Project Description
There is a pressing need to better understand movement patterns and complex life histories of migratory sharks to aid conservation efforts. With important ecosystem-wide effects which cascade down trophic levels the life-history characteristics of sharks (late maturity, slow growth, increased longevities, low reproductive output) leave them vulnerable to human exploitation and environmental change. Quantifying resilience to these changes allows us to predict a species´ future response. Information on the routine distribution of such keystone species across habitats during time and space at different stages of their life-histories is unknown, despite advances in tagging technology. To resolve this knowledge gap, this project aims to reconstruct the environmental histories, feeding and movement patterns of the migratory spurdog shark (Squalus acanthias) by utilizing natural biochemical ‘tags’ (stable isotopes, trace elements) as environmental/trophic proxies1. Currently classed as vulnerable worldwide but endangered in the North-East Atlantic, it is prohibited to commercially fish for spurdog in EU and UK waters, yet paradoxically when spurdog aggregate they are accidentally caught in such large numbers to be considered a choke species in some fisheries. Understanding the basis of these gatherings, their composition, and relevance to this species´ marine functional connectivity is crucial to conservation management.
Cartilage growth rings act as environmental fingerprints and will be analyzed using laser ablation to investigate shifts in habitat use and migration during the lifetimes of individuals. To complement this analysis, the student will use an environmental genomics approach3 to better understand how the genomic characteristics of individuals adapt them to the environmental conditions they experience during their lifetime. Our annotated spurdog genome will allow identification and potential function of genes identified by this approach. Understanding the genetic basis of adaptation in spurdog is critical as their aggregations contain closely related individuals2 and loss of kin groups can rapidly erode genetic diversity of stocks, increasing their vulnerability to climate change. Additional elasmobranchs (white sharks, thornback rays) can be similarly studied, allowing comparison of lifestyles contrasting with spurdog to identify generalizations of ecological life-history reconstructions with genomic markers associated with life-history traits.
Key questions could include: What does the time series of environmental proxies tell us about the habitat(s), locations, migrations, and trophic level(s) an individual experienced during its lifetime? Do estimates of field metabolic rate vary during an individual´s lifetime, with habitat/trophic level, within/between kin aggregations? What associations are there between environmental proxies and genomic data, and how much variation is there within/between recognized aggregations/populations? How do these estimates vary between species, and what ecological/phylogenetic explanations might account for these observations?
The successful applicant will join a group of passionate marine conservation biologists at Aberdeen. Oceans cover more than 70% of the Earth, hosting almost every major phyla, and deliver multiple ecosystem services, several of which shape our society for instance through the provision of food. Hence sustainable management of the seas is vital. Yet, protection of seas lags way behind terrestrial habitats. Marine ecosystems are highly vulnerable to anthropogenic pressures, and most experience multiple threats (habitat loss, overfishing and temperature rise). Over the last 100 years, 90% of marine top predators have disappeared, with many coastal and oceanic habitats lost or severely damaged. Unprecedented losses in marine biodiversity are occurring hence informed actions are needed to mitigate these. Improving knowledge on marine connectivity is a crucial first stage towards understanding these changes and developing ways to promote the resilience of species and habitats to global change.
Essential & desirable candidate skills
Essential: Interest in ‘biochemical tags’ using analytical chemistry (stable isotopes) and their application of conservation biology; Interest in genetics/genomics approaches to conservation. Experience in data handling/statistics.
Desirable: Experience in bioinformatics and population genomics/genetics and/or analytical chemistry and use of stable isotopes.
