IAP-25-047

Leveraging wild hybrids to map the genomic mechanisms of life-history variation in a primitive vertebrate.

Life-history diversity within species is widespread across the tree of life and often manifested in fitness trade-offs in survival, growth, and/or fecundity. Variation in life history within species has been linked to large effect loci, including structural genomic variation, in many species (Mérot et al. 2020). Life-history variation is often associated with variation in a myriad of traits, yet, the underlying genomic and developmental mechanisms, particularly the role of small and complex structural variants, often remain unresolved. This limits our ability to fully understand how life-history variation has evolved and is maintained (Wellenreuther et al. 2025). When life-history forms are able to hybridize and form viable hybrids, they provide a powerful framework for identifying the genomic basis of life-history variation.

While selection has been linked to the maintenance of life-history variation, fitness optima might vary between life-stages, leading to different selection pressures between stages, e.g. with faster growth being advantages for adults but selected against in earlier life-stages, or hybridization being advantageous or neutral early in life but selected against in adults. However, we are only starting to understand how selection landscapes differ between life stages, and what effect this has on life-history evolution.

This PhD project aims to use wild hybrid populations to unravel the genomic basis of life-history evolution and investigate how selection differs across life-history forms and life-stages.

Lampreys, a primitive jawless vertebrate, display an intriguing diversity in adult life history, with the repeated evolution of distinct adult feeding and migratory strategies in relation to differences in the timing of sexual maturation and fecundity (Evans et al. 2018; Hume et al. 2018). The European lamprey (Lampetra sp.) is ancestrally anadromous and parasitic but has evolved a resident non-parasitic form that differs in morphology, physiology, and life-history (Fig.1). While parasitic forms migrate to large lakes or the sea as juveniles to parasitically feed on fish before returning to freshwater to spawn and die, non-parasitic lampreys stay in their natal stream and rapidly mature, spawn and die after metamorphosis. Both forms phenotypically diverge from each other during metamorphosis, yet they are ecologically and phenotypically indistinguishable as larvae.

Previous work, including our own, has shown that European lamprey life-history forms are divergent in a few genomic regions (Rougemont et al. 2017), including structural variants. These forms still hybridise but the proportion of hybrids varies across life-stages, with a more larval hybrids compared to adults, pointing toward selection against hybrids at later life stages. However, the effects of hybridization on development and life-history remain largely unknown.

This PhD project will build on an ongoing NERC-funded project in the PIs lab on the genomic basis of life-history variation in lampreys and will use hybrid populations to map the landscape of divergent selection and viability selection between life-history forms and across life-stages. The PhD student will use new and existing field collections together with modern sequencing approaches to address three central questions:

(1) What is the role of structural genetic variation in life-history evolution?

(2) How do life-history associated phenotypes vary between hybrids and pure parental forms?

(3) What is the role of viability selection in maintaining life-history forms in the face of gene flow?

Addressing these questions requires an integrative approach spanning state-of-the-art genomic analyses with extensive phenotyping. This project has a high likelihood of resulting in high-profile and high-impact publications since it i) addresses fundamental questions in evolutionary biology using a fascinating study system, ii) makes use of state-of-the-art ‘omics and computational approaches, and iii) benefits from an expert supervisory team.

Fieldwork & Phenotypic analyses will be conducted in two complementary hybrid zones in the Loch Lomond catchment with PI Jacobs and in the Oir river (France) with Dr Evanno to collect European lampreys with different life-histories, and their hybrids, across life stages. Long-term monitoring data are available for the Oir system. These samples will be used for phenotypic analyses (e.g. timing of gonad maturation, sperm characteristics, fecundity) in relation to genetic ancestry (genotyping using SNP panels and whole-genome sequencing). Ample tissue samples and genomic data are already in place and provide a great starting point for the project. There will be extensive opportunity for the student to develop and refine field and molecular approaches.

Genomic analyses will be conducted using cutting-edge genomic approaches for new and existing samples to investigate the genomic basis of life-history variation, with a focus on investigating the role of structural variants, identifying signatures of selection, and mapping genotype-phenotype associations in hybrid populations. This project will generate long-read and short-read whole-genome sequencing data to accurately map structural variants. The PhD student will also have access to existing whole genome resequencing data for hundreds of samples and chromosome-scale genomes for multiple individuals that have already been generated. The student will focus on applying state-of-the-art population genomic methods to map genotype-phenotype associations in hybrid populations, investigate signatures of selection, and investigate differences in selection across life-stages. The student will work closely with PI Jacobs and co-I Gaggiotti on state-of-the-art population genomic analyses.

Year 1

– Literature review
– Bioinformatic training through external courses and the supervisory team
– Field collections and phenotypic analysis

Year 2

– Molecular lab work and sequencing.
– Genomic data analysis

Year 3

– Genomic data analysis (continuation)
– Preparation of manuscripts

Year 3.5

– Data analysis and integration
– Dissemination of results by publications, thesis, and conference presentations.

The student will train with experienced and internationally esteemed researchers to acquire a breadth of skills necessary for a career in quantitative, molecular and/or computational jobs: skills in ecology, experimental work, molecular biology for next generation sequencing and advanced bioinformatic analyses for understanding a range of ‘omics data types.

In addition, training in transferable skills will be a core component (e.g. experimental design, statistics, oral and written communication) and are well supported by the outstanding graduate programme at Glasgow.

The project will be based in Glasgow, where the student will join a successful, active, and vibrant research community at an institution of high national and international standing. The data analysis and communication skills gained in this project will have key relevance for employability in conservation, academia, biotech, data analytics, or government research. Furthermore, the student will spend time in France for fieldwork and knowledge exchange (co-I Evanno), and will have the chance for regular knowledge exchanges at the University of St Andrews through co-I Gaggiotti.