The long, drawn-out road to us

Timothy Weaver has an intellectually challenging recent article in the Journal of Human Evolution. He proposes that there was no punctuational "rise of modern humans", but rather a long, drawn-out continuous process since our split with our closest cousins, the Neandertals.

The argument for "no bottleneck" leading up to modern humans in Africa was recently made by Sjödin et al. Weaver examines critically three of the arguments of the "recent Out of Africa" model:

• the shallow coalescence of mtDNA Eve
• the emergence of anatomically modern traits in Africa c. 200ky ago
• the idea that these modern traits are quite different from the ones that preceded them -the idea that a new species was born at the time.

With respect to mtDNA, Weaver makes the argument that the fact that mtDNA Eve coalesces to about 200ky ago (actually 177ky according to the latest estimate) does not mean that there was some bottleneck at the time associated with the rise of modern humans; the same coalescence age could occur under quite different scenaria: perhaps there were bottlenecks all the time, and nothing special happened at that time; or, there were no bottlenecks at all: if the effective population size was constant, then mtDNA would still coalesce at some time, depending on what that effective size was.

This of course raises the question: if we know what the human effective population size is, could we estimate when mtDNA ought to coalesce. First, coalescence theory does not provide a hard time for the coalescence, but rather an expected value; coalescence at 177ky is compatible with lots of different effective sizes, and different effective sizes are compatible with a coalescence at 177ky.

(More importantly, and contrary to popular belief and recent commentary: we have absolutely no idea what the human ancestral effective population size is. Figures like 10,000 people are sometimes quoted around, but we must remember where they come from: there is a triangle of doom between the human-chimp divergence date, the effective population size, and the mutation rate, and you need to know two of these to infer the other. Actually, we are beginning to get a hold of the mutation rate -thanks to the ability to sequence full genomes- but we have absolutely no clue when human-chimp divergence actually happened, at least not within a few million years.)


There is a different blow that can be directed to the idea of using mtDNA to infer a "rise of modern humans": if we look at Denisova and Neandertal hominins, they are autosomally about equidistant to us, but Denisova carries an mtDNA lineage that is about half a million years more ancient. If that doesn't stop us from repeating the "recent mtDNA Eve = recent African origin" meme, I don't know what is.

Getting back to the Weaver article, the author argues that the appearance of cranial modernity is expected if we only make an assumption about the narrow-sense heritability of human traits; that is, working backwards from the present, and taking into account drift and mutation, we expect that "modern traits" will start appearing in the anthropological record at the time of the supposed "rise of modern humans". This is simply a consequence of the fact that anthropologists label traits as modern or archaic with respect to extant human variation; so, there is nothing special about the fact that such "modern" traits appear on the record, since they are expected to do so by the mere fact that the people who lived 100-200ky ago are ever-more related to us.

The final aspect of the Weaver article has to do with the supposed punctuation in the appearance of modern humans in Africa. He makes a good point here, that the African record is so fragmentary that we hardly know what people were like before the supposed rise of modern humans. It's tough to argue about the emergence of a new species when you have no good comparative base. I would also add that even after the supposed emergence, "modern" and "ancient" traits co-exist, with no clear overall pattern discernible in the data. If modern humans suddenly arose in Africa and replaced pre-existing African hominins, the evidence for this sudden emergence and replacement is lacking.

Overall, I would say that Weaver makes a good argument against the idea of us being something special in the grand scheme of things. Perhaps we're not mutant world conquerors after all, but rather the latest phase in a long and drawn-out evolution of Homo. It's a less dramatic and more mellow theory about our origins, but one that may very well be true.

Journal of Human Evolution
Volume 63, Issue 1, July 2012, Pages 121–126


Did a discrete event 200,000–100,000 years ago produce modern humans?

Timothy D. Weaver

Abstract

Scenarios for modern human origins are often predicated on the assumption that modern humans arose 200,000–100,000 years ago in Africa. This assumption implies that something ‘special’ happened at this point in time in Africa, such as the speciation that produced Homo sapiens, a severe bottleneck in human population size, or a combination of the two. The common thread is that after the divergence of the modern human and Neandertal evolutionary lineages ∼400,000 years ago, there was another discrete event near in time to the Middle–Late Pleistocene boundary that produced modern humans. Alternatively, modern human origins could have been a lengthy process that lasted from the divergence of the modern human and Neandertal evolutionary lineages to the expansion of modern humans out of Africa, and nothing out of the ordinary happened 200,000–100,000 years ago in Africa.

Three pieces of biological (fossil morphology and DNA sequences) evidence are typically cited in support of discrete event models. First, living human mitochondrial DNA haplotypes coalesce ∼200,000 years ago. Second, fossil specimens that are usually classified as ‘anatomically modern’ seem to appear shortly afterward in the African fossil record. Third, it is argued that these anatomically modern fossils are morphologically quite different from the fossils that preceded them.

Here I use theory from population and quantitative genetics to show that lengthy process models are also consistent with current biological evidence. That this class of models is a viable option has implications for how modern human origins is conceptualized.

Link

Khoisan genetic prehistory (Pickrell et al. 2012)

This appears to be the first paper using the specialized Affymetrix chip, which was announced some time ago, and used in some of my previous experiments. The new array has been dubbed "Affymetrix Human Origins array" and has been composed by intersecting panels of SNPs ascertained in individuals from several world populations.

It is of course great to see that this paper has appeared as a preprint in arXiv, and hopefully this is a trend that will continue; biology should be like physics, with papers appearing immediately online for commenting, and not hidden away in authors', editors', and reviewers' drawers for months if not years before they become available to all.

I will highlight some points of particular interest to me:

Some caveats of interpretation here are warranted. First, all the Khoisan populations have some level of admixture with non-Khoisan populations. There is thus no single \split time" in their history, and any method (like the one used here) that estimates a single such time will actually be estimating a composite of several signals. Second, we have made the modeling assumption that history involves populations splitting in two with no gene  ow after the split. More complex demographies are quite plausible, but render the interpretation of a split time nearly meaningless (if populations continue to exchange migrants after \splitting", they arguably have not split at all). We thus consider strong interpretations of split times estimated from genetic data to be impossible, but we nonetheless and the estimates to be useful in constraining the set of historical hypotheses that are consistent with the data. 

This echoes (somewhat) my sentiments about split times being a tug-of-war in the presence of admixture. Another interesting bit from the paper:

Interestingly, a few of the Khoe-speaking populations have slightly positive f4 statistics in this com- parison, and in the Shua the f4 statistic is significantly greater than zero. We speculate that some of the Khoe-speaking populations have a low level of east African ancestry, and that the relevant east African population was itself admixed with a western Eurasian population. The Shua also show a detectable signal of admixture LD, though we estimate the admixture date as much older (44 generations). This signal of east African ancestry specifically in Khoe-speaking populations is of particular interest in the light of the hypoth esis that the Khoe-Kwadi languages were brought to southern Africa by a pre-Bantu pastoralist immigration from eastern Africa [Guldemann, 2008] 

The authors also announce an improvement on TreeMix:

In the original TreeMix algorithm, one first builds the best-tting tree of populations. However, this approach is not ideal if there are many admixed populations (as in our application here, where all of the Khoisan populations are admixed). To get around this, we allow for known admixture events to be incorpo- rated into this tree-building step. Imagine that there are several populations that we think a priori might be unadmixed (in our applications, these are the Chimpanzee, Yoruba, Dinka, Europeans, and East Asians). We  first build the best tree of these unadmixed populations using the standard TreeMix algorithm. Now assume we have an independent estimate of the admixture level of each Khoisan population, and imagine we know the source population for the mixture. 

