Razib Khan One-stop-shopping for all of my content

January 18, 2012

The phylogeography of the trans-Caucasus

Randy McDonald points me to this fascinating post, Genetic clues to the Ossetian past. In the post author outlines phylogeographic inferences one can make from uniparental lineages; maternal and paternal lines of descent. Specifically, they are in interested in the origins and relationships of the Ossete people. I assume that one reason Randy pointed me to this post is that the Ossetes are assumed by many to be the descendants or fragments of the Alans. More broadly they’re remnants of a broad array of North Iranian peoples, of whom the Scythians were the most prominent, which have been erased from the pages of history because of the expansion of the Slavs and Turks.


The main lacunae in the above analysis is that it does not cover results from autosomal studies. Some of that has been performed by Dienekes, but more is necessary for a region characterized by as much ethnographic diversity and density as the Caucasus. One peculiarity that emerges in analyses of autosomal data sets is that the Caucasus looms relatively large in a wide array of dispersed populations. For example, there is a genetic signature which ties Indo-Aryan and Caucasian populations together, and others which seem to connect the latter to some Balkan groups.

These are possible hints that the Caucasus is the “mother of nations,” and that the old idea of the “Caucasian race” may have some reality to it. But I would bet on something else: the Caucasus is not the mother of nations, but the repository of forgotten peoples. The Ossetes themselves are presumed to be just such a population. I offer up the hypothesis that one reason that disparate Caucasian populations have diverse and wide-ranging connections has less to do with outward expansion, and more to do with the fact that on the margins of the Caucasus a great range of historic genetic diversity erased by later demographic events (e.g., the Slavic and Turkic expansions from two directions in on the North Iranian peoples) is preserved, as the defeated take refuge.

June 16, 2011

Present genetic variation is a weak guide to past genetic variation

As I’ve been harping on and on for the past few years that the patterns of contemporary genetic variation are probably only weakly tied to past patterns of genetic variation (though Henry Harpending warned me about this as far back as 2004). A major reason that scholars operated under this presupposition is the axiom that most of the variation we see around us crystallized during the Last Glacial Maximum (~20 thousand years before the present).

This may be true in some cases, but I doubt it is true in most cases. I was pointed to a classic case of this problem just today. A reader alerted me to a short paper from this spring which attempts to ascertain the point of origin of the dominant mtDNA haplogroup among the Onge tribe of the Andaman Islanders, M31a1. This is an interesting issue because some researchers proposed, plausibly in the past, that these indigenous people in the Andaman Islands represent the descendants of the first wave “Out of Africa,” who took the rapid “beachcomber” path. Understanding the key to their genetics may then unlock the key to the “Out of Africa” event. Or ...

May 31, 2011

Mediterranean men on the move

ResearchBlogging.orgSeriously, sometimes history matches fiction a lot more than we’d have expected, or wished. In the early 2000s the Oxford geneticist Bryan Sykes observed a pattern of discordance between the spatial distribution of male mediated ancestry on the nonrecombinant Y chromosome (NRY) and female mediated ancestry in the mitochondrial DNA (mtDNA). To explains this he offered a somewhat sensationalist narrative to the press about possible repeated instances of male genocide against lineage groups who lost in conflicts.

Here is a portion of the book of Numbers in the Bible:

15 – And Moses said unto them, Have ye saved all the women alive?

16 – Behold, these caused the children of Israel, through the counsel of Balaam, to commit trespass against the LORD in the matter of Peor, and there was a plague among the congregation of the LORD.

17 – Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.

18 – But all the women children, that have not known a man by lying with him, keep alive for yourselves.

Then there is the rape of the Sabine women. The ethnogenesis of the mestizo and mulatto populations of ...

May 15, 2011

Genetic variation in the Caucasus

The Pith: There is a very tight correlation between language and genes in the Caucasus region.

If the Soviet Union was the “The Prisonhouse of Nations,” then the Caucasus region must be the refuge of the languages. Not only is this region linguistically diverse on a fine-grained scale, but there are multiple broader language families which are found nowhere else in the world. The widespread Indo-European languages are represented by Armenians, Greeks, and Iranians. The similarly expansive Altaic languages are represented by the Turkic dialects. But in addition to these well known groups which span Eurasia there are the Northwest Caucasian, Northeast Caucasian, and Kartvelian, families. These have only a local distribution despite their distinctiveness.

On the one hand we probably shouldn’t be that surprised by the prominence of small and diverse language families in this rugged region between Russia and the Near East. Mountains often serve as the last refuges of peoples and cultures being submerged elsewhere. For example, in the mountains of northern Pakistan you have the linguistic isolate of Burusho, which has no known affinity with other languages. Likely it once had relatives, but they were assimilated, leaving only ...

May 9, 2011

The Solutrean hypothesis vindicated?

Filed under: Archaeogenetics,History,Solutrean hypothesis — Razib Khan @ 1:39 pm

Here’s the model from Wikipedia:

This hypothesises similarities between the Solutrean industry and the later Clovis culture / Clovis points of North America, and suggests that people with Solutrean tool technology crossed the Ice Age Atlantic by moving along the pack ice edge, using survival skills similar to that of modern Eskimo people. The migrants arrived in northeastern North America and served as the donor culture for what eventually developed into Clovis tool-making technology. Archaeologists Dennis Stanford and Bruce Bradley suggest that the Clovis point derived from the points of the Solutrean culture of southern France (19,000BP) through the Cactus Hill points of Virginia (16,000BP) to the Clovis point…This would mean that people would have had to move from the Bay of Biscay across the edge of the Atlantic ice sheet to North America. Supporters of this hypothesis believe it would have been feasible using traditional Eskimo techniques still in use today….

In my opinion there’s all sorts of things crazy with this model. But genome blogger Diogenes has been harping on the possibility that a low level substratum component among Northern Europeans which has affinities to Siberians and Amerindians may be a remnant of the original European hunter-gatherers. It ...

April 19, 2011

Europeans as Middle Eastern farmers

ResearchBlogging.orgThe Pith: Over the past 10,000 years a small coterie of farming populations expanded rapidly and replaced hunter-gatherer groups which were once dominant across the landscape. So, the vast majority of the ancestry of modern Europeans can be traced back to farming cultures of the eastern Mediterranean which swept over the west of Eurasia between 10 and 5 thousand years before the before.

Dienekes Pontikos points me to a new paper in PNAS which uses a coalescent model of 400+ mitochondrial DNA lineages to infer the pattern of expansions of populations over the past ~40,000 years. Remember that mtDNA is passed just through the maternal lineage. That means it is not subject to the confounding dynamic of recombination, allowing for easier modeling as a phylogenetic tree. Unlike the autosomal genome there’s no reticulation. Additionally, mtDNA tends to be highly mutable, and many regions have been presumed to be selectively neutral. So they are the perfect molecular clock. There straightforward drawback is that the history of one’s foremothers may not be a good representative of the history of one’s ...

March 31, 2011

The Bantu völkerwanderung

Filed under: Africa,Archaeogenetics,Bantu Expansion,Genetics,Genomics — Razib Khan @ 2:34 pm


Image Credit: Mark Dingemanse

I recall years ago someone on the blog of Jonathan Edelstein, a soc.history.what-if alum as well, mentioning offhand that archaeologists had “debunked” the idea of the Bantu demographic expansion. Because, unfortunately, much of archaeology consists of ideologically contingent fashion it was certainly plausible to me that archaeologists had “debunked” the expansion of the Bantu peoples. But how to explain the clear linguistic uniformity of the Bantu dialects, from Xhosa of South Africa, up through Angola and Kenya, to Cameroon? One extreme model could be a sort of rapid cultural diffusion, perhaps mediated by a trivial demographic impact. The spread of English exhibits this hybrid dynamic. In some areas (e.g., Australia) there was a substantial, even dominant, English demographic migration coincident with the rise of Anglo culture. In other areas, such as Jamaica, by and large the crystallization of an Anglophone culture arose atop a different demographic substrate, which synthesized with the Anglo institutions (e.g., English language and Protestant religion). The United States could arguably be held up as a in-between case, with an English founding core population, around which there was an ...

December 30, 2010

Are Turks acculturated Armenians?

To the left you see a zoom in of a PCA which Dienekes produced for a post, Structure in West Asian Indo-European groups. The focus of the post is the peculiar genetic relationship of Kurds, an Iranian-speaking people, with Iranians proper, as well as Armenians (Indo-European) and Turks (not Indo-European). As you can see in some ways the Kurds seem to be the outgroup population, and the correspondence between linguistic and genetic affinity is difficult to interpret. For those of you interested in historical population genetics this shouldn’t be that surprising. West Asia is characterized by of endogamy, language shift, and a great deal of sub and supra-national communal identity (in fact, national identity is often perceived to be weak here). A paper from the mid-2000s already suggested that western and eastern Iran were genetically very distinctive, perhaps due to the simple fact of geography: central Iran is extremely arid and relatively unpopulated in relation to the peripheries.

But this post isn’t about Kurds, rather, observe the very close relationship between Turks and Armenians on the PCA. The _D denotes Dodecad samples, those which Dienekes himself as collected. This affinity could easily be predicted by the basic parameters of physical geography. Armenians and Anatolian Turks were neighbors for nearly 1,000 years. Below is a map which shows the expanse of the ancient kingdom of Armenia:

Historic Armenia was centered around lake Van in what is today eastern Turkey. The modern Republic of Armenia is very much a rump, and an artifact of the historic expansion of the Russian Empire in the Caucasus at the expense of the Ottomans and Persians. Were it not for the Armenian genocide there may today have been more Armenians resident in Turkey than in the modern nation-state of Armenia,* just as there are more Azeri Turks in Iran than in Azerbaijan. Many areas once occupied by Armenians are now occupied by Kurds and Turks. But a bigger question is the ethnogenesis of the Anatolian Turkish population over the past 1,000 years.

Dienekes has already shed light on this topic earlier, adding the Greek and Cypriot populations to the mix as well as Turks and Armenians. The disjunction between Kurds and the Armenian-Turk clade suggests to us that Turks did not emerge out of the milieu of Iranian tribes in the uplands of southeast Anatolia and western Persia. Like the Armenians the Kurds are an antique population, claiming descent from the Medes, and referred to as Isaurians during the Roman and Byzantine period.

