Ponds provide clean freshwater environments in farmland and are vital habitats for aquatic biodiversity covering plants, invertebrates, amphibians, fishes, and mammals 1. Recent studies conducted by University College London (UCL) show that ponds are also important for farmland birds through the provision of insect food. In short, good ponds contribute to sustain aquatic biodiversity. In addition, by facilitating the migration of species across the landscape they play a central role in maintaining genetic diversity of species. Genetic diversity has long been accepted to be the foundation of biodiversity (e.g. 2). Regrettably, many ponds have been reclaimed for farming. In the Norfolk area (UK) farming intensification has been particularly severe post World War II (http://www.landscapes.org/researchers-offer-uk-ghost-ponds-new-lease-life/). In this area, many ponds have been claimed by farmers and filled with soil thus reducing landscape connectivity and creating a shortage of water supply. Pond density in this area has decreased from 46,000 farmland ponds before 1950s to just 23,000 today (E. Alderton, unpublished data). However these ponds are not lost and often damp depressions of ‘ghost’ ponds remain in place or former water reservoirs (https://ghostponds.wordpress.com/). Ghost ponds contain the buried sediments, seeds and eggs of the former pond community. By re-excavating these sites we may be able to fight loss of aquatic biodiversity and loss of genetic diversity at regional scale. The restoration of ghost ponds as a resource of biodiversity and genetic diversity is an itriguing one and may radically tranform conservation strategies to maintain or replenish regional bioversity.

This project will be the first to show whether the excavation of ghost ponds may contribute to fight loss of aquatic diversity, with a focus on genetic diversity of a keystone species, responsible for sustaining the food web of aquatic habitats.

The project has three main objectives:

Objective 1: Sample and characterize the genetic diversity of the keystone grazer Daphnia magna from ghost and established ponds in the Norfolk landscape.

Objective 2: Identify migration dynamics between ghost and established ponds via population genetic approaches and assess whether ghost ponds contribute to genetic diversity of established ponds.

Objective 3: Experimentally quantify the extent to which ghost ponds contribute to increase genetic diversity in the landscape.

Ghost pond


Objective 1: Field work. Sample the surface sediment of five ghost (already excavated) and several established surrounding ponds, potentially exchanging migrants. From each pond isolate several Daphnia genotypes and establish isoclonal lines.

Objective 2: Laboratory work. Perform DNA extraction and genotyping on isolates from objective 1 with at least 30 microsatellite markers arranged in multiplexes (following 3) and analyse data. Using population genetic software, identify the migration dynamics between excavated and established ponds.

Objective 3: Laboratory work. Perform competition experiments with isolates from the ghost and the established ponds in different ratios. Genotype laboratory populations after the competition experiment to quantify shifts in genotypic composition. This experiment will provide insights on the number of migrants from ghost ponds needed to increase genetic diversity on the landscape.

Training and Skills

CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to the student's projects and themes. 

The supervisors have a long track record of graduate and postgraduate supervision and have been collaborating on paleogenetic projects. The DR will receive training as field biologist and conservationist from Dr Sayer. He/she will receive training in experimental evolution and population genetics from Dr Orsini. Dr Orsini’ interest is deeply rooted in discovering the molecular targets of natural selection and their contributions to the process of adaptation. Her group at the UoB is part of the Joint Centre for Environmental Omics, which offers training in the most up to date ‘omics’ technologies. The DR will be offered training in these cutting-edge technologies as well as in population genetics.    


Year 1: resurrect Daphnia magna specimens from already excavated ghost ponds and established ponds; establish isoclonal lines of D. magna and collect tissue for DNA extraction and genotyping. Present project plan in a poster at the student conference in Birmingham

Year 2: perform DNA extraction and genotyping and complete data analysis using a suite of population genetic software. Identify migration dynamics between ghost and established ponds. Present preliminary data in a workshop or national conference. Prepare draft of first thesis chapter to be submitted for publication.

Year 3: perform competition experiments and quantify shifts in genotypic composition after the experiment to quantify the contribution of ghost ponds to the regional genetic diversity. Present thesis work in an international conference. Prepare draft of second thesis chapter for publications.

Partners and collaboration (including CASE)

This project merges the expertise of a passionate aquatic conservationist (Dr Sayer) and a population genomicist (Dr Orsini). The DR will have the unique opportunity to work at the interface of fundamental and applied science. He/she will likely contribute to introduce innovative conservation and restoration strategies to preserve or even enhance aquatic biodiversity. Furthermore, the DR will have the opportunity to be trained at two top universities in the UK, UCL London and University of Birmingham. Training at UCL London will happen via regular visits and stays. Throughout the PhD project regular progress report meetings will be arranged with the supervisor team to ensure the reaching of project milestones.

Further Details

For questions about the project contact:

Dr Luisa Orsini

School of Biosciences

University of Birmingham