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Open Access Publications from the University of California

The following Capstone Projects are the result of the innovative, creative and interdisciplinary graduate work done by students in the Master of Advanced Studies Program in Marine Biodiversity & Conservation (MAS MBC) at Scripps Institution of Oceanography, UC San Diego. MAS MBC Capstone Projects tackle the most timely and relevant ocean and coastal challenges we face today. Students integrate the knowledge and experiential learning gained over their year of graduate coursework to design a collaborative project that builds marketable skills and has a real-world application.

Students partner with university faculty, external organizations and state and federal agencies to execute focused and compelling self-directed research that culminates in a written paper, film, educational curriculum, business plan, economic analysis, management plan, or other substantial deliverable. This work further equips students with the tools they need to succeed in their professional careers in ocean and coastal conservation.

We welcome you to this library of past MAS MBC Capstone Projects and encourage you to explore the diversity of topics and solutions presented.

If you have any questions, please contact:

Risa Farrell
MAS MBC Program Coordinator

Cover page of Tide Pooling for a Solution: Strategic Communication to Strengthen the Pūpūkea Marine Life Conservation District

Tide Pooling for a Solution: Strategic Communication to Strengthen the Pūpūkea Marine Life Conservation District


This report focused on a timely marine conservation issue in Pūpūkea, O‘ahu, Hawai’i regarding the lack of enforceable administrative rules in Kapoʻo, also known as the Pūpūkea or Sharks Cove tidepool, that is a part of the Pūpūkea Marine Life Conservation District (MLCD). To support the rule change process to revise the administrative rules, I worked with Mālama Pūpūkea-Waimea (MPW), a local nonprofit, to create and apply an ArcGIS Story Map. To build the Story Map, I explored available published literature, examined human use data from Kapo‘o, and observations from beach closures in response to the COVID-19 pandemic. From theliterature, I gleaned information on the role and function of tide pools in Hawai‘i, impacts from recreational use in coastal environments, marine managed areas in Hawai‘i. From the human use data, I found that the majority of visitors at Kapo‘o engaged in swimming, snorkeling, and shoreline use; and the monthly average number of people participating in these three activities combined increased by 58 people, or 7%, from 2017 to 2019. Observations during a two-month beach closure due to the pandemic included an anecdotal increase of juvenile fish, native algae, and sightings of rarely observed marine life, with no to minimal human disturbance. The Story Map will be used by MPW to educate the Pūpūkea community and visitors and will support the group through the future rulemaking process to make MLCD rules enforceable in Kapoʻo. Future studies will be conducted to understand Kapo‘o’s ecological role in the MLCD, to explore its role as a nursery and refuge for marine life, and to determine the magnitude of fishing andrecreational impacts on the ecosystem.

Cover page of Taking Flight: Building a Culture of Conservation at the Punta Banda Estuary

Taking Flight: Building a Culture of Conservation at the Punta Banda Estuary


Punta Banda, located in Baja California, Mexico, is made up of a five-mile long sandbar that extends into Todos Santos Bay (Bahía de Todos Santos) and creates a protected estuary with salt marsh, mud flat, sand dune, and lagoon zones that provide habitat to a variety of species, including migratory and resident birds. Wetlands and birds can be useful topics for engaging the public in conservation efforts because they are culturally relevant, inspire wonder, encourage connections to the outdoors, and are important components of a healthy coastal and marine ecosystem. Through two interactive ArcGIS StoryMaps, this capstone project aims to share data on the wetlands, shorebirds, and seabirds of the Punta Banda estuary with the public in order to continue to generate support for conservation efforts among locals and visitors. Despite conservation efforts, there are still many anthropogenic threats to the estuary and the birds that use it to feed and nest. This document provides a report of activities conducted as part of a capstone project for the Scripps Institution of Oceanography Master's program in Marine Biodiversity and Conservation.

