A fishery is any activity that leads to the harvesting of fish.  This includes wild harvesting and aquaculture. The main types of fisheries are industrial, small-scale, and recreational.  While all of these methods can be damaging to the environment, industrial fisheries make the largest profits and do the most ecological damage because they are on such a large scale. The physical damages include by-catching, which is the unintentional catching of noncommercial fish, and the destruction to the ocean floor and reefs by utilizing large seafloor trawling nets. Indirect damages to the ecosystem can include changes in the size of reef fish populations, which cause phase shifts in reefs.
A couple of tools managers use to protect fish populations include marine protected areas and marine reserves. Marine protected areas (MPAs) are areas of ocean protected against human development. They can prevent practices such as drilling for oil or laying cables along the sea floor. Marine reserves are a type of MPA that also prevent fishing practices. Marine reserves can vary in their level of protection, ranging from only protecting a few species to preventing harvesting of fish altogether. Such areas are known as no-take areas (NTAs). Well-designed NTAs are extremely effective at increasing fish population size by providing a refuge for fish to reproduce and develop safely . NTAs are not very popular among fishermen, though, as a well placed NTA will protect an area that would otherwise have led to high fishing yields, thus reducing revenue. Even in affluent countries, less than five percent of reefs are designated as NTAs . Protecting coral reefs from overfishing takes a delicate balancing act between effective environmental regulation and the economic needs of the people that rely on fishing for revenue and other stakeholders.
Fishing regulations have been around since the beginning of the 18th century. The main goals of these management policies are to maximize biomass and economic yield and secure and increase employment, food supplies, and export income. However, these interests often conflict with environmental interests. For instance, maximizing biomass yield may not be beneficial to the reefs being fished, especially is the method of harvest is particularly damaging. An example of an effective but damaging method of fish harvest is blast fishing. Blast fishing is the practice of using explosives to stun or kill schools of fish for easy collection. Although it is outlawed in most countries, many developing countries lack the man power needed to regulate and enforce the government fishing policies. As a result, many fisherman cause significant damage to the underlying reefs. The lack of strict regulation is a common problem that fishery management practices face. MPAs are a fairly successful management practice, but without strict management there is little to stop some fisherman from entering them and fishing in the restricted areas anyway. Since MPAs generally protect areas where fish take refuge to reproduce and grow into adults, violating their boundaries to fish illegally can be extremely damaging.
The Nassau grouper is native to the Caribbean and surrounding waters and used to be a staple of fisheries in the Caribbean. However, unsustainable fishery practices in Belize and other regions of the Caribbean have led the Nassau grouper to the edge of extinction. In 2003 the Nassau grouper was placed on the Endangered Species list because of rapid decline in population size. It is estimated that the population is fewer that 10,000 individuals.This reflects a sixty percent decrease in population size in the past three decades. This estimate operates on the assumption that the density of grouper population at each location is the same. The recorded range of percent decreases seen at individual locations ranges from fifty-five percent to ninety-nine and a half percent.
The fisheries use a variety of methods to catch Nassau grouper; however, the different types are generally deployed during breeding season for the grouper. The Nassau grouper breed once a year in the winter for a week. The breeding aggregations range in size from a few dozen to 100,000 individuals.  These breeding aggregations form in relatively open water, such as drop offs or reef spurs. The fisheries use the dependable size and location of breeding aggregations to maximize yields; however, yields have also been decreasing as populations decrease. Off the coast of Belize, landings dropped from 90,900 kilograms in 1984 to 21,000 kilograms in 1991.  This decrease is further evidenced by the decrease in CPUE, which is a measurement of the kilograms of fish caught per boat. St. Thomas saw a seventy-six percent decrease in CPUE between the 1975 and 1976 fishing seasons.
The increase in fishing and the decrease in population size is reflected in the decrease in aggregation sizes across the Caribbean. Off the coast of Belize, about one-third of the breeding aggregations has disappeared due to overfishing.  The largest breeding aggregation has decreased from 15,000 individuals to only 3,000 individuals in twenty-five years. In the Cayman Islands there were five historically identified breeding aggregations.  In 2002 three of these aggregations became inactive meaning there are not enough fish to harvest.
