Biology subjects

Metherell, C.

Publications and source records attributed to Metherell, C..

5 recordsLinked to original sources

bioRxiv2023

Genomic clustering by geography not species in taxonomically complex British and Irish eyebrights (Euphrasia)

Genomic studies of incipient speciation are fundamental to understand the origin and establishment of species. However, a wide range of evolutionary processes and complex evolutionary interactions remain to be explored outside of genetically tractable evolutionary and ecological model systems. Here, we study taxonomically complex British and Irish eyebrights (Euphrasia), as a test case for how different evolutionary factors influence species boundaries across geographic space. Euphrasia is a plant genus that has remarkable diversity in ploidy, mating system and ecology. There are 21 British and Irish Euphrasia species, but with species that are exceptionally difficult to identify based on morphology or DNA barcoding. Here, we test the hypothesis that species boundaries are highly permeable, and taxa experience extensive gene flow despite potential barriers such as ploidy and contrasting mating systems. To understand geographic genetic structure and the nature of species differences, we applied genotyping-by-sequencing (GBS) and spatial-aware clustering methods to 378 population samples from 18 British and Irish species. We find the selfing heathland specialist E. micrantha demonstrates genome-wide divergence in Northern Scotland, indicative of a distinct post-glacial colonisation history and the role of a highly selfing mating system in divergence. In contrast, all other genetic clusters correspond to geographic regions, with extensive gene flow between species and a complete absence of species-specific SNPs. Our results reveal the highly permeable species boundaries present in a recently diverging group, with an overriding signal of geographic genetic structure over and above genetic clustering by species.

evolutionary biology↗

bioRxiv2021

The nature of intraspecific genome size variation in taxonomically complex eyebrights

O_LIGenome size (GS) is a key trait related to morphology, life history, and evolvability. Although GS is, by definition, affected by presence/absence variants (PAVs), which are ubiquitous in population sequencing studies, GS is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific GS variation in taxonomically complex British eyebrights (Euphrasia). C_LIO_LIWe generated GS data for 192 individuals of diploid and tetraploid Euphrasia and analysed GS variation in relation to ploidy, taxonomy, population affiliation, and geography. We further compared the genomic repeat content of 30 samples. C_LIO_LIWe found considerable genuine intraspecific GS variation, and observed isolation-by-distance for GS in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with GS increasing with latitude in outcrossing Euphrasia arctica, but little GS variation in the highly selfing Euphrasia micrantha. Interspecific differences in GS genomic repeat percentages were small. C_LIO_LIWe show the utility of treating GS as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, GS variation may be increased through hybridisation and population subdivision. In addition to selection on associated traits, GS is predicted to be affected indirectly by selection due to pleiotropy of the underlying PAVs. C_LI

evolutionary biology↗

bioRxiv2020

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 hybridisation blur species boundaries. We focus on three closely-related tetraploid species with contrasting ecological preferences, and which 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 demonstrate an allopolyploid origin, with sub-genome divergence of approximately 5%. Using ~2 million SNPs we show sub-genome homology across species consistent with a common origin, with very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland E. micrantha, while grassland E. arctica and coastal E. foulaensis are more closely related. Overall, we show tetraploid Euphrasia is an allopolyploid system characterised by postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.

evolutionary biology↗

bioRxiv2018

Life history evolution and phenotypic plasticity in parasitic eyebrights (Euphrasia, Orobanchaceae)

Premise of the studyParasite lifetime reproductive success is determined by both genetic variation and phenotypically plastic life history traits that respond to host quality and external environment. Here, we use the generalist parasitic plant genus Euphrasia to investigate life history trait variation, in particular whether there is a trade-off between growth and reproduction, and how life history traits are affected by host quality.\n\nMethodsWe perform a common garden experiment to evaluate life history trait differences between eleven Euphrasia taxa grown on a common host, document phenotypic plasticity when a single Euphrasia species is grown on eight different hosts, and relate our observations to trait differences recorded in the wild.\n\nKey resultsEuphrasia exhibit a range of life history strategies that differ between species that transition rapidly to flower at the expense of early season growth, and those that invest in vegetative growth and delay flowering. Many life history traits show extensive phenotypic plasticity in response to host quality and demonstrate the costs of attaching to a low-quality host.\n\nConclusionsCommon garden experiments reveal trait differences between taxonomically complex Euphrasia species that are characterised by postglacial speciation and hybridisation. Our experiments suggest life history strategies in this generalist parasitic plant genus are the product of natural selection on traits related to growth and flowering. However, host quality may be a primary determinant of lifetime reproductive success.

evolutionary biology↗

bioRxiv2017

DNA barcoding British Euphrasia reveals deeply divergent polyploids but lack of species-level resolution

Background and aimsDNA barcoding is emerging as a useful tool not only for species identification but for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode datasets can provide insights into the mechanisms underlying the generation of species diversity. Here, we use DNA barcoding to study evolutionary processes in taxonomically complex British Euphrasia, a group with multiple ploidy levels, frequent self- fertilization, young species divergence and widespread hybridisation.\n\nMethodsWe sequenced the core plant barcoding loci, supplemented with additional nuclear and plastid loci, in representatives of all 19 British Euphrasia species. We analyse these data in a population genetic and phylogenetic framework. We then date the divergence of haplotypes in a global Euphrasia dataset using a time-calibrated Bayesian approach implemented in BEAST.\n\nKey resultsNo Euphrasia species has a consistent diagnostic haplotype. Instead, haplotypes are either widespread across species, or are population specific. Nuclear genetic variation is strongly partitioned by ploidy levels, with diploid and tetraploid British Euphrasia possessing deeply divergent ITS haplotypes (DXY = 5.1%), with haplotype divergence corresponding to the late Miocene. In contrast, plastid data show no clear division by ploidy, and instead reveal weakly supported geographic patterns.\n\nConclusionsUsing standard DNA barcoding loci for species identification in Euphrasia will be unsuccessful. However, these loci provide key insights into the maintenance of genetic variation, with divergence of diploids and tetraploids suggesting that ploidy differences act as a barrier to gene exchange in British Euphrasia, with rampant hybridisation within ploidy levels. The scarcity of shared diploid-tetraploid ITS haplotypes supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, DNA barcoding can reveal insightful evolutionary patterns in taxonomically complex genera.

evolutionary biology↗