Two Denisovan Admixture Events?

Recent genetic analysis suggests that humans mated with the mysterious Denisovans not once, but twice

Asian genomes carry introgressed DNA from Denisovans and Neanderthals

East Asians show evidence of introgression from two distinct Denisovan populations

South Asians and Oceanians carry introgression from one Denisovan population

I can’t read the whole paper, because it’s paywalled, but if correct, this is quite the change. Previously, only small amounts of Denisovan were detected in East Asians, while large amounts (2-6%) were detected in Oceanians (ie, Melanesians, Papuans, and Australian Aborigines.) 

According to Wikipedia:

Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed,[50][51] and that a second introgression event from Denisovans into humans occurred. A study of Han ChineseJapanese and Dai genomes revealed that modern East Asian populations include two Denisovan DNA components: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from the Altai cave. These components were interpreted as representing separate introgression events involving two divergent Denisovan populations. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans.[52]  …

The Denisovans, in case you’re new here, are a human species similar to the Neanderthals who lived… well, we’re not sure exactly where they lived, other than the Altai Cave, Siberia. We also don’t know what they looked like, because we have only found a few of their bones–a finger bone and some teeth–but they might have looked a bit like the Red Deer Cave People. Remarkably, though, these were in good enough condition (Siberia preserves things very well,) to allow scientists to extract sufficient DNA to determine that they are indeed a human species, but one that split from the ancestors of Homo sapiens about 600,000-750,000 years ago, and from the Neanderthals about 200,000 years later. 

Just as Homo sapiens mated with Neanderthals, so Denisovans mated with Neanderthals and Homo sapiens–the human family tree is growing increasingly complex. 

We don’t know exactly where these interbreeding events happened, since we know so little about the Denisovans (at least one of the Neanderthal interbreeding events probably happened in the Middle East, given that all non-Africans [and some Africans] have Neanderthal DNA,) but a clue lies in the DNA of the Negrito peoples. 

The Negritoes are a variety of peoples who live in south east Asia and, like the Pygmies of Africa, are rather short. Some of them, like the Aeta of the Philippines, have almost Papuan levels of Denisovan admixture, while others, like the Onge of India, have almost none. Assuming the Negritos are related to each other and not just isolated examples of island dwarfism, this suggests that the interbreeding event really did take places somewhere east of the major Indonesian islands of Sumatra and Borneo (which probably weren’t islands at the time, but connected to the mainland). The Denisovans may have been clever enough to build boats and cross the Wallace Line, surviving in the more isolated islands of Indonesia and the Philippines. 

On a related note, the article I just linked to from John Hawks, “This is where Scientists Might Find the Next Hobbits,” is truly excellent: 

In May, an international team of scientists led by Thomas Ingicco revealed new archaeological findings from Kalinga, in the northernmost part of Luzon, Philippines. Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old. …

Luzon was never connected to the Asian mainland, even when sea level was at its lowest during the Ice Ages. To get there, ancient hominins had to float. Who were they, and how did they get there?

Timeline of ancient Indonesian and Filipino hominin findings, from John Hawks’s article

I recommend you read the whole thing.

What’s all of this Denisovan DNA good for, anyway? Quoting Wikipedia again:

The immune system’s HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin.[54] The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today.[16] A study involving 40 Han Chinese and 40 people of ethnic Tibetan background identified a region of DNA around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude found in Tibetans is also found in the Denisovan genome.[55][56] In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.[57]

It is a great era in genetics. 


Anthropology Friday: Pygmies and Papuans, pt 3/3

Welcome to Anthropology Friday. Today we are finishing A. F. R. Wollaston’s Pygmies and Papuans, published in 1912, with a focus primarily on the Pygmies of New Guinea and nearby areas (also known as Negritos.)

As usual, quotes will be in “” instead of blockquotes for readability.

Tapiro Pygmies

“At one time or another we took measurements of 40 adult men [of the Tapiro Pygmies], most of them men in the prime of life, and their average height was found to be 144·9 cm. (4 ft. 9 in.). … The height of the smallest man measured was 132·6 cm. By contrast with the Papuans they looked extremely small and, what was rather a curious thing, though many of our Malay coolies were no taller than they, the coolies looked merely under-sized and somewhat stunted men, while the Tapiro looked emphatically little men. They are cleanly-built, active-looking little fellows …

“In consequence of our entire lack of knowledge of their language we were not able to form a very reasonable estimate of their intelligence. …

“A rough test of an uncivilised man’s intelligence is the extent to which he is able to count, but in the case of the Tapiro there is an unfortunate difference of evidence in this respect. Capt. Rawling (Geograph. Journal, Vol. xxxviii., page 246) affirms that they are able to count up to ten. If this is so, it is a very interesting and remarkable fact. On several occasions I tried to make these people count, with a view to learning their numeral words, and I found that like the Papuans they only had words for one and two, and that those two words were the same as the Papuan words; but it appeared that, unlike the Papuans, they had not the custom of using their fingers and toes for the higher numbers.

“On the credit side of their intelligence must be placed their admirably constructed houses, their decorated arrows and ingeniously woven bags, and their cultivation.”

