heterogeneity did not statistically affect genetic diversity. This may be due to the use of selectively neutral microsatellite markers, and possibly by insufficient abiotic selective pressures on habitats examined. Small T. montanum populations in nonoptimal habitats were characterized by reduced genetic and functional trait diversity, and elevated genetic inbreeding and differentiation. This indicates reduced adaptability to current and future environmental changes. The long-term survival of small populations with reduced genetic diversity and beginning inbreeding will be highly dependent on habitat protection and adequate land-use actions.

Geographical Parthenogenesis in Alpine and Arctic Plants

The term "Geographical parthenogenesis" describes the phenomenon that asexual organisms usually occupy larger and more northern distribution areas than their sexual relatives, and tend to colonize previously glaciated areas. Several case studies on alpine and arctic plants confirm the geographical pattern, but the causal factors behind the phenomenon are still unclear. Research of the last decade in several plant families has shed light on the question and evaluated some of the classical evolutionary theories. Results confirmed, in general, that the advantages of uniparental reproduction enable apomictic plants to re-colonize faster in larger and more northern distribution areas. Associated factors like polyploidy seem to contribute mainly to the spatial separation of sexual and asexual cytotypes. Ecological studies suggest a better tolerance of apomicts to colder climates and temperate extremes, whereby epigenetic flexibility and phenotypic plasticity play an important role in occupying ecological niches under harsh conditions. Genotypic diversity appears to be of lesser importance for the distributional success of asexual plants. Classical evolutionary theories like a reduced pressure of biotic interactions in colder climates and hence an advantage to asexuals (Red Queen hypothesis) did not gain support from studies on plants. However, it is also still enigmatic why sexual outcrossing remains the predominant mode of reproduction also in alpine floras. Constraints for the origin of apomixis might play a role. Interestingly, some studies suggest an association of sexuality with abiotic stresses. Light stress in high elevations might explain why most alpine plants retain sexual reproduction despite other environmental factors that would favor apomixis. Directions for future research will be given.

Evolution of Transcriptomes in Early-Generation Hybrids of the Apomictic Ranunculus auricomus Complex (Ranunculaceae)

Hybridisation in plants may cause a shift from sexual to asexual seed formation (apomixis). Indeed, natural apomictic plants are usually hybrids, but it is still unclear how hybridisation could trigger the shift to apomixis. The genome evolution of older apomictic lineages is influenced by diverse processes such as polyploidy, mutation accumulation, and allelic sequence divergence. To disentangle the effects of hybridisation from these other factors, we analysed the transcriptomes of flowering buds from artificially produced, diploid F2 hybrids of the Ranunculus auricomus complex. The hybrids exhibited unreduced embryo sac formation (apospory) as one important component of apomixis, whereas their parental species were sexual. We revealed 2915 annotated single-copy genes that were mostly under purifying selection according to dN/dS ratios. However, pairwise comparisons revealed, after rigorous filtering, 79 genes under diversifying selection between hybrids and parents, whereby gene annotation assigned ten of them to reproductive processes. Four genes belong to the meiosis-sporogenesis phase (ASY1, APC1, MSP1, and XRI1) and represent, according to literature records, candidate genes for apospory. We conclude that hybridisation could combine novel (or existing) mutations in key developmental genes in certain hybrid lineages, and establish (together with altered gene expression profiles, as observed in other studies) a heritable regulatory mechanism for aposporous development.

Untying Gordian knots: unraveling reticulate polyploid plant evolution by genomic data using the large Ranunculus auricomus species complex

