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The genome sequencing of Denisovans DNA shows evidence of autism. Source: kentoh / Adobe Stock.

Did Autism Make the Denisovans Savants of the Prehistoric Age?

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A genetic study hints strongly that the Denisovans, who roamed the earth down to the end of the last ice age, possessed autistic skills, which were then passed on to their modern-human descendants. If correct, then this might at last provide an explanation for the Denisovan’s advanced human behavior and technological innovations.

More than this, it could now help explain the recurrence across many thousands of years of cyclic numbers such as 72, 108, 216, and 432 in ancient king-lists, long-term calendrical systems, and the geometry and design of sacred architecture in southeastern Asia.

The story begins with the sequencing of the Denisovan genome in 2010, achieved using a fragment of finger bone unearthed in Siberia’s Denisova Cave and found to belong to a young girl who lived between 69,000 and 48,000 years ago. This showed that modern human populations shared anything up to 4-6% of their DNA with this now extinct archaic human group, which thrived across the eastern part of Eurasia until around 45,000 years ago, and arguably as late as 15,000 years ago. In other words, interbreeding between the Denisovans and our earliest ancestors resulted in the transfer of genetic materials through what is known as introgression.

The Denisovan finger bone found at the Denisova Cave in 2008. (E.A. Bennett / Science Advances)

The Denisovan finger bone found at the Denisova Cave in 2008. (E.A. Bennett / Science Advances)

Modern human populations benefit from Denisovan introgression in a number of ways, including the EPAS1 protein which allows the indigenous inhabitants of the Tibetan Plateau to thrive at high altitudes where very little oxygen is present. Two other genes—TBX15 and WARS2—inherited from the Denisovans and found among the Inuit of Greenland help them to create the body fats that enable them to exist in the extremely cold climate of the Arctic region.

Tibetan peoples of the Tibetan Plateau gained the EPAS1 high altitude gene from the Denisovans. (Antoinetav / CC BY-SA 3.0)

Tibetan peoples of the Tibetan Plateau gained the EPAS1 high altitude gene from the Denisovans. (Antoinetav / CC BY-SA 3.0)

In addition to this, high-coverage sequencing of the Denisovan genome in 2012 revealed even more about the genes common both to Denisovans and to modern humans. They included ADSL and CNTNAP2, genes that when mutated are known to trigger autism. This raises the question of whether or not the Denisovan brain might have functioned in a manner similar to that of someone on the autistic spectrum today.

Genetic Comparisons

A 2019 scientific study headed by PingHsun Hsieh of the Department of Genome Sciences, University of Washington School of Medicine, Seattle, has found another potential link between Denisovan introgression and autism in modern human populations.

Normally, genetic comparisons between archaic hominins such as Denisovans, Neanderthals, and modern humans tend to focus on what are known as adaptive single-nucleotide variants (SNV). They govern abilities, for example Tibetan peoples have been able to adjust their hemoglobin levels so that they can exist at extremely high-altitudes using a gene inherited from the Denisovans.

The 2019 study, however, instead of focusing on SNVs, analyzed the genome of modern Melanesians looking for something called copy number variants (CNVs). These relate to what is known as gene duplication and reveal the number of copies of an entire gene that are different between individuals. For example, we know that Huntington’s disease results when a specific sub-section of the so-called Huntington gene is replicated to a point where it results in altered protein production.


The researchers found that in the Melanesian genome two specific CNVs could be matched to a hominin inheritance—one to the Denisovan genome and the other to the Neanderthal genome. It is the one coming from the Denisovans that is most crucial to this debate, for it was found that 79% of Melanesians display a duplication on chromosome 16p11.2 in anything up to 383,000 base pairs of DNA strands.

This duplication process derived, the authors of the study predict, from the Denisovan genome as much as 60,000 - 170,000 years ago. This is much earlier than the originally suspected first point of contact between modern humans and Denisovans, estimated to have been around 50,000 years ago.

What is so significant about the 16p11.2 CNV is that it is located adjacent to the area of the genome associated very specifically with autism. In the opinion of the geneticists involved in the 2019 study, the duplication on the 16p11.2 chromosome “exhibits an enrichment of complex recurrent structural rearrangements, which predisposes humans to the second most common genetic cause of autism.”

Organization of DNA in a eukaryotic cell. (PJeganathan / Public Domain)

Organization of DNA in a eukaryotic cell. (PJeganathan / Public Domain)

Autism in Denisovans

So, what exactly is the connection between 16p11.2 and autism? Well, it seems that the 16p11.2 area of the chromosome is both unstable and prone to breakage errors, leading easily to deletion and duplication.

This increases the risk in a person of developmental delay, which can result in intellectual disability, along with impaired language, communication and socialization skills. It can also lead to psychiatric disorders associated with attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). In other words, the duplications and deletions associated with the 16p11.2 chromosome are linked very specifically with the onset of ASD.