Below is a reformatted K = 15 run of ADMIXTURE with Eurasian population. I’ve removed the labels for the ancestral components, but included in populations which have a high fraction of a given ancestral component. The geographical labels are for obscure populations. I’ve underlined the four populations of interest:

First, let’s get out of the way the fact that Turkish samples have non-trivial, though minor, northeast Asian ancestry. The Yakut themselves are a Turkic group situated to the north of Mongolia. The more southerly and central Asian affinities the nomadic ancestors of the Anatolia Turks may have picked up in their sojourns over the centuries between their original homeland in east-central Siberia and Mongolia and West Asia. The rest of ancestry is rather typical of northern West Asian groups. In particular, Armenians! Here is the ancestral breakdown for the four groups I want to focus on using Dienekes’ labels:


Population Greek Cypriots Turks Armenians
West Asian 37.6 54.1 47.2 56.3
Central-South Asian 5.3 8.6 18.2 18.4
North European 25.1 5.6 12 12.3
South European 27.4 20.8 9.4 8.4
Arabian 3.4 8 4.3 3.4
Altaic 0.3 0 2.6 0.1
East Asian 0.3 0.2 2.2 0
Central Siberian 0.1 0.2 1.4 0.2
Chukchi 0 0 1.1 0.2
South Indian 0 0.1 0.8 0.3
Nganasan 0.1 0 0.4 0.2
Koryak 0.1 0 0.2 0.1
East African 0 0.4 0.1 0
West African 0 0 0.1 0
Northwest African 0.3 1.9 0.1 0

And now the correlations between the populations by ancestral components:



Greek Cypriots Turks Armenians
Greek * 0.863 0.823 0.813
Cypriots * * 0.941 0.946
Turks * * * 0.997
Armenians * * * *

Let’s remove the East Eurasian and African components, and recalculate the proportions by taking what remains as the denominator:


Population Greek Cypriots Turks Armenians
West Asian 38.1 55.7 51.8 57.0
Central-South Asian 5.4 8.9 20.0 18.6
North European 25.4 5.8 13.2 12.4
South European 27.7 21.4 10.3 8.5
Arabian 3.4 8.2 4.7 3.4

And the recomputed  correlations:



Greek Cypriots Turks Armenians
Greek * 0.747 0.640 0.647
Cypriots * * 0.901 0.908
Turks * * * 0.999
Armenians * * * *

With all the ~0 ancestral components which were common across these four populations removed the correlations have gone down. Except in the case of the Armenian-Turk pair, because I’ve removed the ancestries which differentiate them.

So what’s a plausible interpretation? A straightforward one would be that the Muslim Turk population of Anatolia has a strong bias toward having been assimilated Armenians, rather than Greeks. The cultural plasticity of Armenians in late antiquity and the early medieval period was clear: individuals of ethnic Armenian to origin rose the pinnacles of the status hierarchy of the Orthodox Christian Greek Byzantine Empire. The Macedonian dynasty of the Byzantines under which the civilization reached its mature peak were descended from Armenians who had resettled in Macedonia. Just as plausible to me is that eastern Anatolia as a whole exhibited little genetic difference between Greeks and Armenians, and the former were wholly assimilated or migrated, while the Armenians remained. One way to test this thesis would be type the descendants of Greeks who left eastern Anatolia during the population exchange between Greece and Turkey in the 1920s. But the difference between Greeks and Cypriots also points us to another possibility: perhaps the Greeks of Greece proper (as opposed to Anatolia) were much more strongly impacted by the arrival of Slavs? One need not necessarily rely solely on the Scalveni migrations either, water tends to be a major dampener to conventional isolation-by-distance gene flow, so the Greek mainland may always have been subject to more influence from the lands to the north.

Whatever the details of ethnogenesis may be, it will be interesting to see how things shake out as we increase sample sizes and get better population coverage. These results may be due to regional selection bias. One might expect that the descendants of Rumelian Turks be more “European” than Anatolian Turks. But, these data do seem to suggest on face value that Armenians are the population which Anatolian Turks have the most genetic affinity with.

* My main hesitation would be that Armenians are a very mobile population, and their numbers within a modern Turkey may have declined simply through emigration, just as those of Christian Arabs have over the 20th century.

December 20, 2010

Some of the Indo-Europeans found?

hunza
School girls in Hunza, Pakistan

A few days ago I observed that pseudonymous blogger Dienekes Pontikos seemed intent on throwing as much data and interpretation into the public domain via his Dodecad Ancestry Project as possible. What are the long term implications of this? I know that Dienekes has been cited in the academic literature, but it seems more plausible that this sort of project will simply distort the nature of academic investigation. Distort has negative connotations, but it need not be deleterious at all. Academic institutions have legal constraints on what data they can use and how they can use it (see why Genomes Unzipped started). Not so with Dienekes’ project. He began soliciting for data ~2 months ago, and Dodecad has already yielded a rich set of results (granted, it would not be possible without academically funded public domain software, such as ADMIXTURE). Even if researchers don’t cite his results (and no doubt some will), he’s reshaping the broader framework. In other words, he’s implicitly updating everyone’s priors. Sometimes it isn’t even a matter of new information, as much as putting a spotlight on information which was already there. Below is a slice of a bar plot from Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. It uses STRUCTURE with K = 7. To the right of the STRUCTURE slice are two plots of individual data on French and French Basque from the same HGDP data set using ADMIXTURE at K = 10 from Dodecad.

fbasq


Repeated runs and higher K’s make it clear that the French Basque lack a “West Asian” aspect which other French, and Iberians as well, have. Some of this is clear in the paper I referenced above as well…the key is you have to look at the supplements at K = 6. Because the Basque are the only native non-Indo-European speakers in Western Europe, their origin and relationship to nearby populations has always been of interest (they also have the highest Rh- frequency of world populations). Granted, the French Basque are very similar genetically to the French as a whole. But, it is obviously highly informative that they lack an ancestral component in totality which seems to exist at low but consistent levels across Western European populations. The only other European population at K = 15 who lack the West Asian component in totality are Finns (the Lithuanians come very close).

This is all preamble to a discussion of a post Dienekes put up today, A solution to the problem of Indo-Aryan origins. Remember that Dienekes has been “playing” with ADMIXTURE for only a few months. To claim to have found a ‘solution’ to a problem as intellectually and politically intractable and explosive as this is rather bold. The crux of the matter is that at a certain confluences of K’s and population sets Dienekes has discovered a distinctive signature of ancestry which seems to be modal on the north slope of the Caucasus, and spans India and Europe. He terms this “Dagestani,” due to the fact that among a population sample from this province in Russia this ancestral component is overwhelmingly dominant. The patterns of Dagestani admixture in Europe and India are curious and suggestive.

1 – In Europe the frequencies are low, but irregularly distributed (excepting around the North Caucasus). Scandinavians and British have appreciable fractions, Finns and Southern Europeans do not. Here’s Dienekes:

Interpreting this pattern is not easy, but it does seem that this component seems to have a V-like distribution, achieving its maximum in Caucasus and its environs, then undergoing a diminution, and achieving a secondary (lower) frequency mode in NW Europe.

The surprising appearance of the homonymous Dagestan component in India suggests a widespread presence of a common ancestry element. The West Asian element, by comparison seems to have a more normal /\-like distribution around its center in Anatolia-Caucasus-Iran region. It does reach the Atlantic coast, but is lacking in Scandinavia and Finland, and also in India itself.

2 – South Indian Brahmins have appreciable fractions, but non-Brahmins in the same region do not. In contrast, those who come from Indo-Aryan speaking backgrounds do seem to have Dagestani ancestral components, irrespective of other aspects of ancestry. For example Pakistanis don’t have that much more Dagestani than South Indian Brahmins or Gujaratis. Also compare the relatively narrow window of Dagestani ancestry variance among Dodecad South Asians (I’m DOD075). DOD088 is from what I recall a Reddy from Andhara Pradesh, a non-Brahmin but non-low caste. It is interesting that they have a high proportion of “Pakistan,” but no Dagestani. I have ~10% Dagestani, but no Pakistani.

Below is K = 10 for a selection of populations. Dienekes has now included in two non-Indo-European speaking Pakistani populations: the Brahui (Dravidian) and Burusho (linguistic isolate in the mountains of Pakistan):
dages

Some general patterns are evident. The light blue is indicative of generic “Indian” ancestry. It is not found in appreciable proportions outside of subcontinental populations (or those of recent subcontinental origin). The same with the red, and light orange. For your reference the dark orange is a “Northern European” component, modal in Lithuania. The light and dark Green are both East Asian components. The dark blue is a “West Asian” component modal in Georgia, and prominent across Europe with declining as a function of distance from the eastern shore of the Black Sea (this is surely the West Asian which distinguishes the French from the French Basque). I believe that the light purple dominant in the Brahui and the light red dominant in the Burusho probably form as a compound the aforementioned Pakistani component. The dark purple is the Dagestani.

587px-Dravidische_SprachenFirst, a word on the Brahui. These are a group of tribes who reside in northern Balochistan in Pakistan. A small number are even to be found in Afghanistan. Historically they have had close relations with the Baloch, an Iranian speaking cluster of tribes who totally envelop the Brahui. The Brahui do speak a Dravidian language, of a family dominant in South India and found in isolated regions of Central and Eastern India. There are two broad models for the existence of a Dravidian language in Pakistan. The first is that the Brahui are remnants of more widely spoken Dravidian languages which date back to the Indus Valley civilization. The second is that the Brahui arrived during the medieval period from another region of South Asia where Dravidian languages were more common. Assuming either model, it has long been presumed that their involution by the Baloch has had a strong impact on the Brahui genetically; the two groups are very close. This is evident in Dienekes’ results as well. But observe that the Baloch are the group which seems more cosmopolitan in ancestry than the Brahui. If the Brahui were Dravidians from deep in India it seems that they would have a greater residual component of India-specific ancestry (light blue and orange). This is not so. In fact the Baloch have more of the Indian ancestral component than the Brahui. The Brahui component is found across Pakistan, and into India, albeit at lower proportions. Naturally, the Baloch have the second highest fraction. I believe these results should shift us toward the position that the Brahui are indigenous in relation to the Baloch, and that the Baloch ethnic identity emerged through the shift of a Brahui substrate, as evidenced by the greater cosmpolitanism of the Baloch. Additionally, Dienekes observes that the Brahui have a lower proportion of the Dagestani component than most other Pakistani groups, and several Indo-Aryan groups in India proper.