I don't think that Sub-Saharan African populations can any longer be considered unadmixed. When one used SNPs ascertained in Eurasian individuals, many Sub-Saharan populations appear symmetrically related to Eurasians, because they lack variation at sites where new polymorphism appeared outside Africa. 

This is not, however, the case when one uses SNPs ascertained in African individuals, and a clear pattern of differential affiliation with West Eurasians across the continent is evident. As I have said before, I strongly suspect that this is due to fairly late back-migration of Eurasians into Africa, carrying Y-haplogroup DE chromosomes. Within haplogroup CT, both its major subclades CF and DE are represented in Eurasia, and both D,E, and DE* as well. In Africa, as far as we know, only DE* and E are native. On balance, the weight of the evidence would suggest a Eurasian origin of the DE-YAP haplogroup.

(I would perhaps be as bold as to extend this into the even more basal clades of the phylogeny which turn up with surprising regularity in Eurasian datasets, and are usually discounted as the result of recent admixture. I'm not so sure; if recent admixture was at fault, then the African signal in Eurasia would be absolutely dominated by E-related lineages: but the A's and B's turn up in quite unexpected places. Are they really all recent Africans, or could they share a much deeper common ancestry? If I had deep pockets, I'd surely invest in genome sequencing the collection of such Eurasian erratics)

As a parting thought, I hope that the data used in this paper will become publicly available in time, perhaps when the article appears in journal form. True open science depends not only in the public availability of research results, but also of the data that produced them.

UPDATE: Here is the ADMIXTURE analysis from the paper (Figure 7):

It would have been nice if the Fst values between ancestral populations were reported in the paper; also, if an East Eurasian group was added in the analysis. In any case, there does appear a pattern of differential affiliation with the French population (K=2). At K=3 the main Sub-Saharan (blue) component emerges, and a few populations continue to exhibit an excess of West Eurasian affiliation.

arXiv:1207.5552v1 [q-bio.PE]
The genetic prehistory of southern Africa

Joseph K. Pickrell et al.

The hunter-gatherer populations of southern and eastern Africa are known to harbor some of the most ancient human lineages, but their historical relationships are poorly understood. We report data from 22 populations analyzed at over half a million single nucleotide polymorphisms (SNPs), using a genome-wide array designed for studies of history. The southern Africans-here called Khoisan-fall into two groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. All individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began 1,200 years ago. In addition, the Hadza, an east African hunter-gatherer population that speaks a language with click consonants, derive about a quarter of their ancestry from admixture with a population related to the Khoisan, implying an ancient genetic link between southern and eastern Africa.

Link

R1b1a2 variants in 1000G data

It's nice to see a group of independent researchers documenting their work using 1000 Genomes data. I've been following on-and-off developments in this field, and I have to say that it requires deep commitment from the persons involved to keep a mental picture of the ever-deepening phylogeny.

But, in a sense, that is what's great about the efforts of citizen scientists tackling a scientific problem: they are deeply invested in understanding their little part of the human Y-chromosome phylogeny, because it's their part and every SNP discovery in it represents a small victory. Thus, they can expend the time and effort to push the discovery process to its technological limits.

It's only too sad that this can at present be done only using 1000 Genomes data, a.k.a. the global collection of full genome data that completely ignores the part of the world between  Italy and China/India. Hopefully, sometime in the future, the ever-better-understood twig of R1b1a2 will be placed within its wider Eurasian context.

PLoS ONE 7(7): e41634. doi:10.1371/journal.pone.0041634


Discovery of Western European  R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach

Richard A. Rocca1*, Gregory Magoon2, David F. Reynolds3, Thomas Krahn4, Vincent O. Tilroe5, Peter M. Op den Velde Boots6, Andrew J. Grierson7

The authors have used an online community approach, and tools that were readily available via the Internet, to discover genealogically and therefore phylogenetically relevant Y-chromosome polymorphisms within core haplogroup R1b1a2-L11/S127 (rs9786076). Presented here is the analysis of 135 unrelated L11 derived samples from the 1000 Genomes Project. We were able to discover new variants and build a much more complex phylogenetic relationship for L11 sub-clades. Many of the variants were further validated using PCR amplification and Sanger sequencing. The identification of these new variants will help further the understanding of population history including patrilineal migrations in Western and Central Europe where R1b1a2 is the most frequent haplogroup. The fine-grained phylogenetic tree we present here will also help to refine historical genetic dating studies. Our findings demonstrate the power of citizen science for analysis of whole genome sequence data.

Link

Broken Hill humerus: date unknown

Recently it was hinted that the Broken Hill skull is younger than has been thought before. Now, a brief communication by Erik Trinkaus in AJPA suggests that the BH humerus which has featured in debates about the evolution of human postcranial morphology lacks proper stratigraphic context, and is from a location where modern human disturbance is likely. The conclusion: it should be avoided in studies about the evolution of humans until it is securely dated.

Redating fossils is a problem that has plagued anthropology for a while. For example, H. sapiens idaltu (Herto) was given a Linnaean moniker and recognized as a precursor of modern humans because of its mix of modern and archaic traits, but shortly thereafter the Omo skulls were re-dated to tens of thousands of years earlier (~195ka), indicating that the more modern morphology of Omo I actually preceded the more archaic one of Herto Man.

When an older fossil is redated to a younger age, what was once seen as showing signs of evolutionary trends leading up to modern humans ends up being an embarrassing survival of archaic traits in a period where they are supposed to have been on their way to replacement. The once popular story of modern humans shedding their archaic traits and attaining modernity in Africa, and then populating the world is increasingly unbelievable, both because the 60,000-year-old coastal migration is bunk, but also because archaic traits persist in some African populations down to the Holocene. I strongly suspect that the story of our origins may be much more interesting than anyone had imagined.

AJPA DOI: 10.1002/ajpa.22118

Brief communication: The human humerus from the broken hill mine, kabwe, zambia

Erik Trinkaus et al.

The distal half of a right human humerus (E.898), recovered ex situ in 1925 by Hrdlicka at the Broken Hill Mine, Kabwe, Zambia, has figured prominently in assessments of Middle Pleistocene Homo postcranial variation and of the phylogenetic polarity and functional anatomy of Pleistocene Homo upper limb morphology. Reassessment of distal humeral features that distinguish modern human and some archaic Homo humeri, especially relative olecranon breadth and medial and lateral pillar thicknesses, confirm previous studies placing it morphologically close to recent humans, as well as possibly to Early Pleistocene Homo. However, it completely lacks stratigraphic context, and there is faunal and archeological evidence for human activity at Broken Hill from the Middle Pleistocene to the Holocene. Given its uncertain geological age and modern human morphology, the Broken Hill E.898 humerus should not be used in analyses of Pleistocene humans until it is securely dated. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.

