Project title

Diversity and distribution of sharks and rays in the Tropical Eastern Pacific using environmental DNA

Mentor name

Dr. Matthieu Leray, STRI Staff
leraym@si.edu, leray.upmc@gmail.com

Location

Naos Laboratories

Project summary and objectives

Human activities are responsible for major declines in population sizes and local species extinctions in most ecosystems across the globe. Marine “defaunation” has disproportionately impacted elasmobranchs (sharks and rays) because of their high economic value. A recent study estimates that the abundance of oceanic sharks has decreased by 71% since 1970 due to overfishing and that three-quarters of species may be at risk of extinction. Yet, the magnitude and ecological consequences of the decline of most coastal and highly mobile species, remain difficult to quantify because of the absence of historical data, and, as inherently shy and elusive animals, they are difficult to census and study. The paucity of information on the distribution and behavior of sharks and rays also challenges the design of effective conservation strategies.

Marine Protected Areas are increasingly advocated as a strategy for protecting and managing shark and ray populations. MPAs are meant to decrease fishing pressure while simultaneously reducing local stressors. Yet, they are often designed without sufficient information on the biology and ecology of sharks and rays. For MPAs already in place, substantial uncertainty remains regarding which species benefit and how. This is because many traditional surveys and monitoring methods for sharks and rays cannot deliver information at the pace needed to support conservation.

Every individual animal on Earth has a unique DNA signature. This genetic material is constantly shed in the surrounding environment in the form of blood, mucus, and waste. We are now able to isolate and sequence DNA barcodes from minute amounts of often degraded DNA molecules in seawater and sediment (environmental DNA or eDNA) to track sharks and rays, including apex pelagic species. We are taking full advantage of these methodological breakthroughs to ask key questions that are critical to advance shark conservation.

Our objectives are:

• Use highly sensitive eDNA sequencing approaches to characterize the distribution of species that have rarely or never been observed in the Tropical Eastern Pacific of Panama, although ecological and environmental conditions in the area suggest that they should be present. That includes low-density migratory apex sharks that potentially use areas of the Tropical Eastern Pacific as feeding and/or reproductive grounds, and endangered species (e.g., sawfish, hammerhead, and whale sharks).
• Identify seasonal migrations of commercially important and protected sharks and rays.
• Characterize the population dynamics of vulnerable sharks and rays using eDNA-based population genetics approaches.
• Develop genomic resources (low coverage genome sequencing) for species of sharks and rays of the Tropical Eastern Pacific.

Mentorship goals

Interns will work directly with a team of Latin American undergraduate and graduate students, with weekly meetings with academic mentor to discuss project goals and progress. Interns will be given the opportunity to participate in every component of this project (fieldwork, laboratory, and data analysis). The project involves the collection and processing of samples in remote locations for genetic analysis, training in the molecular laboratory, processing sequence data for population genetics analysis, analyses of community structure and mapping, and preparing oral and written communications for diverse audiences.

List of suggested readings

Boussarie, G., Bakker, J., Wangensteen, O. S., Mariani, S., Bonnin, L., Juhel, J.-B., Kiszka, J. J., Kulbicki, M., Manel, S., Robbins, W. D., Vigliola, L., & Mouillot, D. (2018). Environmental DNA illuminates the dark diversity of sharks. Science Advances, 4(5), eaap9661. https://doi.org/10.1126/sciadv.aap9661

Davidson, L. N. K., & Dulvy, N. K. (2017). Global marine protected areas to prevent extinctions. Nature Ecology & Evolution, 1(2), 1–6. https://doi.org/10.1038/s41559-016-0040

Dirzo, R., Young, H. S., Galetti, M., Ceballos, G., Isaac, N. J. B., & Collen, B. (2014). Defaunation in the Anthropocene. Science, 345(6195), 401–406. https://doi.org/10.1126/science.1251817

Dulvy, N. K., Simpfendorfer, C. A., Davidson, L. N. K., Fordham, S. V., Bräutigam, A., Sant, G., & Welch, D. J. (2017). Challenges and priorities in shark and ray conservation. Current Biology, 27(11), R565–R572. https://doi.org/10.1016/j.cub.2017.04.038

MacKeracher, T., Diedrich, A., & Simpfendorfer, C. A. (2019). Sharks, rays and marine protected areas: A critical evaluation of current perspectives. Fish and Fisheries, 20(2), 255–267. https://doi.org/10.1111/faf.12337

McCauley, D. J., Pinsky, M. L., Palumbi, S. R., Estes, J. A., Joyce, F. H., & Warner, R. R. (2015). Marine defaunation: Animal loss in the global ocean. Science, 347(6219). https://doi.org/10.1126/science.1255641

Pacoureau, N., Rigby, C. L., Kyne, P. M., Sherley, R. B., Winker, H., Carlson, J. K., Fordham, S. V., Barreto, R., Fernando, D., Francis, M. P., Jabado, R. W., Herman, K. B., Liu, K.-M., Marshall, A. D., Pollom, R. A., Romanov, E. V., Simpfendorfer, C. A., Yin, J. S., Kindsvater, H. K., & Dulvy, N. K. (2021). Half a century of global decline in oceanic sharks and rays. Nature, 589(7843), 567–571. https://doi.org/10.1038/s41586-020-03173-9

Postaire, B. D., Bakker, J., Gardiner, J., Wiley, T. R., & Chapman, D. D. (2020). Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay. Scientific Reports, 10(1), 11847.

Truelove, N. K., Andruszkiewicz, E. A., & Block, B. A. (2019). A rapid environmental DNA method for detecting white sharks in the open ocean. Methods in Ecology and Evolution, 10(8), 1128–1135. https://doi.org/10.1111/2041-210X.13201