The Burusho are event more interesting than the Brahui. Unlike the Brahui the Burusho are very isolated in the mountainous fastness of Baltistan in northern Pakistan. Additionally, their language, Burushashki, is a linguistic isolate. Others of the class are Basque and Sumerian. In general it is assumed that linguistic isolates were once part of broader families of languages which have gone extinct. Burushashki probably persists in large part because of the geography which its speakers inhabit. Mountainous areas often preserve ethnic and linguistic diversity because the terrain allows for the persistence of local variety. I believe it is plausible that the Burusho have been far more isolated than the Brahui. This seems to show up in the ADMIXTURE plot, the Burusho have a greater proportion of their modal ancestral component than the Brahui. Additionally, the Burusho have even an smaller component of Dagestani than the Brahui.

Below is a chart Dienekes constructed ordered by proportion of Dagestani for his South Asian populations. Next to it I’ve placed a chart from a PCA which has some of the same population samples. Compare & contrast:

pcadag

The PCA is looking at between population variation in totality. So naturally the Dagestani component isn’t going to be predictive of that. Rather, it speaks to the possibility which Dienekes is mooting: that the Dagestani component spread in the India subcontinent with the Indo-Aryans specifically, overlying the local resident substrate. In South India this meant that Brahmins brought this, mixing with the indigenous Dravidian population. In Pakistan the Indo-Aryan, and Iranians, were overlain on a substrate which were the ancestors of the Burusho and Brahui. The dominant signal of genetic relationship has to do with the substrate, not the Indo-Aryans. So that’s what’s going to show up on the PCA. In other PCA plots the model where South Indian Brahmins are a linear combination of a Pakistani-like population and a Dravidian population becomes clearer. But when you look at ancestry using something like ADMIXTURE you have the potential to tease apart different components, and so uncover relationships which may have been obscured when looking at aggregate variation.

dieDienekes’ model seems to post three steps in rapid succession ~4,000 years ago. A background variable which must be mentioned is that one must account for the Mitanni, a dominant Syrian power circa 1500 BC where a non-Indo-European language was the lingua franca, and yet a definite Indo-Aryan element existed within the elite. Indo-Aryan specifically because the Indo-European element within the Mitanni was not Iranian, but specifically Indo-Aryan. An easy explanation for this is that the Indo-Aryan component of the Indo-Iranian branch of the Indo-European languages crystallized outside South Asia, and independently reached Syria and India. In Syria it went extinct, while in India it obviously did not. By Dienekes’ model the Mitanni would be rather closer to the urheimat of the Indo-Aryans.

An aspect of his model which I do not understand is why it has to be Indo-Aryan, instead of Indo-Iranian. The South Asian population which the Dagestani component is modal, the Pathans, are Iranian, not Indo-Aryan. Additionally, this model seems to not speak in detail to the existence of the Dagestani element among Europeans. Here is a sorting of European populations (with Iranians included) by the Dagestani component:


Population Dagestan
Urkarah 93
Lezgins 47.9
Stalskoe 38.7
Adygei 16.4
Orcadian (Orkney) 12.6
Georgians 12.4
White_Utahns 11.2
Iranian 10.9
Scandinavian_D 10.2
Armenian_D 9.9
German_D 9.1
Turks 8.8
Armenians 8.4
French 7.9
Hungarians 7.5
Russian_D 6.3
Spanish_D 4.6
North_Italian 4.5
Spaniards 4.4
Romanian 4.1
Finnish_D 4.1
Russian 4
Greek_D 3.8
Portuguese_D 3.6
Tuscan 3.5
Tuscans 3.4
Lithuanians 2.9
S_Italian_Sicilian_D 2.8
Belorussian 2.5
Cypriots 2
Sardinian 1.5
French_Basque 0.7

There is here a strange pattern of rapid drop off from the Caucasus, and a bounce back very far away, on the margins of Germanic Northwestern Europe. This to me indicates some sort of leapfrog dynamic. A well known illustration of this would be the Ugric languages. The existence of Hungarian on what was Roman Pannonia is a function of the mobility and power of Magyar horseman, and their cultural domination over the Romance and Slavic speaking peasantry (their genetic impact seems to have been slight). No one believes that Germanic languages are closely related to Indo-Aryan (rather, if there is structure in Indo-European beyond Indo-Iranian, Celtic, etc., it would place the Indo-Iranian languages with Slavic). So what’s going on? I think perhaps the Dagestani component is part a reflection of the common Indo-European origin in that region. For whatever reason that signal is diminished in much of the rest of Europe. Perhaps Southern Europe was much more densely populated when the Indo-Europeans arrived. Additionally, it seems highly likely that in places like Sardinia, much of Spain, and Cyprus, Indo-European speech came through cultural diffusion (elite emulation) and not population movement. Or perhaps we’re seeing the vague shadows of population admixtures on the Pontic steppe, where distinct Germanic and Indo-Iranian confederations admixed with a common North Caucasian substrate.

Going back to India, let’s revisit the model of a two-way admixture between “Ancestral North Indians,” who were genetically similar to Europeans and West Asians, and “Ancestral South Indians,” who were closer to, but not very close to, East Eurasians. The ANI & ASI. The ASI were probably one of the ancient populations along the fringe of southern Eurasia, all of whom have been submerged by demographic movements from other parts of Eurasia over the past 10,000 years, excepting a few groups such as the Andaman Islanders and some Southeast Asian tribes. The model was admittedly a simplification. But taking that model as a given, and accepting that the Dagestani element is in indeed Indo-Aryan, we can infer that the ANI were not Indo-European. It is notable that the South Indian Brahmins have elevated fractions of both the Brahui and Burusho modal components. This is probably indicative of admixture of the Indo-Aryan element in the Indus Valley, prior to their expansion to other parts of India. I assume one of the languages spoken was Dravidian, though if ancient Mesopotamia was linguistically polyglot at the dawn of history I would not be surprised if the much more geographically Indus Valley civilization was as well.

arai
Aishwarya Rai

The irony is that today when someone refers to a “Dravidian” physical type, they’re not talking about someone who looks like a Pakistani. They’re talking about someone who looks South Indian, where most Dravidian languages are spoken. But combining the inference from Dienekes’ model and the previous two-way admixture model, you reach the conclusion that lighter skin and more West Asian features among South Asians may be more due to Dravidian-speaking ancestors in the Indus Valley, not Indo-Aryans! It goes to show the wisdom of differentiating linguistic classes from biological ones when discussing historical population genetics. Unfortunately wisdom most of us interested in these topics do not show, alas.

As I like to say, interesting times….

Note: If you leave a comment, please don’t be smarter-than-thou in your tone. I have stopped publishing those sorts of comments because the reality is that most of them have not been that smart or informed. At least by my estimation. If you actually are smarter than the average-bear, and impress me with your erudition and analysis clarity, I’ll probably let your comment through no matter your attitude. But I wouldn’t bet on it if I were you, so show some class and humility. Most of us are muddling through.

Image Credit: Georges Biard, iStockPhoto

December 16, 2010

Sons of the farmers, the story of Japan

Filed under: Ainu,Archaeogenetics,Genetics,Genomics,Japan,Japan Genetics,Jomon — Razib Khan @ 1:52 am

800px-AinuGroup
Ainu in 19th century Hokkaido, and rice paddies


Unlike some islands Japan has a long history of human habitation. More interestingly, under the Jomon culture the Japanese archipelago was home to one of the earliest, if not the earliest, societies which used pottery. The Jomon do not seem to have been intensive agriculturalists. Rather, with a widespread marine littoral they likely maintained extremely high population densities, and at least semi-sedentary habitation patterns, simply through a hunting & gathering mode of production. Pacific Northwest Amerindians are likely a good analogy. They also relied on a dense stock of marine life to maintain population densities of a high level and a sedentary lifestyle.

About 2,000 years ago the Yayoi people arrived in Japan. The first Yayoi settlements are in northern Kyushu. These people brought intensive agriculture, in particular rice agriculture, to the Japanese archipelago. The general assumption is that the Yayoi are the precursors of the Japanese who entered into the international system of East Asia during the Tang dynasty in the second half of the first millennium. The Ainu of Hokkaido are presumed to be the descendants of the remaining Jomon people, maintaining a hold in the northern island because of its ecological unsuitability to Japanese agriculture.

The question is: what proportion of the ancestry of modern Japanese is Jomon/Ainu, and what proportion is Yayoi? The dynamics here are nicely constrained by the fact that Japan is a relatively isolated island system. The Yayoi seem to have arrived at one discrete moment in history, and rapidly expanded in ~1,000 years to all the main islands of Japan, though the full settlement of Hokkaido commenced in the 19th century. Interestingly, parts of northern Honshu seem to have had a distinct post-Jomon culture down to ~1000 AD.

Conveniently the HapMap has both Japanese and Chinese samples, but often there hasn’t been too much focus on the differences between these two groups because they’re very close in a global context when compared to the Yoruba or Europeans. In more recent analyses of East Asian groups the coverage seems to be better with various Chinese ethnic groups, but relatively few samples from Siberian populations. The latter are critical because the supposition is that these are the groups which would have the most affinities with the Jomon, due to the culture and contacts of the Ainu which evident during the modern period.

Dienekes most recent post on K = 15 ancestral components in ADMIXTURE clarifies some issues in this regard. There are multiple Han Chinese and Japanese samples, as well as a wide range of East Asian and Siberian groups. I’ve reedited and formatted K = 15 a bit, with the aim of focusing on the relationships of the Japanese in particular.


japan

First, it is reasonable that the Denver and Singapore Chinese sample would have a greater proportion of the orange “Southeast Asian” component, Han in the United States are mostly from southern regions of China. Notice that the Japanese don’t have this component at all. The Japanese have more of the light gray component, which is modal among the Nganassan of the Arctic coast of Central Siberia. Unlike the Chinese the Japanese also have the blue component which is modal in Eastern Siberia, and also found in many North American groups (many omitted). Finally, it is interesting that the Japanese have the light yellow component in both of the samples Dienekes ran through ADMIXTURE. Going through his spread sheet, here’s are some of the populations sorted by this component (number 13):


Population 13
Melanesian 99.99
Paniya (South Indian tribe) 6.18
Malayan 2.85
North Kannada 1.44
Malay, Singapore 1.34
Sakilli (South Indian) 1.02
Japanese 0.71
Japanese #2 0.7
Papuan 0.56
Cambodians 0.53
Ethiopians 0.51
Yizu 0.48
Ket 0.41
Uygur 0.39
Yakut 0.08
Chinese, Beijing 0.06
Chinese, Singapore 0.03
Chukchi 0.03

This is basically Melanesian. Strangely, though at low proportions, the Japanese have much more of this than mainland Chinese, or most East Asians period. They’re in the same range as Cambodians, and topped only by maritime Southeast Asians and Indians. I find this interesting because Japanese Y chromosomes are often of haplogroup D, also common among the Ainu. This lineage spans various isolated regions of eastern Eurasia, such as the Andaman Islands. The implication is that D is a relict of a large set of populations which have slowly been absorbed by expansions of other groups. Additionally, some physical anthropologists have observed similarities in the morphology of the remains of the Jomon people and Australian Aborigines. I am inclined to chalk that up to the general robustness of non-farming populations, but it is something to consider.

