Neanderthal Genome Reveals Incest, Interbreeding and Mystery

For Neanderthals, finding that special someone could have meant looking as far as the next species over - or a close as a cousin, according to the most complete sequencing yet of the Neanderthal genome.

Published in the journal Nature, the study centers on DNA extracted from a 50,000-year-old toe discovered in 2010 in a Siberian cave known to have housed Neanderthals, modern humans and a third group of extinct human relatives known as the Denisovans throughout the ages. By comparing the high-quality sequence of the Neanderthal genome to the other two groups, the scientists have painted the clearest picture yet of the genetic relationship between them.

Neanderthals and Denisovans, the comparison showed, are very closely related, their common ancestor breaking away from the ancestors of modern humans 400,000 years ago. Roughly 100,000 years after that, the two split.

Although the Neanderthals and Denisovans ultimately went extinct, their genetic imprint remains. According to the results, the genomes of non-Africans today contain between between 1.5-2.1 percent Neanderthal genes, while the genomes of Australian aborigines, New Guineans and some Pacific Islanders come in around 6 percent Denisovan. Genomes of Native Americans and Han Chinese, as well as other mainland Asian populations, contain about 0.2 percent Denisovan genes, the researchers estimate.

Intriguingly, the research reveals the genetic influence of a previously unknown player believed to have split from the others more than 1 million years ago.

Kay Prufer is a researcher from the Max Planck Institute for Evolutionary Anthropology and one of the study's lead investigators. He said one candidate for the mystery figure is homo erectus, which lived in Europe and Asia between 1.89 million and 143,000 years ago.

"The paper really shows that the history of humans and hominins during this period was very complicated," said Montgomery Slatkin, a University of California, Berkeley professor of integrative biology. "There was lot of interbreeding that we know about and probably other interbreeding we haven't yet discovered."

The Neanderthal woman the toe came from wasn't only interbred - she was highly inbred as well, her parents either half-siblings, double first cousins (the offspring of two siblings married to siblings), an uncle and a nice, an aunt and a nephew, a grandfather and a granddaughter or a grandmother and grandson.

Going deeper into the data, the researchers suspect that kissing cousins may not have been all that unusual back then due to smaller population sizes over longer stretches of time. According to Slatkin, that such behavior could have contributed to the Neanderthal's demise is doubtful, however.

"Other species, including cheetahs and northern elephant seals have become highly inbred yet have thrived once hunting pressure was removed," he told Nature World News in an email.

Prufer, too, is doubtful. "I have no reason to believe that the inbreeding was a direct cause for the extinction of [Neanderthals]," he said in an email.

Comparing the Neanderthal genome to Denisova, great ape and modern human DNA, the scientists devised a list of 87 genes on which they found at least one amino acid change where the extinct human ancestors have a chimpanzee-like amino acid and modern humans another.

"This means that the mutation must have occurred and risen to 100% frequency in our lineage after modern humans split from other archaic humans," Fernando Racimo, a graduate student from UC Berkeley who participated in the study, said in an email to Nature World News.

"There is no gene we can point to and say, 'This accounts for language or some other unique feature of modern humans,'" Slatkin said. "But from this list of genes, we will learn something about the changes that occurred on the human lineage, though those changes will probably be very subtle."

Co-author Svante Paabo, also from Max Planck, called the list of genes "a catalog of genetic features that sets all modern humans apart from all other organisms, living or extinct."

It's possible, he said, "that in it hide some of the things that made the enormous expansion of human populations and human culture and technology in the last 100,000 years possible."