A world map of Neanderthal and Denisovan ancestry in modern humans

March 28, 2016
This map shows the proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia. Credit: Sankararaman et al./Current Biology 2016

Most non-Africans possess at least a little bit Neanderthal DNA. But a new map of archaic ancestry—published March 28 in Current Biology—suggests that many bloodlines around the world, particularly of South Asian descent, may actually be a bit more Denisovan, a mysterious population of hominids that lived around the same time as the Neanderthals. The analysis also proposes that modern humans interbred with Denisovans about 100 generations after their trysts with Neanderthals.

The Harvard Medical School/UCLA research team that created the map also used comparative genomics to make predictions about where Denisovan and Neanderthal may be impacting modern human biology. While there is still much to uncover, Denisovan genes can potentially be linked to a more subtle sense of smell in Papua New Guineans and high-altitude adaptions in Tibetans. Meanwhile, Neanderthal genes found in people around the world most likely contribute to tougher skin and hair.

"There are certain classes of genes that modern humans inherited from the with whom they interbred, which may have helped the modern humans to adapt to the new environments in which they arrived," says senior author David Reich, a geneticist at Harvard Medical School and the Broad Institute. "On the flip side, there was negative selection to systematically remove ancestry that may have been problematic from modern humans. We can document this removal over the 40,000 years since these admixtures occurred."

Reich and lab members, Swapan Mallick and Nick Patterson, teamed up with previous laboratory member Sriram Sankararaman, now an Assistant Professor of computer science at the University of California, Los Angeles, on the project, which found evidence that both Denisovan and Neanderthal ancestry has been lost from the X chromosome, as well as genes expressed in the male testes. They theorize that this has contributed to reduced fertility in males, which is commonly observed in other hybrids between two highly divergent groups of the same species.

The researchers collected their data by comparing known Neanderthal and Denisovan gene sequences across more than 250 genomes from 120 non-African populations publically available through the Simons Genome Diversity Project (there is little evidence for Neanderthal and Denisovan ancestry in Africans). The analysis was carried out by a machine-learning algorithm that could differentiate between components of both kinds of ancestral DNA, which are more similar to one another than to modern humans.

The results showed that individuals from Oceania possess the highest percentage of archaic ancestry and south Asians possess more Denisovan ancestry than previously believed. This reveals previously unknown interbreeding events, particularly in relation to Denisovans. In contrast, Western Eurasians are the non-Africans least likely to have Neanderthal or Denisovan genes. "The interactions between and archaic humans are complex and perhaps involved multiple events," Reich says.

The study's main limitation is that it relies on the current library of ancient genomes available. The researchers caution against drawing any conclusions about our extinct human ancestors based on the genetics and possible traits that they left behind. "We can't use this data to make claims about what the Denisovans or Neanderthals looked like, what they ate, or what kind of diseases they were susceptible to," says Sankararaman, first author on the paper. "We are still very far from understanding that."

Explore further: How a one night stand in the Ice Age affects us all today

More information: Current Biology, Sankararaman et al.: "The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans" dx.doi.org/10.1016/j.cub.2016.03.037

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rgw
4.3 / 5 (4) Mar 28, 2016
Thank interbreeding for reduced male fertility! I have enough to handle with 8 children. There was a noticeable lack of comments, so I added this one to unleash the hounds of hate.
Osiris1
3.7 / 5 (3) Mar 28, 2016
There are significant differences in humans from east asia and those of the rest of the world. Perhaps the discovery of Denisovian variety of humans explains part of what constitutes orientalness and what makes east asians so different from the rest of humanity. The differences go far deeper than just skin color which appears to be separate other non asian humans from each other but appear to go no deeper than an adaptation to excess UV radiation in tropical climates. Lose the UV then lose the color and dark Lendus and Nilotic Ethiopians go from dark to translucent Icelanders and Swedes.... light in less than ten thousand years all by themselves.
obama_socks
1 / 5 (1) Mar 29, 2016
The Burji, Konso and Beta Israel were sampled from Ethiopia. The Afroasiatic speaking Ethiopians sampled were cumulatively (Fig.5B) found to belong to: 71% in the "Cushitic" cluster, 6% in the "Saharan/Dogon" cluster, 5% in the "Niger Kordofanian" cluster, 3% each in the "Nilo-Saharan" and "Chadic Saharan" cluster, while the balance (12%) of their assignment was distributed among the remnant (9) Associated Ancestral Clusters (AAC's) found in Sub-Saharan Africa.[10] The "Cushitic" cluster was also deemed "closest to the non-African AACs, consistent with an East African migration of modern humans out of Africa or a back-migration of non-Africans into Saharan and Eastern Africa."[11] - from Wikipedia

This is very interesting to me...re Ethiopian demography and genetics. There are so many variations (genetically) where there can be no question as to origin of those variations which have come from Ethiopia's close proximity to the Middle East.
(cont'd)

obama_socks
1 / 5 (1) Mar 29, 2016
(cont'd)

Further from Wikipedia:
Wilson et al. (2001), an autosomal DNA study based on cluster analysis that looked at a combined sample of Amhara and Oromo examining a single enzyme variants: drug metabolizing enzyme (DME) loci, found that 62% of Ethiopeans fall into the same cluster of Ashkenazi Jews, Norwegians and Armenians based on that gene. Only 24% of Ethiopians cluster with Bantus and Afro-Caribbeans, 8% with Papua New Guineans, and 6% with Chinese.[12]

It appears that the Vikings lent their own genetics to 62% of Ethiopians, according to Wiki. How recent is THAT? Does it come from more modern Norwegians...or were Vikings able to arrive in Ethiopia in their long boats via which waterway(s)? The physical appearances of many Ethiopians are distinct from tribes in the Congo, and other African countries of Western Africa. Many Ethiopians are lighter-skinned and have noses that are more long and aquiline than flattened and short.
obama_socks
1 / 5 (1) Mar 29, 2016
The nose knows:
From Wikipedia:
An aquiline nose (also called a Roman nose or hook nose) is a human nose with a prominent bridge, giving it the appearance of being curved or slightly bent. The word aquiline comes from the Latin word aquilinus ("eagle-like"), an allusion to the curved beak of an eagle.[2][3][4] While some have ascribed the aquiline nose to specific ethnic, racial, or geographic groups, and in some cases associated it with other supposed non-physical characteristics (i.e. intelligence, status, personality, etc., see below), no scientific studies or evidence support any such linkage. As with many phenotypical expressions (i.e. 'widow's peak', eye color, earwax type) it is found in many geographically diverse populations.
EnricM
not rated yet Apr 04, 2016
...or were Vikings able to arrive in Ethiopia in their long boats via which waterway(s)?.
Via de mediterranean perhaps?
They worked as mercenaries for the Byzantines and the Normans invaded Sicily and Southern Italy in the 11th century.
EnsignFlandry
not rated yet Apr 04, 2016
@rgw OK, I hate you! Seriously, I find this subject fascinating. There was a report that east Asians brains work differently than others, based on fMRI imaging studies(different areas light up, to oversimplify). Maybe that is why westerners find Chinese "inscrutable", and Chinese called, and sometimes still do, westerners "white devils".

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