But my primary point about writing this post was to offer some judgment as to the provenance of the modern Japanese. I think that looking at these results, and also keeping in mind other results on East Asian genetics, I’m of the mind that Japan looks to be a classic case where farmers totally marginalized hunter-gatherers. In other words, the modern Japanese are predominantly descendants of farmers from the Korean peninsula who arrived ~2,000 years ago.  The alternative is that the Jomon were more similar to mainland East Asians in Korea and China than they were to Siberian peoples, which seems unlikely if the Ainu give us any clue as to the culture of the Jomon. This seems more implausible in light of the fact that the Japanese do seem to have some affinities to Siberian people, to a greater extent than the northern Chinese of Beijing (Beijing is a large city, so likely this sample has people who are descendants of ‘reverse colonists’ from the South as well).

If this inference is correct then it is an amazing instance of demographic expansion and replacement. In much of the civilized world intensive farmers replaced extensive farmers in fertile regions in prehistoric times. Or at least during periods when textual evidence is thin on the ground. In contrast, in Japan the process persisted right up until the margins of written history. Additionally, we can peg the arrival of the Yayoi culture very well chronologically because of the discontinuity. Assuming 25 years per generation, in 40 generations the Yayoi had totally extirpated the post-Jomon cultures across all of the Japanese islands except Hokkaido. And, it is notable that the Jomon are generally judged to have been a relatively numerous for hunter-gatherers. Their longevity in Japan as a continuous culture also attests to their success. This narrow specific case may have larger implications for the demographic-genetic patterns we see in the rest of the world.

December 14, 2010

Re-visualizing European ancestry

I decided to take the Dodecad ADMIXTURE results at K = 10, and redo some of the bar plots, as well as some scatter plots relating the different ancestral components by population. Don’t try to pick out fine-grained details, see what jumps out in a gestalt fashion. I removed most of the non-European populations to focus on Western Europeans, with a few outgroups for reference.

Here’s a table of the correlations (I bolded the ones I thought were interesting):


W Asian NW African S Europe NE Asian SW Asian E Asian N European W African E African S Asian
W Asian * -0.01 -0.18 0.04 0.81 0.59 -0.64 0.39 0.2 0.04
NW African * * 0.19 -0.16 0.23 -0.09 -0.19 0.26 0.67 -0.11
S European * * * -0.38 -0.03 -0.27 -0.42 -0.11 -0.02 -0.36
NE Asian * * * * -0.06 0.5 0.26 -0.04 -0.1 -0.07
SW Asian * * * * * 0.21 -0.62 0.74 0.59 -0.13
E Asian * * * * * * -0.27 0.08 0 0.14
N European * * * * * * * -0.34 -0.28 -0.31
W African * * * * * * * * 0.86 -0.04
E African * * * * * * * * * -0.07

dodenorthdodsouthdodswasiandodwestscatternorthwestscattersouthnorthscattersouthwestscatterwestasiansouthwest

December 13, 2010

Live not by visualization alone

pc1
Synthetic map

In the age of 500,000 SNP studies of genetic variation across dozens of populations obviously we’re a bit beyond lists of ABO blood frequencies. There’s no real way that a conventional human is going to be able to discern patterns of correlated allele frequency variations which point to between population genetic differences on this scale of marker density. So you rely on techniques which extract the general patterns out of the data, and present them to you in a human-comprehensible format. But, there’s an unfortunate tendency for humans to imbue the products of technique with a particular authority which they always should not have.

ResearchBlogging.orgThe History and Geography of Human Genes is arguably the most important historical genetics work of the past generation. It has surely influenced many within the field of genetics, and because of its voluminous elegant visual displays of genetic data it is also a primary source for those outside of genetics to make sense of phylogenetic relations between human populations. And yet one aspect of this great work which never caught on was the utilization of “synthetic maps” to visualize components of genetic variation between populations. This may have been fortuitous, a few years ago a paper was published, Interpreting principal components analyses of spatial population genetic variation, which suggested that the gradients you see on the map above may be artifacts:

Nearly 30 years ago, Cavalli-Sforza et al. pioneered the use of principal component analysis (PCA) in population genetics and used PCA to produce maps summarizing human genetic variation across continental regions. They interpreted gradient and wave patterns in these maps as signatures of specific migration events. These interpretations have been controversial, but influential, and the use of PCA has become widespread in analysis of population genetics data. However, the behavior of PCA for genetic data showing continuous spatial variation, such as might exist within human continental groups, has been less well characterized. Here, we find that gradients and waves observed in Cavalli-Sforza et al.’s maps resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns do not necessarily reflect specific migration events. Our findings aid interpretation of PCA results and suggest how PCA can help correct for continuous population structure in association studies.

A paper earlier this year took the earlier work further and used a series of simulations to show how the nature of the gradients varied. In light of recent preoccupations the results are of interest. Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture:

In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agriculture, in which farmers expanded from the Near East ∼10,000 years ago and replaced the resident hunter-gatherer populations with little or no interbreeding. These interpretations of the PC maps have been recently questioned as the original results can be reproduced under models of spatially covarying allele frequencies without any expansion. Here, we study PC maps for data simulated under models of range expansion and admixture. Our simulations include a spatially realistic model of Neolithic farmer expansion and assume various levels of interbreeding between farmer and resident hunter-gatherer populations. An important result is that under a broad range of conditions, the gradients in PC1 maps are oriented along a direction perpendicular to the axis of the expansion, rather than along the same axis as the expansion. We propose that this surprising pattern is an outcome of the “allele surfing” phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion.

The first figure shows the general framework with which they performed the simulations:

pcab1

You have a lattice which consists of demes, population units, all across Europe. They modulated parameters such as population growth (r), carrying capacity (C), and migration (m). Additionally, they had various scenarios of expansion from the southwest or southeast, as well as two expansions one after another to mimic the re-population of Europe after the Ice Age by Paleolithic groups, and their later replacement by Neolithic groups. They modulated admixture and introgression of genes from the Paleolithic group to the Neolithics so that you had the full range where the final European were mostly Neolithic or mostly Paleolithic.

Below are some of the figures which show the results:

allesurAs you can see the strange thing is that in some models the synthetic map gradient is rotated 90 degrees from the axis of demographic expansion! In this telling the famous synthetic map showing Neolithic expansion might be showing expansion from Iberia. Perhaps a radiation from a post-Ice Age southern refuge?

One explanation might be “allele surfing” on the demographic “wave of advance.” Basically as a population expands very rapidly stochastic forces such as random genetic drift and bottlenecks could produce diversification along the edge of the population wave front. The reason for this is that these rapidly expanding populations explode out of serial bottlenecks and demographic expansions, which will produce genetic distinctiveness among the many differentiated demes bubbling along the edge of expansion. Alleles which may have been at low frequency in the ancestral population can “fix” in descendant populations on the edge of the demographic wave of advance. This is the explanation, more or less, that one group gave last year for the very high frequencies of R1b1b2 in Western Europe. With this, they overturned the classic assumption that R1b1b2 was a Paleolithic marker, and suggested it was a Neolithic one.

Here’s their conclusion from the paper:

A previous study showed that the original patterns observed in PCA might not reflect any expansion events (Novembre and Stephens 2008). Here, we find that under very general conditions, the pattern of molecular diversity produced by an expansion may be different than what was expected in the literature. In particular, we find conditions where an expansion of Neolithic farmers from the southeast produces a greatest axis of differentiation running from the southwest to the northeast. This surprising result is seemingly due to allele surfing leading to sectors that create differentiation perpendicular to the expansion axis. Although a lot of our results can be explained by the surfing phenomenon, some interesting questions remain open. For example, the phase transition observed for relatively small admixture rates between Paleolithic resident and Neolithic migrant populations occurs at a value that is dependent on our simulation settings, and further investigations would be needed to better characterize this critical value as a function of all the model parameters. Another unsolved question is to know why the patterns generally observed in PC2 maps for our simulation settings sometimes arise in PC1 maps instead. These unexplained examples remind us that PCA is summarizing patterns of variation in the sample due to multiple factors (ancestral expansions and admixture, ongoing limited migration, habitat boundary effects, and the spatial distribution of samples). In complex models such as our expansion models with admixture in Europe, it may be difficult to tease apart what processes give rise to any particular PCA pattern. Our study emphasizes that PC (and AM) should be viewed as tools for exploring the data but that the reverse process of interpreting PC and AM maps in terms of past routes of migration remains a complicated exercise. Additional analyses—with more explicit demographic models—are more than ever essential to discriminate between multiple explanations available for the patterns observed in PC and AM maps. We speculate that methods exploiting the signature of alleles that have undergone surfing may be a powerful approach to study range expansions.

What’s the big picture here? In the textbook Human Evolutionary Genetics it is asserted that synthetic maps never became very popular compared to PCA itself. I think this is correct. But, the original synthetic maps have become prominent for many outside of genetics. They figure in Peter Bellwood’s First Farmers, and are taken as a given by many pre-historians, such as Colin Renfrew. And yet a reliance on these sorts of tools must not be blind to the reality that the more layers of abstraction you put between your perception and comprehension of concrete reality, the more likely you are to be led astray by quirks and biases of method.

In this case I do think first-order intuition would tell us that synthetic maps which display PCs would be showing gradients as a function of demographic pulses. And yet the intuition may not be right, and with the overturning of old orthodoxies in the past generation of inferences from the variation patterns in modern populations, we should be very cautious.