In order to counteract the effects of overfishing certain actions have been put in place. The United States has a complete ban any harvesting of Nassau grouper.  Mexico has banned the harvesting of Nassau grouper from breeding aggregations. Belize has instituted a rotation system in which only certain aggregations are available for harvesting each year.
Jamaica’s history of fishing spans back as far as Pre-European settlement. Ostionan and Meillican native peoples relied on Jamaican reef fish as a major source of food . During the 1800s, fishing was revolutionized by the development of large seine nets that could catch large quantities of fish at once, making it easy for newly freed slaves to become self-sustaining .
The biggest blows to coral reef fish populations came with the arrival of the 20th century. Chicken wire replaced wicker in the seine nets, increasing the size and number of fish that could be caught in one haul . The Caribbean became a hot-spot for fishing between 1900-1950. Fishing continued to expand despite the growing concern of scientist. In the 1950s up to the 1970s, government subsidies caused catch rates to skyrocket, the main catches being composed of herbivorous reef grazers like parrotfish . Fish biomass was reduced by up to eighty percent by the 1960s despite reefs appearing healthy until the 1970s . By the time anyone realized how out of control fishing had become, the damage was already done.
Grazing had to be taken over by a non-fished species. A famous seventeen-year study by Terence P. Hughes (1994) collected data from nine points along Jamaica’s coast and monitored the phase-shift that took place during that time. Because overfishing lead to the disappearance of major grazing fish species by the 1970s, the function was taken over by Diadema antillarum, a sea urchin . A single species serving a function once served by many, however, is a far cry from a making resilient system. In 1983, a species-specific disease hit the urchins, resulting in a staggering ninety-nine percent reduction by 1984 .
With the loss of grazing fish and urchins to serve as a control coupled with a sequence of hurricanes bringing nutrients into the system, a massive macroalgae bloom consumed reef systems all across Jamaica, smothering the dominant reef builders Acropora palmatta (elkhorn coral) and Acropora cervicornis (staghorn coral) . According to Hughes, hundreds of kilometers of coral reef area were reduced from having an average fifty-two percent coral cover to three percent and increased in macroalgae cover from four percent to ninety-two percent in a matter of a few decades. This phase-shift has been devastating to local fishermen and to the Jamaican coral reef tourism industry.
Merritt Island National Wildlife Refuge
Merritt Island was established in 1963 making it the oldest fully protected marine reserve in the United States. It contains seven different habitats including saltwater estuaries and marshes.
After the establishment of the refuge, adjacent fisheries began to see positive effects in both population size and density. After the establishment of the refuge, world record sized fish in the adjacent waters increased. Adjacent waters are defined as waters within a 100 kilometer radius. The refuge encompasses only thirteen percent of Florida coastline; however, the waters adjacent to the refuge boast high proportions of world record sized fish. For example, fifty percent of the world record spotted trout came from this region  Adjacent fisheries also saw a rebound in fish populations. For example, the black drum population increased by 12.8 times. These increases are due to the protection of the habitats necessary for the breeding of fish. The saltwater estuaries serve as an area of protected breeding allowing for larger populations to grow each generation.
The Soufrière Marine Management Area (SMMA) was established in 1995 along the southwest side of St. Lucia in the Caribbean. Rapid degration to surrounding coral reef systems prompted the foundation of the refuge. The SMMA protects eleven kilometers of coastline, establishing a chain five marine reserves. The establishment of these reserves reduced coral reef fishing grounds by thirty-five percent, a daunting reduction to local fishermen.
However, the SMMA's impact on reef fishing has proven to be very positive in a short amount of time. Within three years, the biomass of five important reef species tripled within the reserve areas. This massive increase has lead to spill-over into surrounding areas. In fisheries adjacent to the SMMA, biomass of fish nearly doubled. Catches recorded five years after the refuge's establishment show that catch by fishermen using large nets increased by forty-six percent while catches in by fishermen using small nets increased by nearly ninety percent.
When interviewed about the SMMA, local fishermen gave very positive responses about fishing since its establishment. Many feel that they could not thrive without the marine reserves, even though their reef fishing grounds were reduced by thirty-five percent. The opinion of local people matters greatly in a management plan as a tool for the plan's effectiveness at achieving its goals. The SMMA shows that it is possible for both fish and humans to benefit from an increase in protected areas.
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