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Whale, whale, whale

The humpback whales (Megaptera novaeangliae) are one of the larger rorquals, members of the Balaenopteridae family that includes the blue, fin, Bryde's, sei and minke whales. Humpback whales are famous for breaching and showing their tails when they dive. This dramatic sight makes them very popular with whale watchers!

Humpback whale wild head photo © Bill Hunnewell

There are different theories as to how humpback gets its name as some say its because they have a distinct hump in front of their small dorsal fins whereas others say that the name comes from the hump that forms when they arch their back when diving.

They have dark backs ranging in color from dark grey to blue-black, and paler bellies (some completely white, some more mottled). Humpbacks have distinctive knobby heads and jaws, long flippers and broad tail flukes. They can grow to around 15 meters in length and weigh up to 30 tonnes with female humpback whales usually being larger than males.

Humpbacks are known for their long-distance migrations. At the start of winter, humpback whales migrate north past New Zealand to the tropical South Pacific, where they mate and give birth. At the end of winter, they travel back towards Antarctica. The trips between feeding and breeding grounds can cover distances of 8,000 kilometers and more. Researchers have recorded individual whales swimming for as many as nine weeks non-stop!

Like other large whales, the humpback was a target for the whaling industry. The species was once hunted to the brink of extinction; its population fell by an estimated 90% before a 1966 moratorium. While numbers have partially recovered to some 80,000 animals worldwide, entanglement in fishing gear, collisions with ships and noise pollution continue to affect the species. Currently, it is listed as endangered on the red list of IUCN.

The chromosome-length assembly was generated using a skin sample provided to us by Barbie Halaska, Necropsy Manager at The Marine Mammal Center in Sausalito, California. As the world’s largest marine mammal hospital, the Center generates research findings and scientific outputs at volumes similar to top academic institutions. In addition, the Center serves as a resource and thought leader in animal care, education and scientific communities.

Humpback whale, Baker Beach San Francisco. Credit Barbie Halaska © The Marine Mammal Center

This is a $1K-strategy genome assembly with the short-insert draft generated using w2rap contigger (Clavijo et al. 2017) and Hi-C-scaffolded using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details, and check the interactive contact map of the humpback whale’s 22 chromosomes below! Special thanks to Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational and analyses support of the upgrade.

This sample was collected by The Marine Mammal Center under the Marine Mammal Health and Stranding Program (MMHSPR) Permit No. 18786-04 issued by the National Marine Fisheries Service (NMFS) in accordance with the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The work at DNA Zoo was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03.

We thank Barbie Halaska and Ben Neely for their help with this genome assembly. Learn more about the impact of The Marine Mammal Center’s scientific research by visiting the Center’s website at!

Blog post by Parwinder Kaur, with contributions from Daniel Lim, Giancarlo Rulli and Barbie Halaska


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