Link

Volcanic ash didn't kill Neandertals, modern humans did

Related story by Michael Balter:

The team collected samples containing CI cryptotephra from four central European caves where stone tools and other artifacts typical of Neandertals and modern humans have been found. They also gathered the particles from a modern human site in Libya and from marshland and marine sites in Greece and the Aegean Sea. The results, the team argues in a paper published online this week in the Proceedings of the National Academy of Sciences, are incompatible with the hypothesis that the CI was responsible for Neandertal extinction, at least in central Europe. The CI cryptotephra lie above, and so postdate, the transition from Neandertal to modern human stone tool types at all four central European sites, indicating that modern humans had replaced Neandertals before the catastrophic events of 40,000 years ago.

It's a little strange that modern humans arrive in Europe by the late 40,000s cal BP, replace the Neandertals, and shortly -in geological terms- thereafter, a massive volcano goes off on them. Perhaps, a little nemesis?

PNAS doi: 10.1073/pnas.1204579109

Volcanic ash layers illuminate the resilience of Neanderthals and early modern humans to natural hazards

John Lowe et al.

Marked changes in human dispersal and development during the Middle to Upper Paleolithic transition have been attributed to massive volcanic eruption and/or severe climatic deterioration. We test this concept using records of volcanic ash layers of the Campanian Ignimbrite eruption dated to ca. 40,000 y ago (40 ka B.P.). The distribution of the Campanian Ignimbrite has been enhanced by the discovery of cryptotephra deposits (volcanic ash layers that are not visible to the naked eye) in archaeological cave sequences. They enable us to synchronize archaeological and paleoclimatic records through the period of transition from Neanderthal to the earliest anatomically modern human populations in Europe. Our results confirm that the combined effects of a major volcanic eruption and severe climatic cooling failed to have lasting impacts on Neanderthals or early modern humans in Europe. We infer that modern humans proved a greater competitive threat to indigenous populations than natural disasters.

Link

Admixture matters (for polar bears too!)

In Admixture matters, I argued, inter alia, that "admixture can also deflate divergence, if there is subsequent gene flow between the diverged populations."

Interestingly, polar bears are now providing us with a wonderful example of this process in action. It has been abundantly clear for a while now, that polar bears are an arctic-adapted form of non-polar bears, bow how far back in time can there evolutionary relationship be pushed?

A new open access paper in PNAS answers this question:

We first used a simple isolation model (15), comparing pairs of genomes under the assumption of allopatric speciation. However, for all comparisons, we obtained estimates of very recent split times and very large ancestral effective population sizes (Ne ), consistent with mis-specification of the demographic model and suggesting that the true demographics involved are not simple splits but instead initial splits followed by prolonged periods with structured populations and gene flow. WWe therefore applied an extended model estimating an initial split time followed by a period of gene flow before a complete split (SI Appendix). We estimated an initial split between black bears and their sister lineage 4 to 5 Mya followed by gene flow until 100 to 200 kya (Fig. 3)

There you have it: low split times/high effective sizes are inferred in a tree model ("simple isolation model"), but when one does not take into account gene flow between the diverged populations, split times balloon and effective sizes shrink.

Of course in this case, we actually do have extant brown/black/polar samples to work with. But, leaving zoology and going back to anthropology, we only have on extant species (H. sapiens) within the genus Homo and only two (H. Neandertalensis and "Denisovans") of several archaic hominins that once roamed the planet, in some cases, apparently until very recently. Both the cases we do have indicate differential admixture levels with modern human groups.

I think we need to open ourselves to the possibility that shallow divergence times and higher effective population sizes in some human populations may not be the result of Biblical-level bottlenecks as small tribes of humans "conquered the earth", but of thorough and long-term gene flow between populations within the genus Homo.


PNAS doi: 10.1073/pnas.1210506109

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Webb Miller et al.

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

Link

Purifying selection and measures of population differentiation

From the paper:

Because allele frequencies are known to be lower at positions under stronger purifying selection (Subramanian and Kumar 2006), we examined the relationship between population differentiation estimates and minor allele frequencies (MAF). They are also highly positively correlated (Fig. 3A; P less than 10-15). 

... 

Our results suggest that interpreting and comparing results from population genomic studies now should consider this dependence of FST on the frequency of the allele as well as the functional importance (evolutionary rate) of the position. For example, estimates of FST at sites on the Y chromosome and at sites in the mitochondrial genome are sometimes compared to detect the difference in male vs. female migration rates (e.g., Seielstad et al. 1998). In such examinations, we now need to compare FST at sites with similar MAF across populations to detect the difference in migration rates. It is also important when we compare FST at sites among different populations. For example, African populations are known to have higher MAF across populations than non-African populations (Tishkoff and Kidd, 2004). Without consideration of MAF before comparing FST estimates at different positions in the two may lead to incorrect inference of higher degree of population differentiation among one set of populations as compared to the other set of populations.   

I can't say that I am very comfortable with the technical details of this paper, but from my first reading, it would appear that African populations have higher minor allele frequency (MAF) than non-African ones, so measures of population divergence for Africans may be inflated relative to non-Africans, and be reflective of lower levels of purifying selection in African populations.

This would of course have monumental implications for the reconstruction of human prehistory, as it would suggest that high Fst values between different African populations and between Africans and Eurasians may be, at least partially, driven by lower levels of purifying selection in the former. It is also possible, as I've suggested, that excess variation (manifesting itself as higher minor allele frequency) may be the result of admixture between divergent Homo populations.

Biology is a mess, but hopefully statistical geneticists are up to the task!

Mol Biol Evol (2012) doi: 10.1093/molbev/mss187

Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single nucleotide polymorphisms

Takahiro Maruki et al.

An improved understanding of the biological and numerical properties of measures of population differentiation across loci is becoming increasingly more important because of their growing use in analyzing genome-wide polymorphism data for detecting population structures, inferring the rates of migration, and identifying local adaptations. In a genome-wide analysis, we discovered that the estimates of population differentiation (e.g., FST, θ, and Jost’s D) calculated for human single nucleotide polymorphisms (SNPs) are strongly and positively correlated to the position-specific evolutionary rates measured from multispecies alignments. That is, genomic positions (loci) experiencing higher purifying selection (lower evolutionary rates) produce lower values for the degree of population differentiation than those evolving with faster rates. We show that this pattern is completely mediated by the negative effects of purifying selection on the minor allele frequency at individual loci. Our results suggest that inferences and methods relying on the comparison of population differentiation estimates (FST, θ, and Jost’s D) based on SNPs across genomic positions should be restricted to loci with similar minor allele frequencies and/or the rates of evolution in genome-scale surveys.

Link

Archaeometallurgy in the Mediterranean

Continuing a discussion on metallurgical innovation which I began here.