Cover page of A Little Bit of Sargassum Goes A Long Way: Observations and Mapping of Sargassum fluitans and Sargassum natans from NOAA Ship Okeanos Explorer's ROV Deep Discoverer

A Little Bit of Sargassum Goes A Long Way: Observations and Mapping of Sargassum fluitans and Sargassum natans from NOAA Ship Okeanos Explorer's ROV Deep Discoverer


The ocean’s biological pump connects the surface ocean, where light-driven photosynthetic processes fix dissolved carbon dioxide (CO2), to the ocean’s mesopelagic zone (approx. 200 –1000 meters) and beyond. It is a process that depletes the ocean’s surface of CO2 relative to the CO2 in deep water through mechanisms such as the sinking of organic material to the deep Ocean. The Atlantic Ocean features high productivity of the macroalgae genus Sargassum floating on the ocean’s surface in the Sargasso Sea, and in recent years giant blooms of the brown algae Sargassum have been observed stretching from the west coast of Africa to the Gulf of Mexico, the largest macroalgae bloom that has ever been recorded. The sinking of macroalgae from surface waters to the seafloor is considered to be an important carbon sink, but one that is little understood. With the logistical challenges of accessing the deep sea, the record of Sargassum appearing on the seafloor remains limited.

This project utilized an archived exploratory dataset that is freely available to the public in order to make novel discoveries in previously unexplored areas. The following report documents the presence and distribution of Sargassum falls in the deep sea during six dives conducted by NOAA Ship Okeanos Explorer’s ROV Deep Discoverer off the Southeastern United States, in the Gulf of Mexico, and in the Caribbean. Sargassum was observed on each of the dives, in numbers ranging from 6 to 30 observations per dive, with Sargassum being observed an average of every 171 linear meters. This suggests that Sargassum does make its way to the deep sea, in potentially significant amounts.

Cover page of A Review of California's Artificial Reefs: To Help Inform Future Development of a Statewide Management Plan.

A Review of California's Artificial Reefs: To Help Inform Future Development of a Statewide Management Plan.


The California Department of Fish and Wildlife (CDFW) has been involved in the construction of artificial reefs (ARs) since the 1950s. Then in 1985, the California Artificial Reef Program (CARP) was created by legislative statute to address declines in various southern California marine species. The CARP is managed by CDFW but no longer receives funding to manage this program. Before CDFW can support further creation of ARs we need to identify gaps in the program and know how ARs affect marine species and the marine ecosystems. This will ultimately inform a scientifically based statewide AR management plan, which CDFW needs to support in the program. The first step into making informed management decisions of the ARs is to complete a literature review of published material and to survey the type, number, and placement of ARs. The results of this survey need to be standardized and transparent in order for the CDFW to review, compare, and make informed management decisions. Some critical data to include in the surveys will be reef attributes (the quality and specific features of the reef), fish density, biomass, and the assemblage of the AR structure. Identification of gaps in the CARP and the organization and standardization of timely and regular AR assessments will then allow resource managers and stakeholders to use the best available science to make the most informed management decisions possible.  With the ocean continuing to warm and acidify and the world population continuing to increase, fish populations and marine ecosystems are at risk and face unforeseen dangers, including the reduction of fish stocks and the degradation of marine habitat. Rebuilding depleted stocks typically involves conventional fisheries management approaches, such as seasons, quotas, size limits, gear restrictions, MPAs, or even fishery closures. The concept of stock enhancement has been debated as another potential tool in the fisheries management toolbox, and may be possible with the successful implementation of CA’s ARs. CDFW has been involved with the AR program for decades but currently has no statewide management plan to guide placement, development, and testing of AR effectiveness and functionality.

