2024-L6 Understanding the extinction vortex: inbreeding in haplodiploids

Project highlights

Your research will be high impact science geared towards the conservation of the 20% of animal species that are haplodiploid – including essential pollinators and seed dispersers.
You will receive interdisciplinary training and gain experience in a wide variety of sought-after techniques and approaches (e.g. mathematical modelling, GIS and genomics).
You will engage in field work in Spain and present your work in national and international conferences.

Overview

Around 20% of all animals – including all the bees, wasps and ants that are important pollinators and seed dispersers – are haplodiploid (Heimpel and de Boer, 2008). That is, females are diploid and males are haploid. However, the mechanism underlying haplodiploidy, known as complementary sex determination (csd), means that low genetic variation and/or inbreeding can detrimentally reduce reproduction (Zayed and Packer, 2005). This is because diploid offspring erroneously develop as males rather than females (Harpur et al., 2013). Such reduced reproduction lowers population size further, exacerbating the effects in a feedback loop: the extinction vortex (Figure 1A). Given human induced habitat degradation and climate change, insect populations – including many of those with haplo-diploid sex determination – are declining and fragmenting (Sanchez-Bayo and Wyckhuys, 2019). Understanding the extinction vortex is therefore a priority.

Figure 1: A: Extinction vortex caused by diploid male production (Zayed and Packer, 2005); B: relief map of the Iberian Peninsula, darker shading shows higher altitudes; C: Leptothorax acervorum colony showing a queen (yellow arrow), adults workers, developing larvae at various stages of development (gut contents clearly visible).

The objectives of the PhD project are as follows (the emphasis on each element can be tailored to your interests & how the project develops).

Model the effects of inbreeding and diploid male production in haplodiploids. Although there is some theoretical work on the impact of inbreeding and diploid male production on population persistence, you will extend this theory to investigate how life history variation influences outcome.

Estimate inbreeding & diploid male production in a model ant species. You will estimate diploid male production in the well-studied ant, Leptothorax acervorum (Figure 1C), and test if this correlates with effective population size (current and historical) estimated from genetic data. In the southern part of their range (Spain) this species is attitudinally limited being restricted to >1500m (Figure 1B). Populations are often small, have limited gene flow and so population isolation and inbreeding is a real issue and diploid males are regularly produced (Hammond, unpublished data)

Model habitat patch size, occupancy and fragmentation. You will use spatial data to discover suitable habitats for L.acervorum in Spain.  This will allow us to estimate patch size and connectivity and to interpret data gained from objective 2. It will also find new populations to sample for part 2.

Host

University of Leicester

Theme

Climate and Environmental Sustainability
Organisms and Ecosystems

Supervisors

Project investigator

Dr Robert Hammond, [email protected], University of Leicester

Co-investigators

Dr Fabian Freund (modelling, UoL)

Dr Nick Tate (GIS, UoL)

How to apply

Each host has a slightly different application process.
Find out how to apply for this studentship.
All applications must include the CENTA application form.
Choose your application route

Methodology

Modelling: You will develop mathematical models of diploid male production that consider: solitary vs social living, for social species the type of colony founding, mating frequency of females, colony size and female productivity, diploid male fertility and triploid female fertility.
Inbreeding / diploid male production: You will collect samples of the ant, L.acervorum, from known locations, and locations identified by GIS modelling (see 3), in Spain. You will estimate population genetic variation using reduced representation sequencing and the proportion of diploid males will be identified genetically. This will involve molecular genetic lab work and bioinformatic analysis.
Habitat patch size: You will develop GIS models to identify suitable habitat/altitude/aspect patches. This will be done using data derived from known populations / published records and using state of the art GIS software and modelling (e.g. ArcGIS Pro, R).

Training and skills

Students will be awarded CENTA2 Training Credits (CTCs) for participation in CENTA2-provided and ‘free choice’ external training. One CTC equates to 1⁄2 day session and students must accrue 100 CTCs across the three years of their PhD.

You will receive training in a broad array of skills that will prepare you for a career in the environmental sciences: biological / environmental computing and programming (e.g. GIS, bash scripting, R, Linux), mathematical modelling, molecular genetic analysis, manuscript preparation and oral presentation.

In addition to CENTA training you will receive tailored training from:

Supervisors directly (e.g. mathematical modelling, population genetics theory, bioinformatics, GIS).
Ad hoc participation in University of Leicester MSc courses (e.g. Molecular Genetics, Geographical Information Science).
University of Leicester courses (e.g. R, Python).

Partners and collaboration

Dr Rob Hammond has worked on Hymenoptera, especially, L.acervorum, for 20+ years and is experienced in molecular genetics, and the analysis of next generation sequencing data. Dr Nick Tate is an associate professor of the GIS and Remote Sensing Research Group with 20+ years of experience in GIS. Dr Fabian Freund is a mathematical population geneticist with 10+ years’ experience in applying mathematical techniques to biological problems.

Further details

Further details on how to contact the supervisor for this project and how to apply for this project can be found here:

For any enquiries related to this project please contact Dr Rob Hammond (email: [email protected], phone: 0116 252 5302, webpage: https://le.ac.uk/people/rob-hammond).

To apply to this project:

You must include a CENTA studentship application form, downloadable from: CENTA Studentship Application Form 2024.
You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.
Please submit your application and complete the host institution application process via: https://le.ac.uk/study/research-degrees/funded-opportunities/centa-phd-studentships. Please scroll to the bottom of the page and click on the “Apply for NERC CENTA Studentship” button. Your CV can uploaded to the Experience section of the online form. The CENTA application form 2024 can be uploaded to the Personal Statement section of the online form. Please quote CENTA 2024-L6-CENTA2-GENE3-HAMM  when completing the application form.

Applications must be submitted by 23:59 GMT on Wednesday 10th January 2024.

Possible timeline

Year 1

Literature review and training in GIS and mathematical modelling. Development of mathematical models (objective 1) and GIS modelling (objective 3).

Year 2

Paper preparation from mathematical modelling. Fieldwork in Spain collecting ants / testing predictive GIS models. DNA extraction and sequencing and diploid male estimation (objective 2).

Year 3

Analysis of genetic data, paper preparation, international conference presentation, thesis preparation and submission.