The oceans are in trouble—overfishing has led to depletion of fish stocks around the world and has driven many species to critically endangered status. But what to do about it?

Officials have responded to the collapse of fishery stocks with a slew of regulations, many of them forcing fishing operators to be more selective in their harvest, whether by targeting certain species and regional populations, by mandating size or gender restrictions on catches, or by defining open and closed seasons for fishing. For instance, U.S. commercial fishing regulations set minimum-size limits on red snapper and many species of Atlantic tuna. But a perspective paper set to be published online this week in the Proceedings of the National Academy of Sciences argues that such "selective fishing" practices can have unintended consequences. By targeting specific segments of the sea for removal, the authors contend, regulations intended to preserve fish populations can instead nudge a delicate ecosystem out of balance.

Lead study author Shijie Zhou of Australia's Commonwealth Scientific and Industrial Research Organization and his colleagues advocate an alternative approach to fisheries management that they call, perhaps somewhat unappealingly, "balanced exploitation." Using their concept, all fish—regardless of species, size or gender—would be fished in proportion to their abundance and replenishment rate, thereby better preserving the makeup of the ecosystem. Less selective fishing practices would remove a representative slice of the ecosystem while keeping populations above a certain threshold.

"Simply speaking, a balanced exploitation aims to maintain, to the extent possible, natural ecosystem structure to support sustainable fisheries and conserve biodiversity," Zhou says. He adds that the concept seeks to balance relationships both among different species and among subpopulations of a given species such as age groups, gender groups or regional schools. Recent research indicates that selectively targeting subsets of a species can drive unwanted population shifts—say, drastically reducing the number of males relative to females—or even genetic and behavioral changes. Setting a minimum catch size, for instance, applies selection pressure that may unnaturally favor smaller individuals, thereby driving down the size of the species over generations. Similarly, the establishment of legal fishing seasons can affect the timing of salmon runs by selectively killing late or early migrants.

A potentially thorny outcome of fishing a broader range of species is that, in addition to catching high-value species such as salmon, fishing operators would also pull up numerous low-value fish, known as bycatch, that would otherwise be avoided or caught inadvertently and tossed back. Not so under balanced exploitation, wherein species would be harvested according to the carrying capacity of their population rather than their value to consumers. "This concept still supports avoiding bycatch of vulnerable or protected species," Zhou says. But avoiding all bycatch is unnecessary, he adds, and may even be counterproductive from a biodiversity standpoint.

The key would be to develop uses for bycatch species so the harvest would not go to waste. Marie-Joëlle Rochet, a fisheries scientist at the French Research Institute for Exploitation of the Sea who did not contribute to the new research, says that incentives might be more effective than regulations in encouraging less selective fishing. "Probably an important part of the approach would be to develop markets for small things and species you would not judge edible nowadays," she says. Zhou adds that fish need not be suitable for sushi or fish sticks to be of value: other uses include fish oil as well as feed for livestock or even for fish farms cultivating more desirable species.

Rochet has run theoretical models on the effects of fishing practices and has indeed found that selective fishing can negatively impact biodiversity and create ripples in the food web as the balance between predator and prey is upset. "However, this is only theory and needs to be substantiated with empirical analyses," she says.

Jim Scott, assistant director of the fish program for the Washington Department of Fish and Wildlife in Olympia, says that the paper by Zhou and his colleagues raises some good points. "It's important for every person with fisheries management responsibility to understand" the potential concerns about selective fishing, Scott says. "It isn't a panacea," he adds. "You have to be really thoughtful about how you approach it." For instance, he says, gender restrictions on Dungeness crab have led to very high harvest rates among males of the species and may need to be rethought.

At the same time, Scott adds, some ecosystems are already so far out of balance that selectivity is necessary just to stave off total collapse of certain species. "In Washington, we have many species that are either listed under the Endangered Species Act or designated as overfished," he says. "So the idea of moving away from less selective fishing strategies in an environment like Washington—it's not readily apparent to me how we would do that."

Even in more stable fishery environments, Zhou acknowledges that it is "very difficult if not impossible" to design and implement a perfectly balanced exploitation strategy. "We suggest balanced exploitation as an ideal," he says, "and a new approach to consider while scientists and managers critically review the current fishing philosophy that points in the opposite direction."