A large village:

“A few miles further down the river we came to another large village of yet a different character. The houses there were all built on piles, but while a few of them were of the usual small size, the majority were quite unlike anything else we had seen in that part of New Guinea. They were huge barn-like structures raised on piles ten or more feet above the ground, and the length of some of them must have been from one hundred and fifty to two hundred feet. It was quite evident that these were communal dwellings, indicating a social system entirely different from that of the surrounding districts, and it was very tantalising to pass them within a few yards and not to be able to visit them. The village extended for about a mile along the East bank and the natives that we saw must have numbered at least a thousand. ..


Crowds of people lined the river bank and some of them, holding short bamboos in their hands, jerked them in our direction and from the end came out a white cloud of powdered lime, which looked like smoke. …The suggestion that it is a means of imitating the appearance of fire-arms is ingenious, but it can hardly be seriously considered.”

EvX: I think this amusing explanation may well be correct, given the habits of people in many parts of the world to construct replica versions of technology they have seen mainly at a distance.

Here the author quotes a text by Dr. Haddon on the characteristics and cultural traits of local pygmy/negrito groups, “The Pygmy Question“:

“Pygmies, as their name implies, are very short men, and the first question to decide is whether this short stature is normal or merely a dwarfing due to unfavourable environment. … The average human stature appears to be about 1·675 m. (5 ft. 6 ins.). Those peoples who are 1·725 (5 ft. 8 ins.) or more in height are said to be tall, those below 1·625 m. (5 ft. 4 ins.) are short, while those who fall below 1·5 m. (4 ft. 11 ins.) are now usually termed pygmies. One has only to turn to the investigations of the Dordogne district by Collignon and others to see how profoundly la misère can affect the stature of a population living under adverse conditions, for example in the canton of Saint Mathieu there are 8·8 per cent. with a stature below 1·5 m. But when one finds within one area, as in the East Indian region, distinct peoples of medium, short and pygmy stature, living under conditions which appear to be very similar, one is inclined to suspect a racial difference between them, and the suspicion becomes confirmed if we find other characters associated with pygmy stature. …

“Asiatic pygmies have long been known, but it is only comparatively recently that they have been studied seriously, and even now there remains much to be discovered about them. There are two main stocks on the eastern border of the Indian Ocean, who have a very short stature and are respectively characterised by curly or wavy hair and by hair that grows in close small spirals—the so-called woolly hair.

“(i.) The Sakai or Senoi of the southern portion of the Malay Peninsula are typical examples of the former stock, their average stature is slightly above the pygmy limit … All these peoples together with the Vedda and some jungle tribes of the Deccan are now regarded as remnants of a once widely distributed race to which the term Pre-Dravidian has been applied; it is also believed by many students that the chief element in the Australians is of similar origin.

Semang man, Malaysia

“(ii.) For a long time it has been known that there are three groups of ulotrichous (woolly-haired), brachycephalic (broad-headed), dark-skinned, pygmy peoples inhabiting respectively the Andaman Islands, the Malay Peninsula and the Philippines; to this race the name Negrito is universally applied. We can now include in it a fourth element from New Guinea. The physical characters of these several groups may be summarised as follows:

Two Andamanese men

“1. The Andamanese, who are sometimes erroneously called Mincopies, inhabit the Andaman Islands in the Bay of Bengal. Their head hair is extremely frizzly (woolly), fine in texture, lustreless and seldom more than two or three inches long … Hair only occasionally grows on the face and then but scantily. There is little or no hair over the surface of the body. The skin has several shades of colour between bronze or dark copper, sooty, and black, … The average stature of 48 males is 1·492 m. (4 ft. 10-3/4 ins.), the extremes being 1·365 m. (4 ft. 5-3/4 ins.) and 1·632 m. (5 ft. 4-1/4 ins.). …

“2. The Semang live in the central region of the Malay Peninsula, some of them are known under the names of Udai, Pangan, Hami and Semán. The hair of the head is short, universally woolly, and black. Skeat says it is of a brownish black, not a bluish black like that of the Malays, and Martin alludes to a reddish shimmer when light falls on it … Hair is rare and scanty on face and body. Skeat describes the skin colour as dark chocolate brown approximating in some Kedah Negritos to glossy black… The data for the stature are not very satisfactory, the best are a series of 17 males by Annandale and Robinson, the average being 1·528 m. (5 ft. 0-1/4 in.), with extreme, of 1·372 m. (4 ft. 6 ins.) and 1·604 (5 ft. 3 ins.). …

Young Aeta girl, Philippines, 1901

“3. The Aeta live in the mountainous districts of the larger islands and in some of the smaller islands of the Philippines. It is convenient to retain this name for the variously named groups of Philippine Negritos, many of whom show admixture with other peoples. The hair of the head is universally woolly except when mixture may be suspected or is known … Reed says that the beard is very scanty but all adult males have some and that there is very little body hair, but Worcester states that the men often have abundant beards and a thick growth of hair on the arms, chest and legs. The skin is described as being of a dark chocolate brown, rather than black, with a yellowish tinge on the exposed parts (Reed), sooty black (Sawyer), or dark, sooty brown (Worcester). The average stature of 48 men is 1·463 m. (4 ft. 9-1/2 ins.), ranging from 1·282 m. (4 ft. 2-1/2 ins.) to 1·6 m. (5 ft. 3 ins.), but some of these were not pure breeds (Reed); other observations also show a considerable range in height. …

Papuan man accompanied by two Tapiro Pygmies, from Wollaston’s Pygmies and Papuans

“4. The discovery of pygmies in Netherlands New Guinea by the Expedition has drawn public attention to a problem of perennial interest to ethnologists. …

“The racial history of New Guinea has proved to be unexpectedly complicated. We are now justified in recognising at least two indigenous elements, the Negrito and Papuan; the effect of the island populations to the east has not yet been determined, but in the south-west two immigrations at least from Melanesia have taken place, which, with Seligmann, we may term Papuo-Melanesian. … It is, however, almost certain that future researches will reveal that the problem is not so simple as that just indicated.”