Knowledge that the Denisovan contribution to the Melanesian genome is massive, up to 4-6%, strongly hints that the presence in the human genome of Denisovan-based CNVs must have played some beneficial role not just in the Denisovans themselves, but also among the earliest Denisovan-modern human hybrids. How exactly remains unclear with the paleogeneticists involved in the 2019 study suggesting only that it is perhaps linked to the Melanesians living their lives “in an isolated tropical environment.”

Population Adaption

If this is true, then the additional knowledge that the Denisovan genome and modern human genome both share two genes— ADSL and CNTNAP2 that when mutated can trigger ASD again raises of question of whether or not the Denisovans might themselves have possessed savant-like skills.

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Before thinking too much about this, read what the authors of the 2019 study write on the importance of CNVs transferred to modern humans from archaic humans like the Denisovans and Neanderthals: “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.”

What this implies is that any skills resulting from duplication and deletion of CNVs such as 16p11.2 were present in Denisovans before being transferred to modern humans and had to have played some beneficial role. What, however, is unclear.

Just maybe it related to extra sensory faculties, such as increased hearing (a common trait of ASD) and a better connection with the world around them. That said, it is possible that, similar to ASD sufferers today, the Denisovans experienced impaired language, communication and socialization skills, forcing them to exist in isolation within extreme environments both at high altitudes and in very cold climates (the reason why they developed genes for these express purposes).

Accelerated Technological Growth

Yet the effect of CNVs such as 16p11.2 on both the Denisovans and their earliest modern human hybrid descendants might have gone far deeper, for the existence among them of ASD could explain why the last of the Siberian Denisovans went through an accelerated period of technological growth prior to their disappearance around 45,000 years ago. From the creation of the beautiful Denisovan bracelet, a 45,000-year-old choritolite arm bangle displaying signs of sophisticated drilling, design, and polishing, to the invention of bone needles for sewing, the creation of the earliest musical instrument in the form of a whistle or flute, and the development of both microblade stone tool technology and pressure flaking techniques, might all have resulted from an enhanced perception and creativity of a type so often associated with ASD savants.

The 45,000 year-old Denisovan bracelet found in the Denisova Cave. (Anatoly Derevyanko)

The 45,000 year-old Denisovan bracelet found in the Denisova Cave. (Anatoly Derevyanko)

Such a unique mindset might then have been passed by way of CNVs to the genome of the earliest Denisovan-modern human hybrids. In addition to the 2019 study’s prediction that introgression with the ancestors of Melanesians might have occurred as much as 60,000 - 170,000 years ago, another place where modern humans first encountered Denisovans was in northern Mongolia, close to the huge inland sea of Lake Baikal.

Here at an Upper Paleolithic settlement known as Tolbor-16 examples of the same advanced human behavior seen 808 miles (1,300 kilometers) away in the Denisovan layer of the Denisova Cave in southern Siberia have been found. Dating to as early as 45,000 years ago, they include the creation of tubular beads made of ostrich eggshell and a sophisticated microblade technology of the type that would subsequently spread westwards into Europe and southwestern Asia, as well as eastwards in northern China and the Russian Far East. Was this sudden burst of technological advancement among the last of the Siberian Denisovans due to them possessing savant-like skills?

Calendrical Progression

If the Denisovans did themselves experience ASD, and this was passed on to modern human populations via CNVs such as the 16p11.2 chromosome, then how else might this have affected human societies at places like Tolbor-16 in northern Mongolia? The most common savant skill today is calendar counting—the ability of a person to predict what day of a week a date falls either in the future or in the past. (One set of autistic twins were able to calendar count a staggering 40,000 years in the future and into the past.)

Even though such skills are seen as a novelty today, in the past they probably reflected an inherent ability going back to the time of the Denisovans whereby the cycles of the sun and moon were recorded in order to predict eclipses. This in turn might well have generated a complex system of numbers relating to what might be described as calendrical progression, in other words a long-term vision of cyclic time and how to predict it.

Famous savant Kim Peek (1951-2009), the inspiration for the main character in the film “Rain Man”. (Dmadeo / CC BY-SA 3.0)

Famous savant Kim Peek (1951-2009), the inspiration for the main character in the film “Rain Man”. (Dmadeo / CC BY-SA 3.0)

That calendar counting might have in the past been used for more functional purposes involving calendrical progression has long been considered possible. For instance, Dr. Darold Treffert, Clinical Professor of Psychiatry at the University of Wisconsin School of Medicine and a world expert on savant skills writes: “Could it be possible that the calendar calculating ‘chip’ [among savants] is derived inanely from the predictable and constant rhythm of the sun and moon passed on through generations via genetic memory?” If Treffert is right, then calendar counting is a skill that most probably goes back to the age of the Denisovans.

