Information

What percentage of a Neanderthal's DNA could be in a Denisovan?


My questions arose from an online course video at 3:11-19

The professor mentioned that the Neanderthals were inbred with their cousins breeding together but the Denisovans were very diverse , with 70% Neanderthal's DNA, there was found mixing between Denisovans and an even earlier mysterious species. The followings are my questions:

  1. Did he mean that most of Neanderthals were prone to inbreeding? Why?

  2. I'm not sure if that was exectly what he meant by 70% Neanderthal's DNA could exist in a Denisovan. If that were true, why not just called it Neanderthal if only 30% is not Neanderthal?


You should be very careful trying to conclude something from what is known about Neandertal genetics.

To answer question 1: NO! This is probably not what he meant. To date, we have only two high-quality full genomes of archaich humans, one being the (Neandertal from Denisova cave, called Altai Neandertal (Prüfer et al., 2014)) and one being the (Denisovan from Denisova cave (Meyer et. al., 2012)). From this sample (which is exactly one Neandertal) you cannot draw conclusion for the whole population. It seems, however, that this Neandertal individual from the Altai Mountains was indeed inbreed (high runs of homozygosity in the genome) - it does, however, not even tell us in what way her parents were related. Prüfer et al. (2014) write

We conclude that the parents of this Neandertal individual were either half-siblings who had a mother in common, double first cousins, an uncle and a niece, an aunt and a nephew, a grandfather and a granddaughter, or a grandmother and a grandson.

You cannot say more. You also cannot say if this was due to preference in mate choice, or caused by the fact that this group was very isolated, or that this population had an extreme small effective population size (note that it is debated whether the last two effects are actually equivalent).
To make a long story short: based on the available data it is not wise to draw general conlcusions about Neandertal mating behaviour. Altai is the only example where direct inbreeding could be shown, all other genetic data from Neandertals suggest that genetic diversity was just low.

To answer question 2: I do not really know what this means, 70% Neandertal DNA in Densiovans. I can just generally tell you something about Densiovan-Neandertal differences. The Densiovan might be the only (at least mammal) species that was defined based on genetic information alone. Alle that was found were a few teeth and a pinky bone. People thought this was another Neandertal. After sequencing the DNA from that bones to high coverage (vaguely, a measure of qualtiy), one found that the DNA falls both outside the variation of modern humans - showing that this was not a Homo sapiens, but interestingly it also clearly falls outside the variation of known Neandertal sequences - showing that this was not a Neandertal. It also became clear that Densiovans are more closely related to Neandertals than to modern humans (you might now ask yourself how this is possible with just one genome. In fact, there are more genetic data availabe: low coverage genomes, exome sequences, mtDNA and all of them show the same thing: Neandertals and Densiovans are different but more closely related to each other than to modern humans). Overall, Denisovans also seem to have had rather low genetic diversity (which by the way is also a characteristic of modern humans).
Long story short: There seem to have been admixture events between Denisovans and Neandertals but I do not know how to relate this to the 70%. Prüfer et al. (2014) detected about 0.5% contribution from Neandertals in Denisovans.

One last comment about this mysterious species (nobody says it but most people think of Homo erectus): again, Prüfer et al. (2014) found some interesting patterns of derived allele sharing between present-day Africans, Denisovans and Neandertals (this should be equal for African-Denisovan and African-Neandertal comparisons, but present-day Africans share about 7% more derived alleles with Neandertals than with Densiovans - even 13-16% in alleles fixed in present-day Africans). This is either ancient population structure (however, with very deep lineages) or, as suggested in the paper, due to gene flow from a (genetically) unknown archaic hominin into Denisovans.

I hope this clears things up a bit. Feel free to ask in the comment and I will edit the post as it might be a bit unstructured.


What percentage of a Neanderthal's DNA could be in a Denisovan? - Biology

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 genes 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 archaic humans 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 modern humans 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."


DNA Consultants Adopts New Human Migration Map to Reflect Neanderthal and Denisovan Interbreeding

DNA Consultants replaced its “beachcomber route” map of human migrations out of Africa with a “northern route” scheme more aligned with current phylogenetic and phylogeographic theory, said Donald N. Yates, principal investigator. “Although the exact timing and geographical details of the separation of the first Eurasians from Africans remain intensely debated, it is clear that a crossing over the Horn of Africa to Arabia and subsequent coastal route around India and Indonesia to Australia cannot explain the admixture with other hominids preserved in the oldest travelers along that road,” said Yates. “The northern route proposed five years ago by Rosa Fregel and Vicente Cabrera of the University of Laguna in Spain has overwhelming advantages and should be adopted as the new model.”

