Secrets of Dung: Ancient poop yields nuclear DNA

Researchers have extracted remnants of DNA from an unlikely source: the desiccated dung of an extinct ground sloth that lived in Nevada at the height of the last ice age. The feat is the first recovery of genetic material from cell nuclei of fossils that haven’t been sheathed in permafrost. It suggests that scientists may be overlooking caches of fossil DNA preserved in warm arid environments.

Earlier work on fossils had isolated DNA carried in mitochondria, the powerhouses of living cells. However, the DNA in a cell’s nucleus is typically longer and therefore holds much more genetic information about the species and individual from which the cell derived, says Gregory McDonald, a paleontologist with the National Park Service in Denver.

Now, McDonald and his colleagues have isolated snippets of nuclear DNA from a coprolite–or piece of fossilized dung–of a Shasta ground sloth, a 2.3-meter-long, 350-kilogram herbivore. The coprolite, found in a cave in southern Nevada, may be as much as 15,000 years old, says McDonald. The team’s analyses suggest that as many as 4,000 fragments of nuclear DNA measuring at least 100 base pairs in length may be present in each gram of the animal’s desiccated feces. The researchers report their findings in the July 1 Current Biology.

Scientists using only skeletal characteristics and comparisons of mitochondrial DNA have had trouble discerning the relationships among extinct and living sloths, says McDonald. Some of those studies have suggested that the tree-dwelling lifestyle of all living varieties of two-toed and three-toed sloths evolved only once. Other findings suggest that arboreal living arose separately in two-toed and three-toed sloths.

The newly analyzed differences in nuclear DNA suggest that the Shasta ground sloth is more closely related to living three-toed sloths than to the two-toed varieties, which lends credence to multiple origins of tree dwelling.

The key to the preservation of the Nevada sloth’s nuclear DNA was aridity, says McDonald. Lack of humidity desiccated the dung and stymied bacterial degradation of the genetic material in the stable environment provided by the surrounding cave.

The mummifying environment seems to promote long-term preservation of DNA despite the warm conditions, says Julio L. Betancourt, a paleoecologist with the U.S. Geological Survey in Tucson.

In separate analyses of ancient sloth dung from a sheltered ledge outside a cave in the arid foothills of the Argentine Andes, Betancourt and his colleagues may have identified a previously unknown species of extinct ground sloth. Mitochondrial gene sequences extracted from cells in the 16,000-year-old, pecan-size pellets don’t match those garnered from the four other living or extinct sloth species that have been genetically sequenced to date.

The Argentine dung fragments are much smaller than those left by the extinct horse- to elephant-size ground sloths already known to have inhabited the region, Betancourt notes. The dung came either from a species of ground sloth for which bodily remains haven’t yet been found or from a species that also lived in another area but that scientists haven’t yet genetically sequenced. Betancourt and his colleagues reported their findings in the May Quaternary Research.

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