Out-of-Africa Phylogeny from Dental Polymorphisms

I discovered the solution to the problem I was working on. Rather I discovered that Hanihara was struggling with the same problem and that he had figured out the solution by 2008. The population history signal is contained in the neutral drift component of systematic variation in human phenotypes. By neutral, I mean derivation due not to diversifying selection but rather to founder effects and isolation-by-distance. There is definitely a population history signal in cranial and craniofacial characters. A weaker signal is found in phonemic data and postcranial skeletal morphology. All of the above, with the exception of linguistic data, are to a greater or lesser extant confounded by natural selection. And linguistic data has a weak population history signal, certainly at great time depths.

So I have been looking at craniodental data. Metric craniodental data (teeth diameter etc) contains as strong a population history signal as craniometrics. But as it turns out we can do much better. The real gold is in dental polymorphisms. Polymorphisms are discrete variants of phenotypes, eg, blood groups (called RBC polymorphisms), hair color (we get the ginger from Neanderthals), eye color, and so on. Such polymorphisms can usually be found in all populations. The differences in their frequency contains some information on population history. This is usually badly confounded by, say, sexual selection. Think of hair color or eye color.

In the case of dental polymorphisms, there are good reasons to believe that the population history signal is not confounded at all so that frequency differences between populations reflect shared inheritance. The basic operating logic is that of Mayr’s founder effect. All founder populations carry with them only a subset of the phenotypic diversity. Moreover, their smaller effective population size means even greater loss of diversity over time as lineages die out randomly.


Figure 1. Founder effect. Source: Wikipedia Commons.

In a recent paper in Nature, Hanihara and others showed that dental morphology contains an extraordinarily strong population history signal that is highly correlated with the best estimates from molecular anthropology. So this is a very promising line of investigation.

Let me illustrate with some frequency distributions for some of these dental polymorphisms. Figure 2 displays the incidence of shoveling of the first Upper Incisor (UI1) by macro region. Why has this morphotype reached near fixation in northeast Asia and the Americas? Why do the western old worlds and eastern old worlds cluster together and on opposite sides of Africa which is right in the middle? The right answer lies in the details of the Out-of-Africa dispersals. Phylogeographer Stephen Oppenheimer argued forcefully in Out of Eden for a thick version of the southern route or beachcomber hypothesis whereby there a single exit from Africa to India, and it was from the subcontinent that Homo sapiens heading west to Europe, south and east to Sahul, a branch of whom instead went up the coast to China. The morphotype achieved near fixation in northeastern Asia before the founder populations migrated to the Americas across Alaska. Moreover, Oppenheimer argues that the big freeze of the Last Glacial Maximum about 20ka decimated northern populations and reduced their genetic diversity. The actual fixation of this morphotype in northern America may reflect this natural history.


Figure 2. UI1 shoveling incidence rate by macroregion.

In the case of the awkward-to-pronounce Hypoconulid polymorphism, we can see the eastern and western branches going out from India both became derived; in the opposite direction. The morphotype became more frequent in the west and less frequent in the east, with a particularly severe decline in frequency in Australia and northern America. LGM strikes again?


Figure 3. Frequency of the Hypoconulid morphotype.

The premolar accessory cusp morphotype is rather rare outside Australia and Melanesia, suggesting that this is a derivation in these populations after they split from the others. This ancient clade also stands out in metric craniodental traits. The derivation is largely a function of the great time-depth of the split. It is no surprise that geographic isolates display marked derivation in the human species. It holds across the animal kingdom.


Figure. Frequency of premolar accessory cusp morphotype.

Almost simultaneously as their paper in Nature, Hanihara and gang published an extraordinary study in Current Anthropology, where they showed that of all the competing Out-of-Africa dispersal scenarios, Oppenheimer’s beachcomber single-dispersal Out-of-Africa via India scenario (“BSD” in the next figure) is the most consistent with the phylogeny obtained from dental polymorphism frequencies.


Figure 4. Out-of-Africa dispersal scenarios. BSD = beachcomber arc single dispersal; EE = eastward expansion single dispersal; MD = multiple dispersals; MDI = multiple dispersals and Australo-Melanesian isolation.

I like to check things with my own two hands. I used the Hanihara (2008) data on dental polymorphisms to extract a phylogram that reflects our population history. In order to compare the frequency data from different polymorphisms, I converted them to percentile scores. Then I used the Euclidean metric to obtain pairwise phenotypic distances, from which I obtained the phylogram using the standard neighbor-joining algorithm. The accuracy of the resulting phylogram is simply astonishing. I hit pay-dirt alright.


Figure 5. Phylogeny from dental polymorphisms.

One can read off our population history from this diagram. Homo sapiens left Africa via the Red Sea route to India 100-80ka. While many founders stayed behind on the subcontinent, some beachcombers kept going further east. These populations reached Sahul by 60ka. The Negrito populations of the Andaman Islands and Melanesia, and the Australian aboriginal population are actual relict populations from that original dispersal. (BTW, the Negritos aren’t black and fizzy haired because they are close to Africans. Their dark skins reflect directional diversifying selection under similar tropical conditions; like the different origins of depigmentation on either extremity of Eurasia, it’s the classic case of a homoplasy.) On their way to Sahul, some of these founders stayed back in southeast Asia which at time was a large continent called Sunda. Some of them would later go on to become Polynesians and the greatest sea-farers the world has ever seen. Others went up north to northeast Asia and later from there on to the Americas soon after the Last Glacial Maximum. Before all these developments in the far east, pioneer Sapiens ventured forth north and west from India, taking the trans-Caucasus route to Europe where they would go on to “replace” Neanderthals. The move back into Africa (the Ethiopians are the descendents of this reverse migration) followed after southwest Asia was finally peopled (it had been a forbidding desert before).

So here’s the kicker. When Dravidians (9ka) and later Indo-Europeans (4ka) reached India, it was a reunion long in the making. What is astonishing is how this turn table between India and Europe has been turning throughout deep history. In a sense, the paleogeographic logic of this pattern puts the flesh on the bone on Diamond’s insight — that the east-west Eurasian axis was more advantageous than the north-south axes of Africa and the Americas for the simple reason that people, ideas, and technology (and germs) could move faster against the latitude gradient than along it. What is amazing is the emerging picture of how Diamond’s logic worked in practice — at least where pots were moving with people (one can hardly demand more of physical anthropology).

Oppenheimer argues that the Upper Paleolithic revolution in Europe (it is to paleoanthropologists what the Industrial Revolution is to modern economic historians and the Neolithic revolution is to prehistorians) was the handiwork of founders from the Indian subcontinent. He traces both the people who authored the Aurignacian culture c. 43ka as well as the later arrivals who authored the Gravettian c. 35ka, the great mammoth hunters of north-central Eurasia, to the subcontinent. But that deepens the paradox of the Upper Paleolithic. If the authors of the Aurignacian came from the subcontinent and so did those of the Gravettian, they why does the Upper Paleolithic not reach India until tens of thousands of years later? Was it combined and uneven development structured by our Heliocentric geometry? Or was something even deeper at play. That’s the big open question of paleoanthropology.



Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s