It was Stephen Oppenheimer’s The Real Eve that suggested as long ago as 2003 that the main out-of-Africa migration of humans proceeded across the mouth of the Gulf of Suez and around the coasts of Arabia, India and Southeast Asia—the “beachcomber” or southern route. Opposing Oppenheimer, an Oxford genetics professor, was an older theory of multiple dispersals through the Levant, championed by Cambridge University geneticists Marta Mirazon Lahr and Robert Foley.

In 2009, a massive project spearheaded by the Chinese seemed to put that question to rest. The 40-institution HUGO Pan-Asian SNP Consortium “strongly concludes the southern route made a more important contribution to East and Southeast Asian populations than the northern route,” said Li Jin, a population geneticist at Fudan University in Shanghai, China. Jin was one of the lead authors of a study reported in Science, vol. 326, no. 5959, p. 1470, “SNP Study Supports Southern Migration Route To Asia,” by Dennis Normile.

But the issue did not rest with SNPs. In 2010 began the era of ancient DNA. The bombshell arrived with the May 7, 2010 issue of Science Magazine. Entitled “A Draft Sequence of the Neandertal Genome,” it presented the years-long attempt of an international team of scientists to derive DNA from ancient female Neanderthal bones and determine if there was any genetic overlap with humans. There was, quite a lot. Later studies zeroed in on Denisovan, Neanderthal-Denisovan hybrid, Homo erectus, and “unknown hominid” admixture.

Our new map pays homage to the article, “Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asia Route,” published in PLoS One, June 8, 2015, by Rosa Fregel, Vicente Cabrera, Jose M. Larruga, Khaled K. Abu-Amero and Ana M. González (all at Spanish institutions).

According to the Spanish team, ancient DNA sequences embedded in modern samples showed that East Asians actually had more Neanderthal than Europeans, and Austronesians had significant Denisovan. Arabians and Indians had little of either. A northern dispersal route of some 5,000 years duration through territory with proven Neanderthal and Denisovan fossils made imminently more sense than the beachcomber route, which wasn’t supported by any fossils. Phylogenetics and phylogeography agreed.

“Combined genetic, archeological and bioclimatic evidence suggest that, although the early anatomically modern human was born in Africa, the nursery of the modern humans that colonized Eurasia, Oceania and the New World might be first at the south Siberia northwest China core and later in Southeast Asia,” the team concluded in 2015, more than five years ago.

“In the old model, the arrows mostly went east and then north, backtracking west,” said Yates. “In the new map our earliest ancestors are shown going north and then east and finally south, in a fundamentally opposite pattern.”

Lest anyone think that all problems are solved, there are still the matters of a possible Homo erectus contribution to humans’ family tree and the place of a recently discovered “mystery hominid in North Africa.” Debate between the continental and universal origins of humans continues. Also, the controversy has not abated over whether Macrohaplogroup L3 (the parent of the first haplogroups considered non-African) arose inside Africa or outside it, with or without Neanderthal input.


Not all inheritance is the same

Importantly, just because one has Densivoan or Neanderthal DNA in their genome that doesn’t mean that inheritance is going to show up in their genes in the same way. Each human population has a specific history, and ancient hominins interbred with modern humans at different times and in different places.

“That is why introgressed genes are sometimes specific to a population,” Gouy says. “Different people can carry the same amount of Neanderthal DNA, but it can be found in different places of their genome.”

For example: The region of the genome that may be involved in resistance to malaria among Papua New Guineans is inherited from Denisovans. These mutations are almost always found in Melanesians and Aboriginal Australians — which is why they aren’t present across the global population.

It’s also not as simple as saying because a person with Neanderthal DNA has ADHD, then Neanderthals had ADHD. While this study points out that Denisovan and Neanderthal-inherited genes are related to health and behavior, “it remains very difficult to quantify precisely the effect of those mutations,” Guoy says.

“What we can say so far is that some introgressed mutations have been associated to neurological processes,” he says. “We cannot know yet precisely how it will affect the health or behavior of an individual, based on genomic data only.”