Citation: Olivier François, Mathias Currat, Nicolas Ray, Eunjung Han, Laurent Excoffier, & John Novembre (2010). Principal Component Analysis under Population Genetic
Models of Range Expansion and Admixture Mol Biol Evol

December 11, 2010

Excavating the Neolithic genetic strata

After linking to Marnie Dunsmore’s blog on the Neolithic expansion, and reading Peter Bellwood’s First Farmers, I’ve been thinking a bit on how we might integrate some models of the rise and spread of agriculture with the new genomic findings. Bellwood’s thesis basically seems to be that the contemporary world pattern of expansive macro-language families (e.g., Indo-European, Sino-Tibetan, Afro-Asiatic, etc.) are shadows of the rapid demographic expansions in prehistory of farmers. In particular, hoe-farmers rapidly pushing into virgin lands. First Farmers was published in 2005, and so it had access mostly to mtDNA and Y chromosomal studies. Today we have a richer data set, from hundreds of thousands of markers per person, to mtDNA and Y chromosomal results from ancient DNA. I would argue that the new findings tend to reinforce the plausibility of Bellwood’s thesis somewhat.

The primary datum I want to enter into the record in this post, which was news to me, is this: the island of Cyprus seems to have been first settled (at least in anything but trivial numbers) by Neolithic populations from mainland Southwest Asia.* In fact, the first farmers in Cyprus perfectly replicated the physical culture of the nearby mainland in toto. This implies that the genetic heritage of modern Cypriots is probably attributable in the whole to expansions of farmers from Southwest Asia. With this in mind let’s look at Dienekes’ Dodecad results at K = 10 for Eurasian populations (I’ve reedited a bit):


neolith

Modern Cypriots exhibit genetic signatures which shake out into three putative ancestral groups. West Asian, which is modal in the Caucasus region. South European, modal in Sardinia. And Southwest Asian, which is modal in the Arabian peninsula. Cypriots basically look like Syrians, but with less Southwest Asian, more balance between West Asian and South European, and far less of the minor components of ancestry.

Just because an island was settled by one group of farmers, it does not mean that subsequent invasions or migrations could not have an impact. The indigenous tribes of Taiwan seem to be the original agriculturalists of that island, and after their settlement there were thousands of years of gradual and continuous cultural change in situ. But within the last 300 years settlers from Fujian on the Chinese mainland have demographically overwhelmed the native Taiwanese peoples.

During the Bronze Age it seems Cyprus was part of the Near East political and cultural system. The notional kings of Cyprus had close diplomatic relations with the pharaohs of Egypt. But between the end of the Bronze Age and the Classical Age Cyprus became part of the Greek cultural zone. Despite centuries of Latin and Ottoman rule, it has remained so, albeit with a prominent Turkish minority.

One thing notable about Cyprus, and which distinguishes it from mainland Greece, is the near total absence of a Northern European ancestral component. Therefore we can make the banal inference that Northern Europeans were not initially associated with the demographic expansions of farmers from the Middle East. Rather, I want to focus on the West Asian and Southern European ancestral components. One model for the re-population of Europe after the last Ice Age is that hunter-gatherers expanded from the peninsular “refugia” of Iberia and Italy, later being overlain by expansions of farmers from the Middle East, and perhaps Indo-Europeans from the Pontic steppe. I have a sneaking suspicion though that what we’re seeing among Mediterranean populations are several waves of expansion out of the Near East. I now would offer the tentative hypothesis that the South European ancestral element at K = 10 is a signature of the first wave of farmers which issued out of the Near East. The West Asians were a subsequent wave. I assume that the two groups must correlate to some sort of cultural or technological shift, though I have no hypothesis as to that.

From the above assertions, it is clear that I believe modern Sardinians are descendants of that first wave of farmers, unaffected by later demographic perturbations. I believe that Basques then are a people who emerge from an amalgamation of the same wave of seafaring agriculturalists with the indigenous populations preceding them (the indigenes were likely the descendants of a broad group of northern Eurasians who expanded after the end of the last Ice Age from the aforementioned refugia). They leap-frogged across fertile regions of the Mediterranean and pushed up valleys of southern France, and out of the Straits of Gibraltar. Interestingly, the Basque lack the West Asian minority element evident in Dienekes’ Spaniards, Portuguese, as well as the HGDP French (even up to K = 15 they don’t shake out as anything but a two way admixture, while the Sardinians show a minor West Asian component). Also, the West Asian and Southern European elements are several times more well represented proportionally among Scandinavians than Finns. The Southern European element is not found among the Uyghur, though the Northern European and West Asian one is. I infer from all these patterns that the Southern European element derived from pre-Indo-European farmers who pushed west from the Near East. It is the second largest component across much of the Northwestern Europe, the largest across much of Southern European, including Greece.

A second issue which First Farmers clarified are differences between the spread of agriculture from the Near East to Europe and South Asia. It seems that the spread of agriculture across South Asia was more gradual, or least had a longer pause, than in Europe. A clear West Asian transplanted culture arrived in what is today Pakistan ~9,000 years ago. But it does not seem that the Neolithic arrived to the far south of India until ~4,000 years ago. I think that a period of “incubation” in the northwest part of the subcontinent explains the putative hybridization between “Ancient North Indians” and “Ancient South Indians” described in Reconstructing Indian population history. The high proportion of “Ancestral North Indian,” on the order of ~40%, as well as Y chromosomal markers such as R1a1a, among South Indian tribal populations, is a function of the fact that these groups are themselves secondary amalgamations between shifting cultivators expanding from the Northwest along with local resident hunter-gatherer groups which were related to the ASI which the original West Asian agriculturalists encountered and assimilated in ancient Pakistan (Pathans are ~25% ASI). I believe that the Dravidian languages arrived from the Northwest to the south of India only within the last 4-5,000 with the farmers (some of whom may have reverted to facultative hunter-gathering, as is common among tribals). This relatively late arrival of Dravidian speaking groups explains why Sri Lanka has an Indo-European presence to my mind; the island was probably only lightly settled by farming Dravidian speakers, if at all, allowing Indo-European speakers from Gujarat and Sindh to leap-frog and quickly replace the native Veddas, who were hunter-gatherers.

Note: Here is K = 15.

* Wikipedia says there were hunter-gatherers, but even here the numbers were likely very small.

December 3, 2010

The great northern culture war

A new paper in The New Journal of Physics shows that a relatively simple mathematical model can explain the rate of expansion of agriculture across Europe, Anisotropic dispersion, space competition and the slowdown of the Neolithic transition:

The front speed of the Neolithic (farmer) spread in Europe decreased as it reached Northern latitudes, where the Mesolithic (hunter-gatherer) population density was higher. Here, we describe a reaction–diffusion model with (i) an anisotropic dispersion kernel depending on the Mesolithic population density gradient and (ii) a modified population growth equation. Both effects are related to the space available for the Neolithic population. The model is able to explain the slowdown of the Neolithic front as observed from archaeological data

The paper is open access, so if you want more of this:
fareq

Just click through above. Rather, I am curious more about their nice visualization of the archaeological data:


euroneolithic

Note how much variance there is in terms of the rate of change of the clines. As I’ve observed before there was a “break out” of the LBK farmers into Central Europe nearly 7,000 years ago, but it took much longer to close the gap between the farms on the frontier and the sea. This is well known from the archaeology, as there seems to have been a pause of ~1,000 years across much of the north European plain. On the scale of 10,000 years that’s not much time, but that’s about 40 generations. In Frisia it looks like the spreading of farming stopped for nearly ~2000 years!

Why the abatement of the spread of farming? I think the authors of the above paper are correct in their acceptance of the conventional wisdom of greater Mesolithic densities in Northern Europe. But I think perhaps a better description might be maritime Northern Europe. We often imagine early farmers displacing hunters and gatherers of game and herb, but what if in much of the world the main clash numerically was between dense populations oriented toward the sea, and those who were depended on the land? About seven years ago a study came out which argued for a rapid transition from seafood to meat in the diets of early Britons, Why Did Ancient Britons Stop Eating Fish?:

When cattle, sheep, pigs, and wheat arrived on the shores of Great Britain about 5,000 years ago, fish quickly fell off the Neolithic menu, according to an analysis of human bones scattered throughout the island.

“Farming really took off in Britain during the Neolithic. The main questions concerning the speed of change relates to how quickly Mesolithic peoples adapted—or otherwise—to the new farming methods and/or the spread of farming into Britain by new farming communities,” he said.

The research by Richards and colleagues Rick Schulting at Queen’s University Belfast and Robert Hedges at the University of Oxford tracks the shift in diet by examining the dietary signature stored in the bones.

They find that the shift was rapid and complete at the onset of the Neolithic. “Marine foods, for whatever reason, seem to have been comprehensively abandoned,” the researchers conclude in the September 25 issue of the journalNature.

“We determined that after the introduction of domesticates, as well as the other artifacts associated with the Neolithic, the isotope values showed that marine foods were not used anymore,” he said. “We then infer that this is a switch from wild foods such as fish and shellfish to the new domesticates that arrive at this time.”

Richards said there are three plausible reasons why the British abandoned seafood from the beginning of the Neolithic: the domesticated plants and animals presented a steady source of food; the shift was forced by a climate change; or cultural pressure.

In the early 2000s the idea of wholesale rapid demographic replacement was not in the air. I think we need to put that back on the table. Here is the chart on isotope ratios from the 2003 paper:
culwar

Notice the sharp discontinuity. Richards et al. in 2003 interpreted this as a rapid cultural acquisition of the Neolithic lifestyle ~2500-3000 BC. They note in the media reports that later Britons, for example at the time of the Roman conquest, seem to have utilized fish a bit more in their diet than these early Neolithics. This stands to reason, much of Britain is not too far from the sea. To me the very sharp drop in marine consumption is indicative more of a food taboo, than a practical shift. Obviously farmers would primarily be subsistent on grain, but there’s no necessary reason to avoid meat or fish, but as it happens in many parts of the world societies preserve and perpetuate exactly such norms. These norms may have spread through cultural diffusion, for example through an adoption of a new religion. Or, the norms may have been brought by a new group which arrived in large numbers and replaced the indigenous population.

Here is an equivalent chart from Denmark from an earlier paper by the same group:

denmark

800px-Saami_Family_1900pacnortWhen we think of peoples who aren’t farmers, we often think of marginalized nomadic or semi-nomadic groups. Many of the remaining hunter-gatherers such as Bushmen, as well societies which supplement their conventional lifestyle with a lot of hunting & gathering, such as the indigenous peoples of Siberia or the Sami of northern Scandinavia, occupy territory which is simply not viable for conventional agriculture. But this was not so in the past. Before the farmers arrived the rich bottom-lands were occupied by hunters & gatherers, of fish, game, grain, and nuts. In certain ecologies, such as around productive estuaries one could imagine enormous aggregations of these peoples. Additionally, it seems likely that a sedentary lifestyle predates farming. A good contemporary analog for what ancient Northern Europe may have been like was the Pacific Northwest before the European settlement. These native tribes were relatively affluent because of the abundance of salmon runs, and engaged in lavish signalling, such as with their famous potlatches. Seeing as how there are Atlantic salmon runs in places like Norway and Scotland one can make even closer correspondences perhaps!