Photo credit: Fenella Wood
Supervisors
Catherine JonesPrimary Supervisor: | Profile: Catherine Jones Email: c.s.jones@abdn.ac.uk Institution: University of Aberdeen Department/School: School of Biological Sciences |
Andrew MehargSecondary Supervisor: | Profile: Andrew Meharg Email: aa.meharg@qub.ac.uk Institution: Queen's University, Belfast Department/School: School of Biological Sciences |
Kara LaytonAdditional Supervisor: | Profile: Kara Layton Email: kara.layton@abdn.ac.uk Institution: University of Aberdeen Department/School: School of Biological Sciences |
References
Delaval, A., Frost, M., Bendall, V., Hetherington, S. J., Stirling, D., Hoarau, G., Jones, C. S. & Noble, L. R. (2022). Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis. Evolutionary Applications, 15(1), 78-94. https://doi.org/10.1111/eva.13327
Delaval, A. N., Bendall, V., Hetherington, S., Skaug, H., Jones, C.S. & Noble, L. R. (2022). Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population. Evolutionary Applications. https://doi.org/10.1111/eva.13474
Schwanck, T. N., Delaval, A., Noble, L. R., Wright, P. J., Donnan, D. & Jones, C. (2022). The complete mitochondrial genomes of the flapper skate Dipturus intermedius and the longnose skate Dipturus oxyrinchus. Mitochondrial DNA Part B: Resources, 7(5), 897-899. https://doi.org/10.1080/23802359.2022.2064248
Delaval, A., Wagner, C. I., Schwanck, T., Wood, F. R., Jones, C. S., Hoarau, G. & Noble, L. R. (2021). Endangered Coastal Elasmobranchs of the North-East Atlantic. In Reference Module in Earth Systems and Environmental Sciences Elsevier. https://doi.org/10.1016/B978-0-12-821139-7.00094-5
Lieber, L., Hall, G., Hall, J., Berrow, S., Johnston, E., Gubili, C…… Jones, C.S. & Noble, L.R. (2020). Spatio-temporal genetic tagging of a cosmopolitan planktivorous shark provides insight to gene flow, temporal variation and site-specific re-encounters. Scientific Reports, 10, [1661].https://doi.org/10.1038/s41598-020-58086-4
Delaval, A., Schwanck, T., Kopp, M. E. L., Hoarau, G., Jones, C. S. & Noble, L. R. (2020). The complete mitochondrial genome of the blue skate Dipturus batis. Mitochondrial DNA Part B: Resources, 5(3), 2488-2489. https://doi.org/10.1080/23802359.2020.1778572
Frost, M., Neat, F. C., Stirling, D., Bendall, V., Noble, L. R. & Jones, C. S. (2020). Distribution and thermal niche of the common skate species complex in the North-East Atlantic. Marine Ecology Progress Series, 656, 65-74. https://doi.org/10.3354/meps13545
Thorburn, J., Neat, F., Burrett, I., Henry, L-A., Bailey, D. M., Jones, C. S. & Noble, L. R. (2019). Ontogenetic Variation in Movements and Depth Use, and Evidence of Partial Migration in a Benthopelagic Elasmobranch. Frontiers in Ecology and Evolution, 7, [353]. https://doi.org/10.3389/fevo.2019.00353
Jeffery, N.W., Lehnert, S.J., Kess, T., Layton, K.K.S., Wringe, B.F., & Stanley, R.R.E. (2022). Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy. Frontiers in Genetics. 22, 13:886494. https://www.frontiersin.org/articles/10.3389/fgene.2022.886494/full
Newth, J.L., Cromie, R.L., Brown, M.J., Delahay, R.J., Meharg, A. A. et al. Poisoning from lead gunshot: still a threat to wild waterbirds in Britain. European Journal of Wildlife Research 59, 195–204 (2013). https://doi.org/10.1007/s10344-012-0666-7
Expected Training Provision
This project provides training in core and generic skills, with cutting edge technologies (population genomics, bioinformatics, stable isotopes, multi-elemental fingerprinting) integrating Biodiversity and Earth Systems to translate findings into improved policy and practice for effective conservation management of endangered marine species.
Impact
This project promises to be both impactful and insightful because of its novel approach employing two disparate approaches to improve the precision at the individual level of profiling in terms of gene-environment interactions. As a valuable commercial species spurdog fisheries in the North Atlantic were exploited until they crashed. Currently commercial fishing for spurdog prohibited with the exception of bycatch. There are indications that the status of the NE Atlantic stock is improving yet the stock remains low compared to historic levels. Pressure to reopen spurdog fisheries in UK/European waters makes a better understanding of their movement ecology, aggregating behaviour, and genomics a vital precursor. Additionally, this species is an important epibenthic predator, so its abundance can have ecosystem-wide implications, making effective conservation a priority. Indeed, an over wintering area (Loch Etive) has been identified in Scotland, but conservation management, policy, and strategic positioning of potential marine protected areas require further spatio-temporal details on point of origin, pupping areas, aggregation sites, and ontogeny of environmental preferences in relation to movements.