Neanderthal, Denisovan DNA Found Near Autism Genes in Modern Humans

One of the most interesting questions of hominin evolution is exactly how much of our vanished cousins remains in us. Between 1-4 percent of the modern human genome is derived from Neanderthals everywhere but sub-Saharan Africa. In addition, between 4-6 percent of the modern Melanesian genome has been shown to be derived from a separate species of archaic hominin, Denisovans. Now, a new paper focused on comparing a specific type of genetic variance has found evidence suggesting that Denisovans and Neanderthals made large-scale, long-term positive contributions to the human genome. Our understanding of the impact of these changes is currently limited, but they occur in a rather interesting place.

Most of the studies that compare differences in human populations (or differences between archaic and modern hominins) focus on adaptive single-nucleotide variants (SNV). It was a single nucleotide variation that gave archaic northwest Europeans the ability to digest lactose, and the ability to do so is a textbook case of human natural selection. The image below shows the prevalence of adult lactase persistence as a percentage of the total population.

Single nucleotide variations found in the genome of the Tibetan people are associated with greater acclimatization to high-altitude conditions. These originated in the Denisovan genome. While the Denisovan addition occurred much earlier than the adaptation for adult lactase digestion, both of them have been conserved (meaning they have persisted since initial evolution).

This new research isn’t focused on SNVs. Instead, it analyzed the modern Melanesian genome for signs of copy number variants (CNVs). Copy number variation is when the number of copies of an entire gene are different between individuals. Huntington’s disease, for example, is caused when a specific sub-section of the Huntingtin gene is repeated to the point that it causes altered protein production. CNVs are much larger than SNVs and they tend to exert very strong selective pressure. Any evidence of conserved CNVs in the Melanesian population that could be traced to the Denisovan or Neanderthal genomes would, therefore, be evidence that these variants conferred benefits.

One thing to know up front is that the impact of CNVs on the human genome is an active field of study. SNVs have historically received far more attention. The discovery of conserved CNVs in the Melanesian population from archaic Denisovan and Neanderthals is significant in its own right. It’s still not clear, however, exactly what either variation actually does. Part of the difficulty of analyzing CNVs is the fact that they’re much larger than SNVs with a much larger range of potential effects.

Denisovan and Neanderthal Contributions

The researchers found two specific CNVs — one associated with the Denisovan genome, and one associated with Neanderthals. 79 percent of Melanesians carry a duplication on chromosome 16p11.2 of >383,000 base pairs (kbp) that originated from Denisovans and was introduced into the native population 60,000-170,000 years ago.

The second variation was introduced by Neanderthals and is carried by some 44 percent of modern Melanesians. It’s located on chromosome 8p21.3 and consists of a

What’s particularly interesting about the Denisovan addition to the human genome is its location. According to the researchers, the specific area of 16p11.2 they identified as being Denisovan in origin is part of a locus which “exhibits an enrichment of complex recurrent structural rearrangements, which predisposes humans to the second most common genetic cause of autism, accounting for

1% of patients.” To be more specific, the Denisovan CNV is directly adjacent to the area of the chromosome where genes known to be associated with autism are.

This specific section of the human genome is known to be unstable and prone to breakage errors. Previous research on 16p11.2 has found that an earlier duplicative transposition of the BOLA2 gene some 282,000 years ago “simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.”

The fact that the Denisovan contribution to the human genome is 1). Huge 2). Built in the metaphorical swamp of 16p11.2, and 3). Highly conserved suggests it was important to retain. The Neanderthal CNV encompasses TNFRSF10D (tumor necrosis factor receptor superfamily 10D). According to the researchers, “TNFRSF10D has been reported as one of the primate-specific genes preferentially expressed in progenitor cells of the human fetal neocortex.”

What’s It All Mean?

Honest answer: Nobody is sure. The researchers theorize that these genes likely conveyed an evolutionary benefit to the Melanesians, probably one linked to their lives in an isolated tropical environment.

“Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation,” the study authors wrote.

The problems with CNV analysis have made it difficult to apply until now. The application of these techniques suggests we may see them used more widely in the future, but the newness of the approach means we’ll be figuring out what these variances do for quite some time to come.

Written with assistance from Jessica Hall. Feature image is a comparison of early Homo sapiens with Homo neanderthalensis. Credit: Wikipedia.


Recently, a Neanderthal toe bone yielded enough DNA to sequence the full genome of the woman whose remains were found in the Denisova Cave in the Altai Mountains, shown above. This information was published in the Journal Nature in an article titled “The complete genome sequence of a Neanderthal from the Altai Mountains” by Prufer et al. I wrote about what was found here, but it wasn’t until I really read the 200+ pages of supplemental information that I found additional buried information.