Speciation via hybridization and polyploidization is a major evolutionary force in plant evolution but is still poorly understood for neopolyploid groups. Challenges are attributed to high heterozygosity, low genetic divergence, and missing information on progenitors, ploidy, and reproduction. We study the large Eurasian Ranunculus auricomus species complex and use a comprehensive workflow integrating reduced-representation sequencing (RRS) genomic data to unravel reticulate evolution, genome diversity and composition of polyploids. We rely on 97 312 restriction site-associated DNA sequencing (RAD-Seq) loci, 576 targeted nuclear genes (48 phased), and 71 plastid regions derived from 78 polyploid apomictic taxa and four diploid and one tetraploid putative sexual progenitor species. We applied (phylo)genomic structure, network, and single nucleotide polymorphism (SNP)-origin analyses. Results consistently showed only 3-5 supported and geographically structured polyploid genetic groups, each containing extant sexual and one unknown progenitor species. Combined analyses demonstrated predominantly allopolyploid origins, each involving 2-3 different diploid sexual progenitor species. Young allotetraploids were characterized by subgenome dominance and nonhybrid SNPs, suggesting substantial post-origin but little lineage-specific evolution. The biodiversity of neopolyploid complexes can result from multiple hybrid origins involving different progenitors and substantial post-origin evolution (e.g. homoeologous exchanges, hybrid segregation, gene flow). Reduced-representation sequencing genomic data including multi-approach information is efficient to delimit shallow reticulate relationships.

Greater reproductive assurance of asexual plant compared with sexual relative in a low-density sympatric population: Experimental evidence for pollen limitation

High reproductive assurance is regarded as a key advantage of uniparentally reproducing organisms for establishing a new population. This demographic benefit should especially be relevant for plants with autonomous apomixis, that is those which produce seeds completely independently from mates and pollinators. Indeed, many autonomous apomicts occupy larger distributional ranges when compared to their sexual relatives, showing geographical parthenogenesis patterns. However, uniparental reproduction advantage has only rarely been quantified in natural populations and results provided a mixed support, partly because allopatric sexual and asexual populations were exposed to different environmental and pollination conditions causing considerable between-population variation in the level of reproductive assurance. Here, we compared the level and stability of reproductive assurance between sexual self-incompatible and asexual autonomously apomictic plants of Hieracium alpinum (Asteraceae) cultivated in a sympatric low-density population with two levels of spatial clumping of sexual plants. Overall, we found that the realized seed set (i.e. proportion of well-developed seeds per capitulum) of asexuals was ca. 3 times greater than that of sexuals (83% vs. 27%), whereas the variance of this trait expressed as coefficient of variation was ca. 4 times smaller in asexuals compared with sexuals (19% vs. 83%). Solitary sexual plants had more than 2 times lower realized seed set when compared to clumps composed of two spatially close (20-30 cm) sexual plants (13% vs. 34%). Our study provides experimental evidence for benefit of uniparental reproduction of asexuals in a sympatric situation when the availability of mates is limited. This, together with unpredictability of pollinator environment could provide autonomous apomicts with an ultimate demographic superiority during colonization reflected in geographical parthenogenesis observed in this species.

Moving beyond assumptions: Polyploidy and environmental effects explain a geographical parthenogenesis scenario in European plants

Geographical parthenogenesis (GP) describes the phenomenon that apomicts tend to have larger distribution areas and/or occur at higher altitudes or latitudes compared to sexual relatives. However, the complex effects of genome-wide heterozygosity, ploidy, reproduction mode (sexual vs. apomictic), and environment shaping GP of plants are still not well understood. We ascertained ploidy and reproduction mode by flow cytometry of 221 populations, and added genomic RADseq data (maximum 33,165 loci) of 80 taxa of the Ranunculus auricomus polyploid plant complex in temperate Europe. We observed 7% mainly diploid sexual, 28% facultative apomictic (mean sexuality 7.1%), and 65% obligate apomictic populations. Sexuals occupied a more southern, smaller distribution area, whereas apomicts expanded their range to higher latitudes. Within the complex, we detected three main genetic clusters and highly reticulate relationships. A genetically-informed path analysis using GLMMs revealed several significant relationships. Sexuality of populations (percent of sexual seeds) was higher in diploids compared to polyploids, associated with more petals, and similar between forests and open habitats. In contrast to other apomictic plant complexes, sexuality was mainly positively correlated to solar radiation and isothermality, which fits the southern distribution. We found up to three times higher heterozygosity in polyploids compared to diploids, and generally more heterozygous individuals in forests compared with open habitats. Interestingly, we revealed a previously unknown positive association between heterozygosity and temperature seasonality, suggesting a higher resistance of polyploids to more extreme climatic conditions. We provide empirical evidence for intrinsic and extrinsic factors shaping the GP pattern in a polyploid plant complex.