EvX: Just as my favorite map is the one where large tracts of Antarctica are marked “Unexplored,” so I find interesting the experience of simply discovering new groups of humans who had previously been unknown to outsiders.

New Guinea was, for mostly geographic reasons, one of the last places on Earth to be competently explored by outsiders, and thus held some of the last ‘undiscovered’ peoples.


“Finally Guppy, Ribbe and Rascher report the occurrence of very short people in the interior of the larger islands of the Bismarck Archipelago and of the Solomon Islands; recently Thurnwald refers to very small people in the mountainous interior of Bougainville who speak a non-Melanesian language, one man from Mari mountain had a stature of 1·39 m. (4 ft. 6-1/2 ins.). In the mountains the mixed population consists of types recalling the Solomon Islanders and “representatives of a small short-legged, broad-faced, short-skulled, very hairy, wide-nosed people.” …

“Discussing the pygmies of Melanesia von Luschan referred in 1910 (Zs. f. Ethnol. XLII., p. 939) to bones brought a century ago from the Admiralty Islands which must have belonged to individuals 1·32-1·35 m. (4 ft. 4 ins.-4 ft. 5 ins.) in stature; it is unlikely that the type persists, though Moseley mentions an unusually short man, a little over 5 ft. (Journ. Anth. Inst. 1877, p. 384). In the collection made by the German Marine Expedition there are a number of extremely small skulls from New Ireland, which von Luschan is convinced belong to pygmies. Finsch brought from New Britain over thirty years ago the smallest known skull of a normal adult person; it came from the S.W. coast of Gazelle Peninsula. …

“At the same time that the Expedition discovered pygmies in Netherlands New Guinea, Mr. R. W. Williamson was investigating the Mafulu, a mountain people on the upper waters of the Angabunga river in the Mekeo District. … The average stature is 1·551 m. (5 ft. 1 in.) ranging from 1·47 m. (4 ft. 10 ins.) to 1·63 m. (5 ft. 4 ins.). They are fairly strong and muscular, but rather slender and slight in development. …

“It is worth noting that Pöch had in 1906 measured two Fergusson Island men with statures 1·403 and 1·425 m. (4 ft. 7-1/4 ins., 4 ft. 8 ins.), who told him that “all the people in that tribe were as small or smaller.” …

“On reading through the brief synopses which I have given it is apparent that, with the possible exception of the Andamanese, each of the Negrito peoples shows considerable diversity in its physical characters and this is more evident when more detailed accounts and photographs are studied…

“The Negritos have certain cultural characters more or less in common, some of which differentiate them from their neighbours. There is very little artificial deformation of the person. … The Semang women possess numerous bamboo combs which are engraved with curious designs of a magical import, similar combs are possessed by nearly every Aeta man and woman. The Andamanese have no combs.

“The Andamanese make three kinds of simple huts on the ground and large communal huts are sometimes built. The Semang construct “bee-hive” and long communal huts and weather screens similar to those of the Andamanese. They also erect tree shelters, but direct evidence is very scanty that pure Semang inhabit huts with a flooring raised on piles; they sleep on bamboo platforms. The Aeta usually make very simple huts sometimes with a raised bamboo sleeping platform inside. …

“All the Negritos have the bow and arrow. The Great Andamanese bow is peculiar while that of the Little Andamanese appears to resemble that of the Semang. The Great Andamanese and the Tapiro have very long bows. Harpoon arrows with iron points are used by the Andamanese and Aeta, the arrows of the Andamanese, Semang and Aeta are nocked, but only those of the two latter are feathered.  …

“So far as is known the social structure of the Negritos is very simple. … Our knowledge concerning the Semang and Aeta is extremely imperfect but they probably resemble the Andamanese in these points. The Andamanese and Semang are strictly monogamous, polygyny is allowed among the Aeta, but monogamy prevails. The only restriction at all on marriage appears to be the prohibition of marriage between near kindred, and divorce is very rare. All bury their dead, but it is considered by the Andamanese more complimentary to place the dead on a platform which is generally built in a large tree, and the more honourable practice of the Semang is to expose the dead in trees. The Mafulu bury ordinary people, but the corpses of chiefs are placed in an open box either on a platform or in the fork of a kind of fig tree.”

EvX: That’s all for today. Next week, I have a book from Appalachia planned.

Some Historical Photos of Negrito People

Young Negrito Girl from the Philippines

There’s this weird divide between physical anthropology (which talks about what people look like,) and cultural anthropology (which talks about what they do.) When I read about what people are doing, I always want to know what they look like, especially if they’re from obscure groups I’ve never met anyone from in real life.

But when talking about people whose lifestyles have changed radically over the past hundred years or so, you run into a sharp divide between historical photos,
(depicting nearly naked hunter-gatherers in a nearly Edenic environment,) and modern photos of young women at the mall. With few exceptions, the folks Anthropologists love to study still exist–they did remain in the 1800s–even if Wikipedia contains no updated information on their modern lives.