Cover page of Indigenous Aquaculture: A Tool to Support Food Security

Indigenous Aquaculture: A Tool to Support Food Security


Fears of food insecurity are a reality for vulnerable island nations and coastal communities, especially with impending climatic and environmental disasters. The 2020 breakout of SARS-CoV-2 further highlighted fundamental problems with the current centralized food system, inspiring more people to value local, community-produced options. Restoring indigenous aquaculture systems, such as Pacific Northwest clam gardens and Hawaiian loko iʻa (fishponds), holds great promise in helping small coastal communities adapt to a changing climate. Their integrated, low trophic level models increase natural seafood production without feeds or antibiotics. In turn, they increase the health of their surrounding ecosystem as well as the physical and mental health of those who utilize them. To do so, the systems rely on hyper-local traditional ecological knowledge (TEK) accumulated over centuries. But indigenous aquaculture is only a solution if it can function in climate change. Here we explore how the TEK embedded in indigenous aquaculture can withstand climate changes, while helping communities adapt to and mitigate the associated challenges.

Cover page of Putting the Cat Back in the Bag: Turning the Invasive Lionfish Scourge into a Conservation Opportunity

Putting the Cat Back in the Bag: Turning the Invasive Lionfish Scourge into a Conservation Opportunity


In the last few decades, invasive lionfish from the Indo-Pacific, Pterois volitans and Pterois miles, have proliferated throughout the Gulf of Mexico and Caribbean Sea. This diaspora has caused major concerns for the health of marine ecosystems in this region. Research has shown that invasive lionfish can have potentially extremely detrimental impacts on the native reef fish populations which, in turn, can result in extensive ecologic shifts, thereby negatively affecting coral reef communities as a whole. In response to this epidemic, many of the region’s coastal and island communities and nations have instituted culling programs in an attempt to reduce lionfish populations and mitigate the damage.

This study aimed to find strategies that can best be implemented to pursue lionfish mitigation by capitalizing on this unexpected resource to create viable conservation opportunities for coastal communities that depend on healthy reef ecosystems for sustenance and economic well-being. Due to the vagaries of designing a market around a resource that is ultimately intended to be depleted, it was found that a large scale commercial fishery is not economically feasible. It appears that small-scale artisanal and subsistence fisheries, coupled with engaging the multitude of recreational divers that visit the region to participate in culling efforts, will be the most cost effective and efficient way to keep lionfish populations low in order to protect the coral reef ecosystems on which so many coastal communities depend.

Cover page of Exploring the Spatial Relationships between Resorts and Reef Fish in the Maldives

Exploring the Spatial Relationships between Resorts and Reef Fish in the Maldives


Over the last few decades, the tourism industry in the Maldives has experienced exponential growth. This rise in tourism has created a new demand for reef fish and anecdotal reports indicate that exploitation of reef fish is increasing; however, currently, there is little monitoring of the reef fish fishery. This project integrated fish biomass data from underwater visual fish surveys with locations of resorts to examine correlations between fish populations and tourism development. Maps of human presence throughout the archipelago were used to classify surveyed reefs as community, resort or uninhabited. Spatial statistics and regression analysis suggest that distance to a resort has no significant impact on the amount of fish biomass found at nearby reefs. However, the breakdown of biomass by trophic level show an absence of apex predators across all sites, which likely indicates fishing pressure and resource exploitation of large-bodied species readily caught through hook and line fisheries. Additionally, a high level of herbivore biomass across all sites could be playing an important role in reef recovery. As the fishery develops and reef fish demand grows, the Maldives will need to create a management plan that allows for the recovery of apex predators, as well as protects the abundance of herbivores.

Cover page of Fighting Beneath the Surface: Exploring How Community-Based Marine Debris Cleanups Can Be Therapeutic Recreation for Active Duty Service Members and Veterans

Fighting Beneath the Surface: Exploring How Community-Based Marine Debris Cleanups Can Be Therapeutic Recreation for Active Duty Service Members and Veterans


There is a substantial amount of plastic polluting our oceans. Increasing numbers of our military suffer from mental health issues like post-traumatic stress disorder (PTSD), traumatic brain injury, and depression. Wouldn’t it be great if we could use the marine debris problem to help alleviate mental health issues among military service members and veterans? We can - through Blue Ocean Warriors (BOW), which will be the first military-centered environmental nonprofit organization.

