JOB OPENING – Bioinformatician – Closing Date: 13 October 2021
Job Title and Grade: Research Officer (ASR); Grade 7
Contract: Fixed-term, Full-time. This post is fixed-term until 31 July 2022 due to funding.
Hours: Your hours of work are as required to perform the duties of your role, for a full-time employee this is normally 36 hours per week
Salary: £31,406 – £34,304 per annum
Purpose of role: Undertake genomic bioinformatic analysis of NGS data for population genomics and phylogenomics research
We are seeking an individual with a strong background in quantitative skills to conduct bioinformatic and genomic research within grant-funded deep-sea connectivity research. This is a full-time post for a contact of 9 months. The next generation sequencing data (in the form of ultra-conserved elements) is already available. We require a bioinformatician to clean, quality control, and analyse this data for two purposes i) analysis of population connectivity of 4 species of Antarctic deep-sea octocorals ii) phylogenomic analysis of deep-sea octocorals. This research is entirely computer-based so location (as long as you are eligible to work in the UK and have internet) is not constrained.
Full details: https://bit.ly/3oxdEh9
Interviews are planned for: TBC
Expected start date: 1 November 2021, or as soon as possible thereafter.
Projects looking for someone to make their own (research degrees at Essex start in Jan/April/Oct) :
MSD (1 yr Masters project): Do marine convergence zones form separate biomes?
It has long been seen that different marine communities are found in different water masses (Agogué et al., 2011; Cartes et al. 2014). Convergence zones between these waters masses have had less focus and there is a burgeoning body of evidence that these relatively small zones have distinct fauna from their neighbouring water masses (particulate organic carbon, microorganisms, Djurhuus et al., 2015; midwater Crustacea, Letessier et al., 2015; cephlapods, Laptikovsky et al., 2015).
This project will look at deep-sea video (collected from a ROV; remotely operated vehicle) from across a convergence zone to investigate if communities of VME (vulnerable marine ecosystems), such as corals and sponges, are distinct north, within, and south of the zone.
The student undertaking this research will learn about the metadata commonly collected in remotely operated vehicle surveys, how to format and use that data, the environmental data often used in large-scale deep-sea research, as well as fauna identifications from video, how such data is transcribed and collated, how image data sets are created and maintained, as well as standard community and diversity analyses.
Email firstname.lastname@example.org to discuss.
Agogué H, Lamy D, Neal PR, Sogin ML, Herndl GJ. 2011. Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Mol. Ecol. 20, 258–274.
Boersch-Supan PH, Rogers AD, Brierley AS. 2015. The distribution of pelagic sound scattering layers across the Southwest Indian Ocean. Deep Sea Res. Part II: Top. Stud. Oceanogr. 136, 108–121.
Cartes et al. 2014. Distribution and biogeographic trends of decapod assemblages from Galicia Bank (NE Atlantic) at depths between 700 and 1800 m, with connexions to regional water masses. Deep-sea Research II, 106:165-178.
Djurhuus A, Read JF, Rogers AD. 2015. The spatial distribution of particulate organic carbon and microorganisms on seamounts of the SouthWest Indian Ridge. Deep Sea Res. Part II: Top. Stud. Oceanogr. 136, 73–84.
Letessier TB, De Grave S, Boersch-Supan PH, Kemp KM, Brierley AS, Rogers AD. 2015. Seamount influence on mid-water shrimp (Decapoda) and gnathophausiids (Lophogastridea) of the South-West Indian Ridge. Deep Sea Res. Part II: Top. Stud. Oceanogr. 136, 85–97.
Laptikovsky V, Boersch-Supan P, Kemp K, Letessier T, Rogers AD. 2017. Cephalopods of the Southwest Indian Ocean Ridge: a hotspot of extreme biological diversity and absence of endemism. Deep Sea Res. Part II: Top. Stud. Oceanogr. 136, 98–107.
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.
Small projects – as part of a taught masters
- 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. Are seamounts shark nursery habitats? Using video analysis to look at shark habitat in the deep sea.
Video analysis – watching videos and recording incidences of shark eggs and sharks at sites around Greenland. Desk-based. Skills to learn and practice in this project include: benthic ID, shark ID, data collection, R, spatial statistics.
Work linked with academics at the National Oceanography Centre.
3. Deep-sea benthic communities of Marguerite Bay, Antarctica
Substantial data collection already completed. Requires “fresh eyes” to cross check video and community data. Novel community analyses required. Skills to learn and practice in this project would include: R, community statistics, and QGIS (map making).
Email Dr Taylor for more info : email@example.com
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.