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Ancient Mitochondrial DNA Provides Clues to Ice Age Megafauna Extinction Causes

NEW YORK (GenomeWeb) – A new ancient DNA study suggests the culprit in Ice Age megafauna extinctions in South America was not humans alone, but a combination of humans and warming climate.

In an effort to understand what brought so many of these megafauna — such as giant sloths and Smilodon cats — to a seemingly abrupt end during the Late Pleistocene period, an international team led by investigators in Australia and the US did mitochondrial DNA sequencing on dozens of bone and teeth samples from Patagonia in southern South America.

By tying in radiocarbon data for many more bone samples, the researchers got a look at how megafauna relationships and extinctions corresponded to climate and to human colonization some 14,600 to 15,000 years ago. Their results, appearing online today in Science Advances, point to a main stretch of megafauna extinctions that took place fewer than 12,300 years ago when the climate began warming after a cold snap known as the Antarctic Cold Reversal stadial.

"[H]uman colonisation didn't immediately result in extinctions, but only as long as it stayed cold," senior author Alan Cooper, director of the Australian Centre for Ancient DNA, said in a statement. "Instead, more than 1,000 years of human occupation passed before a rapid warming event occurred, and then the megafauna were extinct within a hundred years."

The fossil records reveal a rich megafaunal history in Patagonia — from giant short-faced bears and saber-toothed cats to giant ground sloths and South American horses, Cooper and his co-authors noted. Past estimates suggest more than 80 percent of megafaunal genera in South America disappeared at some point in the Late Pleistocene, though the precise timing and cause have been controversial.

Starting from 175 bone or teeth museum samples from megafaunal animals from the Holocene and Late Pleistocene, the team did targeted mitochondrial DNA sequencing on 89 of the samples using established ancient DNA sequencing methods, along with radiocarbon analyses on 71 samples.

In a subsequent phylogenetic analysis, the researchers identified an extinct South American jaguar that appears to have belonged to the Panthera onca mesembrina sub-species and an ancient Patagonian puma with mitochondrial haplotypes resembling those that remain in South America.

They also uncovered a new camelid species called Lama gracilis that fell in the same clade as the vicuna, Vicugna vicugna, a proposed alpaca ancestor that appears to have survived the extinction event. A genetically distinct group of extinct Patagonian camelids from the L. guanicoe species fell in a distinct clade with L. guanicoe guanacos that did make it through the extinction, the investigators explained, surviving to be the ancestors of present-day llamas.

"The ancient genetic data show that only the late arrival in Patagonia of a population of guanacos from the north saved the species, all other populations became extinct," first author Jessica Metcalf, an ecology and evolutionary biology researcher affiliated with the Australian Centre for Ancient DNA and the University of Colorado at Boulder, said in a statement. 

The team's radiocarbon dating on the youngest megafauna samples indicated that many of the other megafauna species disappeared around 12,280 years ago, roughly 1,000 to 3,000 years after human colonization.