Giant crab's dietary analysis as a proxy

Dietary analysis as a proxy for habitat biodiversity and integrity: A case study of the giant crab, a fishery under stress

Degree type

PhD

Closing date

6 March 2023

Campus

Hobart

Citizenship requirement

Domestic/International

About the research project

It is estimated that exploitable biomass of the giant crab has declined from a maximum of approximately 1500 tonnes in the early 1990's to 244 tonnes in 2009/10, equating to 16% of the original unfished exploitable biomass (Hartman and Gardner 2011). Total biomass and egg production have also decreased to 19% of their initial levels. The reasons for decline of stock levels could be diverse ranging from overfishing to habitat loss associated with damaging fishing practices such as deep-water trawling.  There is a clear concern about this stock and viability of its fishery. Therefore, a better understanding of habitat diversity, prey availability, stock structure and decoupling of fishery drivers are necessary to guide and sustainably manage the fishery into the future.

The project will combine morphological, observational and molecular approaches to analyse the faeces content of the giant crab as a proxy to infer dietary diversity of the species that may be diagnostic to fishing grounds along the East and West coasts of Tasmania. Specifically, the project will;

  1. Observe in situ habitat and prey diversity of the giant crab along the East and West coasts of Tasmania;
  2. Analyse spatial and temporal diversity of faeces content of the crab using a DNA meta bar code strategy; and
  3. Identify potential drivers that may be contributing to the habitat specific diversity observed in 1 and 2

Methods

Briefly, established in situ underwater field observation strategies will be deployed, including camera systems attached to traps used by commercial fishers and water samples for eDNA analysis. Crab samples from multiple fishing grounds along the coast of Tasmania will be obtained and their gut contents collected. Where available, these will be complimented with faecal samples. DNA extraction and meta barcoding will employ standard protocols. Taking into account the number of samples/sites available and the issues involving sampling times of the year, a suitable statistical analysis will be explored. For example, a Jaccard dissimilarity index of the presence/absence data will performed in R using the Vegan (Oksanen et al., 2016) and labdsv (Roberts, 2016) pack-ages. A nested nonparametric multivariate analysis of variance will be used to determine whether the giant crab diet differs significantly between the sampling areas, with pairwise comparison to ascertain the contribution of each sites. Nonmetric multidimensional scaling will be used to visualise relationship of sampling sites.  An estimate of indicator value (Dufrêne & Legendre (1997) will also be calculated to determine which taxa significantly influences potential differences in the giant crab diet between the coasts and among sites within each coast. Primarily the analysis will be limited to presence/absence data, but relative abundance of NGS reads will also be explored.

The project is directly aligned to the ongoing management of the Tasmanian giant crab fishery.

References

Berry, O., Bulman, C., Bunce, M., Coghlan, M., Murray, D. C., & Ward, R. D. (2015). Comparison of morphological and DNA metabarcoding analyses of diets in exploited marine fishes. Marine Ecology Progress Series, 540, 167–181.

Dufrêne, M., & Legendre, P. (1997). Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological Monographs, 67, 345–366.

Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.

Hartman, K and Gardner, C (2011). Tasmanian giant crab fishery. University of Tasmania. PP36

Oksanen, J., Guillaume Blanchet, F., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P R., O'Hara, R. B., Simpson, G. L., Solymos, P., Henry M., Stevens, H., Eduard Szoecs, E., Wagner, H. (2016). vegan: Community Ecology Package. R package version 2.3-0. (http://CRAN.R-project.org/package=vegan)

Pompanon, F., Deagle, B. E., Symondson, W. O. C., Brown, D. S., Jarman, S. N., & Taberlet, P. (2012). Who is eating what: Diet assessment using next generation sequencing. Molecular Ecology, 21, 1931–1950.
Roberts, D. W. (2016). labdsv: Ordination and Multivariate Analysis for Ecology. R package.

Primary Supervisor

Meet A/Prof Sean Tracey

Funding

Applicants will be considered for a Research Training Program (RTP) scholarship or Tasmania Graduate Research Scholarship (TGRS) which, if successful, provides:

  • a living allowance stipend of $28,854 per annum (2022 rate, indexed annually) for 3.5 years
  • a relocation allowance of up to $2,000
  • a tuition fees offset covering the cost of tuition fees for up to four years (domestic applicants only)

If successful, international applicants will receive a University of Tasmania Fees Offset for up to four years.

As part of the application process you may indicate if you do not wish to be considered for scholarship funding.

Eligibility

Applicants should review the Higher Degree by Research minimum entry requirements.

Additional eligibility criteria specific to this project/scholarship:

  • Applicants must be able to undertake the project on-campus

Selection Criteria

The project is competitively assessed and awarded.  Selection is based on academic merit and suitability to the project as determined by the College.

Essential criteria:

  • A degree (MSc, honours) in fields related to marine biology, physiology or molecular biology.

Desirable criteria :

  • Advanced molecular biology (including NextGen sequencing and or genomics) and quantitative ecology skills are highly desirable, so is experience in crustacean biology. Quantitative skills and familiar with programming languages such as R or MatLab.

Application process

There is a three-step application process:

  1. Select your project, and check you meet the eligibility and selection criteria;
  2. Contact the Primary Supervisor, A/Prof Sean Tracey to discuss your suitability and the project's requirements; and
  3. Submit an application by the closing date listed above.
    • Copy and paste the title of the project from this advertisement into your application. If you don’t correctly do this your application may be rejected.
    • As part of your application, you will be required to submit a covering letter, a CV including 2 x referees and your project research proposal.

Following the application closing date applications will be assessed within the College. Applicants should expect to receive notification of the outcome by email by the advertised outcome date.

Apply now Explore other projects

Why the University of Tasmania?

Worldwide reputation for research excellence

Quality supervision and support

Tasmania offers a unique study lifestyle experience