Mock Research Proposal Introduction


Trying to manage a fish population is an endeavor with several factors, both known and unknown. Currently, there is a big push for the better understanding and management of Long-Lived fish populations. These populations are hard to study and harder to manage because there is so little known about them and how to manage a k strategist (an individual that focuses onXXXX). The Yelloweye Rockfish (Sebastes ruberrimus) is a k strategist species of fish that lives on the Pacific Coast ranging from California to Alaska. The lower populations of this rockfish are showing signs of overharvesting and habitat destruction, the population located in Puget Sound (Washington) has been listed as “Threatened” by the National Oceanic and Atmospheric Administration. This population is currently protected and unless a management procedure is implemented it is likely the population will be lost. The Yelloweye brings several obstacles to management efforts; their inability to be brought to surface and survive due to barotrauma (XXXX) makes it hard to protect the species from mortality due to by catch (xxxx). Their longevity (xxxx) and delayed sexual maturity (xxxx) make it highly difficult to get the population to successfully reproduce; with an estimated age of sexual maturity around 20 years old, it is hard to ensure survival of the offspring without directly controlling it. Thus, it would be highly productive for the scientific community to understand how to manage k-strategist since most of them are easily overharvested and recover poorly from fishing efforts.

Purpose of the Study

The purpose of this study is to better understand how to manage a long-lived marine species. There are several goals that are accomplished by successfully design a management method for the Yelloweye Rockfish. These goals include reviving the threatened Yelloweye population in Puget Sound, study the benefits of hybridization in k-strategists, and increase the ecosystem health of Puget Sound by improving water quality, habitats, and increasing species richness (the number of species found in a habitat; the higher the number, the more diverse the habitat is and the healthier the ecosystem is).


Back-Cross – “The mating of a hybrid organism (offspring of genetically unlike parents) with one of its parents or with an organism genetically similar to the parent.”

Barotrauma– The expansion of the air-filled swim bladder during ascent that may result in injury or death of the fish.

Critical Habitat– “A specific geographic area(s) that contains features essential for the conservation of a threatened or endangered species and that may require special management and protection”

Fitness– An individual’s ability to reach sexual maturity, locate a mate, and produce viable offspring.


Hybridization– “ The process of interbreeding between individuals of different species (interspecific hybridization) or genetically divergent individuals from the same species (intraspecific hybridization). Offspring produced by hybridization may be fertile, partially fertile, or sterile.”


Introgression– “Back-cross of a hybrid individual with one of its progenitors (parent or ancestor)”

Iteroparity-An individual that can reproduce multiple times in one lifetime.


K-selected traits– Long adult lifespan, delayed maturity, ability to reproduce multiple times in a life, traits that maximize fitness when resources are scarce but somewhat constant, much like they are when the population is at carrying capacity (K).

Marine Reserves-Protected areas of the ocean where there is no killing, harming, or harassing of any plants or animals permitted

Slot-limits– A size limit for a species that limits the minimum and maximum size that the fish can be, thus it must be able to fit in the given slot.


Significance of the Investigation

By properly managing the Yelloweye Rockfish population the methods used can be implemented onto similar cases of k-strategist species that may be currently suffering a population decline. Commercial fishing is on the rise and is one of the lead reasons that k-strategist populations are on the decline. K-strategist species are evolved to survive at a population maximum for their ecosystem, their longevity and delayed sexual maturity is a way to keep their population from surpassing the carrying capacity (the maximum number of individuals in a species that can survive in an ecosystem, usually nutrient dependent)  of their ecosystem and causing a population collapse. This strategy is detrimental when a population is being harvested faster than it can reproduce and thus it is r-strategists that can better survive high levels of harvesting. Thus, there are several species that are currently in a population decline and because they naturally occur at the carrying capacity  they appear to be abundant and unaffected by fishing practices when truly populations are rapidly declining and, unless they are protected and managed, will be lost in the near future.

Literature Review

Managing Long-lived marine species is not in the forefront of science currently, as stated earlier, many populations are on the decline but are yet to reach threatened levels and are thus not a current concern for scientists. The best compilation of papers relating to conservation and management of long-lived species is “Life in the Slow Lane: Ecology and Conservation of Long-Lived Marine Animals” compiled by J.A. Musick. The three articles in this book that I focused on were: “Ecology and conservation of long-lived marine animals,” “Management of Long-Lived Marine Resources: A Comparison of Feed back-Control Management Procedures,” and “Management and conservation of temperate reef fishes in the grouper-snapper complex of the southeastern United States.” These three articles came to similar conclusions, current management methods implemented on non-long-lived species will not work on long-lived species, k-strategists are more susceptible to collapsing due to over fishing, and the best way to protect these species is to make their critical habitats marine reserves (areas that it is illegal to kill, harm, or harass life).