Stonehenge-GreenAs I have stated before just because we have no written records of this period, we can not assume that these were necessarily the fragmented and scattered “small-scale societies” which we’re familiar with today. There may have been ideologically motivated political coalitions and alliances which broke down along ethnic and cultural lines. In the paper above the authors argue that there is evidence that a climatic constraint, crops which do not have a good yield in cooler or warmer temperatures, is a weak hypothesis. If so I wonder if it is a bit too pat to simply model the dynamics as a diffusive “bottom up” process. Seems plausible enough for much of Europe where Mesolithic populations were thin on the ground because of local carrying capacity, but I suspect that the encounter between dense agglomerations of farmers and fishermen resulted in an inevitable ramp up of political integration and consolidation, as villages and tribes had to coordinate together because of a positive feedback loop of conflict.

Image Credit: Lordkinbote, Mactographer

November 29, 2010

No Romans needed to explain Chinese blondes

uyghurboy
Uyghur boy from Kashgar

Every few years a story crops up about “European-looking” people in northwest China who claim to be of Roman origin. A “lost legion” so to speak. I’ll admit that I found the stories interesting, amusing, if  implausible, years ago. But now it’s just getting ridiculous. This is almost like the “vanishing blonde” meme which always pops right back up. First, let’s quote from The Daily Mail,* DNA tests show Chinese villagers with green eyes could be descendants of lost Roman legion:

For years the residents of the remote north western Chinese village of Liqian have believed they were special.

Many of the villagers have Western characteristics including green eyes and blonde hair leading some experts to suggest that they may be the descendants of a lost Roman legion that settled in the area.

Now DNA testing of the villagers has shown that almost two thirds of them are of Caucasian origin.

The results lend weigh to the theory that the founding of Liqian may be linked to the legend of the missing army of Roman general Marcus Crassus.
Enlarge

In 53BC, after Crassus was defeated by the Parthians and beheaded near what is now Iran, stories persisted that 145 Romans were captured and wandered the region for years.

As part of their strategy Romans also hired troops wherever they had conquered and so many Roman legions were made up not of native Romans, but of conquered men from the local area who were then given training.

250px-Statue-AugustusLet’s start from the end. The last paragraph indicates a total ignorance of the nature of military recruitment during the late Republic. In the year 110 BC the Roman army was composed of propertied peasants. These were men of moderate means, but means nonetheless. They fought for the Republic because it was their duty as citizens. They were the Republic. Due to a series of catastrophes the Roman army had to institute the Marian reforms in 107 BC. Men with no means, and who had to be supplied with arms by the Republic, joined the military. This was the first step toward the professionalization of the Roman legions, which naturally resulted in a greater loyalty of these men to their leaders and their unit than the Republic. Without the Marian reforms Sulla may never have marched on Rome. By 400 AD the legions were predominantly German in origin, and supplemented with “federates,” who were barbarian allies (though alliances were always subject to change). But in 53 BC this had not happened yet. The legions who marched with Crassus would have been Roman, with newly citizen Italian allies in the wake of the Social War. The legions of the Julio-Claudians were probably still mostly Italian, a century after Crassus (service in the legions, as opposed to the auxiliaries, was limited to citizens, who were concentrated among Italians). So that objection does not hold.


But really, do we need the Roman hypothesis? Those big blonde Romans? Here’s one section of the piece: “Archaeologists discovered that one of the tombs was for someone who was around six foot tall.” Because of issues of nutrition the Roman soldiers were notoriously short relative to the Celts and Germans (who had more meat and milk in their diet). Perhaps they had the potential for greater height, which they realized in the nutritional surfeit of…China?

Anyway, there’s a straightforward explanation for the “Chinese Romans”: they’re out of the same population mix, roughly, as the Uyghurs. Before the year 1000 AD much of what is today Xinjiang was dominated by peoples with a European physical appearance. Today we call them Tocharians, and they spoke a range of extinct Indo-European dialects. It seems likely that there was also an Iranian element. The archaeology is rather patchy. Though there were city-based Indo-Europeans, it is clear that some of them were nomadic, and were among the amorphous tribes that the ancient Chinese referred to as the “Rong and Di.” The Yuezhi and Wusun were two mobile groups who left China in the historical period and are recorded in the traditional annals.

Meanwhile, between 500 AD and 1000 AD the Indo-European substrate of the Tarim basin was absorbed by Turkic groups coming from Mongolia. They imposed their language on the older residents, but genetically assimilated them. The modern Uyghurs are a clear hybrid population. In the papers published on the Uyghurs they shake out as about a 50/50 West/East Eurasian mix. But the DODECAD ANCESTRY PROJECT has them in the sample, and here’s how they break down by a finer grain:
uad

Uyghurs are the third population from the bottom. Below them are the Yakut and Chinese. The Yakut are the northernmost Turkic people, and the Turkic element which settled in Xinjiang and assimilated the Tocharians was from the north. The Chinese-like element may simply be that the proto-Uyghurs were already admixed with the Han populations, or, that that element has a geography-conditional cline where the Yakuts are at an extreme. In any case, the other components of Uyghur ancestry are not East Asian. Like many European popualtions the Uyghurs have a West Asian and Northern European aspect, but they lack the South European ancestry. This is important, because it is dominant in both the Tuscans and North Italians.  If the “Roman Chinese” are genuinely Roman, they will have this specific southwest European ancestry, which will put them at a distinction from the Uyghurs.

As it is, I don’t think that’s what’s going on.  On the order of 4,000 years ago the domestication of the horse allowed for the expansion of Indo-European populations from east-central Eurasia across the steppe. Eventually they they also percolated into the underpopulated zones between the taiga and the highlands around the Himalayan massif. I believe that these were the groups which introduced nomadism and agriculture to the Tarim basin, and their genetic and cultural impact was a function of the fact that they simply demographically swamped the few hunter-gatherers who were indigenous to the region.

In the period between 1000 BC and 1000 AD the flow of people reversed. The expansion of the Han north and west, and the rise of a powerful integrated state which could bully, and could also be extorted, changed the dynamics on the steppe and in the oasis cities beyond. The vast swaths of Central Asia which were Indo-European in speech became Altaic in speech. But many of these populations absorbed the Indo-European groups, and came out genetically admixed. A clear residual of West Eurasian admixture can also be found among peoples who presumably never interacted much with Indo-Europeans, such as the Mongols, though at lower levels.

The villagers of Liqian are a different part of the story. Clearly substantial numbers of “barbarians” were assimilated into a Han identity on the northern frontier. In the case of tribes such as the Xianbei and Khitan they even did the assimilating themselves, through top-down sinicizing edits. In areas like Gansu these elements contribute a greater proportion of the ancestry, and just as the Uyghur are Turkic speaking, and yet have equal portions of West and East Eurasian ancestry, so the people of Liqian are Chinese speaking, and have equal portions of West and East Eurasian ancestry.

I find it curious that the piece above didn’t mention Uyghurs at all. No idea if politics was involved, but I won’t be surprised if I get some angry Han and Uyghur comments because of what I’m saying here (I’m not totally clear what these sorts of commenters are angry about really, they’re usually pretty inchoate).

Addendum: East and West Eurasian ancestry seems pretty equitably distributed among the Uyghurs. But the number of genes which code for racially salient traits are far smaller than the total set which can be used to estimate ancestry. So within a large enough population allelic combinations across loci will segregate so that some individuals exhibit a “pure” ancestral phenotype. What colloquially might be termed a “throwback.” This little boy comes strikingly close.

* I am aware of the reputation of this newspaper. Nevertheless, it’s being picked up by the international press and some blogs, so I’m going to address it.

Image Credit: Gusjer

September 17, 2010

Of Iran, Turan, and Turks

uzbekmanThere’s a new paper out in The European Journal of Human Genetics which is of great interest because it surveys the genetic and linguistic affinities of two dozen ethno-linguistic groups from the three Central Asian nations of Uzbekistan, Kyrgyzstan, and Tajikistan. This is what the Greeks referred to as Transoxiana, and the Persians as Turan. Originally inhabited by peoples with close cultural affinities with those of Persia, indeed, likely the root of the peoples of Persia, by the historical period Turan developed a distinctive identity as a frontier or march. It was in Turan where the Turk met the Iranian (a class which included non-Persian groups, such as the Sogdians), from the pre-Islamic Sassanians down to the present day. It is a region of the world which has a very ancient urban culture, cities such as Merv, as well as peoples that were only recently nomads, forcibly made sedentary by the Soviet regime.

To add another twist to the picture many of the ethno-linguistic groups which we are familiar with today and which serve as the cores of the new Central Asian nations only came into being within the last few centuries, with a particular “push” from Russian Imperial and Soviet ethnologists who were tasked with fleshing out national identities with which the center could negotiate. A “Tajik” is after all simply part of the Persian-speaking residual population of Central Asia, spreading down into Afghanistan. The carving out of an independent Tajikistan out of the Central Asian landscape is as much a creation of the modern age as the state of Israel. The “Uzbek” identity was once simply that of the ruling caste of Transoxiana who came to power after the decline of the Timurids. Today it is an appellation which brackets the settled Turkic speaking peoples of Uzbekistan and beyond.

ResearchBlogging.orgInto this near Gordian knot of history and ideology walk the naive and well-meaning geneticists. There is no great objection one can make to the genetics within the paper, but the historical framework and some of the assertions are peculiar and tendentious indeed. It’s a problem which starts within the abstract. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations:

Located in the Eurasian heartland, Central Asia has played a major role in both the early spread of modern humans out of Africa and the more recent settlements of differentiated populations across Eurasia. A detailed knowledge of the peopling in this vast region would therefore greatly improve our understanding of range expansions, colonizations and recurrent migrations, including the impact of the historical expansion of eastern nomadic groups that occurred in Central Asia. However, despite its presumable importance, little is known about the level and the distribution of genetic variation in this region. We genotyped 26 Indo-Iranian- and Turkic-speaking populations, belonging to six different ethnic groups, at 27 autosomal microsatellite loci. The analysis of genetic variation reveals that Central Asian diversity is mainly shaped by linguistic affiliation, with Turkic-speaking populations forming a cluster more closely related to East-Asian populations and Indo-Iranian speakers forming a cluster closer to Western Eurasians. The scattered position of Uzbeks across Turkic- and Indo-Iranian-speaking populations may reflect their origins from the union of different tribes. We propose that the complex genetic landscape of Central Asian populations results from the movements of eastern, Turkic-speaking groups during historical times, into a long-lasting group of settled populations, which may be represented nowadays by Tajiks and Turkmen. Contrary to what is generally thought, our results suggest that the recurrent expansions of eastern nomadic groups did not result in the complete replacement of local populations, but rather into partial admixture.

