Excavating the Neolithic genetic strata

By Razib Khan | December 11, 2010 7:15 pm

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.

CATEGORIZED UNDER: Anthroplogy, Culture, Genomics
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  • http://washparkprophet.blogspot.com ohwilleke

    “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.”

    I am inclined to agree based on linguistic evidence of time-depth and the close association between the range and age of Dravidian languages and the South Indian Neolithic that Dravidian emerged in the south of India with farmers (some of whom may have reverted to hunter-gathering), although I would put the date closer to 5,500 years ago in line with the archeology of the South Indian Neolithic. But, an origin for Dravidian in Northwest India seems unlikely.

    The lack of expansion of the Harappans out of Northwest India to the rest of India has an obvious explanation. Near Eastern Neolithic founder crops grow in Northwest India but not in the climate of South India where African Sahel crops grow much better, and the South Indian Neolithic involved crops domesticated in the African Sahel, which arrived later in a separate event.

    There is really no archaeological evidence to support anything more than a thin trading relationshp between the Harappans and the South Indian Neolithics. And, the case that there is a Dravidian substrate in early Rig Vedic Sanskrit is increasingly viewed as weak, despite the fact that if the Harappans or their ancestors were the first people subjected to Indo-Europeans from Central Asia and were also the source of Dravidian, there should have been such a substrate. Finally, the crops argue against that origin.

    Indo-European expansion is also quite sufficient to explain the ANI genetic component in South Indian Dravidian population. The evidence that Dravidian farming practices and language have a source in a Niger-Kordifani speaking population of Sahel farmers in Africa, as argued by Sergent, increasingly looks more likely to me, and has support from crops, from linguistics and from cultural carryovers. Given the lack of an mtDNA trace of that event, I think it is likely that the seed population of the Dravidian culture was probably a group of colonizing men and that Y-DNA haplogroup T, a haplogroup whose distribution coincides neatly with the linguistically inferred location of proto-Dravidian, is the genetic trace of this seed population. See some supporting evidence cited here.

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  • http://blogs.discovermagazine.com/gnxp Razib Khan

    dude,

    1) i followed some of your links. they’re old. that doesn’t invalidate them, but the genetic stuff i know has been superseded.

    2) there’s no autosomal data to corroborate the hypothesis. in fact, lots of to refute it. that’s more for the people who read your comment. don’t care what you think about the issue, it’s pretty clear to me that the overwhelming preponderance of evidence weighs against you in the ‘afro-dravidian’ hypothesis.

  • http://washparkprophet.blogspot.com ohwilleke

    I certainly don’t claim to have autosomal or mtDNA evidence to support the hypothesis (and, of course, one doesn’t need to have extant genetic evidence of any kind to the extent that the Afro-Dravidian hypothesis, which is mostly a linguistic and cultural sourcing claim involves more cultural transfer than a demic replacement by outsiders).

    But, the genetic argument that I have made, which is to associate Y-DNA T with the Afro-Dravidians may be possible to show in a suitably designed autosomal study. But, since Y-DNA T is not uniform across Dravidian speakers (one presumes based on Y-DNA data that there was an initial demic expansion in the core proto-Dravidian area followed by expansions that is proportionately more culturally transmitted in the wider Dravidian area), in a way that goes beyond the ANI v. ASI cline, one would expect a search looking for Dravidian v. non-Dravidian components to have a hard time parsing out this subpart of a proto-Dravidian population.

    Most autosomal studies have offered inputs in the form of linguistic groups or macrolinguistic groups, with an aim to discerning if autosomal genetic clusters form along those lines and they do. The autosomal data, while not unequivocal, does show a distinction between ANI and ASI. And, with enough clusters permitted (as Dienekes does in his recent analysis) almost every subpopulation can be distinguished from almost every other subpopulation as a distinct autosomal population that matched closely the input groupings without using a process that relies on the labels assigned to the input genomes. The hard part is to discern larger dimensional trends within an ASI component.

    But, the fact that a population is distinct from other populations autosomally doesn’t tell you much about where its autosomal mix came from. Pure cluster analysis doesn’t itself distinguish between admixed and non-admixed populations, or determine how many components went into that population’s mix when (except in cases where recent merger of populations leaves mostly unadmixed as cryptic subpopulations).

    To test the genetic part of an Afro-Dravidian hypothesis you would need to take a fine grained set of samples from populations that are Dravidian and are hypothesized to be Dravidian and look to see which autosomal markers, if any, corrolate to the prevalence of Y-DNA T in that population, and then compare those autosomal markers to autosomal markers that corrolate with Y-DNA T that is phylogenically similar to the Y-DNA T found in South Indian populations.

    We certainly aren’t there yet and I don’t claim that this is anything more than a hypothesis. Y-DNA T was just recognized as a distinct haplogroup at all in the last few years, and I haven’t been able to locate any sources that I can read (i.e. that aren’t behind paywalls) that even do a phylogenic comparison of Y-DNA T subhaplogroups by geography (which could itself make or break the genetic part of the hypothesis), and since there are almost no pure Y-DNA T populations, providing pure types to use as comparisons in first order autosomal analysis, it isn’t easy work.

    But, it is a hypothesis with considerable supporting evidence from multiple different disciplines including the Y-DNA studies, so it is worth the effort to investigate.

    While there may be cases where autosomal studies reveal connections that patrilines and matrilines fail to reveal (for example, in cases where one instance of patriline dominated replacement by invaders to an existing population is followed by a second such instance that obliterates the Y-DNA traces of the first invasion wave), there shouldn’t be any cases where strong Y-DNA or mtDNA traces are entirely invisible in autosomal DNA evidence, even though the autosomal DNA evidence is much more formidable to work with in multiple loci at the same time (if you use individual allels and genes, it is only modestly more difficult). Autosomal data don’t make uniparental market data obsolete, it only adds nuance to it.

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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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