Looking at more non-contemporary aspects of conservation of species I have decided to bring in hybridization. Hybridization (the crossing of two species to create a new species) is a controversial practice and if not for the success it has had I would not include it in this study. Dr. Andrew Martin of University of Colorado Boulder has been involved in several hybridization projects to help preserve species that are on the brink of extinction. His work with the Devils Hole Pupfish and the Greenback Cutthroat Trout were vital to increasing population size, species richness, and genetic flow in small inbred populations. Two papers that he was involved in (“Hybridization Dynamics between Colorado’s Native Cutthroat Trout and Introduced Rainbow Trout” and “Dramatic shifts in the gene pool of a managed population of an endangered species may be exacerbated by high genetic load”) provide evidence for the success of hybridization. It is my hope that by crossing the Yelloweye Rockfish with a shorter lived rockfish there may be a decrease in longevity and an increase in fecundity, there have been instances of other Rockfish hybridizing naturally (assessed by Piper Schwenke in her Master’s thesis “History and extent of introgressive hybridization in Puget Sound rockfishes (Sebastes auriculatus, S. caurinus, and S. maliger)”). Thus, with such high success rates in other areas and naturally amongst rockfish I feel that there will be a high chance of success for this to aid in reestablishing the Yelloweye Rockfishes population.

Thesis and questions

The Yelloweye Rockfishes (Sebastes ruberrimus) population maybe successfully managed and returned to historical populations size via a combination of habitat restoration, importation of Yelloweye Rockfish from other healthy localities, hatcheries, hybridization, marine reserves, and educating the public on conservation. I believe this multistep plan will allow for successful management of the species, and by spreading out the efforts into multiple parts it increases the likelihood that the Yelloweye population will respond to one of the methods.  There are several unknowns in this study, the biggest question is can the Yelloweye hybridize and if so will it help increase the fecundity of the population? It is also important to ask if the niche that the Yelloweye typically fills has been taken over by another species, thus making it harder for the population to take hold in the given habitat. Finally, if these methods of management are successful, can they be implemented on other long-lived species that are experiencing a decline in population size?

Annotated Bibliography

Annotated Bibliography (MLA)

Blaxter, J. H. S. “The Enhancement of Marine Fish Stocks.” Ed. BT  – Advances in Marine Biology. Vol. 38. Academic Press, 2000. 1–54. ScienceDirect. Web. 31 Mar. 2016.

-Professor John Blaxter who the J.H.S. Blaxter Award, an award given by the American Fish Society honoring Professor Blaxter’s contribution to the understanding of larval fish ecology, is named after, focuses primarily in this paper on the efforts and history of “Enhancing” fish stock. Enhancing fish stock is primarily done via hatcheries where historically done by releasing larvae and yolk sac’s (embryos) into a habitat in hopes that the captive bred fish would help replenish the declining species population size. Initial efforts did not work, but through time we have been able to realize components that control the success of enhancement. I plan to use this article to evaluate the use of hatcheries as a viable way to increase population size whilst noting the various stipulations that predict the success of enhancement.

Heppell, Selina et al. “Effects of Fishing on Long-Lived Marine Organisms.” Marine Conservation Biology (2005): 211–231. Print.

-Dr. Heppell is currently a Professor at Oregon State University who runs a lab (Heppell Lab) and has been a part of 63 publications. This article goes over several aspects of conservation of long-lived marine organisms, she addresses several views on how they should be managed and current efforts to limit by-catch mortality. I plan to use this article to both define key terms for my paper as well as a reference for the struggle of trying to manage long-lived species. Her in depth view on the variables that make over exploitation of long-lived marine species will be implemented throughout my paper and be helpful with bring pathos into the subject.

López-Pujol, Jordi et al. “Should We Conserve Pure Species or Hybrid Species? Delimiting Hybridization and Introgression in the Iberian Endemic Centaurea Podospermifolia.” Biological Conservation 152 (2012): 271–279. ScienceDirect. Web.