Some interesting excerpts from a book chapter:

Tin bronze first appeared in Mesopotamia and Anatolia during the third millennium B.C., or Early Bronze Age (Pare 2000a:6–7). In the Mediterranean,the transition from arsenical to tin bronze took place during the course of the Middle Bronze Age (late third to early second millennium B.C.in the eastern Mediter-ranean, somewhat later in the west). The implication (Renfrew 1972:313–319) that tin bronze was an independent development in the northeast Aegean is contradicted by lead isotope analyses which show that most copper or bronze objects from sites such as Troy, Poliochni, and Kastri were not produced from local ores (Muhly and Pernicka 1992; Pernicka 1998:140–141). Exactly what caused the transition from arsenical to tin bronze is not well understood: as an alloy, tin bronze is not mechanically superior to arsenical copper (Pernicka 1998:135–136).Unlike arsenic, moreover, tin is not widely available as a mineral, and new trade networks would have been required to enable its distribution. However, it may have been easier to control the quality of tin bronze, and the production of tin bronze would have overcome the problem of working with toxic arsenic fumes (Charles 1978:30;Pare 2000a:7).

Given the limited number of tin deposits in the region, the source(s) of tin usedin the prehistoric eastern Mediterranean has always been a highly controversial issue. The suggestion that Afghanistan served as a prime source of tin for Bronze Age eastern Mediterranean societies is based in part on the existence of its rich tin resources (Muhly and Pernicka 1992:315;Weeks 1999:60–61).Muhly (1999:21) recently argued that Afghanistan or central Asia provided the tin that supplied the bronze industries of Mesopotamia, Anatolia, and the eastern Mediterranean, including Cyprus. Cuneiform documents from the early second millennium B.C., moreover, point to a trade network that brought tin from the east to the early states of Anatolia and Mesopotamia (Maddin et al.1977:41:Weeks 1999),and thence to the Mediterranean. Weisgerber and Cierny (2002,with fuller references) now maintain that prehistoric tin mining (second millennium B.C.), attested at the sites of Karnab (Uzbekhistan) and Musciston (Tajikistan), provided an important source of tin for Anatolia and Mesopotamia, if not for the Mediterranean. In contrast, Yener and Vandiver (1993) have argued that (very limited) tin deposits in the Taurus Mountains of southern Turkey were exploited during the Early Bronze Age. Their argument has been challenged by several scholars (e.g.,Muhly 1993;Weisgerberand Chierny 2002:180–181;papers in Journal of Mediterranean Archaeology 5[1995]) who maintain that the archaeological evidence is unclear,and far too limited to demonstrate anything beyond local use. Even if tin from the Taurus were mined during the Early Bronze Age, it now seems more likely that central Asia provided at least some of the tin used during the Middle-Late Bronze Ages,when tin bronze was far more widely produced, traded, and consumed in the Mediterranean. 

... 

By the Late Neolithic period (ca.4800–3100 B.C.), most people living in the Mediterranean region produced their own food, lived the year round in sedentary communities and increasingly were involved in intricate social and economic exchanges. By the beginning of the Bronze Age, certain alliances, special-interest groups, or even individual local leaders came to control access to raw materials in demand: obsidian, precious or semi-precious stones, metals such as gold, silver, copper, and tin, and a range of more perishable goods. From about 3000 B.C.onward – corresponding to the Chalcolithic period (Argaric culture) in Spain, the Final Neolithic in Italy, and the Early Bronze Age in the Aegean and eastern Mediterranean – the production and trade in metals increasingly became a key factor in promoting social change (Giardino 2000b;Knapp 1990a;Levy et al.2002;Manning 1994;Ruiz Taboada and Montero Ruiz 1999).  

...  

Technological innovations may be seen as progressive by managers and elites, but for the people who mined ores or smelted metals they were also potentially disruptive, forming the backdrop for social change as well as social abuse (Heskel andLamberg-Karlovsky 1980:260–261;Stollner 2003:427–429). Miners and metal-smiths often use ideology as a means to maintain, resist,or change their power base within society. Because elites who control and organize metallurgical produc-tion often use material culture to restructure relations of power (Gamble 1986:39), we may also expect such transformations to be visible in the archaeological record. 

...  

Consequently, there is little room to doubt that innovations in technology had deep-seated and long-lasting social and ecological effects, placing constraints as well as conferring benefits on Bronze Age mining and metallurgical production. In social terms, whereas the intensified production of copper employing an advanced technology did not preclude a strong sense of local community, such factors served to increase social distinctions between those at the top of the control structure and those at the bottom (Hardesty 1988:102,116;Knapp 1986b;2003). 

...  

The trade in metals during the Chalcolithic period was carried out on a very limited scale, and most metals were certainly consumed in the same area where they were produced (cf.Gale 1991). During the Early Bronze Age (third millennium B.C.), technological innovations like the longboat and sail facilitated the bulk transport of raw materials or manufactured goods on a much larger scale than ever before (Broodbank 1989). 

... 

Metals and metallurgy wielded an immense impact on Mediterranean Bronze Age societies, clearly evident in all the fundamental changes seen in the archaeological record from the end of the Chalcolithic period (Copper Age) onward. During the Bronze Age,innovations in maritime transport and the earliest cultivation of olives and vines stimulated the economy of the Mediterranean region and spurred some of its inhabitants to produce metals, take part in maritime trade, manufacture distinctive artifacts, and build domestic and public structures that represented the earliest towns and ceremonial complexes in the Mediterranean. The advent and spread of metallurgy promoted greater social distinctions,as certain individuals or groups acquired new wealth and prestige items. Because tin had to be imported in order to produce bronze, long-distance trade was stimulated. Duringthe second millennium B.C., gold, silver, copper, and tin came to represent what Sherratt (2000:83) has termed “convertible”value, both in an economic sense and in the literal sense that they could be consumed, stored, redistributed, or recycled in diverse forms and for various symbolic or ideological ends.Such documentary evidence as exists, exclusively in the eastern Mediterranean, is frequently preoccupied with these self-same metals (Liverani 1990:205–223,247–266;Moran,inKnapp 1996:21–25).

A remarkable series of social and economic changes thus were linked closely to all the innovative developments in extractive and metallurgical technologies,and tothe increasingly widespread and intensified production and distribution of metalsand metal objects. These changes include but are not limited to: (1) the proliferation of settlements and the emergence of town centers;(2) the development and expansion in interregional trade;(3) the growth of palatial regimes and city-state kingdoms,with their attendant writing systems (notably in the eastern Mediterranean);(4) the development and refinement of craft specialization and the spread of an iconographic koine;(5) the elaboration of mortuary rituals and burials with large quantities of precious metal goods;(6) the widespread occurrence of metal hoards and the related trade in recycled and scrap metal. The circulation of goods, ideas, and ideologies across geographic,cultural,and economic boundaries represents a social transaction,one that entangled producers, distributors, and consumers in wider relations of alliance and dependence, patronage and privilege, prestige and debt (Thomas 1991:123–124). Certain occupational identities came to be focused around metallurgical production and trade, and Cyprus even gave its name to the island’s most prominent product: copper ore (Muhly 1973:174–175).The coming of the Age of Iron, subsequent to all the developments discussed in this study, itself relied on extractive and smelting technologies developed during theBronze Age,together with the use of carburization, all of which are linked directly(albeit over the millennia) to the dramatic social and economic changes that ushered in the Industrial Revolution and the beginnings of the modern era.If it is indeed the case that “metals make the world go round” (Pare 2000b),nowhere can this slogan be better and more widely illustrated than in the prehistoric Bronze Age of the Mediterranean.