So with that caveat, this post is devoted to historical photos of Negritos, with the emphasis on historical. Outside of the Sentinelese, who have remained independent and preserved their historical lifestyle by killing anyone who gets too close to their island, most modern Negritos no longer live like the folks depicted in these photos.

But the past is still fascinating.

The Negrito couple on the left hails from the lovely Andaman Islands (of which North Sentinel Island is part,) off the west coast of Indo-China and today part of India; the remaining Andamanese are designated a Scheduled Tribe[1] under Indian law.

To the right: Two Great Andamanese men, circa. 1875.

The Andamanese are believed to have arrived in the area around 26,000 years ago, about the time of the last glacial maximum, when lower sea levels made getting to such isolated places much easier.

Unfortunately, contact with the outside world has devastated the population, estimated at 7,000 in the late 1700s and only 400-450 today (and the Jangil are completely gone,) despite access to at least some of the modern medicines and technologies that are allowing populations to explode elsewhere.

The following photo is one of my favorites:

Perhaps this Andamanese fellow–a young man or teen, I assume–was showing off for the camera, but that is quite the leap he made in pursuit of the turtle he is spearing.

The boat (as you can see in other pictures) is quite long and can hold several fishermen (or warriors) at once.

I don’t know the purpose of the enclosure in the background; perhaps it also served to catch fish?

This fellow is not carrying about the skull of his defeated enemy, but a memento of a loved relative. According to the Handbook to Ethnographical Collections, “The dead are buried within the encampment in a sitting posture and wrapped up in leaves. The encampment is then deserted forthree months, after which the body is exhumed, and washed in the sea. Necklaces are then made of the bones, which are worn as mementoes by relations and friends, and are thought to cure pain or disease. Thus a man afflicted with toothache ties such a necklace round his face… The skull of the deceased is also worn round the neck as a mark of affection.”

Here is a jawbone worn in similar style, and a necklace made of what look like finger bones.

Their villages looked something like this village from Car Nicobar Island, with a thatched roof raised well above the ground. Here is another village, which shows how the huts could come right over the water, and a view of the inside of a large hut.

Here is a view of the outside of a large hut; this one’s sides go all the way to the ground–perhaps it belonged to a different tribe than the folks with the elevated huts.

The huts of the Jangil Negritos of the Andaman islands were completely different and look more like temporary sun-shelters than houses. (Though I note they are very similar to this double-decker storage and lounging hut.) When the weather is warm all year long, you just don’t need much in the way of house.

This young woman to the right is wearing a “tail skirt,” a piece of traditional finery that Wikimedia speculates may have led to legends of “monkey-tailed people” inhabiting the Andaman Islands.

Here is a photograph of Riala, Age 35, Andamanese-English interpreter from the Aka-Kede tribe, showing a traditional Andaman hairstyle (1890s), and here is a photo showing a traditional Andaman Negrito scarification pattern.

The Negritos of the Philippines, of course, having long inter-married with the other Filipinos, look a great deal like their neighbors.

This illustration of two pre-Hispanic Filipino Negrito warriors comes from the Boxer Codex, created around 1590. The Boxer Codex is filled with lovely illustrations of the various ethnic groups of the Philippines at the time of first contact with the Spanish, including Tagalogs, Visayans, Zambals, Cagayanes or possibly Ibanags, as well as several non-Filipino groups like Chinese and Vietnamese who had also settled there.

The Codex is (probably intentionally) also a guide to relative social class, with wealthier folks wearing far more (and colorfully dyed) clothes than than poor folks like these nearly-naked warriors.


Some 300 years later (1899), the Smithsonian published a near-recreation of the illustration, featuring two Negritos from Luzon, demonstrating their skill with the bow:

Here is another photograph of the same men plus several of their fellow tribesfolk (including three women), showing off their extremely long bows and fine hats.

Sadly, Wikimedia doesn’t seem to have any photos of Malaysian or other mainland Negritos.

For the most part, the Philippine Negritos appear to have tightly curled hair similar to the Andamanese, Papulans, and Melanesians, but some have wavy hair, more similar to the Australian Aborigines (though the effect is probably due entirely to marrying a non-Negrito neighbor.

(I note as well that the lady on the right is a bit taller than her friend on the left, which also suggests intermarriage–leaving us with a different question: Why do Aborigines have wavy hair?)

I have also met Vietnamese women with wavy hair (though perhaps not as wavy as this woman’s.) It contrasts with the extremely straight hair associated with Chinese and Japanese people, and I also wonder where it came from, though perhaps it’s just within the range of totally normal human variation.

The Negritos of Sundaland, Sahul, and the Philippines

Ati (Negrito) woman from the Philippines

The Negritos are a fascinating group of short-statured, dark-skinned, frizzy-haired peoples from southeast Asia–chiefly the Andaman Islands, Malaysia, Philippines, and Thailand. (Spelling note: “Negritoes” is also an acceptable plural, and some sources use the Spanish Negrillos.)

Because of their appearance, they have long been associated with African peoples, especially the Pygmies. Pygmies are formally defined as any group where adult men are, on average 4’11” or less and is almost always used specifically to refer to African Pygmies; the term pygmoid is sometimes used for groups whose men average 5’1″ or below, including the Negritos. (Some of the Bushmen tribes, Bolivians, Amazonians, the remote Taron, and a variety of others may also be pygmoid, by this definition.)