-Dr. Jordi López-Pujol has his PhD in Ecology, Botany, and Genetics; his uses a scientific voice to assess the pros and cons of hybridization in the plant species Centaurea podospermifolia. This will be my ethics piece for the paper because it analyzes the use of hybridization which is a very controversial topic. I plan to use this paper to help support the implementation of hybridization in hatcheries and the Yelloweye Rockfish’s critical habitat (Puget Sound/ Georgia Basin). By hybridizing the species there is an increase in genetic diversity which may potentially aid in the increase of species number. Hybrid species are commonly unstable thus making them a temporary source of genetic flow that may be able to jumpstart the population into a healthy and maintainable reproductive cycle.

Pribyl, Alena L. “A Macroscopic to Microscopic Study of the Effects of Barotrauma and the Potential for Long-Term Survival in Pacific Rockfish.” (2010): n. pag. Web. 9 Apr. 2016.

-Dr. Pribyl is another current Professor at Oregon State University with a Phd in Fishery Science. Her article on the effects of barotrauma in Pacific Rockfish goes into the short and long term effects of barotrauma in Rockfish. This is an important conservation point to be brought up in my proposal because it adds another layer difficulty to preserving the Yelloweye Rockfish. It is important to identify the many limiting factors that make the Yelloweye an important and difficult species to preserve.

Protected Resources Webmaster, Office of Protected Resources. “Yelloweye Rockfish – Office of Protected Resources – NOAA Fisheries.” N.p., n.d. Web. 31 Mar. 2016.

-This is an article put together by the NOAA to help define the Yelloweye Rockfish. It uses a scientific voice that does not delve too deeply into terms so that a wide variety of people can read and understand this article. I plan to use this article primarily to help describe the fish and use its characteristics to mold conservation methods. The Yelloweye Rockfish is a long lived fish that has a high number of eggs produced annually making it an interesting fish to design a plan for conservation. Having this general summary of the Yelloweye Rockfish is important for ensuring the limitations that the species introduces into conservation methods.

Sawchuk, Jennifer Heibult et al. “Using Stakeholder Engagement to Inform Endangered Species Management and Improve Conservation.” Marine Policy 54 (2015): 98–107. ScienceDirect. Web.

-Dr. Sawchuk is a Professor at the University of Washington in the school of Marine and Environmental Affairs, she is also an employee for the National Oceanic and Atmospheric Administration. Her article on stakeholder engagement for management and conservation in Puget Sound overlooked stakeholder (fishers) opinions on conservation and management of species. Their approach of informing the fishers and allowing them to respond with ideas and fill out a survey on their feelings toward potential conservation and management efforts brought out the stake holders positive opinions on conservation. This article is how I will address the stakeholders opinion on the protection of the Yelloweye because overall fishers did want to preserve endangered species to various degrees, and thus this paper will also help support the area of my proposal to educate the public.



Preliminary research:

It is important to understand the historical population sizes, habitat type, and water quality of Puget Sound and the Yelloweye Rockfish before there is any attempt to establish a healthy population. The time used to research the historical qualities of Puget Sound can be done early in the study whilst other aspects are being worked on. The most important aspect of any biological restoration is attempting to reproduce a historically healthy habitat. Puget Sound has been known for its pollution since the 80’s when they discovered high levels of POP’s, and declared 2 superfund sites in Puget Sound.


Habitat Restoration

Restoring the natural and historical habitat of the Rockfish in Puget Sound is not an easy task and will take several years to accomplish. There are several departments working currently on reducing the pollution levels in Puget Sound so for this project the focus will be primarily on the restoration of the rocky corals and boulder fields, these should be implemented throughout Puget Sound including the production of shallow rocky reefs and boulder fields. Introducing a wider habitat with more coverage may attribute to the protection of rockfish and other species that utilize the rocky protection. Yelloweye are known for having a very small home range, potentially living solely in one rock pile. The production of new rocky reef and boulder fields could be readily protected by banning fishing and mooring in certain areas of Puget Sound. Marine reserves need to be implemented XXXX…



Importing Yelloweye Rockfish both (juveniles and adults) from Alaska and British Columbia, where populations are thriving, could be utilized in multiple ways. The first would be to stock Puget Sound, primarily in protected areas (both artificially made rocky reefs and boulder fields and naturally occurring ones). This not only would increase the population size but it would also increase genetic flow in the dwindling Puget Sound population. It is important to slowly acclimate these fish both in capturing and releasing due to the chance of death due to their inability to readily release oxygen from their swim bladders(XXXX). This acclimation period is one where they are readily preyed upon and thus need to be protected until fully acclimated. Another important use of importation is utilizing this population in a hatchery on Puget Sound. This hatchery (focused on in next section) will utilize the juveniles and adults in an effort to both produce healthy offspring within their own population and with a population harvested from Puget Sound and potentially for the production of a hybrid species (explained in forthcoming section).