Archaeometallurgy in the Mediterranean: The Social Context of Mining, Technology, and Trade

Vasiliki Kassianidou and A.Bernard Knapp

Link

Anthropological Investigation of the S. Greece population’s composition in the Bronze Age

Here is a link to S. K. Manolis's 1991 dissertation which complements the previous one by G. Panagiaris, since it includes data from the Peloponnese and Crete. I might translate parts of it in the space below. The author seems to argue for an environmental cause of brachycephalization during the Bronze Age; personally I think that the more likely explanation is intrusion by mountain-folk from either the Pindos area or Anatolia, associated with metallurgy. In any case, I am hopeful that some of the Ancient Greek osteological material, some of which has been excavated many decades ago may still possess usable DNA that could be exploited in future studies that may overcome the limits of craniometry.

A physico-anthropological study of skeletal material from Neolithic age to Hellenistic times in Central Greece and surrounding region

I have located the text of George Panagiaris important 1993 doctoral thesis on Greek skeletal material. This may be one of the most comprehensive efforts to study the Ancient Greek population from a physical anthropological perspective (413 male and 354 female crania, using 65 biometric characters as well odontological traits).

Panagiaris' conclusions in English can be found in p.10 of the document. He confirms that the greater period of discontinuity in the material is observed during the Helladic period (=Bronze Age in Greek archaeology), where broad-headed incoming groups appear, side by side with the older Mediterranean population. He attributes this to the arrival of such people from the highlands Pindos range, although he sees the possibility of Anatolian influences as well, but has no comparative data. He cites the tendency for broader skulls in higher latitudes, although this general trend in H. sapiens probably does not explain the local trend within Caucasoids where the key difference is between mountaineers (where the Alpine, Dinaric, Armenoid, and Pamir-Ferghana types are well-represented) and lowland folk. Perhaps, if various ancient DNA projects manage to study some Greek material we may be able to ascertain the events that were taking place in Greece at that time.


Of course, the issue cannot be seen in isolation, because at this time we see an increase in brachycephalic types in Crete and Anatolia, the appearance of the intrusive brachycephalic Bell Beaker folk in Western Europe, and perhaps even the presence of the interfluvial type (Pamir-Ferghana type) in the eastern Saka. 

Personally, I see something important in these developments: why would broad-headed mountaineers make their appearance in the lowlands at this time in history? I am strongly leaning towards the idea that this has to do with metallurgical innovation during this time. According to Roberts et al. (2009), from which the figure on the left is taken:

Metallurgy in Eurasia originated in Southwest Asia due to the widespread adoption of, and experimentation in, pyrotechnology and the desire for new materials to serve as aesthetic visual displays of identity, whether of a social, cultural or ideological nature. This can be demonstrated through the early use of metal for jewellery and the use of ore-based pigments along with the continued use of stone, bone, and other materials for most tools. The subsequent appearance of metals throughout Eurasia is due to the acquisition of metal objects by individuals and communities re-inventing traditions of adornment, even in regions hundreds of kilometres from the nearest sources of native metals or ores. The movement of communities possessing metallurgical expertise to new ore sources and into supportive societies led to the gradual transmission of metallurgy across the Eurasian landmass. By the second millennium BC, metallurgy had spread across Eurasia, becoming firmly rooted in virtually all inhabitable areas (Sherratt 2006). The ability to smelt different ores, create different metals or increase metal production did not occur in a linear evolutionary fashion throughout Eurasia, but rather appeared sporadically over a vast area – a result of regional innovations and societal desires and demands. 

There is no evidence to suggest that metallurgy was independently invented in any part of Eurasia beyond Southwest Asia. The process of metallurgical transmission and innovation created a mosaic of (frequently diverse) metallurgical traditions distinguished by form, composition and production techniques. It is within this context that innovations such as the earliest working of gold in the Balkans or the sudden emergence of distinctive tin-bronze working in Southeast Asia should be seen. 

The richest ore deposits were found in mountain areas as Thornton (2009) makes clear:

Models for the development of metallurgy in Southwest Asia have for a long time been focussed on research carried out in the lowland regions of the Levant and Mesopotamia. These models do not take into account the different developmental trajectories witnessed in the resource-rich highlands of Anatolia, the Caucasus, and Iran. In this paper, the beginnings of the use and production of metals in Iran will be juxtaposed with a cursory overview of the lowland model (the ‘Levantine Paradigm’) in order to highlight these differences. By synthesizing data from a number of current research projects exploring the early metallurgy of the Iranian Plateau, this paper demonstrates how at least one of the highland regions of Southwest Asia was at the very forefront of technological innovation from the seventh through the second millennium BC.  

I had planned to write a separate post on the interplay between metallurgy and the rise in social complexity that led to the spread of (at least some branches of-) Indo-European and Semitic during time, but this is probably as good a place as any to summarize the argument:

The practice of metallurgy launched the first globalization: in order to produce high quality metal objects, one needed a variety of specialized workers: prospectors, miners, metalworkers. The necessary ores do not occur everywhere on the map, and production requires a complex logistic operation to manage resources and talent. One needed, in addition, to establish a network of traders and warriors to carry out and supervise the trade, since demand for metal objects was wide and not limited to the vicinity of their production.

Production and trade networks facilitated the flow of ideas, and necessitated the flow of peoples, both because expertise was non-local, and also because the producers wanted to supervise their profitable business. There is an advantage to being an early adopter of new technology; many of the shifts in power in world history depended on a technology differential (European guns in the New World, mounted archers on the Eurasian steppe, triremes in the Mediterranean, Macedonian long-spears vs. Persian light infantry being some examples).

The technology differential eventually dissipates as everyone gets access to the new inventions. This process may take several centuries, but in the meantime those monopolizing them enjoy a triple advantage:

1. There is demand for their product
2. They have the better weapons
3. They are part of broader communities that can muster resources against anyone who crosses them

It is no accident that the Bronze Age started with technological innovation and ended up in a series of military conflicts. What began as a transformation of Neolithic communities by monopolizing guilds of the bearers of the new technologies ended up with everyone having access to them, and of course they went to war.

Getting back to the topic of Panagiaris' dissertation, I might try my hand at translating some interesting portions. These will be posted as updates in the space below.

Clarifying the phylogeny of Y-chromosome haplogroup C3c

A short and to the point paper that addresses the issue of classification within Y-haplogroup C3c and refines our knowledge about the distribution of both C3c* and C3c1. I wish more researchers would publish such short technical papers that refine the classification of their Y-chromosome samples as more phylogenetic information becomes available.

From the paper:

In our study, the highest frequencies of subhaplogroup C3c1-(M77, M86) were observed in Tungusic-speaking people of North-Eastern Asia, such as Evens and Evenks, as well as in Turkic-speaking Altaian Kazakhs and Mongolic-speaking Kalmyks. These results are in agreement with previous observations based on separate or joint genotyping of M77 and M86 markers.3,9,12,16

C3c* haplotypes were detected in aboriginal populations of North- Eastern Asia—Koryaks (28.2%) and Evens (1.6%) from the Sea of Okhotsk coast (Magadan region) and West Evenks (2.4%) from Central Siberia (Evenki Autonomous District) (Table 1). Earlier, two Evenk individuals from southern part of Yakutia, one Yakut-speaking Evenk and one Yukaghir were found to belong to C3c*.2,3 Therefore, the geographic distribution of subhaplogroup C3c* is limited to the eastern part of Siberia.

