Seascape genomics of Antarctic deep-sea coral: Groundtruthing larval dispersal models with genetic connectivity data

CASE award with Centre for Environment Fisheries and Aquaculture Science (Cefas) (TAYLOR_E20ARIES)

Seascape genomics of Antarctic deep-sea coral: Groundtruthing larval dispersal models with genetic connectivity data

CASE award with Centre for Environment Fisheries and Aquaculture Science (Cefas) (TAYLOR_E20ARIES)

Project Description

Supervisors

Dr Michelle Taylor, School of Life Sciences, University of Essex

Dr Oliver Hogg, Centre for Environment Fisheries and Aquaculture Science (Cefas)

Dr Rebecca Ross, Institute of Marine Research, Norway

CASE studentship to investigate connectivity of Southern Ocean deep-sea coral; a rare opportunity to verify larval dispersal models with genomic data.

Scientific background

Detailed understanding of dispersal and genetic connectivity is critical in determining processes underpinning population persistence and productivity, speciation, appropriate scales for management, and the potential for recovery from detrimental impacts e.g. climate change and/or fishing.

Larval dispersal models (LDMs) integrate mathematical hydrodynamic models with species’ biological data to predict population connectivity. They are economical, in time and effort, compared to genetic connectivity research (no sampling/expensive laboratory analyses). For this reason, LDMs are increasingly used in marine environments to investigate connectivity (Ross et al., 2016; 2019), especially in areas challenging to sample, e.g. deep sea. However, very few LDMs are validated with genetic connectivity data. This project creates LDMs and then compares outputs with ground-truthed genomic connectivity data – a combined approach called “seascape genomics” (Selkoe et al., 2016). By using environmental data alongside genomic data, the drivers of connectivity across this rapidly-changing region are investigated. The study focuses on deep-sea octocorals from sub-Antarctic UK overseas territories – some are MPAs giving this project an applied output with great potential for management impacts.

Research methodology

Collate oceanographic and environmental datasets and investigate the utility of various oceanographic models, combined with Lagrangian particle simulators, to predict larval dispersal in deep-sea octocorals. Compare dispersal model outputs with known genomic connectivity between study sites. Research will be undertaken at UoE using a high performance computing server. On regular visits to Cefas, model utility will be assessed and outputs integrated into practical protection measures.

Training

Mathematical modelling – Oceanographic models and Lagrangian particle simulators.

Mapping/geographic data analyses skills using ArcGIS / QGIS / R.

Analysing genomic connectivity data – STACKS, BAYESCAN, STRUCTURE, and adegenet in R.

Communicating science to policy makers (minimum 3 months at Cefas).

Person specification

This PhD suits a quantitatively-minded candidate with some experience in statistical or mathematical modelling. Suitable degrees could cover topics such as genetics, MTH, physics and/or biologists with an interest in modelling. Essential – working knowledge and experience in R/ Matlab, Desirable – an interest in deep-sea ecology.

References

  • Ross, R. E., W. A. M. Nimmo-Smith, et al. (2016). Increasing the depth of current understanding: Sensitivity testing of deep-sea larval dispersal models for ecologists. PLOS ONE 11(8): e0161220.
  • Ross, R.E. et al. (2019). Modelling marine larval dispersal: a cautionary deep-sea tale for ecology and conservation. bioRxiv, https://doi.org/10.1101/599696
  • Selkoe KA, et al. (2016). A decade of seascape genetics: contributions to basic and applied marine connectivity. Mar Ecol Prog Ser. 554:1-19
  • Taylor, M. L., & Roterman, C. N. (2017). Invertebrate population genetics across Earth's largest habitat: The deep‐sea floor. Molecular Ecology, 26(19), 4872-4896.
  • Hogg, O. T., Huvenne, V. A., Griffiths, H. J., Dorschel, B., & Linse, K. (2016). Landscape mapping at sub-Antarctic South Georgia provides a protocol for underpinning large-scale marine protected areas. Scientific Reports, 6, 33163.

Key Information

  • This project has been shortlisted for funding by the ARIES NERC Doctoral Training Partnership, and will involve attendance at mandatory training events throughout the course of the PhD.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship - UK and EU nationals who have been resident in the UK for 3 years are eligible for a full award.
  • Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses in the subject area (see https://www.aries-dtp.ac.uk/supervisors/additional-funding/).
  • This studentship will start on 1st October 2020, and the closing date for applications is 12:00 on 7th January 2020.
  • Shortlisted applicants will be interviewed on 18/19 February 2020.
  • For further information, please contact the supervisor.
  • Please note that the joint NERC-ESRC ARIES-SeNSS studentship projects have different deadlines and funding arrangements. For full details please visit https://senss-dtp.ac.uk/aries-senss-joint-studentship, or contact SeNSS.dtp@uea.ac.uk.

Studentship Open for Applications

Please apply by sending a CV (including contact details of two academic referees) and a cover letter explaining your motivation and suitability for the PhD.

They should be sent to Emma Revill  ariesapp@essex.ac.uk  by 7th Jan 2020