Past and Current research

Current Research Projects

Pinniped diet reconstruction using metabarcoding and bias corrections based on quantitative metabarcoding methods (Contract WDFW ongoing)

Research contracted by WDFW Marine Mammal researchers to take the updated methods, create valid corrections for digestion and tissue makeup bias in mtDNA detection, and implement a previously validated Bayesian model to correct for PCR amplification bias to sequencing results. All resulting in a more accurate assessment of diet proportion from pinniped scat. 

Development and validation of a long-read sequencing assay to determine Chum sex proportions and/or stock ID from pinniped scat samples using MinION nanopore sequencing technology (Contract WDFW ongoing)

Based on results from previous exploration studies, we are aiming to find targeted long-read sequencing methods, test them and validate them for use in identifying threatened Chum runs in pinniped scat and/or the proportion of male and female salominds in the prey via scat sampling.

Effect of extreme tidal events as future sea-level rise scenarios on Heʻeia fish communities in areas of biocultural restoration (Contract University of Hawaii ongoing)

Bioinformatics and statistical analysis of eDNA metabarcoding data to assess the effect of extreme tidal events as a proxy for future sea-level rise on fish communities in an estuary on O'ahu undergoing indigenous biocultural restoration of land and sea management. Working to assist researchers and native communities in Hawaii to address climate change impacts with molecular ecology. 

Past Research Projects

Feasibility of the use of Nanopore technology for prey identification from sea lion scat (Contract WDFW 2022-2023)

Research contracted by WDFW Marine mammal researchers to determine the feasibility of using longer read sequencing via nanopore technology to obtain genetic information of prey from sea lion scat.

Development of GTseq panel for individual ID of harbor seals from scat (Contract WDFW 2022-2023)

Research contracted by WDFW Marine mammal researchers to develop a GTseq panel for the identification of individual harbor seals from their scats in order to determine individual specificity of diets.

Modification and updating of diet metabarcoding methods for pinnipeds (Contract WDFW 2022-2023)

Research contracted by WDFW Marine mammal researchers to update and improve the metabarcoding methods used by WDFW to measure diet from pinniped scats.

Single species detection with CRISPR Cas12a/Cas13a

Research granted by WSDOT to develop easy-to-use CRISPR Cas12a/Cas13a assays to detect endangered species in aquatic systems for environmental risk assessments.

Isothermal Cas12a assays for wildlife pathogen detection in eDNA samples

Develop easy-to-use CRISPR Cas12a/Cas13a assays to detect bacterial pathogen (Renibacterium salmoninarum) DNA from water samples to speed up management decisions for antibiotic treatment in hatcheries. 

Molecular laboratory techniques: Easy/fast DNA extraction method development/use, primer design, CRISPR Cas guide RNA design, isothermal amplification, CRISPR enzymatic assay design and implementation, lateral flow test development.

Implementing eDNA methods to assess changes in community and salmon movements during restoration of creeks

Using eDNA technologies to update NEPA-style environmental impact assessments, validate method for governmental use via use case in salmon bearing creeks undergoing restoration.

Molecular laboratory techniques: DNA extraction, PCR, library preparation. Bioinformatics using Python and R platforms to handle sequence data and analyze results. 

Microbial community changes throughout the gastrointestinal tract of two wombat species

Characterize the microbiota throughout the gastrointestinal tract of a common wombat and a southern hairy nose wombat. Determine the distribution of fermenting bacteria which contribute to their digestion of plant matter. 

Molecular biological techniques such as DNA extraction, PCR and DNA quality assessment were used before high-throughput amplicon sequencing was conducted. Use of Qiime2 in Python and R statistical packages were used to computationally analyze the amplicon sequence data. 

Congenital diseases in harbor seals from the Salish Sea

Characterize the congenital diseases found through necropsies of harbor seals in Washington state, US. Using retrospective data we characterized the types of congenital diseases in a wild marine mammal population, as well as their prevalence, distribution, and associated spatiotemporal trends.

Microbial connections between salmon aquaculture and wild fur seals in Tasmania

Assessing microbial community shifts in fur seals around Tasmania based on their foraging on farmed salmon through a large-scale comparative study of both fur seal and salmon gut microbiota. Identifying any potential pathogenic bacteria in fur seal populations of Tasmania, specifically any being shared between farmed salmon and fur seals. Determine presence and characteristics of antimicrobial resistant pathogenic bacteria in fur seals guts due to exposure to farmed salmon industry activities.

Skills used to complete these research objectives included: marine mammal captures and handling in the field, necropsies, sample collection and processing, bacterial culture of potential pathogens, DNA extraction, PCR, sequence analysis, direct antimicrobial susceptibility testing, epidemiological analysis and metagenomic analysis/bioinformatics.    

