IAP-25-048

Using functional genomics to assess population health after a local reintroduction of the field cricket in Cornwall

Background

Human induced environmental change is having unprecedented impacts on biodiversity. Many species are under threat of local extinction, but this often goes unnoticed in the case of small, less charismatic animals, like many insects. This is a serious issue as insects play key roles in terrestrial ecosystems. Their disappearance can have catastrophic ecosystem-wide consequences through all trophic levels. Strategic translocations have been successfully implemented to protect vertebrate species against habitat loss, inbreeding, and local extinction. However, translocations are rarely used for insects and whether such strategies could be effective remains unclear. Black field crickets (Gryllus campestris) are large ground dwelling annual insects that were once common in England, but are now virtually extinct (Fig. 1). Together with natural England we have reintroduced this species to Cornwall by translocating individuals from Spain. The population has thrived, with the current generation representing the great-grand offspring from the founders. Though the reintroduction is seen as successful in terms of the present population size, we currently do not know whether the Cornwall population is healthy from a population genetic perspective, and whether they will continue to thrive in the future. Genetic variation will have been affected by the translocation. There will also have been strong selection, given the different climate in Cornwall compared to the environmental conditions of the source populations in Spain. The translocation event may have caused inbreeding and reduced overall fitness. The Cornwall cricket project present a unique opportunity to study local adaptation after an environmental change, providing important insights into the resilience of these and other insects to environmental change. This project also serves as a novel case study to determine the potential for translocation as effective tool in insect conservation ecology.

Research aims

Using modern population genomics, the PhD candidate will investigate the consequences of translocation for genetic variation, inbreeding depression, and evolution. This will be achieved by conducting fieldwork in Cornwall (Fig. 2) to catch and collect tissue samples from adult crickets to sequence their genomes. A fully annotated genome is not yet available for this species, but genomes have been published of closely related field cricket species. The PhD candidate will exploit these resources to create a high-resolution annotated genome. This will enable the PhD candidate to investigate the effects of the translocation event on inbreeding, and to study the impacts of subsequent selection on functional genomic regions by comparing and reconstructing genomic shifts relative to the ancestor population in Spain.

Engaging non-academic stakeholders

The project will be in close collaboration with Natural England, local stakeholders, and the (enthusiastic) landowner. By the end of the PhD, the candidate will not only have gained experience in fieldwork, molecular genomics, and other general academic skills, but will also have engaged with these stakeholders to gain valuable experience in public outreach and engagement with professional bodies, as well as contributing to the debate about the need for efficient conservation policy revolving around insects.

The student will conduct annual fieldwork in south-west Cornwall, UK. This work will take place over two- to three years aimed at developing methods to monitor the population, to catch individual crickets from their burrows, and to obtain tissue samples. The fieldwork will typically last for around 2 months per year during the summer. Samples will be prepared in the lab in Glasgow, including DNA extractions and library preparations. Sequencing will be outsourced. The analyses will initially focus on the creation of a detailed annotated genome and to estimate runs of homozygosity to estimate inbreeding depression. More detailed analyses will follow linking genomics to the ancestors for which we have samples stored. This will enable a more detailed study into the genomic responses following the translocation.

Year 1

This year will consist of a literature review, training in programming language and Bayesian statistics, and quantitative genetics, all supervised by Boonekamp. Jacobs will provide training in genomics, and a start will be made with the genome assembly. Two months of field work will take place during the summer. Boonekamp will join the student to train them in field methods.

Year 2

This year will focus on the lab work, DNA extractions, library preparations, and the genome assembly. A start will be made with the genomics data analysis. Two months of field work will take place during the summer to continue data collection.

Year 3

This year will focus on the functional genomics data analyses. The student will receive further training on genomics during a secondment to Nathan Bailey in St. Andrews. Initial findings will be shared with Natural England and presented at a suitable conference.

Year 3.5

Writing of the thesis chapters and submission of the thesis.

The studentship provides an opportunity to receive training from a diverse team of internationally recognized experts to develop skills in cutting-edge research techniques consistent with NERC’s mission. For example, numeracy will be developed through engagement with statistical quantitative genetics analyses. Best practice for lab technique plus proficiency in quantitative and genomic analyses will equip the student with skills that can be applied in other settings or systems during their future career. We will encourage the student to identify relevant external workshops in molecular evolution and local adaptation and enable them to pursue sub-specialities of their own interest. Fieldwork training will be facilitated by the PIs, and the student will be embedded within a highly collegiate postgraduate environment at Glasgow that offers both formal and informal mentoring, access to seminars and more informal discussion groups. The student and supervisors will take advantage of the DTP scheme to arrange for a secondment to St Andrews to facilitate knowledge exchange through institutional seminars or workshops, thus widening the network of potential contacts, colleagues and collaborators for the student. The project will benefit from matured genomic resources including an annotated genome, gene expression data, comparative genomic resources for the superfamily of crickets (Grylloidea) containing Gryllus campestris including established bioinformatic pipelines for genome assembly and annotation, and includes a secondment to co-supervisor Bailey’s lab at the University of St Andrews. Taken altogether, this project will enable diverse training goals thus avoiding pigeonholing the student into narrowly defined career options in research.