Daphnia represent sentinel species in assessing the health of freshwater systems, and are key indicators of ecosystem resilience to environmental change1. Fundamental to their survival is being able to enter a specialised dormant state, termed diapause, to avoid unfavourable conditions. Seasonal changes in many environmental factors (light, temperature, food availability etc.) program the diapause response, and this shifts populations from a cycle of asexual reproduction to the sexual production of diapausing eggs (Fig. 1)2.  This switch plays a fundamental role in regulating Daphnia phenology, in turn influencing freshwater food webs and nutrient cycling. While most diapausing embryos resume development the following spring, some do not and can remain viable in lake sediments for hundreds of years 3.  This provides a unique window into examining the ecology of historic populations (resurrection ecology4), as well as understanding what biological processes enable such prolonged periods of suspended animation. Through our ongoing work with the Daphnia Genomics Consortium (DGC), Daphnia is emerging as one of the best characterized genomic systems5, yet we currently know almost nothing about the molecular mechanisms underpinning Daphnia diapause, including how they cope with environmental stresses during dormancy.  Yet this information is critical to modelling the impact of continued environmental change on freshwater systems.

Core objectives of the project are:

  1. i) Provide the first molecular characterisation of diapause in Daphnia using both ‘omic and systems biology approaches; ii) Quantify the stress tolerance limits of diapausing embryos to determine tipping points in population survival. iii) Determine how the decision to enter diapause is affected by increased pollution and climate change.
Life cycle of Daphnia magna6.


Standard Daphnia culturing protocols for asexual and sexual reproduction.

Objective 1: Next-Gen  RNA sequencing of transcriptional changes underpinning key transition points in diapause vs. non-diapause pathways (Fig 1).

Objective 2: Standardised stress treatments and survival assessments. RT-PCR and metabolomic analysis of responses to stress treatments in diapause vs non-diapause embryos.

Objective 3: Climate change environment simulations and pollution dose treatments combined with monitoring of life history trajectories through to diapause termination.  RNAseq (comparison with Obj. 1) to determine disrupted processes.

Training and Skills

CENTA students will attend 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. 

SH, JC and LO are based within the Biosystems and Environmental Change (BEC) theme, providing training in the use of state-of-the art facilities at the vanguard of systems biology and environmental research. The DR will receive specialist training in high throughput sequencing and bioinformatic analysis as well as culturing Daphnia under different environmental scenarios.  They will also become expert in addressing key knowledge gaps in our understanding of Daphnia biology and freshwater systems more widely. 


Year 1: Establish control Daphnia cultures, conduct time series assessment of transcriptional changes (RNAseq) underpinning key transitions in the diapause vs. non-diapause life history pathways (Fig 1.). Expose cultures to different environmental scenarios mimicking predicted climate change and/or pollution levels to determine impact on diapause phenotypes.

First UK Conference end of Yr 1

Preparation of manuscripts for publication.

Year 2: Continue with analysis of RNAseq data.  Quantify the stress tolerance limits (range of stressors) of diapausing embryos, to determine tipping points/at what point local extinction might occur.  Contrast stress response of diapause vs. non-diapause embryos – RTPCR of key stress genes.

Ongoing submission of manuscripts.

Year 3: RNAseq treatments identified in Yr 1 that disrupt diapause pathway to discern mode of action.  Identify targets for diapause termination based on candidate mechanisms from RNAseq time series.

International conference and ongoing submission of manuscripts.

Partners and collaboration (including CASE)

This collaborative partnership between SH, JC and LO at UoB, integrating expertise and multidisciplinary approaches in genomics, physiology and ecology. SH is a world expert on diapause and stress biology.  JC leads the DGC, and LO is an expert in Daphnia resurrection ecology.

Further Details

Any further questions about the project, please contact:

Dr Scott Hayward

School of Biosciences

University of Birmingham

e-mail: s.a.hayward@bham.ac.uk