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A short furrytail

Off the coast of southern California, there is a group of small islands - Channel Islands. About 7000 years ago, mainland grey foxes (Urocyon cinereoargenteus) got onto these islands (and we still do not know how exactly). The foxes thrived, and are now their own separate species called the island fox (U. littoralis).

Island fox by Christian Schwarz, [CC BY-NC], via

Over the centuries, the foxes got smaller in size; average weight is only about 2 kg (~4 lb) making them the smallest fox in North America! They also lost a few tail vertebrae making their tails shorter. The island foxes are docile and are not afraid of humans. They enjoy life in woods, grasses, and on the beaches of islands by hunting mostly at dawn and dusk on small mammals (deer mice), insects (crickets), lizards, birds (and their eggs), and frogs.

The Santa Catalina Island fox (U. littoralis catalinae) is one of six subspecies of the island gray fox. The Santa Catalina population was almost wiped out in 1999 by the devastating outbreak of canine distemper virus. The epidemic left less than 100 foxes alive. The severe bottleneck has decreased the levels of genetic diversity in the fox population and increased the frequency of potentially deleterious variants. It is likely that these variants are responsible for the unusually high occurrence of ear tumors (ceruminous gland carcinoma) in these foxes after the distemper epidemic (Hendricks et al., 2022).

Over the last two decades enormous conservation efforts of Santa Catalina Island Conservancy together with the National Park Service, The Nature Conservancy, and the Institute for Wildlife Studies brought the number of foxes back to over 2000. Catalina Island fox survival is a remarkable tribute to well-planned science-based conservation strategies: fox vaccinations, captive breeding, radio-collar monitoring, predator control (Golden eagle), strict limits on mainland-derived pets, wildlife, parasites, and human impact monitoring etc. We hope that the genome assembly we share today will contribute to these conservation efforts including long-term monitoring of the carcinoma alleles as well as overall genetic diversity, and provide crucial information for the long-term persistence of the threatened fox population.

The ear sample that was used for this genome assembly was kindly provided by Julie King from the Catalina Island Conservancy and was collected with Winston Vickers. The primary fibroblast cell line ULI-623 was established by Polina Perelman from the biopsy of the 10-year-old female Catalina Island fox #36966 (affected by ceruminous gland carcinoma) at the Laboratory of Genomic Diversity led by Stephen O’Brien. Passage #3 was used to construct the short-read DNA-Seq and Hi-C libraries. We thank Drs. Melody Roelke-Parker, Carlos Driscoll, Christina Barr, and David Goldman for preserving LGD cell line collection.

Browse the 33 chromosomes of the island fox in the interactive Juicebox.js session below, and check out the assembly page for more information about this genome!


Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox (Urocyon littoralis catalinae). Genes (Basel). 2022 Aug 22;13(8):1496. doi: 10.3390/genes13081496.

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