The article itself talks about some of the findings relative to Native Americans, but the supplemental information provides additional detail and the supporting charts.

In the paper, the Mixe and the Karitiana people of Mexico and Brazil, respectively were most often used to represent Native Americans. There are about 90,000 Mixe language speakers alive today, so their population is not small. However, the Karitiana are just the opposite, with only about 320 people in a very remote region of Brazil. The Karitiana shun contact with outsiders. In some parts of this study, additional population groups were used for additional Native samples.

Here’s what the article itself has to say about Neanderthals, Denisovans and Native Americans.

Denisovan gene flow in mainland Asia

We used the two high-coverage archaic genomes and a hidden Markov model (HMM) to identify regions of specifically Neanderthal and specifically Denisovan ancestry in 13 experimentally phased present-day human genomes (Supplementary Information sections 4 and 13). In the Sardinian and French genomes from Europe we find genomic regions of Neanderthal origin and few or no regions of Denisovan origin. In contrast, in the Han Chinese, the Dai in southern China, and the Karitiana and Mixe in the Americas, we find, in addition to regions of Neanderthal origin, regions that are consistent with being of Denisovan origin (Zscore54.3 excess relative to the Europeans) (Supplementary Information section 13), in agreement with previous analysis based on low-coverage archaic genomes. These regions are also more closely related to the Denisova genome than the few regions identified in Europeans (Supplementary Information section 13). We estimate that the Denisovan contribution to mainland Asian and Native American populations is ,0.2% and thus about 25 times smaller than the Denisovan contribution to populations in Papua New Guinea and Australia. The failure to detect any larger Denisovan contribution in the genome of a 40,000-year-old modern human from the Beijing area suggests that any Denisovan contribution to modern humans in mainland Asia was always quantitatively small. In fact, we cannot, at the moment, exclude that the Denisovan contribution to people across mainland Asia is owing to gene flow from ancestors of present-day people in Oceania after they mixed with Denisovans. We also note that in addition to this Denisovan contribution, the genomes of the populations in Asia and America appear to contain more regions of Neanderthal origin than populations in Europe (Supplementary Information sections 13 and 14).

The fascinating part of this, aside from the fact that Native people also carry both Denisovan and Neanderthal DNA, and that they carry more than Europeans, is that the Denisovan and Neanderthal DNA that they carry is different than that carried by Europeans. In fact, it appears that not all Europeans carry Denisovan DNA and this paper lowers the estimated percentage of Neanderthal for all Europeans.

This difference in the Neanderthal and Denisovan DNA might be able to help solve a long-standing mystery, and that’s whether or not part of the Native population of the Eastern seaboard, and in particular, the far Northeast part of that region, was populated by or admixed with Europeans long before the time of Columbus and other European pre-colonial explorers. This information, of course would have to come from pre-contact burials, but they do exist and with this new information in hand, they might just yield answers never before available.

Dr. Ricki Lewis, in her DNA Science Blog, mentioned something else quite interesting culled from a Christmas Day issue of Nature titled “Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico.” In a nutshell, from article introduction, we find this commentary:

“The risk haplotype carries four amino acid substitutions, all in SLC16A11 it is present at

50% frequency in Native American samples and

10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals.”

Ricki extrapolated on this further:

“Researchers determine the degree to which a mutant gene differs from the most common sequence (wild type), then impose a time scale in the form of known mutation rates. The SLC16A11 five-site haplotype is so divergent that it goes back to nearly 800,000 years ago — before our ancestors expanded out of Africa.

The most plausible explanation, unexpected I suspect, seemed to be that the haplotype came from an archaic human – a Neanderthal or Denisovan or their as-yet unnamed contemporaries. And the haplotype indeed shows up in the skeleton of a Neanderthal found in the Denisovan cave in Siberia.”

And so, it seems that the Native American people today indeed inherited their propensity for type 2 diabetes from their ancient Neanderthal ancestors who lived in the Altai Mountains. It also appears that this genetic predisposition did not carry forward to Europe, if indeed this group of Neanderthals was ancestral to Europeans at all.

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Scientists Sequence Y Chromosome DNA of Denisovans and Neanderthals

The genomes of our closest relatives, Neanderthals and Denisovans, have been sequenced and compared with that of modern humans. However, most archaic individuals with high-quality sequences available have been female. In new research, a team of geneticists from the United States, China and Europe has sequenced the paternally inherited Y chromosomes from three Neanderthals and two Denisovans comparisons with archaic and modern human Y chromosomes indicated that, similar to the maternally inherited mitochondrial DNA (mtDNA), the human and Neanderthal Y chromosomes were more closely related to each other compared with the Denisovan Y chromosome this result supports the conclusion that interbreeding between early Homo sapiens and Neanderthals replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals.