Re-emergence of Guadalupe fur seals in the Pacific Northwest: The epidemiology of strandings 2005-2016

Conducting stranding response, necropsies, data collection and management, then analyzing associated health and demographic data to discern spatiotemporal trends in strandings and causes of death for a threatened marine mammal.

Terrestrial predation and scavenging effects on haul-out dynamics of Harbor Seals

Master’s thesis study on the effects of a novel and frequent predation and scavenging at a harbor seal haul-out by raccoons and coyotes.

Maternal traits effect on rearing success in Harbor Seals

Master’s thesis study on the effects of age, pupping history, mass and behavior on the rearing success of female harbor seals as determined by the health and size of the pup at weaning. 

PUBLICATIONS

D’Agnese, E., Chase, D. M., & Andruszkiewicz-Allan, E. (2023). Isothermal recombinant polymerase amplification and CRIPSR (CAS12A) assay detection of Renibacterium salmoninarum as an example for wildlife pathogen detection in environmental DNA samples. Journal of Wildlife Diseases, 59(4), 545-556.

Allan, E. A., Kelly, R. P., D'Agnese, E. R., Garber‐Yonts, M. N., Shaffer, M. R., Gold, Z. J., & Shelton, A. O. (2023). Quantifying impacts of an environmental intervention using environmental DNA. Ecological Applications, 33(8), e2914.

D’Agnese, E., McLaughlin, R. J., Lea, M. A., Soto, E., Smith, W. A., & Bowman, J. P. (2023, June). Comparative Microbial Community Analysis of Fur Seals and Aquaculture Salmon Gut Microbiomes in Tasmania. Oceans (Vol. 4, No. 2, pp. 200-219). MDPI.

Gold, Z., Shelton, A., Casendino, H., Duprey, J.,Gallego, R., Van Cise, A., Fisher, M., Jensen, A., D’Agnese, E., Andruszkiewicz-Allan, E., Ramon-Laca, A., Garber-Yonts, M., Labare, M., Parsons, K., Kelly, R. (2023) Distinguishing Signal from Noise: Understanding Patterns of Non-Detections to Inform Accurate Quantitative Metabarcoding. Plos one, 18(5), e0285674.

Shelton, A., Gold, Z., Jensen, A., D'Agnese, E., Andruszkiewicz-Allan, E., Van Cise, A., Gallego, R., Ramón-Laca, A., Garber-Yonts, M., Parsons, K., Kelly, R. Toward quantitative metabarcoding. Ecology. 2022. 104( 2): e3906. https://doi.org/10.1002/ecy.3906

Penrose, B., MacIntosh, A., Parbhakar-Fox, A., Smith, L., Sawyer, T., D'Agnese, E., Carver, S. Heavy Metal Wombats? Metal Exposure Pathways to Bare-Nosed Wombats (Vombatus Ursinus) Living on Remediated Tin Mine Tailings. STOTEN. 2022. 835:155526. http://dx.doi.org/10.2139/ssrn.4034521

Eisenhofer, R., D’Agnese, E., Taggart, D., Carver, S., Penrose, B. Microbial biogeography of the wombat gastrointestinal tract. PeerJ. 2022. 10: e12982 https://doi.org/10.7717/peerj.12982

D’Agnese, E., Lambourn, D., Olson, J.K., Huggins, J., Raverty, S., Garner, M., Calambokidis, J., Scott, A., Jeffries, S., Gaydos, J.K. Congenital disease in harbor seals (Phoca vitulina richardsii) from the Salish Sea. Journal of Wildlife Disease. 2021. 57(3): 672-677. https://doi.org/10.7589/JWD-D-20-00179

D’Agnese, E., Lambourn, D., Rice, J., Duffield, D., Huggins, Spraker, T., Raverty, S., Kuzmina, T., Grigg, M., Smith, W. Re-emergence of Guadalupe fur seals in the Pacific Northwest: The epidemiology of stranding events during 2005-2016. Mar Mam Sci. 2020. 1-18. https://doi.org/10.1111/mms.12678

D’Agnese, E.R. A One Health Approach to the effects of Fisheries and Aquaculture on Recovering Fur Seal Populations. 2020. UC Davis Dissertation Collection.

Warlick, A.J., Duffield, D.A., Lambourn, D.M., Jeffries, S.J., Rice, J.M., Gaydos, J.K., Huggins, J.L., Calambokidis, J., Lahner, L.L., Olson, J., D'Agnese, E., et al… Spatio-Temporal Characterization of Pinniped Strandings and Human Interaction Cases in the Pacific Northwest, 1991-2016. Aquatic Mammals. 2018. 44(3), pp. 299-318.

D'Agnese, E.R. The effect of maternal traits on rearing success in pacific harbor seals (Phoca vitulina richardsii). 2015. WWU Masters Thesis Collection. 425.