BOW’s mission is to enrich our military’s lives through community-based marine debris cleanups while empowering them in the fight to eradicate marine plastic pollution. BOW envisions a world where our military is not impaired by mental health concerns. A world without plastic-filled oceans, lakes, rivers, and beaches. A world where local communities embrace and support their military community members and where the military treats local communities with respect. BOW envisions a circular economy society where everyone reuses resources and does not waste them. BOW will be led by a marine debris expert passionate about helping our military with a unique psychology, nonprofit business, entrepreneurship, and science background. BOW’s goal is to transform our service members and veterans into ocean advocates by spreading the environmental knowledge and love for the ocean they gain from marine debris cleanups to their peers, while supporting others to make positive environmental changes in their own lives. Marine debris is polluting our oceans and mental health concerns among our military are worsening, leading to increased suicide and destructive behaviors, but through the concept of “Blue Mind” both problems can be alleviated. Therefore, we need Blue Ocean Warriors to not only improve the health of the ocean, but to improve mental health issues among military service members and veterans.

Spatial Dispersion of Red Abalone (Haliotis rufescens) Environmental DNA (eDNA) in a Controlled Marine Environment and Applications of eDNA to Monitor Critically Endangered Abalone (Haliotis spp.) Populations in the Wild


The analysis of environmental DNA (eDNA) from water samples is improving species monitoring by offering enhanced detection of rare, cryptic, and endangered taxa over traditional survey methods. This study aimed to investigate the dispersion of red abalone (Haliotis rufescens) eDNA in a controlled marine environment and assess the feasibility of detecting presence of abalone (Haliotis spp.) eDNA in the ocean. Genus-specific primers were used to amplify red abalone eDNA, and multiple experiments revealed the eDNA permeated a two million liter volume of seawater within 18 hours of introduction. Field validation was conducted with seawater samples from two locations where abalone are known to occur along the California coast, and both samples amplified presumed abalone eDNA using the same genus-specific primers. Environmental DNA is a promising tool to detect the presence of cryptic and endangered abalone species in the ocean, with the potential to complement and strengthen current visual survey methods.

Cover page of Seafood is off the Chain! How do we integrate Blockchain Technology for Seafood Traceability?

Seafood is off the Chain! How do we integrate Blockchain Technology for Seafood Traceability?


The seafood supply chain is largely opaque, which allows for overfishing, organized crime,

and even human rights abuses. Illegally caught fish enter the supply chain at various points, and

important data about the fish (e.g. species, provenance, catch method, etc...) can be lost or

fabricated. Although some third-party auditors offer to trace an actor’s supply chain, these services are expensive and the data are siloed away, leaving only the third-party’s guarantee. One option for seafood traceability lies in blockchain technology, which marries a network of computers to an immutable, add-only ledger of transactions. In a supply chain managed by digital ledger technology, the potential for transparency is far greater than in the status quo. However, because the global seafood supply chain is so fragmented, and adoption of blockchain technology requires stakeholder buy-in at all levels of the supply chain, there exists no reliable roadmap for implementation. This Capstone Research Project will use a start-up company – DockChain – as a proxy to examine how to incentivize actors in the seafood supply chain to adopt blockchain technology.

DockChain is a blockchain-enabled restaurant distributor and direct-to-consumer seafood subscription service. Dockchain aims to use blockchain in order to connect local seafood consumers with San Diegan fishermen through the use of a distributed application, and QR codes. This application will allow seafood consumers to scan a QR code to access a story showing all relevant key data elements and critical tracking events, such as the identity of the harvester, and where the seafood had been processed and filleted. The business will have three phases of development in which it will focus on particular markets for adoption. The primary fish that DockChain will purvey will be opah, because of its potential as to grow in popularity. Although opah will be the primary fish the company deals, DockChain will be eager to distribute other fish as well.