Funded Phd – Seascape genomics of Antarctic deep-sea coral: Groundtruthing larval dispersal models with genetic connectivity data. Deadline 7th Jan 2020!
Full details here.
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.
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.
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).
This PhD suits a quantitatively-minded candidate. Suitable degrees could cover topics such as genetics, mathematics, physics and/or biologists with an interest in modelling. Essential – some experience in statistical or mathematical modelling. Desirable – working knowledge and experience in R/ Matlab, an interest in deep-sea ecology.
How to apply
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 to Emma Revill email@example.com. If you have any questions please feel free to contact any member of the supervisory team
Projects looking for someone to make their own:
MSD (1 yr Masters project) – Stylasteridae habitat suitability modelling
Stylasteridae, lace corals, are the second most speciose group of calcifying corals (290 species; Linder et al., 2014, Zootaxa) with a global distribution (Arctic to Antarctic) and living from shallow (0m) to deep areas (2789m; Cairns, 2011, PLoS ONE). They are classified as forming vulnerable marine ecosystems (United National General Assembly UNGA, 2007; 2009) and play a central role in deep-sea ecosystems and the carbon cycle. Fishing interactions with VMEs are an ever-increasing problem in deep-sea areas (Victorero et al., 2018, Front. Mar. Sci) and there is strong evidence that stylasterids are especially vulnerable to fishing damage (Taylor, 2013, Imperial College London). With stylasterids living at or below the aragonite saturation horizon they may be close to their environmental tolerances – an important consideration with ongoing ocean acidification. Learning more about what environmental factors define where stylasterid coral exist is therefore an important undertaking. One method would be to look the drivers of habitat suitability. Habitat suitability models involves investigating what common environmental factors occur in locations where stylasterids are found and then projecting where other similar areas are located.
Global environmental data layers e.g. bathymetry (for aspect, roughness etc), oxygen concentration, temperature etc, will be collected. Stylasterid locations from the database will be used to investigate what factors are driving stylasterids presence.
Student will learn data harvesting, data collection, database creation, map creation programmes (ARCgis and /or QGIS), presence-only habitat suitability modelling analyses (ENFA, Maxent). This project would suit a candidate who is interesting in large-scale global processes, the deep-sea, and whom has an interest in mathematical modelling.
Masters research projects:
1. Resource partitioning and niche differentiation in herbivorous coral reef fish
Supervisors: Amy Sing-Wong and Dr Michelle Taylor
Herbivorous coral reef fish are known to provide crucial functional process to the ecosystem through grazing activity. Environmental change due to the compounding effects of global disturbances coupled with local pressures, it is evident to maintain the functional activity within the reef. The resilience of a reef can be largely down to the organisms which inhabit them which varies spatially and temporally. Herbivores can control and even prevent major regime shifts through algae grazing (Edwards et al., 2014). Herbivores can be further divided into secondary functional groups (Green and Bellwood, 2009), which can reveal finer partitioning within this guild. Herbivorous fish and their realised niche (actual utilisation of the biotic and abiotic environment) are poorly understood (Brandl and Bellwood, 2014).
In order to investigate the functional niche/resource partitioning within secondary functional groups, we can view differences in their behavioural traits through video analysis, and morphological traits (Kelly et al., 2016) in order to model the functional niche (Mouillot et al., 2005; Villéger et al., 2011; Fox and Bellwood, 2013).
Overarching Aim: To understand the underlying mechanisms in which functionally similar fish are able to co-exist and partition resources.
Skills gained: Video analysis, fish identification, benthic identification, ethogram development, statistical analysis, niche modelling,
Outcome: This is part of a wider project and has the potential to be published, as part of the project or even as single paper (result dependent).
Suitability: Interest in coral reef ecosystems, behavioural ecology, functional ecology, community ecology, statistics and modelling.
– Total of 45 videos, approximately 20 – 25 mins long (Species dependent, minimum observation time study already complete).
– 3 fish species, Acanthuridae family – Acanthurus pyroferus, Zebrasoma scopas & Ctenochaetus binotatus
– Data collected from Hoga Island, Wakatobi National Park, SE Sulawesi, summer 2018
Brandl and Bellwood (2014) ‘Individual-based analyses reveal limited functional overlap in a coral reef fish community’, Journal of Animal Ecology. Edited by Hays, 83(3), pp. 661–670.
Edwards et al. (2014) ‘Global assessment of the status of coral reef herbivorous fishes: evidence for fishing effects’, Proceedings of the Royal Society B: Biological Sciences, 281(1774), pp. 20131835–20131835.
Fox and Bellwood (2013) ‘Niche partitioning of feeding microhabitats produces a unique function for herbivorous rabbitfishes (Perciformes, Siganidae) on coral reefs’, Coral Reefs, 32(1), pp. 13–23.
Green and Bellwood (2009) Monitoring Functional Groups of Herbivorous Reef Fishes as Indicators of Coral Reef Resilience A practical guide for coral reef managers in the Asia Pacifi c Region, Science.
Kelly, Eynaud, Clements, Gleason, Sparks, Williams and Smith (2016) ‘Investigating functional redundancy versus complementarity in Hawaiian herbivorous coral reef fishes’, Oecologia. Springer Berlin Heidelberg, 182(4), pp. 1151–1163.
Mouillot, Stubbs, Faure, Dumay, Tomasini, Wilson and Chi (2005) ‘Niche overlap estimates based on quantitative functional traits: A new family of non-parametric indices’, Oecologia, 145(3), pp. 345–353.
Villéger, Novack-Gottshall and Mouillot (2011) ‘The multidimensionality of the niche reveals functional diversity changes in benthic marine biotas across geological time’, Ecology Letters, 14(6), pp. 561–568.
2. An octocoral nursery: Using barcoding to investigate species ID of eggs found on deep-sea octocorals.
Involves genetic barcoding of deep-sea samples. Laboratory-based.
3. Are seamounts shark nursery habitats? Using video analysis to look at shark habitat in the deep sea.
Involves video analysis so is office-based. Work links with colleagues at the National Oceanography Centre.
Email Dr Taylor for more info : firstname.lastname@example.org
PhD self-funded research projects
I have a wealth of deep sea specimens and several PhD projects ready to go. At the moment these include:
Deep-sea population genomics and seascape genomics of bivalve across the North Atlantic
A global study of deep-sea connectivity of the solitary coral, Desmophyllum
Ocean-scale population genomics – from north to south Atlantic.
The above plethora of samples, with some sequencing and consumable finance, could answer are some interesting ecological questions. If you are interested in my field of research and join our lab as a postdoc here is a link to a list of fellowships: https://asntech.github.io/postdoc-funding-schemes/
Email me to discuss ideas.