Pacific Islands Fisheries Science Center Young Scientist Opportunity

Project 1. Fisheries Electronic Monitoring and Machine Learning

Schematic of an electronic monitoring system.

Mentors

Keith Bigelow, Jenny Stahl, Matthew Carnes

Background

Hawaiʻi-based fisheries are highly suitable for electronic monitoring, which is likely more cost effective than on-board human observers. In order to supplement observer coverage, however, it would take 27 video reviewers to watch 100 percent of the fishing activity in our fisheries. With machine learning, we intend to lower the amount of video needing human review to more manageable levels.

Objectives

"Pacific Islands Fisheries Science Center (PIFSC) Electronic Monitoring" is a fisheries data toolbox that is modernizing fisheries science. It uses machine learning to identify species and monitor the amount of fish being caught. The selected student will assist the PIFSC electronic monitoring team with the creation of machine learning libraries to train machine learning algorithms to better identify fish in video. This internship provides experience in fisheries using cutting-edge technologies.

Duties and Responsibilities

• Work with team members to implement machine learning technology on video from electronic monitoring.
• Work with trade secret fishing data (the intern must sign a non-disclosure agreement).
• Investigate new technologies.
• Shadow team members during on-vessel and dockside meetings with fishermen.
• Assist in developing tools that provide data to manage sustainable commercial fisheries.

Preferred Qualifications

• Knowledge of Pacific islands pelagic fish species.
• Some understanding of computer vision and convolutional neural networks.
• Efficiency with Linux computer systems.
• Demonstrated ability to remain flexible in a changing work environment.

Project 2. Investigation Into the Early Life History of Bigeye Tuna (Thunnus obesus) Around Hawai'i

Larval tuna. Photo: NOAA Fisheries/Jonathan Whitney.

Mentors

Johanna Wren, Don Kobayashi, Emily Contreras

Background

The Hawaii-based, deep-set longline fishery is the most valuable fishery in the state. Its target species is bigeye tuna. Despite the importance of bigeye tuna, we know very little about its early life history stages and the environment it lives in.

In 2020, we will conduct a bigeye oceanography research cruise to collect oceanographic data and zooplankton. We will also examine plankton samples, which were collected off Oʻahu in 2017, for the presence, absence, and abundance of bigeye tuna larvae. Bigeye tuna spawning in the vicinity of the Hawaiian Islands is not documented in the scientific literature, but there are enough fishery observations of adult, spawning-ready bigeye tuna to warrant further investigation.

Objective

This project will yield important insights into the early life history of bigeye tuna around Hawaiʻi. There may be an opportunity for the student to participate on a 25-day oceanographic research cruise and sample processing, depending on the timing and availability of the student and the research cruise. Otherwise, the internship will focus on a more detailed examination of the historical plankton samples taken off Oʻahu, and preliminary analysis of electronic data streams collected during the 2020 cruise. This would include conductivity temperature depth (CTD) data, ocean current data from an acoustic doppler current profiler (ADCP), and gear profiles from the time depth recorder (TDR). Please note that a field component to this internship is not guaranteed, as there are many aspects of ship operations that are beyond the control of the mentors.

Duties and Responsibilities

Over the course of this internship, the student will participate in the following activities:

1. Work with data streams collected during an oceanographic cruise and learn how to clean, analyze, and visualize these data. 

2. Sort and identify zooplankton samples collected during an oceanographic research cruise. Focus will be on identifying and enumerating larger taxonomic groupings with an emphasis on larval fish.

Qualifications

The ideal candidate will have familiarity and interest in zooplankton identification and experience working with laboratory equipment including proficiency with operating a dissecting microscope and proper handling of zooplankton samples. Some project components may require proficiency with Microsoft Excel as well as working with statistical software such as R or MatLab. Length of internship is expected to be 12 weeks. An interest and established competency in seagoing scientific operations is desirable.

Project 3. Identifying Marine Cultural Keystone Species for the Hawaiian Archipelago

Mentors

Kirsten Leong, Danika Kleiber, Hing Ling Chan

Background and Description

In the Western Pacific, fishing is an integral part of the daily life affecting all cultures and communities. Pacific island communities have sustained themselves for generations with marine resources from surrounding waters, and continue to depend upon the ocean for food and many other activities and products. Recognizing the cultural importance of marine species, and monitoring the most culturally important species (cultural keystones) may ensure their sustained use by fishing communities.

Culturally important marine species are reflected throughout Hawaiian culture—in myths, legends, songs, and place names. However, there has not been a systematic review of cultural importance for marine species that are federally managed. This project will begin that process by documenting marine species in key historic documents, including the Kumulipo (Hawaiian creation chant) and collection of moʻolelo, stories that explain how the world works.

Objectives

The overall goal of this project is to begin to identify marine cultural keystone species in Hawaiʻi, based on use in key historic documents. Specific objectives include the following:

• Conduct systematic content analysis of key historic documents.

• Identify the federally managed marine species most foundational to Hawaiian culture.

• Produce outreach materials such as blog posts, infographics, or a story map.

Duties and Responsibilities

With guidance from mentors, the selected student will analyze historic documents to identify marine cultural keystone species in the Hawaiian Archipelago. The student will learn how to perform systematic content analysis of textual sources, including the following:

• Identification of an appropriate collection of texts (the corpus, or dataset), which may include archival research.
• Qualitative coding of text, based on a codebook of definitions.
• Data organization and basic analysis

The student will also produce outreach materials for the general public.