However, genetic testing has long indicated that they, along with other Melanesians and Australian Aborigines, are more closely related to other east Asian peoples than any African groups. In other words, they’re part of the greater Asian race, albeit a distant branch of it.

But how distant? And are the various Negrito groups closely related to each other, or do there just happen to be a variety of short groups of people in the area, perhaps due to convergent evolution triggered by insular dwarfism?

From Wikimedia

In Discerning the origins of the Negritos, First Sundaland Peoples: deep divergence and archaic admixture, Jinam et al gathered genetic data from Filipino, Malaysian, and Andamanese Negrito populations, and compared them both to each other and other Asian, African, and European groups. (Be sure to download the supplementary materials to get all of the graphs and maps.)

They found that the Negrito groups they studied “are basal to other East and Southeast Asians,” (basal: forming the bottom layer or base. In this case, it means they split off first,) “and that they diverged from West Eurasians at least 38,000 years ago.” (West Eurasians: Caucasians, consisting of Europeans, Middle Easterners, North Africans, and people from India.) “We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups.” (Denisovans are a group of extinct humans similar to Neanderthals, but we’ve yet to find many of their bones. Just as Neanderthal DNA shows up in non-Sub-Saharan-Africans, so Denisvoan shows up in Melanesians.)

Figure 1 (A) shows PC analysis of Andamanese, Malaysian, and Philippine Negritos, revealing three distinct clusters:

In the upper right-hand corner, the Aeta, Agta, Batak, and Mamanwa are Philippine Negritos. The Manobo are non-Negrito Filipinos.

In the lower right-hand corner are the Jehai, Kintak and Batek are Malaysian Negritos.

And in the upper left, we have the extremely isolated Andamanese Onge and Jarawa Negritos.

(Phil-NN and Mly-NN I believe are Filipino and Malaysian Non-Negritos.)

You can find the same chart, but flipped upside down, with Papuan and Melanesian DNA in the supplemental materials. Of the three groups, they cluster closest to the Philippine Negritos, along the same line with the Malaysians.

By excluding the Andamanese (and Kintak) Negritos, Figure 1 (B) allows a closer look at the structure of the Philippine Negritos.

The Agta, Aeta, and Batak form a horizontal “comet-like pattern,” which likely indicates admixture with non-Negrito Philipine groups like the Manobo. The Mamanawa, who hail from a different part of the Philippines, also show this comet-like patterns, but along a different axis–likely because they intermixed with the different Filipinos who lived in their area. As you can see, there’s a fair amount of overlap–several of the Manobo individuals clustered with the Mamanwa Negritos, and the Batak cluster near several non-Negrito groups (see supplemental chart S4 B)–suggesting high amounts of mixing between these groups.

ADMIXTURE analysis reveals a similar picture. The non-Negrito Filipino groups show up primarily as Orange. The Aeta, Agta, and Batak form a clear genetic cluster with each other and cline with the Orange Filipinos, with the Aeta the least admixed and Batak the most.

The white are on the chart isn’t a data error, but the unique signature of the geographically separated Mananwa, who are highly mixed with the Manobo–and the Manobo, in turn, are mixed with them.

But this alone doesn’t tell us how ancient these populations are, nor if they’re descended from one ancestral pop. For this, the authors constructed several phylogenetic trees, based on all of the data at hand and assuming from 0 – 5 admixture events. The one on the left assumes 5 events, but for clarity only shows three of them. The Denisovan DNA is fascinating and well-documented elsewhere in Melanesian populatons; that Malaysian and Philippine Negritos mixed with their neighbors is also known, supporting the choice of this tree as the most likely to be accurate.

Regardless of which you pick, all of the trees show very similar results, with the biggest difference being whether the Melanesians/Papuans split before or after the Andamanese/Malaysian Negritos.

In case you are unfamiliar with these trees, I’ll run down a quick explanation: This is a human family tree, with each split showing where one group of humans split off from the others and became an isolated group with its own unique genetic patterns. The orange and red lines mark places where formerly isolated groups met and interbred, producing children that are a mix of both. The first split in the tree, going back million of years, is between all Homo sapiens (our species) and the Denisovans, a sister species related to the Neanderthals.

All humans outside of sub-Saharan Africans have some Neanderthal DNA because their ancestors met and interbred with Neanderthals on their way Out of Africa. Melanesians, Papuans, and some Negritos also have some Denisovan DNA, because their ancestors met and made children with members of this obscure human species, but Denisovan DNA is quite rare outside these groups.

Here is a map of Denisovan DNA levels the authors found, with 4% of Papuan DNA hailing from Denisivan ancestors, and Aeta nearly as high. By contrast, the Andamanese Negritos appear to have zero Denisovan. Either the Andamanese split off before the ancestors of the Philippine Negritos and Papuans met the Denisovans, or all Denisovan DNA has been purged from their bloodlines, perhaps because it just wasn’t helpful for surviving on their islands.

Back to the Tree: The second node is where the Biaka, a group of Pygmies from the Congo Rainforest in central Africa. Pygmy lineages are among the most ancient on earth, potentially going back over 200,000 years, well before any Homo sapiens had left Africa.