The authors apply the evolutionary mutation rate -although they acknowledge that molecular dating is controversial- to obtain ages of 9.9 (C3c), 6.5 (C3c1), and 4.5 (C3c*). While I don't trust the ability of Y-STR-based molecular dating to provide reasonably accurate age estimates, I would not be surprised if C3c1 was somehow implicated in the deeper origins of the Altaic language family, at least in the "narrow-sense" (Mongolian-Tungusic-Turkic).

J Hum Genet. 2012 Jul 19. doi: 10.1038/jhg.2012.93. [Epub ahead of print]

On the Y-chromosome haplogroup C3c classification.

Malyarchuk BA, Derenko M, Denisova G.

Abstract As there are ambiguities in classification of the Y-chromosome haplogroup C3c, relatively frequent in populations of Northern Asia, we analyzed all three haplogroup-defining markers M48, M77 and M86 in C3-M217-individuals from Siberia, Eastern Asia and Eastern Europe. We have found that haplogroup C3c is characterized by the derived state at M48, whereas mutations at both M77 and M86 define subhaplogroup C3c1. The branch defined by M48 alone would belong to subhaplogroup C3c*, characteristic for some populations of Central and Eastern Siberia, such as Koryaks, Evens, Evenks and Yukaghirs. Subhaplogroup C3c* individuals could be considered as remnants of the Neolithic population of Siberia, based on the age of C3c*-short tandem repeat variation amounting to 4.5±2.4 thousand years.

Link

Admixture matters

Until recently, tree models dominated models of human demography. Under such models, populations split off from each other in a branching pattern. African populations, and especially African hunter-gatherers, which are the most divergent occupy the basal positions in the tree. The story has been repeated many times: Africans are more genetically diverse, Eurasians carry a subset of African genetic variation, a small subset of Africans left the continent and colonized the world after going through a severe bottleneck and so on.

It's a simple and attractive story, but one which is wholly dependent on ignoring admixture. There are two types of admixture that are pertinent: one is admixture between modern human groups. An example of this is Ethiopia. Many studies have presumed to identify a signal of Out-of-East Africa based on diminishing distance from East Africa. But it is completely unclear how this model fares when one takes into account that East Africans are a recently admixed population: their great genetic diversity may be due to the recent intermingling of two very divergent groups of people (Caucasoids and aboriginal East Africans).

Or, consider two Englishmen, one with a Nigerian and another with a Chinese grandparent. These two individuals might appear greatly diverged from each other genetically and phenotypically, but this is the aggregate of sharing 3/4 of quite recent common ancestry (from their English grandparents), and not sharing 1/4 each of highly divergent ancestry (from their Chinese and Nigerian ones).

The situation is more interesting when we realize that admixture can occur not only between modern human groups, but also between modern humans and archaic ones. Both archaic genomes published so far (Neandertal and Denisova) show differential affiliation to modern human groups, and indirect evidence suggests that some African groups also admixed with archaic species that once lived in Africa.

Of course, levels of archaic admixture inferred from these studies are usually small, but we must remember that a little archaic goes a long way. This is due to the fact that modern humans and archaic ones diverged from each other a long time ago. Their admixture, even in highly favorable (for modern humans) proportions introduces a substantial amount of new genetic variation. As a result, populations harboring archaic admixture appear more divergent from each other.

This point is made quite well in a new article:

If human populations do not all have the same level of archaic introgression, the current genetic structure of human populations might be partly shaped by differential admixture. Estimates of population sizes and divergence times between human populations should thus be affected by past admixture events. The divergence time between an admixed and a non-admixed population should be overestimated if admixture is not properly modelled. Similarly, the effective size of admixed populations should be overestimated as archaic lineages inflate genetic diversity. In Figure 2, we report a simulation study of this bias in a very simple case of population divergence without migration. The overestimations of divergence time and admixed population size are almost linearly increasing with admixture rate (Figure 2). For instance, a divergence time of 1,600 generations (40,000 y assuming a 25-y generation time) is perfectly recovered if none of the populations is admixed, but is overestimated by 100 generations (2,500 y) with 1% admixture in one population, and already by 350 generations (8,750 y) with 5% admixture. Even though our simulated scenario is unrealistically simple, it is likely that differential admixture should affect population genetic affinities under more complex models of population differentiation. The proper interpretation of human genetic affinities should thus probably be re-evaluated in the light of these results. In particular, the divergence between Africans and Oceanians (showing up to 5% archaic admixture [16]) could be more recent than previously reported (62–75 Kya [24]). It remains unclear whether the method used by Rasmussen et al. [24] to date this divergence is also sensitive to differential introgression, but, if that was the case, the colonization wave to Oceania thought to well predate that towards East Asia [24] could have occurred at roughly the same time once differential admixture had been taken into account.

This is an important point: the inferred early dispersal of Oceanians could in fact be the result of archaic admixture in both Africans and Oceanians. 


Lower levels of archaic admixture are sufficient to make two individuals or populations appear much more distant from each other. Archaic Homo populations may be as much as an order of magnitude more divergent to H. sapiens that particular H. sapiens groups are to each other.

But, admixture can also deflate divergence, if there is subsequent gene flow between the diverged populations. As an example, Near Eastern Arab populations: have both diverged from Europeans due to receiving African admixture, and also converged with them by the fact that Europeans have Neolithic Near Eastern admixture which renewed bonds between Europe and the Near East. It means little to speak of "when" Europeans and Near Eastern people diverged from each other: it's a balancing act of centrifugal and centripetal influences: if a Crusader lands on the Levant and marries a local woman, he diminishes apparent Europe-Near East genetic divergence; if a Somali does the same, he increases it. So, in the end, the apparent "divergence" between Europe and the Near East may have little to do with how much time has transpired since the colonization of a new region, and more to do with "who had sex with whom" in the intervening period.

In fact, the ability of admixture to "converge" populations is the basis of the multi-regional evolution theory, although that is usually posited in terms of gene flow. But, the basic idea is still the same: our relatively uniform human species may not be entirely the result of tree-like divergence of populations from an original African population, but rather of a confluence of streams of ancestry derived from Lower and Middle Paleolithic populations of Homo.

Admixture may not only lead us to overestimate divergence between populations: it might lead us to wrongly estimate the directionality of migration itself. 

Consider a future geneticist, working thousands of years after a collapse of civilization in the near future which led into a breakdown of long-distance travel. Such a scientist would perhaps conclude that the highest genetic diversity is to be found in North America, and conclude that North America colonized the rest of the world.

In some cases, it can well be argued that serial founder effects/bottlenecks restrict genetic variation/effective size. For example, the colonization of the Americas in three waves created a population that is clearly a subset of the East Eurasian parental population. But, notice that researchers trying to understand it had to carefully disentangle the various migration waves and cleanse their data from recent European admixture. The directionality of migration can be recovered through a diligent treatment of the evidence.