Hatcheries are a way to produce a population of fish that may be strongly affected by high mortality (death) in its offspring prior to reaching sexual maturity. The Yelloweye Rockfish is a long-lived fish and takes roughly 20 years to reach sexual maturity. Thus, the use of imported juveniles and breeding adults will help speed the process of restoring the population to more historical levels and supporting the population in the future. The Yelloweye is known to produce up to 2,700,000 eggs and give birth to live young, by protecting these offspring through their juvenile years until maturity could readily restore the Puget Sound population and potentially make the Yelloweye a sport fish once again. Hatcheries are known to cause a number of issues including disease, reduced gene flow, bias selection, and a comfortability with human interaction (reviewed in the limitations section). To minimize this, the facility will use methods that reduce selection bias, monitor disease, and minimize human interaction. Reducing human interaction will not play too large of a role as the juveniles change feeding methods and habitat upon reaching sexual maturity where they begin eating fish and crustaceans in lieu of plankton and other small organisms and move to deeper levels in the ocean. Yelloweye adults released from the hatchery should be visibly tagged to enable proper calculations of population size.



Hybrids have been known to help conserve an aspect of the genetic code of an endangered species and potentially create a stronger species. This will require researching genetic sequences and finding a close relative to the Yelloweye, which may not be in Puget Sound, and attempting to hybridize the two species. The preferred species for the Yelloweye to hybridize with would be on that reaches sexual maturity earlier in life, decreasing the Yelloweye hybrids life span may increase the number of offspring an individual may produce because so many individuals fail to reach sexual maturity. This is a potentially dangerous practice and should be approached cautiously as the introduction of fish may have detrimental effects on the ecosystem. Yet, the addition of a viable hybrid may increase genetic flow, species richness, and potentially provide fishers with a sport fish that is not protected. These species should be tagged to identify them as a separate species from the Yelloweye.



Educating the public is always an important effort for any attempt to restore an ecosystem. With the public’s understanding, support, and input we can both increase effectiveness of the implemented processes and decrease the cost of these processes. Utilizing the public for volunteering, fundraising, and publicity will greatly benefit the project and make the goals readily accessible.


Field Data Collection Methods

Set dive transects will be implemented to analyze the population size of the Yelloweye and the species richness of the rocky habitats. Divers will be on 50 meter transects in the Boulder fields and Rocky Coral beds. They will record population data for the Yelloweye and other potential inhabitants. Another set of transect data will be attained using Manta tow technique, where a diver is pulled behind a boat with a board to record data. The diver is pulled at a predetermined speed (~4km/hr) for two minute increments, every 2 minutes they stop and the diver records all of the data for the last two minutes and then the transect is continued. Divers will make special note of tagged specimens which will later be used to estimate population size of the Yelloweye using a mark recapture method.


Historical Research

The use of Historical research will be used to generate ideal goals for the habitat type, size, and health as well as the population size of the Yelloweye. It is important to realize that we will not be able to return Puget Sound to historically pristine conditions due to the high level of anthropogenic pollution and activity. The historical data will be used to produce goals that are reachable and manageable through the years. The main goal of this historical research is to find a number that can be maintained with minimal stocking efforts and be able to resist decline due to fishing activities (both active and by-catch).


The restoration of the Puget Sound Yelloweye Rockfish is a project that will encompass several fields and be a lasting endeavor. The wide variety of expertise needed to accomplish the goals of the project requires the collaboration of several individuals who may bring a skill set ideal for a branch of the project. My personal contribution will primarily be population analysis, this is only a small portion of the project but it is the central goal of the project to restore the population. Though I do plan to participate in all areas of this project, I will have several individuals conducting the various branches of this project.

