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California's Endangered Island Foxes Have Low Genetic Diversity, Study Suggests

Channel island fox

NEW YORK (GenomeWeb) – Island foxes living on California's Channel Islands have some of the lowest levels of genetic diversity yet documented in mammals, according to a new study published today in Current Biology.

Researchers from the US and China sequenced the genomes of seven individuals from the Channel Island fox species, Urocyon littoralis, representing all six islands the animals inhabit. Their analyses indicated that the island foxes have far lower levels of genetic variation and markedly higher homozygosity, even at some deleterious alleles, compared with the populations of mainland gray foxes they split from thousands of years ago.

On one of the islands, San Nicolas Island, the team saw little to no genetic variation over most of the genome, though a few hotspots of genetic variation turned up in sequences that are especially variable in fox ancestors, including olfactory receptor genes.

"The degree to which the San Nicolas foxes have lost genetic variation is remarkable, upholding a previous observation that they may be the least genetically variable population of wild animals known," co-senior author Robert Wayne, an ecology and evolutionary biology researcher at the University of California, Los Angeles, said in a statement. "It suggests that under some conditions, genetic variation is not absolutely essential for the persistence of endangered populations."

The Channel Island foxes are believed to have evolved from gray foxes transported to the islands 7,000 or more years ago, leading to a distinct species that is roughly two-thirds the size of the modern-day mainland gray fox, U. cinereoargenteus. Four of the six U. littoralis sub-species are currently classified as endangered by the US Endangered Species Act, the team noted, spurring interest in the genetic diversity of the remaining populations.

To assess genetic features in the island foxes, the researchers used the Illumina HiSeq 2000 to sequence samples from six island foxes: one fox apiece from five of the Channel Islands and two from San Nicolas Island.

Samples included in the study were collected in 1988, before island fox populations on four islands declined due to disease and the presence of non-native golden eagles that pick off the animals.

The sequence reads were aligned to the canFam3.1 reference genome for the domestic dog, as were sequences generated using genomic DNA from a mainland gray fox from southern California.

Whereas the mainland animal had relatively robust levels of heterozygosity and genetic diversity, heterozygosity dipped by between three- and 84-fold in the island foxes. That decline was most dramatic in the two San Nicolas foxes tested, which were almost identical to one another genetically, differing at just two bases for every 100,000 on average.

Genetic variability and heterogeneity was limited in the other island foxes as well, though not to the same extent as the San Nicolas foxes, hinting that small population sizes might not be the lone factor in the population's low diversity.

"[A]lthough a critical variable, long-term small population size does not completely account for the striking lack of diversity in San Nicolas foxes," Wayne and his co-authors wrote, noting that this population appears to have experienced a pronounced bottleneck in the 1970s, followed by low effective population sizes — on the order of a few dozen foxes — for much of their recent history.

The animals' demographic history also seemed to explain the rise in deleterious alleles that have made their way into island fox genomes, the authors noted.

"The absence of obvious negative effects on population persistence from genetic deterioration may in part reflect a more benign island environment," they wrote, "given the lack of competitors and predators that exist on the mainland."