But, let's forget about the nested-subset analogy: the fact that a population X may appear to be a subset of another Y does not indicate that Y founded X any more than the fact that the genetic variation of any single European country is a subset of the cosmopolitan populations of the Americas will indicate an America-to-Europe migration to the future geneticist. Sometimes, X is a subset of Y because Y has a superset of variation formed by union with a divergent other population.

Sub-Saharan Africa is one example of a terra incognita for the historian. In the absence of written sources, science is mostly clueless as to what was going on there for thousands of years after the invention of writing in Mesopotamia. In some areas, due to the moist climate/abundant vegetation/political instability even archaeological evidence is lacking. What this means is that we are in the dark about what admixtures were going in the Dark Continent. Thankfully, people are working on it.

My own position is that while an origin of anatomically modern humans in Africa still seems to be correct, the pattern of divergence and reduced effective size of Eurasians from Africans is not wholly due to a small group of them leaving the continent at some Middle Pleistocene epoch.

How much of the African divergence and higher African effective population size is due to a Biblical-level bottlenecks coinciding with Out-of-Africa? As readers of the blog know, I don't buy the recent Out-of-Africa model, especially in its "endangered but crafty tribe of pioneers following the coast 60,000 years ago" variety. Archaic admixtures in Eurasia and Africa inflate divergence times; back-migration may deflate them. It's yet another balancing act.

Hopefully statisticians, with a little help from archaeology and palaeoanthropology can untangle the palimpsest of events and present us with a believable story about our own origins. It's time to give up trees and embrace networks!


PLoS Genet 8(7): e1002837. doi:10.1371/journal.pgen.1002837

Genomic Data Reveal a Complex Making of Humans

Isabel Alves et al.

In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.

Link

Redating of the Early Upper Paleolithic site of Riparo Mochi (Italy)

There are two possibilities on how the early Aurignacian entered Europe. According to one hypothesis, its bearers followed the Danube, which formed a natural corridor into the heartland of the continent which was, at the time, thickly forested. A different hypothesis is that the early Aurignacian entered Europe via the Mediterranean. Distinguishing between the two hypotheses depends on obtaining reliable chronological estimates for the Mediterranean and Central European Aurignacian

A recent dating of a site in the Swabian Jura suggested that the Aurignacian was earlier attested in Central Europe. But, another paper in the Journal of Human Evolution examines meticulously the sequence in the Moch rockshelter and finds that it is just as early.

Comparisons with dates for other Upper Palaeolithic contexts outside Italy suggest that the date of the Protoaurignacian of Mochi compares closely. In Fig. 9a the start boundaries for the earliest Aurignacian evidence at the sites of Geissenklösterle (Germany), Abri Pataud and Isturitz (France) are compared to the start boundary for unit G in Mochi. The first two sites were dated recently in Oxford with reliable methodologies (Higham et al., 2011; Higham et al., in press) while for Isturitz only a small number of dates exist for the earliest Upper Palaeolithic (Szmidt et al., 2010). This comparison reveals that the lowermost Aurignacian levels at Geissenklosterle (AHIII) and Isturitz (C4d) date to the same period as Mochi G, at around 42.7-41.5 ka cal BP (68.2%). The earliest Aurignacian of Abri Pataud dates slightly later to around 41e40 ka cal BP (68.2%), but the assemblage there has always been considered more evolved, so this is not surprising. No Mousterian dates are included in any of these calculations, therefore the start boundaries in the Bayesian models are not well constrained at their earliest end. What is interesting is that there appears to be a close similarity between the dates for the Protoaurignacian and Early Aurignacian sites in Germany on the Danube and on the Mediterranean coast. This might suggest a rapid dispersal of both variants of the Aurignacian across Europe at c. 44-42 ka cal BP.

It does appear that the Aurignacian was a continent-wide punctuational event in Europe which occurred in the middle to late 40 thousands ka cal BP.

Either there were two streams into Europe (Danubian and Mediterranean), or one stream that quickly inundated much of the continent. Given that the argument for the Danubian Corridor is partly related to the ease of access it provided, it is difficult to imagine how the people who followed it would quickly stray far from it all the way to Italy. Overall, it does appear that there were multiple streams into Europe, and perhaps new research in the Balkans, Eastern Europe, and West Asia, may help us trace the earlier predecssor of these streams before they followed their separate ways into Europe.

Journal of Human Evolution DOI:10.1016/j.jhevol.2011.11.009

A new chronostratigraphic framework for the Upper Palaeolithic of Riparo Mochi (Italy)


Katerina Douka et al.


The rockshelter of Mochi, on the Ligurian coast of Italy, is often used as a reference point in the formation of hypotheses concerning the arrival of the Aurigancian in Mediterranean Europe. Yet, the site is poorly known. Here, we describe the stratigraphic sequence based on new field observations and present 15 radiocarbon determinations from the Middle Palaeolithic (late Mousterian) and Early Upper Palaeolithic (Aurignacian and Gravettian) levels. The majority of dates were produced on humanly modified material, specifically marine shell beads, which comprise some of the oldest directly-dated personal ornaments in Europe. The radiocarbon results are incorporated into a Bayesian statistical model to build a new chronological framework for this key Palaeolithic site. A tentative correlation of the stratigraphy to palaeoclimatic records is also attempted.

Link

Huge study on Y-chromosome variation in Iran (Grugni et al. 2012)

This is the equivalent of a box of candy for anyone interested in Eurasian (pre-)history. I will have digest all the goodies within, and post any of my comments as updates to this post.

UPDATE I: Here is the table of haplogroup frequencies for easy reference:

One of the most interesting finds is the presence of a few IJ-M429* chromosomes  in the sample. Haplogroup IJ encompasses the major European I subclade, and the major West Asian J subclade. The discovery of IJ* chromosomes is consistent with the origin of this haplogroup in West Asia; it is widely believed that haplogroup I represents a pre-Neolithic lineage in Europe, although at present there are no Y chromosome-tested pre-Neolithic remains.

There is also a wide assortment of Q and R in Iran. While some of these may be intrusive (e.g., the 42.6% of Q1a2 in Turkmen, likely a legacy of their Central Asian origins), the overall picture appears consistent with a deep presence of these lineages in Iran. This is especially true for haplogroup R where pretty much every paragroup and derived group is present, excepting those likely to have originated recently elsewhere.

UPDATE II: From the paper:

Although accounting only for 25% of the total variance, the first two components (Figure 3) separate populations according to their geographic and ethnic origin and define five main clusters: East-African, North-African and Near Eastern Arab, European, Near Eastern and South Asian. The 1stPC clearly distinguishes the East African groups (showing a high frequency of haplogroup E) from all the others which distribute longitudinally along the axis with a wide overlapping between European and Arab peoples and between Near Eastern and South Asian groups. The 2ndPC separates the North-African and Near Eastern Arabs (characterized by the highest frequency of haplogroup J1) from Europeans (characterized by haplogroups I, R1a and R1b) and the Near Easterners from the South Asians (due to the distribution of haplogroups G, R2 and L). Iranian groups do not cluster all together, occupying intermediate positions among Arab, Near Eastern and Asian clusters. In this scenario, it is worth of noticing the position of three Iranian groups: (i) Khuzestan Arabs (KHU-Ar) who, despite their Arabic origin, are close to the Iranian samples; (ii) Armenians from Tehran (THE-Ar), whose position, in the upper part of the Iranian distribution, indicates a close affinity with the Near Eastern cluster, while their position near Turkey and Caucasus groups, due to the high frequency R1b-M269 and other European markers (eg: I-M170), is in agreement with their Armenia origin; (iii) Sistan Baluchestan (SB-Ba) that clusters with its neighbouring Pakistan.