To analyze the population it is important that there is not damage done to the population so it is important that population demographics are done via dives. Tagging of released individuals from fisheries will be used as a means to reproduce a mark recapture study; we will not recapture individuals though. XXXXX

The primary data that will be used for analyzing will be the population demographics. The starting population will be assessed via comparing current estimates with data collected via dive transects, these transects will be used again during mark recapture efforts, though there will be no recapturing in this study. It will be important to take sample specimen of the population throughout the study and monitor the level of inbreeding, parasite loads, and population estimates for size and age (using otoliths). This data will be collected and analyzed semiannually to ensure there are no spikes or drops in population size or health. XXXXX


There are several ethical dilemmas that this project must face. Primarily this project will have to confront the local fishing population and implore them to understand the importance of marine reserves, limiting bottom troweling, and other practices that are known to be destructive to the Yelloweye habitat. This long term project will take the continual effort of the team and community to properly reestablish the population, thus there must be some incentive offered to the local fishers. This is where the hybrid rockfish may play an economically beneficial role, if it does take off as a species. Rockfish, commonly known as Snappers on the West Coast are an expensive and sought after fish. Introducing a new fishable Snapper that can be stocked and possibly survive the impact of sport fishing could be the solution for appeasing the fishing community so they allow for the Marine Reserves in Puget Sound.

The introduction of a new species is another ethical dilemma, a hybrid species can be considered both more and less detrimental in the public’s eye. Many hybrids can be genetically altered so they are sterile thus reducing the likelihood that they will decimate the ecosystem, and thus creating a sterile population that is continually stocked into Puget Sound may be another alternative for helping protect the Yelloweye. Creating a hybrid is an invasive procedure and many of the public may find the idea of the project “playing god” to be unappealing and may lead to further ethical dilemmas.


The methods being implemented in this project are aimed to do minimal damage to the target species and the other inhabitants of Puget Sound. These methods for monitoring population size are commonly used in areas where it is important to minimize the stress typically related to other capture methods. Using a typical mark recapture method, where the individual must be recaptured to estimate population size, is one that would be a death sentence to the individual as many adult Yelloweye’s cannot survive being brought to surface rapidly (XXXX). It is also important to revisit the idea that the Yelloweye has a very small home range, making them less likely to be counted multiple times while on transect; thus by using set transect data there will be minimal damage to the population and the estimate of the population will still be accurate.

Years Progress
0-1 Preliminary research completed, start rebuilding habitat, begin collecting specimen for hatchery
1-2 Continue rebuilding habitat, begin breeding in hatchery, look at genetic code for relatives of the Yelloweye
2-4 Finish rebuilding habitat, establish marine reserves continue breeding in the hatchery, introduce imported adults to marine reserves, begin trying to hybridize individuals.
4-6 Continue to stock marine reserves with imported adults, continue breeding in hatchery, continue hybridizing individuals, begin monitoring the Marine Reserves via manta tow and fixed SCUBA transects semiannually, analyze data recorded.
6-19 Continue to stock marine reserves with imported adults, continue breeding in hatchery, continue hybridizing individuals, continue monitoring the Marine Reserves via manta tow and fixed SCUBA transects semiannually, analyze data recorded. Potentially begin introducing hybrid individuals.
20 Continue to stock marine reserves with imported adults, continue breeding in hatchery, continue hybridizing individuals, continue monitoring the Marine Reserves via manta tow and fixed SCUBA transects semiannually, analyze data recorded, continue to release tagged hybrid individuals, begin releasing tagged adults that were raised in the hatchery.
20+ Continue to stock marine reserves with imported adults, continue breeding in hatchery, continue hybridizing individuals, continue monitoring the Marine Reserves via manta tow and fixed SCUBA transects semiannually, analyze data recorded, continue releasing tagged adults and hybrids that were raised in the hatchery.




Dive boat (rent), Scuba gear (rent), manta tow gear. XXXXX


  • Budget-(for research aspect only, the rest of the population restoration is likely a billion dollar effort with too many variables to estimate)


Materials Cost
Dive boat rental $300 / day
SCUBA gear rental $110 / day
Manta Tow Gear Build for ~ $100


The biggest limitation of this project is time. Finding funding for long term research and conservation is difficult because results will not be available for several years, thus it is easy to loose public support. People want results and this study cannot guarantee results for several years, even stocking Puget Sound may take years for the fish to become properly established, thus it is important to give a realistic timeline to the public and supporters.

It is important to realize that the management of a long-lived species is very different from the management of other fish. It requires time and most importantly a cease in fishing efforts in the reserves. Thus, we must exclude any paper describing management methods used for species that are not long-lived. It is also important to exclude any analysis of mark recapture that involves the physical capturing of the individuals because of the Yelloweye’s struggle surviving changes in depth.

The successful revival of the Yelloweye population would be a great stepping off point for several other management efforts for long-lived species. If the project is successful it will be important to publish the methods, data, and results making the process replicable for other populations that are threatened or endangered due to overfishing or habitat degradation.  If the results are not what we hoped for they are important to share too, that way others may develop new methods and ideas from our short comings.