It is only in recent years that targeted fishing of whale sharks has been outlawed in countries like Taiwan and India.
"While whale sharks may be protected [in some national waters], once they move 200 miles [320 kilometers] off the coast they are in the high seas, where fisheries remain almost completely unregulated," Hogan said.
Hogan leads the Megafishes Project, a three-year effort funded by the National Geographic Society to document the 20-plus species of freshwater fish that measure at least 6.5 feet (2 meters) in length or 220 pounds (100 kilograms) in weight.
(National Geographic News is part of the National Geographic Society.)
(Read: "Megafishes Project to Size Up Real 'Loch Ness Monsters'" [July 24, 2007].)
Whale sharks are not a freshwater species, but Hogan has come to La Paz, on the Gulf of California, to learn more about these giant creatures, because they face many of the same threats that large fish living in lakes and rivers around the world encounter.
"Large freshwater fish like the Mekong giant catfish share some of the same life-history traits with these large migratory sharks," he said.
"They live a long time, don't reproduce until a late age, and often need vast areas to survive.
"This makes them more vulnerable to threats like overfishing and habitat destruction," he added.
Deni Ramirez Macias is a doctoral student at the Northwestern Center for Biological Research in La Paz, who studies whale sharks.
She has been tagging and taking tissue samples of whale sharks in the Bay of La Paz and comparing them with larger populations found around Holbox Island, near Cancun in the Gulf of Mexico (see map of Mexico).
The results show that the two populations are genetically different from each other.
Photographing the whale sharks, whose patterns of spots on their backs are unique to each individual, also helps scientists identify the animals to learn more about their movement and habits.
"We know for example that 30 percent of the sharks return each year to the Bay of La Paz," Ramirez said.
"We see juveniles aggregating in the coastal waters here, and we also see pregnant females.
"We think that the southern waters of the Gulf of California is like a nursery or feeding area for juveniles and therefore we have to make a big effort to protect and conserve this critical habitat for the whale sharks," she added.
Scientists have also enlisted the public's help in the photo identification of whale sharks.
Brad Norman is the director of ECOCEAN, a marine conservation organization based in Perth, Australia, which runs a Web-based photo-ID library that tracks whale sharks around the world.
Divers are encouraged to submit any photos they take of whale sharks to the Web site, which uses a computer program originally developed by NASA to identify the sharks.
"We'd like to think of this program as citizen science," Norman said.
"You can be a tourist or a member of the general public and help us identify individual whale sharks around the globe, and from that we can understand more about their numbers and their movement worldwide."
In La Paz—and many other places around the world—whale sharks are sparking a boom in ecotourism.
Alex Antoniou is the La Paz field director for the Shark Research Institute, a Princeton, New Jersey-based organization that hosts tourist divers on research expeditions.
"Shark ecotourism is a renewable resource and an annual source of income," Antoniou said.
"It creates a value for the shark as a living species as opposed to one that you find in the market."
Despite their giant size, whale sharks are harmless to divers and snorkelers. Since the fish feed near the surface and swim slowly, tourists can usually get close-up, uninterrupted looks at the creatures.
"To swim with these sharks is breathtaking," said David Kaplowitz, a diving enthusiast from Austin, Texas, who visited La Paz to swim with whale sharks for the first time.
"It's like a spiritual experience to be with these animals in their natural habitat."
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