Life history evolution, species differences, and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

Phenological responses of alpine snowbed communities to advancing snowmelt

Climate change is leading to advanced snowmelt date in alpine regions. Consequently, alpine plant species and ecosystems experience substantial changes due to prolonged phenological seasons, while the responses, mechanisms and implications remain widely unclear. In this 3-year study, we investigated the effects of advancing snowmelt on the phenology of alpine snowbed species. We related microclimatic drivers to species and ecosystem phenology using in situ monitoring and phenocams. We further used predictive modelling to determine whether early snowmelt sites could be used as sentinels for future conditions. Temperature during the snow-free period primarily influenced flowering phenology, followed by snowmelt timing. Salix herbacea and Gnaphalium supinum showed the most opportunistic phenology, while annual Euphrasia minima struggled to complete its phenology in short growing seasons. Phenological responses varied more between years than sites, indicating potential local long-term adaptations and suggesting these species' potential to track future earlier melting dates. Phenocams captured ecosystem-level phenology (start, peak and end of phenological season) but failed to explain species-level variance. Our findings highlight species-specific responses to advancing snowmelt, with snowbed species responding highly opportunistically to changes in snowmelt timings while following species-specific developmental programs. While species from surrounding grasslands may benefit from extended growing seasons, snowbed species may become outcompeted due to internal-clock-driven, non-opportunistic senescence, despite displaying a high level of phenological plasticity.

Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone?

PREMISE

Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross-ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross-ploidy hybrid combinations have been reported based on morphology.

METHODS

We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross-ploidy hybridization and introgression.

RESULTS

Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single-nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (F_ST  = 0.44). However, the F_ST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation.

CONCLUSIONS

Our results suggest that recent cross-ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross-ploidy introgression to take place.

Phenolic acids as chemotaxonomic markers able to differentiate the Euphrasia species

The objective of this study was to get the answer on the question, which phenolic compounds may serve as chemical markers in taxonomy of Euphrasia spp. (E. nemorosa, E. rostkoviana, E. stricta) collected from the wild. Moreover, it is still unknown how and which environmental parameters can impact on the quantity of polyphenols, flavonoids and phenolic acids. To the authors' knowledge, this is the first study that analyses such a broad spectrum of phenolic compounds in the genus Euphrasia and takes into account the habitat conditions of their synthesis. The species of Euphrasia differ significantly in the content of phenolic compounds. Euphrasia rostkoviana has the highest total content of polyphenols and flavonoids. Euphrasia stricta contains the largest amounts of phenolic acids, such as 5-O-caffeoylquinic, p-coumaric, protocatechuic and salicylic acid. It has been evidenced that the content of metabolites in the Euphrasia herb depends on a number of habitat parameters. The increased content of phenolic acids in E. stricta can be attributed to the fact that this species occupies drier habitats, with lower content of nitrogen and organic carbon compared to E. nemorosa and E. rostkoviana. The compounds that can be considered as chemotaxonomic markers are salicylic and protocatechuic acid for E. stricta, 5-O-caffeoylquinic acid for E. rostkoviana and ferulic acid for E. nemorosa. These findings provide theoretical and empirical basis for a chemotaxonomic classification of those species, which taken together with morphological characteristics should prevent misidentification.

Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)

Disentangling the phylogenetic relationships of taxonomically complex plant groups is often mired by challenges associated with recent speciation, hybridization, complex mating systems, and polyploidy. Here, we perform a phylogenomic analysis of eyebrights (Euphrasia), a group renowned for taxonomic complexity, with the aim of documenting the extent of phylogenetic discordance at both deep and at shallow phylogenetic scales. We generate whole-genome sequencing data and integrate this with prior genomic data to perform a comprehensive analysis of nuclear genomic, nuclear ribosomal (nrDNA), and complete plastid genomes from 57 individuals representing 36 Euphrasia species. The species tree analysis of 3,454 conserved nuclear scaffolds (46 Mb) reveals that at shallow phylogenetic scales postglacial colonization of North Western Europe occurred in multiple waves from discrete source populations, with most species not being monophyletic, and instead combining genomic variants from across clades. At a deeper phylogenetic scale, the Euphrasia phylogeny is structured by geography and ploidy, and partially by taxonomy. Comparative analyses show Southern Hemisphere tetraploids include a distinct subgenome indicative of independent polyploidy events from Northern Hemisphere taxa. In contrast to the nuclear genome analyses, the plastid genome phylogeny reveals limited geographic structure, while the nrDNA phylogeny is informative of some geographic and taxonomic affinities but more thorough phylogenetic inference is impeded by the retention of ancestral polymorphisms in the polyploids. Overall our results reveal extensive phylogenetic discordance at both deeper and shallower nodes, with broad-scale geographic structure of genomic variation but a lack of definitive taxonomic signal. This suggests that Euphrasia species either have polytopic origins or are maintained by narrow genomic regions in the face of extensive homogenizing gene flow. Moreover, these results suggest genome skimming will not be an effective extended barcode to identify species in groups such as Euphrasia, or many other postglacial species groups.

Performance of generalist hemiparasitic Euphrasia across a phylogenetically diverse host spectrum

Generalist hemiparasites may attach to many different host species and experience complex parasite-host interactions. How these parasite-host interactions impact on the fitness of hemiparasitic plants remain largely unknown. We used experimentally tractable eyebrights (Euphrasia, Orobanchaceae) to understand parasite-host species interactions affecting the performance of a generalist hemiparasitic plant. Common garden experiments were carried out measuring Euphrasia performance across 45 diverse hosts and in different parasite-host combinations. We show that variation in hemiparasite performance can be attributed mainly to host species and host phylogenetic relationships (λ = 0.82; 0.17-1.00 CI). When variation in performance is considered temporally, annual host species cause earlier flowering, and lead to poorer performance late in the season. While Euphrasia species typically perform similarly on a given host species, some eyebrights show more specialized parasite-host species interactions. Our results show that generalist hemiparasites only benefit from attaching to a limited, but phylogenetically divergent, subset of hosts. The conserved responses of divergent Euphrasia species suggest hemiparasite performance is affected by common host attributes. However, evidence for more complex parasite-host species interactions show that a generalist hemiparasite can potentially respond to individual host selection pressures and may adapt to local host communities.

The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights

BACKGROUND AND AIMS

Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species.

METHODS

We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples.

KEY RESULTS

We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small.

CONCLUSIONS

We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.

Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island

Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here, we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity, and hybridization blur species boundaries. We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole-genome sequencing and a novel k-mer approach we call "Tetmer", we demonstrate that the species are of allopolyploid origin, with a sub-genome divergence of approximately 5%. Using ∼2 million SNPs, we show sub-genome homology across species, with a very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland Euphrasia micrantha, while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related. Overall, we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.