This work will measure genetic diversity in sharks and contributes to the growing debate concerning the need for global conservation policy to action the largely neglected protection and monitoring of genetic diversity—one of the three main pillars of biodiversity.
A tractable, easily caught, and widespread sport fish, the spurdog is used extensively in biomedical research, encouraging production of an annotated genome. Its abundance in coastal locations, such as Scottish sea lochs, for which high resolution environmental datasets exist make it the ideal elasmobranch to develop as a model for integrating environmental reconstructions with genomic parameters to develop more precise models of genotype-environment interactions.
Proposed Supervision
The Aberdeen elasmobranch research group lead by Cath Jones investigates the conservation genetics and connectivity of many marine top predators from coastal batoids including the largest European skate, the critically endangered flapper skate, it’s close relative the blue skate to small benthic sharks like the spurdog, through to iconic oceanic sharks such as white sharks, porbeagles and basking sharks1-8. The group is interested in the role of marine protected areas (MPAs) and the challenges this brings for protecting highly migratory species. One of our ongoing projects funded by Save Our Seas Foundation involves developing monitoring tools for North-east Atlantic elasmobranchs. https://saveourseas.com/project/a-genetic-tool-to-help-monitor-sharks-and-skates-in-the-north-east-atlantic/
Co-supervisor Kara Layton at Aberdeen uses field and lab systems alongside genomic tools to resolve systematic and biogeographic patterns in marine taxa, to identify drivers of marine speciation and adaptation and to predict how biodiversity will respond to future climate change. Additionally, Kara is interested in the application of ‘omic tools’ to assist the design of MPAs9. Training in genomic approaches and associated bioinformatic analyses will be provided at Aberdeen.
This studentship is unique in having a co-supervisor at Queens University Belfast, Andy Meharg, whose research focuses on how harmful toxins such as arsenic, make their way from the soil, into crops, and on into the human and animal food chain. Andy also applies his expertise in trace element fingerprinting and stable isotope analysis to wildlife issues10. Training will be provided in Andy’s lab in trace element fingerprinting and stable isotope analysis using laser ablation ICP MS to reconstruct the ecological life history.
Proposed Timetable
Year 1: Compile existing metadata for aggregation samples; literature review. Identify appropriate additional training courses (e.g. stable isotope and trace element analyses, population genomic and bioinformatic analyses). Establish a protocol for trace element fingerprinting and stable isotope analysis of spurdog vertebrae collected from bycatch aggregations to reconstruct the ecological life history. Vertebrae will be cleaned and sectioned to expose growth bands. Elemental profiles will be quantified from the focus of the vertebral centrum to its edge using laser ablation ICP MS, thereby encompassing the complete life history of the individual. Individuals will be categorized according to cohort using a published growth model.
Year 2: Vertebral elemental patterns will be compared between capture localities, between juveniles, subadults and adults to investigate ontogenetic shifts in habitat use and metabolism. Elemental patterns will be investigated from skeletal and white muscle to allow for additional samples from localities where vertebral material is unavailable. Paper 1 – reconstructed environmental life history profiling. Obtain and curate genome-wide single nucleotide polymorphisms from existing and additional material. Conduct population genomic analyses and relatedness estimates, together with environmental/seascape genomics to identify outlier sequences, or those associated with specific behaviours (such as migration) or environmental parameters. Scan the available annotated genome of the spurdog to identify the gene region(s) associated with SNPs identified from these analyses. Where necessary employ molecular strategies to explore these gene regions further. Assess the potential for design of specific SNP assays for monitoring in additional spurdog populations. Paper 2 – genotype-environmental interactions.
Year 3: Additional elasmobranch material (white shark and thornback rays) can be used to compare lifestyles contrasting with that of spurdog. These will be considered for further ecological life-history reconstructions and identification of genomic markers associated with life-history traits. Paper 3 – Cross-species comparisons of ecological and genomic interactions.
Year 4: Thesis write up.
QUADRAT Themes
- biodiversity
- earth-systems
- environmental-management
Partners
Not applicable at this time.
