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  • TIBURON, CALIFORNIA - APRIL 23: Scientists and volunteers with the...

    TIBURON, CALIFORNIA - APRIL 23: Scientists and volunteers with the Marine Mammal Center and California Academy of Sciences perform a necropsy on a beached grey whale on April 23, 2019 in Tiburon, California. Scientists are studying the causes of death of 7 whales that have washed up on the shores of the San Francisco Bay and along the coast in the past month. It was determined that four of the whales died from malnutrition and three have died from ship strikes. (Photo by Justin Sullivan/Getty Images)

  • TIBURON, CALIFORNIA - APRIL 23: Marine Mammal Center Director of...

    TIBURON, CALIFORNIA - APRIL 23: Marine Mammal Center Director of Veterinary Science Dr. Pádraig J. Duignan stands on top of a beached grey whale as scientists and volunteers with the Marine Mammal Center and California Academy of Sciences perform a necropsy on the whale on April 23, 2019 in Tiburon, California. Scientists are studying the causes of death of 7 whales that have washed up on the shores of the San Francisco Bay and along the coast in the past month. It was determined that four of the whales died from malnutrition and three have died from ship strikes. (Photo by Justin Sullivan/Getty Images)

  • TIBURON, CALIFORNIA - APRIL 23: Moe Flannery, (R) Ornithology and...

    TIBURON, CALIFORNIA - APRIL 23: Moe Flannery, (R) Ornithology and Mammalogy collections manager at California Academy of Sciences, and Jackie Isbell, research intern at the Marine Mammal Center, inspect a dead grey whale before performing a necropsy with scientists and volunteers with the Marine Mammal Center and California Academy of Sciences on April 23, 2019 in Tiburon, California. Scientists are studying the causes of death of 7 whales that have washed up on the shores of the San Francisco Bay and along the coast in the past month. It was determined that four of the whales died from malnutrition and three have died from ship strikes. (Photo by Justin Sullivan/Getty Images)

  • TIBURON, CALIFORNIA - APRIL 23: Scientists and volunteers with the...

    TIBURON, CALIFORNIA - APRIL 23: Scientists and volunteers with the Marine Mammal Center and California Academy of Sciences perform a necropsy on a beached grey whale on April 23, 2019 in Tiburon, California. Scientists are studying the causes of death of 7 whales that have washed up on the shores of the San Francisco Bay and along the coast in the past month. It was determined that four of the whales died from malnutrition and three have died from ship strikes. (Photo by Justin Sullivan/Getty Images)

  • TIBURON, CALIFORNIA - APRIL 23: The carcass of a male...

    TIBURON, CALIFORNIA - APRIL 23: The carcass of a male grey whale sits on the beach as scientists and volunteers with the Marine Mammal Center and California Academy of Sciences perform a necropsy on a female grey whale (rear) on April 23, 2019 in Tiburon, California. Scientists are studying the causes of death of 7 whales that have washed up on the shores of the San Francisco Bay and along the coast in the past month. It was determined that four of the whales died from malnutrition and three have died from ship strikes. (Photo by Justin Sullivan/Getty Images)

  • Experts from The Marine Mammal Center and its partners at...

    Experts from The Marine Mammal Center and its partners at California Academy of Sciences confirm a 1-year-old gray whale died of severe malnutrition after performing two separate necropsies at Angel Island State Park. (Cara Field/The Marine Mammal Center)

  • Scientists from The Marine Mammal Center and California Academy of...

    Scientists from The Marine Mammal Center and California Academy of Sciences start an investigation into the death of a seven gray whale in the San Francisco Bay Area this year. This whale was found recently in Pacifica. (Laura Sherr/Marine Mammal Center)

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Gray whales currently are making their annual trip to Alaska. After breeding in the coastal lagoons of Baja, California, they’re traveling 10,000 miles north to eat. Adult males are the first to migrate. Young, nonbreeding whales follow suit.

But their journey this year has been fraught with peril. So far, seven migrating whales have been reported dead in the San Francisco Bay — some from colliding with ships, which is not unusual, others from starvation, which is rare.

“When there isn’t enough food … it’s going to be the younger, less experienced animals or the older, less fit animals who will have challenges finding enough food,” said Padraig Duignan, Chief Research Pathologist at the Marine Mammal Center, who performed necropsies on these dead whales. “That seems to be playing out here.”

Sure enough, the first two whales found dead in the Bay in early March were about a year old. The third was an older adult male, stranded near Rodeo.

The three whales that collided with ships were “perfectly healthy.” Justin Greenman, assistant stranding coordinator for National Oceanographic and Atmospheric Association, suspects that use of near-shore waters put the whales in contact with boaters who weren’t used to or expecting to see them this far in.

But the migration season is just picking up. Females with calves will only start migrating later in April. Researchers are wondering what’s to come as the season progresses.

“In a typical year, we see two or three gray whales come into San Francisco Bay,” said William Keener, a marine mammal biologist with the Golden Gate Cetacean Research. “They’ll come for a day or so and then leave.”

They could be lost, curious, and if it’s a mom with a calf, she could be moving close to the shore to protect her baby from orcas or sharks.

But this year, Kenner observed at least two whales using the near-shore Bay for a prolonged period. Using photographs to ID them, he was sure that they were the same individuals hanging around since mid-February. And they were skinny. “You can see the backbone show a little bit more than it should,” he said.

Michael Pierson, a naturalist with San Francisco Whale Tours, even noticed some evidence of whales feeding, thanks to mud trails they’d left behind in the water. When gray whales eat, they head to deep waters, dig their faces into the seafloor sediments, take in mouthfuls of mud and tiny creatures inhabiting it, and then filter out this mud and water through their baleens. This generates the mud plumes.

Active feeding in this area and at this time is unusual. Outside the summer months that whales spend feasting voraciously in the Arctic waters, they’re often fasting.

“We’re not used to seeing this much utilization of the near-shore and in-shore habitats like we’ve seen this year,” Greenman said. “The number of deaths this year, and this early in the season, has been surprising.”

But were there visible signs of distress at the breeding grounds, too?

Steven Swartz, a marine biologist who has studied whales of the San Ignacio Lagoon in Mexico for over 40 years, observed more skinny whales this past winter.

In the last five or six years, he’d seen 7 to 8 percent skinny whales in the entire San Ignacio gray whale population. This winter, that number spiked to 26 percent. “This is alarming,” he said. Swartz also counted fewer calves this winter. “We’ve seen 70, sometimes 100, newborn calves …  and this year we haven’t seen more than 20.”

It reminded him of a similar period between 1999 and 2000, when gray whale deaths spiked. Thousands died, and their numbers were down by a third. Twenty-four gray whales were stranded in the San Francisco Bay during that period. “It was a nutritional problem,” Duignan said. ”It wasn’t trauma related, it wasn’t disease, but they were mostly in poor body condition.”

“What might be happening now is that the skinny whales we saw in Mexico this past winter … are basically running out of gas,” Swartz said.

There must be something going on with their food availability in the North Pacific. According to Swartz, the recent warm water “blob” that depleted nutrients essential for life in these waters and climate change could be potential suspects.

“If there is enough food to support 25,000 whales, then they’re fine,” he said. “If oceanographic conditions are changing and that volume of food production is not happening … we’re going to see a reduction in gray whale populations” if that is what’s happening.

Keener and others hope that an event similar to 1999-2000 doesn’t repeat itself.

“But this is certainly a very unusual year,” he said.