Petr et al. performed targeted sequencing of the paternally inherited Y chromosomes from three Neanderthals and two Denisovans. Image credit: Neanderthal Museum.

A growing number of ancient DNA studies on Neanderthals, Denisovans and Homo sapiens suggest intertwined evolutionary and population histories, including several admixture events between early modern and archaic humans.

However, ancient nuclear and mtDNA sequences revealed phylogenetic discrepancies between the three groups that are hard to explain.

For example, autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans more than 550,000 years ago.

However, all but the earliest Neanderthal mtDNA samples are far more similar to those of modern humans than to those from Denisovans.

These studies suggest that Neanderthals originally carried a Denisovan-like mtDNA, which was later replaced through early admixture with early modern humans, likely between 350,000 and 150,000 years ago.

While genomic data for the paternally inherited Y chromosome would help resolve puzzling gene flows, virtually none of the male Neanderthal and Denisovan remains studied to date contain well-preserved Y chromosome DNA.

To address this gap, Dr. Martin Petr from the Max Planck Institute for Evolutionary Anthropology and his colleagues used a targeted capture-based DNA sequencing approach to enrich and extract Y chromosome sequences from the remains of three male Neanderthals and two male Denisovans.

The researchers found that, like maternally inherited mtDNA, modern human and Neanderthal Y chromosomes were more related to each other than to the Denisovan Y, supporting the suggestion that interbreeding between early humans and Neanderthals and subsequent selection led to the total replacement of more ancient Denisovan-like genetic material in late Neanderthals.

“This was quite a surprise to us,” said Dr. Petr, first author of the study.

“We know from studying their autosomal DNA that Neanderthals and Denisovans were closely related and that humans living today are their more distant evolutionary cousins.”

“Before we first looked at the data, we expected that their Y chromosomes would show a similar picture.”

The authors also found that the Y chromosomes of Denisovans split around 700,000 years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370,000 years ago.

“We speculate that given the important role of the Y chromosome in reproduction and fertility, the lower evolutionary fitness of Neanderthal Y chromosomes might have caused natural selection to favor the Y chromosomes from early modern humans, eventually leading to their replacement,” Dr. Petr said.

“If we can retrieve Y chromosome sequences from Neanderthals that lived prior to this hypothesized early introgression event, such as 430,000-year-old Neanderthals from Sima de los Huesos in Spain, we predict that they would still have the original Neanderthal Y chromosome and will therefore be more similar to Denisovans than to modern humans,” said study senior author Dr. Janet Kelso, also from the Max Planck Institute for Evolutionary Anthropology.


Why Do Modern Humans Have Some Neanderthal DNA?

The current view is that shared Neanderthal DNA is due to interbreeding between the species. This may have occurred at several different times and regions. The earliest period would have been some time after modern humans migrated from Africa into Europe.

When I was growing up, our teachers told us grimly that humans had hunted the poor Neanderthals into extinction. My school days were during the Cold War, and I think we were supposed to draw some alarming analogies.

I had to chuckle recently at a quip that summed up recent thinking as: it was a case of making love, not war.

This entire topic is changing year by year with further research. One fascinating discovery is that modern African populations have more Neanderthal DNA than previously thought. It seems that some of our ancestors doubled back on their migration path into Europe and returned to Africa – carrying pieces of Neanderthal DNA.

Our genetic history is truly a complex interwoven tapestry.


What&rsquos the use of knowing if you are Neanderthal or not?

There is not currently much use in knowing whether or not you have Neanderthal ancestry. In fact, if you don&rsquot have substantial modern African roots, then you probably find Neanderthal in your DNA.

The main benefit in knowing whether you have Neanderthal DNA is primarily to have something cool to talk about at a cocktail party.

Science might continue to develop more insight into the significance of having Neanderthal ancestry, but for now, it&rsquos basically just proof that you can use to insult your brother when he makes you mad.


A world map of Neanderthal and Denisovan ancestry in modern humans

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 genes 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 archaic humans 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 modern humans 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."

The authors were supported by the National Institutes of Health, the National Science Foundation, and the Howard Hughes Medical Institute.

Current Biology, Sankararaman et al.: "The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans" http://dx. doi. org/ 10. 1016/ j. cub. 2016. 03. 037

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