8.02.2011

Infectious cancers, genotyping, and indirect extinction pressure

The cover story of last week's PNAS covers attempts by scientists to analyze the Tasmanian devil genome. The hope is that by doing so they might better understand the devils' vulnerability to the infectious cancer that's currently wiping them out at an alarming pace:
The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we report a whole-genome analysis of two animals originating from extreme northwest and southeast Tasmania, the maximal geographic spread, together with the genome from a tumor taken from one of them. A 3.3-Gb de novo assembly of the sequence data from two complementary next-generation sequencing platforms was used to identify 1 million polymorphic genomic positions, roughly one-quarter of the number observed between two genetically distant human genomes. Analysis of 14 complete mitochondrial genomes from current and museum specimens, as well as mitochondrial and nuclear SNP markers in 175 animals, suggests that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations.
Devil facial tumor disease manifests itself in a fashion as horrific as one might guess, and is considered a major threat to the species' existence. Infectious cancers are more common outside of humans, though DFTD is still particularly odd: it isn't viral but rather consists of parasitic cells which spread from host to host via blood-to-blood contact. It's very similar to canine cancers with similar behavior and is believed to originate in a subtype of neural cell called Schwann cells (want to scare a friend? show them the title to the Schwann cell Science paper and underline "clonally transmissible cancer").

DFTD is interesting to think about above and beyond its clinical oddness for the fact that it seems to be largely our fault: humans likely introduced the cancer in the first place via dogs (an invasive species in Tasmania), and are doubly at fault for having reduced the devil population (the 100 year old dip in genetic diversity mentioned above) thereby reducing genetic variation and the potential for resistance. Short of a human intervention soon (researchers are apparently trying to figure out why a very small number of females are partly immune), the species will likely go extinct.

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