Monday, March 19, 2018

Humans Interbred with Denisovans and Neanderthals: Ancient DNA Still with Us

Two distinct interbreeding events with Denisovans, a sister group to Neanderthals, contributed to the ancestry of modern East Asians, according to a genetic data analysis.An early 20th century painting of East Asian women combing and washing cotton.

Modern humans co-existed and interbred not only with Neanderthals, but also with another species of archaic humans, the mysterious Denisovans. While developing a new genome-analysis method for comparing whole genomes between modern human and Denisovan populations, researchers unexpectedly discovered two distinct episodes of Denisovan genetic intermixing, or admixing, between the two. This suggests a more diverse genetic history than previously thought between the Denisovans and modern humans.

East Asian art

A report on archaic DNA in the genomes of modern people, published March 15 in Cell, expands the understanding of human origins.

“This finding offers us a more nuanced understanding of the mixing of modern humans and archaic populations when humans moved out of Africa,” said lead author Sharon Browning, a professor of biostatistics in the UW School of Public Health. “Through DNA analysis, we knew there were at least two interbreeding events—with Neanderthals and with Denisovans. We now know there were at least three inbreeding events—at least one with Neanderthals, and at least two with Denisovans.”

Prior to this study, it was known that the genomes of certain populations, such as Papuan individuals, contained about 5% Denisovan ancestry, and that Denisovan ancestry throughout Asia was present to a lesser degree. However, comparison of DNA sequences shows a much closer Denisovan match among Han Chinese, Chinese Dai, and Japanese sequences.

Neanderthals and two populations of Denisovans contributed to the ancestry of current-day humans (Sharon Browning and Serena Tucci, 2018).

 Credit: Analysis of human sequence data reveals two pulses of archaic Denisovan admixture.

Denisovans are a distinct branch of the Homo family tree whose existence came to light in 2010. Analysis of a bone fragment and molars found in Denisova Cave in Siberia revealed a complete genome for a previously unknown human. But other than their DNA, little is known about the Denisovans. No evidence exists that reveals what they looked like, what they ate or what tools and technologies they possessed.

Browning, along with the other researchers who worked on the project, applied a new reference-free statistical method call Sprime (pronounced, s-prime) to existing genetic data from the 1000 Genomes project and the Simons Genome Diversity Project. The new Sprime method allowed them to search 5,639 whole genome sequences from present day people in Eurasia and Oceania and identify segments of DNA that were likely inherited from archaic human populations. These genetic variants were compared with Neanderthal and Denisovan sequences.

In the future, Browning and her colleagues plan to study additional Asian populations as well as others, including Native Americans and Africans. “We hope to use Sprime to find signatures of introgression from other archaic humans,” said Browning. “We may be able to partially reconstruct the genomes of archaic human populations that did not leave remains with viable DNA for direct sequencing, such as populations that lived in warm and humid regions of the world where DNA decays rapidly."

In a paper published in Cell on March 15, scientists at the University of Washington in Seattle determined that the genomes of two groups of modern humans with Denisovan ancestry--individuals from Oceania and individuals from East Asia--are uniquely different, indicating that there were two separate episodes of Denisovan admixture.

This graphical abstract shows two waves of Denisovan ancestry have shaped present-day humans.

 Credit: Browning et al./Cell

"What was known already was that Oceanian individuals, notably Papuan individuals, have significant amounts of Denisovan ancestry," says senior author Sharon Browning, a research professor of biostatistics, University of Washington School of Public Health. The genomes of modern Papuan individuals contain approximately 5% Denisovan ancestry."

Researchers also knew Denisovan ancestry is present to a lesser degree throughout Asia. The assumption was that the ancestry in Asia was achieved through migration, coming from Oceanian populations. "But in this new work with East Asians, we find a second set of Denisovan ancestry that we do not find in the South Asians and Papuans," she says. "This Denisovan ancestry in East Asians seems to be something they acquired themselves.
After studying more than 5,600 whole-genome sequences from individuals from Europe, Asia, America, and Oceania and comparing them to the Denisovan genome, Browning and colleagues determined that the Denisovan genome is more closely related to the modern East Asian population than to modern Papuans. "We analyzed all of the genomes searching for sections of DNA that looked like they came from Denisovans," says Browning, whose team relied on genomic information from the UK10K project, the 1000 Genomes Project, and the Simons Genome Diversity Project.

"When we compared pieces of DNA from the Papuans against the Denisovan genome, many sequences were similar enough to declare a match, but some of the DNA sequences in the East Asians, notably Han Chinese, Chinese Dai, and Japanese, were a much closer match with the Denisovan," she says.

What is known about Denisovan ancestry comes from a single set of archaic human fossils found in the Altai mountains in Siberia. That individual's genome was published in 2010, and other researchers quickly identified segments of Denisovan ancestry in several modern-day populations, most significantly with individuals from Oceania but also in East and South Asians.

"The assumption is that admixing with Denisovans occurred fairly quickly after humans moved out of Africa, around 50,000 years ago, but we do not know where in terms of location," Browning says. She theorizes that perhaps the ancestors of Oceanians admixed with a southern group of Denisovans while the ancestors of East Asians admixed with a northern group.

Going forward, the researchers plan on studying more Asian populations and others throughout the world, including Native Americans and Africans. "We want to look throughout the world to see if we can find evidence of interbreeding with other archaic humans," says Browning. "There are signs that intermixing with archaic humans was occurring in Africa, but given the warmer climate no one has yet found African archaic human fossils with sufficient DNA for sequencing."

Contacts and sources:
Jeff Hodson
University of Washington

Joseph Caputo
Cell Press

Read the article in Cell: Analysis of human sequence data reveals two pulses of archaic Denisovan admixture

Other co-authors of the paper include Brian Browning, UW professor of medical genetics and adjunct professor of biostatistics; Ying Zhou, UW postdoctoral scholar; Serena Tucci, Princeton University postdoctoral scholar; and Joshua Akey, Princeton University professor of ecology and evolutionary biology and the Lewis-Sigler Institute for Integrative Genomics.

Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM110068.

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