The next group that splits off from the rest of humanity are the Yoruba, a single ethnic group chosen to stand in for the entirety of the Bantus. Bantus are the group that you most likely think of when you think of black Africans, because over the past three millennia they have expanded greatly and conquered most of sub-Saharan Africa.

Next we have the Out of Africa event and the split between Caucasians (here represented by the French) and the greater Asian clade, which includes Australian Aborigines, Melanesians, Polynesians, Chinese, Japanese, Siberians, Inuit, and Native Americans.

The first groups to split off from the greater Asian clade (aka race) were the Andamanese and Malaysian Negritos, followed by the Papuans/Melanesians Australian Aborigines are closely related to Papuans, as Australia and Papua New Guinea were connected in a single continent (called Sahul) back during the last Ice Age. Most of Indonesia and parts of the Philippines were also connected into a single landmass, called Sunda. Sensibly, people reached Sunda before Sahul, though (Perhaps at that time the Andaman islands, to the northwest of Sumatra, were also connected or at least closer to the mainland.)

Irrespective of the exact order in which Melanesians and individual Negrito groups split off, they all split well before all of the other Asian groups in the area.

This is supported by legends told by the Filipinos themselves:

Legends, such as those involving the Ten Bornean Datus and the Binirayan Festival, tell tales about how, at the beginning of the 12th century when Indonesia and Philippines were under the rule of Indianized native kingdoms, the ancestors of the Bisaya escaped from Borneo from the persecution of Rajah Makatunaw. Led by Datu Puti and Datu Sumakwel and sailing with boats called balangays, they landed near a river called Suaragan, on the southwest coast of Panay, (the place then known as Aninipay), and bartered the land from an Ati [Negrito] headman named Polpolan and his son Marikudo for the price of a necklace and one golden salakot. The hills were left to the Atis while the plains and rivers to the Malays. This meeting is commemorated through the Ati-atihan festival.[4]

The study’s authors estimate that the Negritos split from Europeans (Caucasians) around 30-38,000 years ago, and that the Malaysian and Philippine Negritos split around
13-15,000 years ago. (This all seems a bit tentative, IMO, especially since we have physical evidence of people in the area going back much further than that, and the authors themselves admit in the discussion that their time estimate may be too short.)

The authors also note:

Both our NJ (fig. 3A) and UPGMA (supplementary fig. S10) trees show that after divergence from Europeans, the ancestral Asians subsequently split into Papuans, Negritos and East Asians, implying a one-wave colonization of Asia. … This is in contrast to the study based on whole genome sequences that suggested Australian Aboriginal/Papuan first split from European/East Asians 60 kya, and later Europeans and East Asians diverged 40 kya (Malaspinas et al. 2016). This implies a two-wave migration into Asia…

The matter is still up for debate/more study.

Negrito couple from the Andaman Islands

In conclusion: All of the Negrito groups are likely descended from a common ancestor, (rather than having evolved from separate groups that happened to develop similar body types due to exposure to similar environments,) and were among the very first inhabitants of their regions. Despite their short stature, they are more closely related to other Asian groups (like the Chinese) than to African Pygmies. Significant mixing with their neighbors, however, is quickly obscuring their ancient lineages.

I wonder if all ancient human groups were originally short, and height a recently evolved trait in some groups?

In closing, I’d like to thank Jinam et al for their hard work in writing this article and making it available to the public, their sponsors, and the unique Negrito peoples themselves for surviving so long.

Why is India so dark?

source: Wikipedia
source: Wikipedia

Take a closer look at the 20th parallel:


South of the 20th, India and Africa match pretty well, though south east Asia, Indonesia, the Philippines, and Latin America are noticeably lighter. North of the 20th parallel, even most of Africa is lighter than most of India.

My theory is that one of the first groups out of Africa (if not the first) was a dark-skinned group (all of the groups that left Africa were dark-skinned, of course,) that took a coastal route though (modern) Yemen and Oman, along the southern coast of Pakistan, and then spread into the abundant, hospitable lands around the Indus, Ganges, Narmada, and other rivers.

Some of them continued on, into Tibet, Indochina, and Indonesia. These guys were competent boat-builders, who made it to the Andaman Islands, Australia, Melanesia, and possibly up to Japan (the Ainu) and the New World (where we are now finding what looks like Melanesian DNA deep in the rainforests of Brazil.) This all happened somewhere between 100,000 years ago (out of Africa, maybe) and 40,000 years ago (people reached Australia.)

More-or-less meanwhile, other groups headed northward, then circled back around. By the time they came back, they’d lightened. Several groups back-migrated into Africa, (most recently the Arab conquests, but we also have evidence of migrations 3 thousand and 23 thousand years ago;) they probably conquered Iran and Indochina from the north. From Taiwan spread another group, the Polynesians, who might have partially displaced the Melanesians and settled many islands they hadn’t been able to reach. The Ainu got pushed out and even Australia got a small invasion, though in its case, by folks from India, so its skin color didn’t change.

But India is a tough place to conquer from the north. There are some awfully big mountains in thew way. India has certainly been conquered during the long expanse of history–I suspect this accounts for the violet blob that pierces central India, perhaps due to the Indo-European expansion–but they’ve probably been conquered less, overall, than places like China.