Mal’ta Plate

On the western side of Lake Baikal, not too far from the archaeological site of Tolbor-16 in northern Mongolia, is the Upper Paleolithic site of Mal’ta. Here, around 24,000 years ago, an incredibly important plate was fashioned from mammoth ivory. On one of its two flat surfaces are three cobra-like snakes in outline, while on the other the artist has used a sharp instrument to peck out seven distinct spiral patterns.

The 24,000-year-old mammoth ivory plate found at Mal’ta in southern-central Siberia. (Public Domain)

The 24,000-year-old mammoth ivory plate found at Mal’ta in southern-central Siberia. (Public Domain)

Russian archaeologist Vitaly Larichev (1932–2014) noted that the number and arrangement of these spiral patterns preserve calendrical information regarding the movement of the sun and moon, along with knowledge of the 54-year triple saros eclipse cycle. What’s more, the Mal’ta plate, as well as an archaic calendar still in use today among the shamanic peoples of the Altai region of southern Siberia and northern Mongolia, both display a definite understanding of cyclical time and calendric progression revolving around key numbers such as 9, 54, 72, 108, 216, and 432. These numbers are found repeatedly in association with the cosmological myths and legends of various ancient Eurasian cultures, as well as within the design of sacred architecture in various parts of the world including Angkor Wat in Cambodia and Borobudur in Java.

Borobudur temple in Java, where 432 Buddha statues are placed inside individual stupas. (22Kartika / CC BY-SA 3.0)

Borobudur temple in Java, where 432 Buddha statues are placed inside individual stupas. (22Kartika / CC BY-SA 3.0)

The significance of numbers such as 54, 72, 108, 216, 432, and multiples thereof, most likely derive from perceived synchronizations between the 54 year triple saros eclipse cycle and a separate 72 year cycle based on an awareness of axial precession (which moves at a rate of 1 degree every 72 years). If so, did this profound understanding of cyclic number sequences, so important in shamanic traditions across eastern Eurasia, derive originally from the savant-like minds of Denisovans?

Was this information passed on to their hybrid descendants who occupied the high plateaus and forest-steppe of the Altai-Baikal region when the Mal’ta settlement was in full flow some 24,000 years ago?

If so, then how and why did they create them in the first place? What use did they have?

Calendar round displaying the proposed grand calendrical system of the Altai-Baikal region, which is at least 24,000 years old. (Andrew Collins)

Calendar round displaying the proposed grand calendrical system of the Altai-Baikal region, which is at least 24,000 years old. (Andrew Collins)

Functional Probability

Another key aspect of ASD that could help us better understand the apparent obsession with calendric progression among savants is the manner in which the human brain uses a system of functional probability to predict likely outcomes on a moment to moment basis. What this means is that if the brain has repeatedly registered that when B follows A then C will inevitably follow, then the next time B follows A, then C will always be expected to occur.

Such a calculated anticipation of future events is something critical to brain function in the animal world, and although present in the brain responses of modern humans, it is likely to have been more important among archaic humans such as the Denisovans and Neanderthals.

The study of functional probability, related to the concept of what in neuropsychology is called the predictive mind, is today being recognized as important in autism, the work of Belgian psychologist Peter Vermeulen, the author of many books on ASD, being a prime example.

If correct, then this could explain the necessity for ASD sufferers to calendar count, something that inevitably involves a predictive calculability of future fixed points, in other words the day of the week either future or past dates fall on. Yet in the distant past, among both Denisovans and their hybrid descendants, any perceived breakdown in functional probability might have been addressed in a slightly different way — one involving the constant creation of fixed points in the future or the past involving the movement of the sun and moon. This then becomes just one of a whole number of benefits that might have been bestowed on us by the Denisovans in their potential role as the savants of the prehistoric age.

Top image: The genome sequencing of Denisovans DNA shows evidence of autism. Source: kentoh / Adobe Stock.

By Andrew Collins

Andrew Collins is a history and science writer, and the author of Denisovan Origins, co-authored with Greg L. Little (Inner Traditions, 2019). His website is

Updated on April 9, 2021.


Treffert, D. 2010. Islands of Genius. Jessica Kingsley Publishers.

Larichev, V. 1986. Malta Plate from Mammoth Ivory. Institute of Archaeology and Ethnography at the Russian Academy of Sciences.

Larichev, V. 1989. The Wisdom of Snakes: Primitive Man, Moon and Sun. Nauka.



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Andrew Collins is one of the world’s foremost experts on Göbekli Tepe, having first visited the site in 2004. He has been investigating its Pre-Pottery Neolithic culture for over 20 years, and is the author of various books that feature... Read More

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