In my initial comment on this paper in a link round-up I wondered what the authors were thinking making such a comment: anyone who knows Central Asians would see on their faces that the Turks did not completely replace the local populations. The image above is of an Uzbek man, who does not exhibit any visible “Mongolian” features. This is not the norm, but is not unheard of. Even populations which are presumed to have less Iranian admixture, such as the Kazakhs, exhibit a range of physical types. It would be one thing if this reference was an isolated peculiarity, but there are other comments within the paper which indicate to me that the research group’s familiarity with the non-genetic literature is cursory at best. They refer to Huns as having “brought the East-Asian anthropological phenotype to Central Asia.” There is no clear definite foundation for this assertion. Unfortunately historians do not have a clear idea what the ethno-linguistic character of the Huns was. By the time Roman observers encountered them the Hunnic horde seems to have been predominantly German, with a Iranian (Alan) secondary component, the Huns themselves being a small elite (Attila’s name itself may be Gothic). In light of subsequent eruptions into Europe of Turkic and Ugric nomads it is easy to slot the Huns into this exotic category, but the primary literature makes it clear that you can’t ascertain their ethnic character from the contemporary sources (the “White Huns” of Central and South Asia had no real connection to the Huns of Europe).

Near the end of the paper they say something really peculiar: “The Westernized view of westward invasions usually emphasizes the extreme violence and cruelty of the hordes led by Attila the Hun (AD 406–453), or that from the Mongolian empire led by Genghis Khan. However, our results somehow challenge this view and rather suggest that these more recent expansions did not lead to the massacre and complete replacement of the locally settled populations….” It is true that European observers of the Mongol expansion did not have a sanguine attitude. But the idea that Mongols were genocidal exterminationists really comes to us via the Islamic historians, for whom the Mongol conquests were totally shocking and a literal world-turned-upside-down moment. The Mongol conquests did seem to result in a decline in population between Mesopotamia and Transoxiana. Whole cities in Central Asia were depopulated. There is an assumption that the Mongol conquests marks the turning point where Central Asia passed from being a predominantly Iranian world with a Turkic military elite (which was to be the nature of Iran proper until the 20th century) to a Turkic world with a large Persian minority. Though the military conquests of the Mongols were important punctuating events, I do not believe that scholars today would assume that they produced an ethnic shift in toto. On the contrary, the null hypothesis is generally against migrationism.

With those preliminaries out of the way, what’s going on with the genetics? Below are the less interesting tables & figures. The first is important because it has the abbreviations which they use. Basically anything that starts with a “T” are Indo-Iranian Tajiks, and everything else is Turkic, except LUzn LUza, who are Indo-Iranian Uzbek nationals, but I presume would be ethnic Tajiks in Uzbekistan (this stuff is really confusing in regards to labels, because as I said the national categories are to some extent ad hoc impositions on more ancient identities which don’t always follow the European language = nation formula). The second image is a figure which shows the sampling of locations, as well as pie charts with ancestral quanta. The third image is a table which shows that Indo-Iranians are genetically more varied than Turks. While the fourth is a STRUCTURE plot which I reedited to zoom in on peoples of interest for this study, as well removing some of the lower K’s. Remember that each K is a putative ancestral population. As Dienekes notes since they used only 27 microsatellite markers across their 26 populations, the plot may inflate minor ancestral contributions.

Of more interest is the correspondence analysis, which is conceptually similar to principal component analysis. The variate inputs are allele counts. I’ve obviously reedited the figure a bit, and added some labels (yeah, I ended up thinking that rotating after I’d added some labels was best, sorry). Note the clear color-coding of Turkic vs. Iranian Central Asian groups.

turkiraneurasian

There’s a clear separation linguistically between Iranian speaking and Turkic speaking groups in Central Asia. Some of the Turkic groups are close to Iranian groups, closer than to other Turkic groups, but still the two broad sets have a coherent identity. Undergirding the linguistic variation is classical geographic variation. The eastern Turkic groups seem the least impacted by the Iranian substrate which was dominant before the arrival of Turks, while the Turcoman group sampled from western Uzbekistan seems to have been the most genetically “Iranized.” In a world wide context the central position of Central Asians is not surprising. Interestingly the Iranian groups of Central Asia seem to overlap rather well with the Indo-Iranian groups from the HGDP data set. In contrast, the Turkic groups are distributed along a linear axis from East Asians to the Iranian cluster. This is the same pattern evident among African Americans as individuals. It’s a two-way admixture, with different dosage degrees by population as a function of history and geography (I presume you’d see the same pattern if it was broken down on individuals with a SNP-chip).

admixMoving to the explicit admixture estimates, the labels leave something to be desired. The shaded area is for Turkic speakers. The very last group, TJY, indicates the Yagnobis of Dushanbe. I happen to know offhand that the Yagnobis are reputed to be descendants of the Sogdians, having preserved their language and Zoroastrian religion relatively late in history before switching to Tajik and Islam. Like many ethno-linguistic relics these people preserved their independent identity after the Arab conquest, which saw the decline of Sogdian influence on the Silk Road, by taking refuge in isolated regions. It is no surprise then that this group shows the least East Asian admixture of all the Iranian samples, as they were isolated from many of the social and historical processes which were operative in Transoxiana after the conquest by the Arabs, and the later pushing in of the zone of Turkic hegemony after the fall of the Samanids.

These admixture estimates definitely put the spotlight on the role of Central Asia as a nexus of sorts. In the archaeology and history it is clear that Central Asia has been affected by peoples of European, South Asian, Middle Eastern, and East Asian origin. Central Asia itself has been the mother of empires, famously the seat of Timur, but also the original base of what later became the Abbasid dynasty. At one point the Caliphate was split between western and eastern factions and there was a possibility that the capital would be relocated from Baghdad to the Central Asian city of Merv! I do not believe that the Arabs had a strong genetic impact, nor was there a large South Asian migration in recent periods into Central Asia. So the admixture estimates adduced for these groups may be due to the natural cline in allele frequencies which are found in different peripheral Eurasian populations. Frequencies which are naturally intermediate in Central Asia. The main caveat is that it is probable that local conditions will vary a great deal. In contrast we have strong reason to suspect that the East Asian component arrived relatively recently with the Turks, and we see that its aspect is most evident among the groups which were nomadic within living memory, the Kazakhs and Kyrgyz. These two ethnicities, which are really compounds of several tribes or “hordes,” were only marginally integrated into sedentary Islamic society where the Tajik element would be prominent (shamanism among many of these tribes only disappeared under the influence of the Islamic missionaries sponsored by Russian Empire). I think this pattern is reinforced by what we saw in the correspondence analysis, where the Turkic groups exhibited a linear distribution toward East Asia, while the Iranian ones were placed where you’d expect them geographically. Finally, I want to note that Dienekes observes that using South Asians as a Central Asian population source is strange since South Asia is more appropriately thought of as a demographic sink for Turan. True, but the HGDP populations are strongly biased toward groups with relatively little indigenous South Asian ancestry, with the Sindhi being the only Indo-Aryan speakers within the set. So I think that objection is mitigated by these factors. Rather, the Iranian-speaking Pakistani groups serve as proxies for the original Central Asian Iranian substrate, from which both they and the Tajiks presumably derive.

Moving back to the Turk vs. Iranian distinction, the authors note that the Turkic groups exhibit a strong degree of genetic homogeneity on the Y chromosomal lineages. This points to the possible manner in which the East Asian genetic element spread in Central Asia, not necessarily just through population displacement, but also through polygamy and the high reproductive fitness of particular “super-male” lineages. The children of elite Turkic men who took Iranian wives presumably adopted the culture of their fathers, including the linguistic identity. This may have been particularly easy in Central Asia because they did not have to repudiate their maternal heritage in totality, as Persian culture still had great status and currency. If we partition the ancestry into “East Eurasian” and “West Eurasian” components the Turkic groups have much more of the latter than the Iranian ones have of the former. That stands to reason as the Turks were newcomers, and an elite which the locals would wish to assimilate to if they had the opportunity. In contrast, the shift from Turk to Iranian may have been rarer, and a switch which individuals would wish to avoid since the latter did not have the same level of temporal power. Over ~1,500 years gene flow does occur between the groups, and even the Yagnobis have appreciable East Asian ancestry. Eventually the linguistic differences would probably be dwarfed by the geographical ones, but currently we’re taking a snapshot of a “transient.”

It’s complicated. And one has to be very careful about using terms like “Turk” in a localized context, vs. a more international one. The Turks of Turkey are overwhelming derived from the same source populations as their Balkan (because of Rumelian Turks), Iranian, and Armenian, neighbors. The decline in East Asian fraction is evident even in this sample, as the Turcomans from western Uzbekistan have the least eastern ancestry of any of the groups. But this paper is an excellent within into a critical geographical hinge of genetic variation and historical tumult (though one must set aside some of their tacked-on historical speculations).

Citation: Martínez-Cruz B, Vitalis R, Ségurel L, Austerlitz F, Georges M, Théry S, Quintana-Murci L, Hegay T, Aldashev A, Nasyrova F, & Heyer E (2010). In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations. European journal of human genetics : EJHG PMID: 20823912

Image Credit: Wikimedia

March 27, 2010

The science of human history as written by Herodotus

The following passage is from the epilogue of The Real Eve: Modern Man’s Journey Out of Africa by Stephen Oppenheimer:

In this book I have offered a synthesis of genetic and other evidence. Everything points to a single southern exodus from Eritrea to the Yemen, and to all the non-African male and female gene lines having arisen from their respective single out-of-Africa founder lines in South Asian (or at least near the southern exit). I regard the genetic logic for this synthesis as a solid foundation, and I have based the rest of my reconstruction of the human diaspora upon it. Obviously, the ‘choice’ of starting point (mine or theirs) determined all the subsequent routes our ancestors and cousins took. Tracing the onward trails is only possible as a result of marked specificity in regional distribution of the genetic branches The geographic clarity of both male and female gene trees is a big departure from the fuzzy inter-regional picture shown by older genetic studies. The degree of segregation of lines into different countries and continents is in itself good evidence that once they got to their chosen new homes, the pioneers generally stayed put, at least until the Last Glacial maximum forced some of them to move. This conservative aspect of our genetic prehistory also provides a partial explanation for the fact that when we look at a person, we can usually tell, to the continent, where their immediate ancestors came from, and underlies differences that some of us still call ‘race.’