UPDATE III: There are lots of little details in the haplogroup distribution that make historical sense. For example, C3 exists in Assyrians from Azarbaijan, and both C*, C3, and O exists in Zoroastrians from Yazd. It is often forgotten that before the spread of Islam, and quite time thereafter, Inner Asia was teeming with Zoroastrians and Nestorian Christians. It seems quite likely that these outliers represent a legacy of these communities.

UPDATE IV: I have a feeling that Razib will take exception with this statement: "Ancient Persian people were firstly characterized by the Zoroastrianism. After the Islamization, Shi'a became the main doctrine of all Iranian people."


UPDATE V: This confirms my observation from the recent studies in Afghanistan, that there is an inverse relationship of J2a and R1a in Iranian-speaking groups, with an excess of the latter among the eastern Iranians, and of the former among the Persians. From the paper:

Among the different J2a haplogroups, J2a-M530 [46] is the most informative as for ancient dispersal events from the Iranian region. This lineage probably originated in Iran where it displays its highest frequency and variance in Yazd and Mazandaran (Figure 2). Taking into account its microsatellite variation and age estimates along its distribution area (Tables S3 and S7), it is likely that its diffusion could have been triggered by the Euroasiatic climatic amelioration after the Last Glacial Maximum and later increased by agriculture spread from Turkey and Caucasus towards southern Europe. The high variance observed in the Italian Peninsula is probably the result of stratifications of subsequent migrations and/or of the presence of sub-lineages not yet identified. Of interest in the M530 network (Figures 2 and S3) is the presence of a lateral branch that is characterized by a DYS391 repeat number equal to 9. Differently from previous observations [46], this branch is not restricted to Anatolian Greek samples being shared with different eastern Mediterranean coastal populations. The M530 diffusion pattern seems to be also shared by the paragroups J2a-M410* and J2a-PAGE55*. In addition, the variance distribution of the rare R1b-M269* Y chromosomes, displaying decreasing values from Iran, Anatolia and the western Black Sea coastal region, is also suggestive of a westward diffusion from the Iranian plateau, although more complex scenarios can be still envisioned because of its non-star like structure.

Of course, the idea that the diffusion of J2a related lineages ties in with early agricultural expansions has been with us for a long time, but it is time to abandon it. First of all, as we have seen, J2a diminishes greatly as we head towards South Asia; it certainly doesn't look like the lineage of the multitude of agricultural settlements that sprang up along the southeastern vector soon after the invention of agriculture. Second, it is lacking so far in all ancient Y chromosome data from Europe down to 5,000 years ago. It seems much more probably that J2 related lineages spread from the highlands of West Asia much later. 


The "age estimates" are the result of using the inappropriate "evolutionary mutation rate", and become even older because of the inclusion of the DYS388 marker that is very stable in many haplogroups but very mutable within haplogroup J. On the left you can see frequency, Y-STR variance, and haplotype network structures for various J-related groups.


It is unfortunate that there is no progress in the phylogeographic assessment of R1a in this paper. There have been substantial discoveries of SNPs within this haplogroup as a result of commercial testing; however there is clearly an ascertainment bias in the newer discoveries, as almost all these SNPs have been detected in Europeans. The new paper confirms the high levels of Y-STR variance in India, Pakistan, and Iran. Together with the cornucopia of related paragroups in Iran, there is little doubt that this haplogroup originated in the general area of Central/South Asia.


Personally, as I have stated before, I would relate this R1a with Neolithic peoples living east of the Caspian, in contrast to the R1b bearers who lived west and south of it. These two populations came under the influence of the Indo-Europeans and spread in different directions. The Indo-Iranians were then initially the mixed descendants of the Indo-Europeans and the R1a old agricultural population, and were formed in the territory of the Bactria-Margiana Archaeological Complex. 


This also explains the contrast between Iranian and Armenian groups: the latter mostly lack the R1a lineage, contrasting with all Iranian groups (even their Kurdish neighbors) who possess it. Conversely, Iranian groups, and especially eastern Iranians and Indo-Ayrans lack the R1b lineage. This is due to the fact that neither R1a nor R1b were originally part of the Indo-European community, but their geographical position was such that they came under the influence of the Indo-Europeans when the latter began their expansion.


UPDATE VI: I have created my own dendrogram using the Y-haplogroup frequencies and the hclust package of R (default parameters):

From top to bottom, one can identify some clusters:

• Eastern Europe, further broken down into Balkans and Slavic+Hungary
• West Asian/Caucasus
• Iranian Proper
• Arab

These correspond largely to the clusters identified by the authors, with India and the Turkmen sample emerging as the clear outliers. I omitted the Ethiopian samples, since E-M78 was not resolved phylogenetically, causing the Ethiopians to group with the likely E-V13 from the Balkans.

UPDATE VII: I have also run MCLUST over the haplogroup frequency data over the MDS representation of the distance matrix. The maximum number of 10 clusters occurred with 5 MDS dimensions retained. Population assignments in the 10 clusters can be found in the table below:

Iran/Azerbaijan_Gharbi+Tehran_(Assyrian)	1
Iran/Lorestan_(Lur)	1
Iran/Tehran_(Armenian)	1
Iran/Azerbaijan_Gharbi_(Azeri)	2
Iran/Hormozgan_(Bandari+Afro-Iranian)	2
Iran/Hormozgan/Qeshmi	2
Iran/Khorasan_(Persian)	2
Iran/Kurdistan_(Kurd)	2
Iran/Sistan_Baluchestan_(Baluch)	2
Pakistan	2
Iran/Fars+Isfahan_(Persian)	3
Iran/Gilan_(Gilak)	3
Iran/Yazd+Tehran_(Zoroastrian)	3
Turkey/Central	3
Turkey/East	3
Turkey/West_	3
Iran/Golestan_(Turkmen)	4
India	4
Iran/Khuzestan_(Arab)	5
Egypt_(Arab)	5
Iraq/Baghdad	5
Oman	5
Saudi_Arabia	5
Tunisia	5
United_Arab_Emirates	5
Iran/Mazandaran_(Mazandarani)	6
Iran/Yazd_(Persian)	6
Balkarian	6
Georgia	6
Albania	7
Greece	7
Bosnia	8
Croatia	8
Slovenia	8
Czech_Republic	9
Hungary	9
Poland	9
Ukraine	9
Iraq_(Marsh_Arab)	10
Qatar	10
Yemen	10

We can ignore cluster #4 which consists of the two outliers (India + Turkmen). The rest of the clusters seem relatively coherent. Notice, for example, the Arabian cluster #10, Balkan cluster #8, Eastern European cluster #9, Greek-Albanian cluster #7, Mixed Arab cluster #5.

PLoS ONE 7(7): e41252. doi:10.1371/journal.pone.0041252

Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians

Viola Grugni et al.


Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.

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