There are a lot of small, interesting groups that I suspect are ultimately descended from what was once a large group of people that stretched around the south eastern curve of Asia (and its islands), but are now quite isolated–

source Wikipedia
Negrito couple from the Great Andaman Island

Andamanese people hunting turtles
Andamanese people hunting turtles

Young Aeta girl, Philippines, 1901
Young Aeta girl, Philippines, 1901

Semang man from Malaysia (old picture, I know)
Semang man from Malaysia (old picture, I know)

Semang people, Malaysia
Semang people, Malaysia

Young Negrito Girl from the Philippines
Young Negrito Girl from the Philippines


Not so obscure Australians

Folks from Papua New Guinea
Folks from Papua New Guinea

Naural blond hair
Two Melanesian girls from Vanatu




Species of Exit: The Sentinelese, the world’s most isolated people

North Sentinel Island
North Sentinel Island

Map showing location of North Sentinel Island (red) relative to the rest of the Andaman Islands
Map showing location of North Sentinel Island (red) relative to the rest of the Andaman Islands

Map showing the distance between the Andaman Islands and land.
Map showing the distance between the Andaman Islands (small islands south of Myanmar) and land.

The Sentinelese appear to have split off from the rest of humanity approximately 48,500 years ago, and aside from occasional contact with other members of the Andaman islands, have remained isolated ever since.

People have occasionally landed on or near Sentinel island, but the islanders have all resisted contact, generally by shooting arrows at anyone who gets too close. Even National Geographic hasn’t got any pictures of them–when they tried to make a documentary on the island, armed with gifts, they had to retreat after the director took an arrow in the thigh. The last guys whose boat accidentally drifted onto their beach got killed and buried in shallow graves on the beach.

North Sentinel Island is technically owned by India, but India has given up trying to make peaceful contact, and it would probably look bad to just bomb the place.

So what do we know about the Sentinelese?

Obviously not a whole lot, since most of what we know of them has been observed from a distance.

The whole island is about the size of Manhattan, and probably inhabited by 40-500 people. They’re generally characterized as Negritos, a term used for the shorter than average but taller than Pygmies, dark-skinned people of the Andaman Islands and certain groups in the Philippines, Thailand, and Malaysia. The term is only descriptive; different Negrito tribes may not be related to each other at all. (I promised I’d get around to the Negritos eventually.)

Aside from stuff that has randomly washed up on their island or was given to them by folks trying to make contact, they have only stone tools and, according to the Wikipedia, appear not to have fire.

But a little more research suggests that Wikipedia may just be wrong on this point; during the search for the lost Malaysian jetliner, smoke was observed rising from North Sentinele, which implies that the people there probably do have fire.

At any rate, we do know that they have bows and arrows, boats, and spears.

When National Geographic tried to make contact, they left a plastic toy car, coconuts, a live pig, a doll, and aluminum cookware on the beach before getting shot at. After they retreated, they observed the Sentinelese shoot and bury the pig (not eat it?) and, if the Wikipedia is accurate, shoot and bury the doll. They took the coconuts and pans; no word of the car’s fate.

In 1970, a group of Indian anthropologists that came near the island had a decidedly strange incident:

Quite a few discarded their weapons and gestured to us to throw the fish. The women came out of the shade to watch our antics… A few men came and picked up the fish. They appeared to be gratified, but there did not seem to be much softening to their hostile attitude… They all began shouting some incomprehensible words. We shouted back and gestured to indicate that we wanted to be friends. The tension did not ease. At this moment, a strange thing happened — a woman paired off with a warrior and sat on the sand in a passionate embrace. This act was being repeated by other women, each claiming a warrior for herself, a sort of community mating, as it were. Thus did the militant group diminish. This continued for quite some time and when the tempo of this frenzied dance of desire abated, the couples retired into the shade of the jungle. However, some warriors were still on guard. We got close to the shore and threw some more fish which were immediately retrieved by a few youngsters. It was well past noon and we headed back to the ship…

Virtually nothing is known about the Sentinelese language, though it is speculated that it is related to the Onge language of the Andaman islands. However, attempts at using the Onge as translators have failed, as the Onge themselves cannot understand a word of Sentinelese.

A British expedition in the 1880s that got a decent look at the island claimed that, of all the nearby groups, Sentinelese culture most closely resembled Onge culture, so it is still possible that the languages are related, albeit distantly.

Since much more is known about the Onge, I’m going to speak briefly about them:

A member of the Onge collecting Honey on the Andaman Islands
Onge man collecting honey, Andaman Islands

The Onge are marked in blue on the map above; today they live chiefly on Little Andaman Island in the south, but in the past they ranged further north, closer to to the Sentinelese. Contact with the outside world has reduced their population from almost 700 people (1900) to about 100. (There may well have been >700 people before 1900, that’s just the first date I have numbers for.) Strangely, the Onge appear to be the world’s least fertile people, with 40% of couples suffering infertility. Wikipedia estimates their Net Reproductive Rate (similar to TFR, but only looks at daughters) at 0.91, which is below replacement, however, their population appears to have held steady for the past 30 years, so perhaps the problem is working itself out.

Why such infertility? The most obvious guesses (IMO) are some sort of environmental poison/effect; some sort of diseased-induced infertility, like gonorrheal scaring (please note that I have no idea if any of the Onge have ever had gonorrhea, but it is a common cause of infertility;) or a side effect of inbreeding/lack of genetic diversity following their extreme population collapse.