Oppenheimer wrote the above in the early aughts, as his book was published in 2003. Much of this is generally in line with the ‘orthodoxy’ of the day. I believe that Oppenheimer’s assertion that there was one southern migration out of Africa by anatomically modern humans has gained some advantage over the alternative model of two routes, northern and southern, over the past ten years (Spencer Wells’ The Journey of Man sketches out the two wave model). Other assertions and assumptions have not stood the test of time. In particular, I would contend that generally the ‘conservative aspect of our genetic prehistory’ can no longer be taken for granted. Specifically, it seems likely now that much occurred after the Ice Age and during the Neolithic.


420px-AGMA_HérodoteThe false inferences of the early aughts were due to two primary problems. First, they relied heavily on the powerful new techniques of extraction and analysis of uniparental ineages; the male and female direct line of descent. Concretely, mtDNA and the nonrecombintant portion of the Y chromosome. The lack of recombination allows for relatively easy reconstruction of phylogenies assuming a coalescent model. Second, the inferences attempt to make connections between the patterns of variation in modern populations, and what one may infer about the past from those patterns. Obviously constructing a phylogeny, or plotting haplogroup frequencies as a function of geography, is rather straightforward science. But using these results to generate inferences of the past is often more of an art than a science, and implicit assumptions lurk behind the causal chains. Consider for example the utilization of modern Anatolian (i.e., Turkish) genetic variation as a reference for the expansion into Europe of Neolithic farmers from the Near East. This of course presumes that modern Anatolians are a good proxy for ancient Anatolians. There are various suggestive reasons for why this is a plausible assumption, but assemble enough plausible assumptions, and rely on their joint likelihood, and you construct a very rickety machinery of possibility.

In early 2007 I began to have serious doubts about the orthodoxy of genetic conservatism. The primary trigger was the story of the Etruscans. Here is the crux of the issue: there are two models for the origins of the Etruscans, first, that they were the pre-Indo-European autochthons of Italy, or, that they were the migrants from the eastern Mediterranean, in particular Anatolia. The second may seem an outlandish hypothesis, but there were several tendrils of evidence to support it. But perhaps the ’support’ which weighed most against it is that the fact that the Anatolian model has an ancient source, the Greek historian Herodotus. I should perhaps put historian in quotes as well, because Herodotus is often viewed more as a repeater of myths, and derided by some as the ‘father of lies’ (in this he stands in sharp contrast to contemporary perceptions of the ‘modern’ Thucydides, though revisionists have begun to challenge this narrative). In contrast, the model that Etruscans are indigenous to Italy, and that their ‘exotic’ foreign traits were simply acquired through trade and cultural diffusion, dovetailed well with the post-World War II ‘pots not peoples’ paradigm. That cultural change was ubiquitous, while at the same time populations were immobile. It was boring, prosaic, and conservative, and so an ideal null hypothesis.

But here it turns out that Herodotus was right, and archaeologists were wrong. Genetic analysis of modern Tuscans from isolated villages shows that some are surprisingly closely related to extant eastern Mediterranean lineages. Genetic analysis of Tuscan cattle showed that they were surprisingly closely related to extant eastern Mediterranean lineages of cattle. Finally, extraction of ancient Etruscan DNA showed that they were closely related to extant eastern Mediterranean lineages. The overlap was often with Anatolia, and combined with fragmentary linguistic and archaeological data, the evidence clearly points to an exogenous origin for the Etruscans. The boring null hypothesis was wrong. After these genetic stories gained prominence I went and reread recent archaeological texts on the Etruscans, and there were many models which showed exactly how Etruscan cultural uniqueness derived back to prehistoric Italy. It seems in hindsight that the prior assumption served as an interpretative filter, and people saw patterns that they were primed to see based on what they ‘knew’ to be the history of prehistoric and early Iron Age Tuscany.

Of course to refute the primacy of Oppenheimer’s conservative model of genetics one has to offer more examples than that of the Etruscans, and in particular, examples which are of greater scope and weight. I believe those examples exist. In the early aughts based on the mtDNA evidence the likelihood was that South Asian genetic variation is by and large a product of changes wrought upon the basic elements extant in the region around the end of the last Ice Age. The Y chromosomal data was more confused, though it did imply a closer relationship to groups in western Eurasia. But based on the mtDNA Oppenheimer posited a model whereby India was the mother of all non-Africans, that is, all non-African lineages derived from roots within the Indian subcontinent before the Last Glacial Maximum. This is at sharp variance with colonialist narratives of an Aryan invasion of the subcontinent, and the subjugation of the natives by quasi-European overlords, who are the ancestors of the moder upper castes. The charged ideological import of this model is transparently obvious.

Unfortunately the reality is likely more complex. I suspect that some form of Oppenheimer’s model is correct, insofar as South Asia was likely an important way station for modern humans as they left Africa, and pushed into other regions of Eurasia, on to Australasia and the New World. This interpretation does gain support from mtDNA, the direct maternal lineage. But a new analysis of South Asian genetic variation using a substantial proportion of the autosomal genome implies in fact that South Asians are possibly descendants of an ancient hybridization event between a native population with deep roots in the subcontinent, and a quasi-European population which was exogenous to the subcontinent.* Genetically the quasi-European population is quite close to northern Europeans, similar to the genetic distance between modern Finns and Italians, not trivial, but far closer than that between modern South Asians and Europeans. Was this the ancient Aryan invasion? I remain skeptical of this particular detail for various reasons, as I suspect that the history of the Indian subcontinent is in fact even more complex than has been assumed before (I think it is more likely that the quasi-Europeans came before the Indo-Aryans, who arrived late, and had a stronger cultural than genetic influence).

Finally, there is another region of the world where it seems likely that the old orthodoxies of genetic conservatism will be overthrown. That region is Europe. The scientific orthodoxy of deep time continuity is strong enough that it has percolated into the public consciousness, the leader of the British National Party even referred to the deep roots of white British in demarcating who he believed ‘indigenous people’ of the Isles were. But newer data is more supportive of the hypothesis that in fact Neolithic farmers who arrived from elsewhere are the likely ancestors of most Europeans, not the hunter-gatherers who remained after the Ice Age. Extraction of ancient DNA has yielded a set of results which simply are not explicable assuming the older models of genetic continuity, which were based on inferences made from modern population variation. If I had to hazard a guess, I would have some, though not high, confidence in the following story. First, the indigenous hunter-gatherers are assimilated or marginalized by waves of Neolithic farmers pushing out from the eastern Mediterranean. The demographic expansion does not necessarily sweep outward along a southeast-northwest axis, rather, it follows the Mediterranean and Atlantic fringes, as well as along river systems in the interior. Its impact is weakest in the northeast of Europe, where Middle Eastern crops are least suitable, and the natives have the most time to absorb the cultural toolkit of the newcomers so as to resist their advance. Second, and far later, there was another wave pushing out from the region of the Ukraine to the Volga, likely the ancestors of the Indo-Europeans. Tentatively I would contend that these were the carriers of the Kurgan culture, and also brought the allele for lactase persistence. Again, for ecological reasons the populations of the northeast Baltic and into the forests of northern Russia were most insulated from this push (and non-Indo-European languages persisted in Iberia down to Roman times, and specifically in the Basque-country down to modern times, though I suspect this is a function of distance). So modern European populations may be assumed to be tri-hybrid, first a synthesis of Middle Eastern farmers overlain upon the Paleolithic substrate, and second a synthesis of Indo-Europeans from the east overlain upon pre-Indo-European substrate. Unlike the case of India I suspect teasing out these patterns in modern populations is more difficult because the genetic distance between the three ancestral populations is far smaller than between the indigenous peoples of India before the quasi-Europeans arrived.

This leaves much of the world untouched by my speculations, but I believe showing that the genetically conservative null hypothesis is now in serious doubt in South Asia and Europe is sufficient to knock it from being a necessarily default assumption through which we must filter our interpretations. I do not believe that the reordering of human variation and the welter of population movement after the Ice Age was equivalent in effect to the Out of Africa migration, but I do believe that it was important enough to make the world of 2000 BCE very different from that of 15000 BCE in regards to genetic variation. In some cases, such as Central Asia from the Caspian to the Taklamakan the world of 2000 CE is fundamentally different from the world of 0 CE.

I will then end with a prediction, one in which I do not have much confidence, but which may no longer be wrong on the face of it with these new data in mind. Here is a passage from page 7 of Jared Diamond’s Guns, Germs, and Steel:

Initially, archaeologists considered the possibility that the colonization of Australia/New Guinea was achieved accidentally by just a few people swept to sea while fishing on a raft near an Indonesian island. In an extreme scenario the first settlers are pictured as having consisted of a single pregnant young woman carrying a male fetus…..

Let me stipulate that Diamond seems skeptical of the extreme model, but it illustrates the consensus that Australian Aboriginal populations are descended from the first settlers. That is, the modern populations of indigenous Australians are the direct descendants of those who swept Out of Africa along the fringe of the Indian ocean, through Southeast Asia, and arrived in Australia (more specifically, Sahul), on the order of 40 to 60 thousand years ago. From what genetic data I have seen this may be true. But I do not know of any extractions of ancient DNA, and it seems to me that the analysis of the phylogenetics of Australian Aboriginals is relatively sketchy. Therefore, I will suggest that within the last 10,000 years there has been a major new migration of people into Australia, and the modern range of genetic variation of Australian Aboriginals is significantly different from that of the populations of the Ice Age. I suggest this primarily because the dingo arrived within the last 10,000 years, more likely as recently as 4,000 years ago. With the expansion of the utility of ancient DNA extraction and analysis this question may be answered in the near future. I would still bet I’m wrong with the hypothesis I just offered, but I’m far less sure than I would have been 2 years ago.

Note: This post emerged from a conversation I had with Kevin Zelnio and Dave Munger.

* I say ‘quasi-European’ because the population may have origins outside of the boundaries of modern Europe at the Urals. Perhaps in western Siberia. Additionally, the idea of ‘Europe’ is relatively new, and exhibits little ancient cultural coherency.

Image source: Wikipedia

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