Qualifications

Although not required, the ideal candidate would have familiarity with Hawaiian names for common marine species, coursework in anthropology or other social sciences, familiarity with database and spreadsheet software and qualitative coding of text. Applicants should have a strong work ethic, willingness to learn, and ability to work both independently and as part of a team. Length of internship is expected to be 12 weeks.

Project 4. Hawaiian Green Sea Turtle Research: Integrating Climate Projections into a Population Model, Understanding Age of Recruitment or Sexual Maturity, or Archiving Samples

Basking green sea turtles on Tern Island, French Frigate Shoals, Northwestern Hawaiian Islands.

Mentors

Camryn Allen, Shawn Murakawa, Alexander Gaos, Summer Martin

Background

The Marine Turtle Biology and Assessment Program conducts research to monitor the status and trends of marine turtle populations throughout the Pacific Islands region (Hawaiian Archipelago, Marianas Archipelago, American Samoa, and the Pacific Remote Island Areas). This requires understanding the biology, ecology, and population dynamics of multiple turtle populations of five species (green, hawksbill, leatherback, loggerhead, and olive ridley turtles). Additionally, researchers in the program study the impacts of anthropogenic threats, such as fisheries bycatch and climate change, on Pacific Islands turtle populations to inform fisheries and protected species management decisions. 

Objectives

The selected student will work directly with scientists in the Marine Turtle Biology and Assessment Program. They will be mentored in general topics of wildlife and fisheries research and endangered species conservation, and will be exposed to multiple facets of the research program beyond their project area. They will receive specific training on the data sets and general methods necessary to succeed in their internship project as well as basic analytical tools for their analysis and reporting. A 12-week internship is preferred. 

As part of the program's research team, the student will work on a project to help fill gaps in our understanding of fisheries bycatch patterns and impacts on Pacific turtle populations. Specific projects may include those defined below, but will depend on the qualifications and interests of the selected intern. The applicant should specify which project is the best fit for them in their cover letter:

1. Explore fisheries bycatch patterns in the Hawaiʻi longline fishery for olive ridley or leatherback turtles using statistical models, such as generalized additive models, and characteristics of the fishery (e.g., season, location) and/or environmental conditions (e.g., sea surface temperature, or chlorophyll concentration). This project could allow a student to further develop their skills related to programming and modeling in R, mapping and spatial analysis in ArcGIS, manipulating large data sets in both programs, and potentially exploring remotely sensed oceanographic data. The results from this project will provide valuable input to fisheries managers. 
2. Develop a user interface to assess fisheries impacts using a computer coding language such as R for a turtle population model that allows users to adjust bycatch levels and determine resulting population impacts of proposed levels of allowable fisheries bycatch. This would be an implementation project for an intern with coding skills who is interested in developing a useful tool for fisheries managers and protected species biologists. The population model code and general idea for the interface would be provided by the marine turtle biology and assessment team, and the intern would work creatively to design code for this specific use. The resulting product will provide a valuable tool for fisheries managers. 
3. Assist with age and growth laboratory research projects utilizing skeletochronology, endocrinology, stable isotopes, or genetic analyses to determine age of recruitment, age of sexual maturity, or kinship.
4. Archive samples through sample database creation, data entry, sample labeling, and accessioning.

Duties and Responsibilities

The student will help to further refine the project idea and develop research questions or implementation solutions within their selected project area. They will work with fisheries data and/or population models provided by the turtle research team and report findings as they progress. While working on their project, they will meet with mentors regularly, take part in team meetings, and gain experience in multiple areas of the research program as other duties are assigned. Specific duties pertaining to potential project areas may include the following:

Project (1) Fisheries Bycatch Patterns or (2) Fisheries Impacts Assessment Interface 

• Manipulate a large multi-year dataset of fishery catch, bycatch, and environmental variables.
• Create bycatch maps in ArcGIS for various turtle species.
• Construct, evaluate, and use statistical models (preferably using R code) to explore the relationship of different operational and environmental variables to variation in bycatch rates.
• Document the steps of the modeling exercise in a format that can be used in a scientific manuscript and internal NOAA report.
• Develop a user-interface for a turtle population model with adjustable fishery bycatch mortality.

Project (3) Age & Growth Laboratory Research

• Necropsy and humerus bone collection, sample preparation, micromilling, aging, and stable isotope analysis.
• Conduct hormone assays to determine sea turtle sex and hormone concentrations.

Project (4) Sample Archiving

• Sample database creation, data entry, sample labeling, and sample accessioning.

Qualifications

The Intern will receive on-site guidance and context necessary for their project. Helpful skills for all projects include the following:

• Interest in population dynamics of marine species, fisheries management, protected species science.
• Programming skills, preferably in R.
• Extreme attention to detail.
• Remain focused, especially while working with large data sets, solving coding problems, writing in lab notebooks, labeling samples, and analyzing data.
• Excellent writing and communication skills.
• Ability to complete a 12-week internship.

Additional skills for projects (1) & (2):

• Interest in and aptitude for quantitative/statistical wildlife problems.
• Advanced R programming skills (or another language for advanced programmers, but the MTBAP team uses R); advanced coding skills are essential for the user interface project.
• Some ArcGIS mapping experience.
• Some statistical and modeling coursework and knowledge (ecological/biological/economic statistics).
• Strong interest in coding, debugging, and problem solving.

Questions? Please contact pifsc.pyso@noaa.gov.

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