The article Malnutrition and high childhood mortality among the Onge tribe of the Andaman and Nicobar Islands suggests that the real cause of the low NRR is high childhood mortality due to malnutrition/insufficient food, probably due to loss of their traditional hunting/gathering grounds.

Genetically, the Onge appear to have been isolated for an extremely long time. They all share the same mitochondrial DNA, haplotype M32, which is not found anywhere outside of the Andaman Islands. (The larger umbrella-group M, to which all M-varieties belong, is one of the world’s most wide-spread lineages, emerging either shortly before the Out of Africa event, or shortly after it, but is most reliably concentrated in Asia, with several ancient lineages in India.)

The Onge language is related to the languages of some of the other tribes in the Andaman Islands, and speculated to be part of the greater Austronesian language family. (Considering that the whole Indo-European language family is about, what, 4-6,000 years old, I am a little skeptical of our ability to reconstruct too much about a language that may have diverged 40,000+ years ago.)

Onge Y-DNA belongs to Haplogroup D-M174, which emerged in Asia about 60,000 years ago and isn’t found outside of Asia. It is found today among Tibetans, the Ainu, and the Andaman Islanders, suggesting that these people are all (at least partially) descended from a common source that split off from other humans around 60,000 years ago, or just after the OoA (relatively speaking.) D-M174 is also found in small amounts in China and central/east Asia.

The Ainu, IIRC, also have a particular tooth shape that is commonly found in Melanesia, but not outside of it, and a small amount (about 15%, I think,) of Siberian DNA. And, of course, we now have evidence of Melanesian DNA showing up in the Amazon rainforest, not to mention the curious concentration of archaic Denisovan admixture in Melanesians, despite the only Denisovan remains we’ve found so far coming from Russia. However, it appears that there is no Denisovan DNA in the Andaman Islanders, so maybe they split off before the Denisovan admixture advent.

The sum of the evidence suggests a single band of people, perhaps most closely resembling the Negritos, spread 60,000 years ago along the coast of southern Asia and spread far into the interior, reaching at least as far as Tibet, the Andaman Islands, and northern Japan, and possibly even crossing the Bering Strait and down to the tip of South America. (Since Melanesians do not appear to have ever spread to Polynesia, I suspect they did not boat straight across the Pacific, but maybe we just haven’t yet found Melanesian remains in Polynesia.)

Over the ensuing millenia, later population waves, like the Polynesians and the common ancestors of east Asians like the Han and the Japanese, migrated into the area, leaving only a few isolated remnants of Haplogroup D-M174 in far-flung, difficult to reach places like the Andaman islands, the Himalayan Plateau, and the coldest parts of Japan. Likewise, Melanesian DNA in the New World seems to have best survived in one of its harshest, most difficult to penetrate habitats: the rain forest.

This all gets back to my theory of genetic survival at the fringes, (discussed here,) which I hope to devote a full post to soon. The history of the world is the group with better tech conquering the group with worse tech, and then getting conquered in turn by a group with even better tech.

The island of Taiwan illustrates this well; the most recent immigration wave happened in 1949, when the ROC lost their war with the PRC and evacuated 2 million of their people to Taiwan, a nation of 6 million at the time. Taiwan had previously (temporarily) been conquered by the Japanese, and before that, by other Chinese people, who began arriving around 1300. They’ve been gradually defeating/replacing the aboriginal Taiwanese, who are now a very small population, and the aboriginal Taiwanese themselves have legends about having wiped out a negrito-like people who predated their arrival, but I consider such legends only potentially true. Each group got conquered by the next group with better tech.

A couple more pictures of Andaman Islanders:

source Wikipedia
Onge mother and child, Wikipedia


source Wikipedia
Andamanese Couple, Wikipedia

Anyway, back to the Sentinelese.

The available evidence suggests that they split off from the rest of the human population ages upon ages ago, and have been effectively isolated from everyone but their immediate neighbors ever since. Though technically their island is considered part of India, as a practical matter, they govern themselves. They have managed to retain their independent status for so long by living on a tiny, hard-to-reach island and enforcing a strict immigration policy of killing anyone who shows up on their beach.

Given that the Sentinelese would probably all die of the common cold if they ever did let foreigners onto their island, their policy is not unreasonable. You wouldn’t want to let some plague-bearing foreigner kill you with their germs, either. Unfortunately, the disease situation is unlikely to reverse itself; their population is just too small to withstand contact with the outside world. Too-long isolation in such a tiny place has cut them off from all the technological progress of the past 40,000 to 60,000 years, and their population is too small to develop much tech internally. To be fair, their strategy has worked so far. But now they’re stuck, maintaining their tiny island against the odds until someone decides to show up with guns and do some logging, fishing, or whatever they feel like, at which point there’s a good chance they’ll be wiped out.

Long term, total isolation is a policy with very low survival odds.

After some thought, the best option I can think of for the Sentinelese, other than continuing as they are and hoping for the best (after all, the rest of the world could destroy itself in a nuclear holocaust and leave them behind to continue doing their thing for the next 40,000 years,) is to expand their numbers and send excess people to the other Andaman Islands. Sure, most of those people would probably get colds and die, and if not the colds, alcohol’s a likely culprit, but as long as they keep exporting people, eventually some of them will survive, and create a breeding population/intermix with the other Andamanese until they have the numbers/immunity to interact with the outside world.