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Likely an individual with derived allele on KITL locus (Credit: David Shankbone)

An individual polymorphic on the KITL locus? (Credit: David Shankbone)

Pigmentation is one of the few complex traits in the post-genomic era which has been amenable to nearly total characterization. The reason for this is clear in hindsight. As far back as the 1950s (see The Genetics of Human Populations) there were inferences made using human pedigrees which suggested that normal human variation on this trait was controlled by fewer than ten genes of large effect. In other words, it was a polygenic character, but not highly so. This means that the alleles which control the variation are going to have reasonably large response, and be well within the power of statistical genetic techniques to capture their effect.

I should be careful about being flip on this issue. As recently as the mid aughts (see Mutants) the details of this trait were not entirely understood. Today the nature of inheritance in various populations is well understood, and a substantial proportion of the evolutionary history is also known to a reasonable clarity as far as these things go. The 50,000 foot perspective is this: we lost our fur millions of years ago, and developed dark skin, and many of us lost our pigmentation after we left Africa ~50,000 years ago (in fact, it seems likely that hominins in the northern latitudes were always diverse in their pigmentation)

A new paper in Cell sheds some further light on the fine-grained details which might be the outcome of this process. Being a Cell paper there is a lot of neat molecular technique to elucidate the mechanistic pathways. But I will gloss over that, because it is neither my forte nor my focus. A summary of the paper is that it shows that p53, a relatively well known tumor suppressor gene, seems to have an interaction with a response element (the gene product binds in many regions, it is a transcription factor) around the KITLG locus. This locus is well known in part because it has been implicated in pigment variation in human and fish. So KITLG is one of the generalized pigmentation pathways which spans metazoans. There are derived variants in both Europeans and East Asians which are correlated with lighter skin, though there is polymorphism in both cases (it has not swept to fixation).

The wages of adaptation? (Credit: Hoggarazzi Photography)

The wages of adaptation? (Credit: Hoggarazzi Photography)

But this is a Cell paper, so there has to be a more concrete and practical angle than just evolution. And there is. It turns out that a single nucleotide polymorphism mutation in the p53 response element results in a tendency toward upregulation of KITLG and male germ line proliferation. The latter matters when it comes to tumor genesis, and in particular testicular cancer. This form of cancer is one where there doesn’t seem to be a somatic cell mutation of p53 itself. Additionally, the authors observe that testicular cancer manifests at a 4-5 fold greater rate in people of European descent than African Americans. And, presumably the upregulation of KITLG is somehow related to increased melanin production. The authors posit that because of lighter skin in Europeans due to selection at other loci there has been a balancing effect at KITLG (increased tanning response). There is evidence of selection at this locus (a long haplotype and increased homozygosity), so this is not an unreasonable conjecture, though the high frequency of loss of function alleles suggests that the model is likely complex.

I don’t know if this particular story is correct in its details (though I am intrigued that variation in KITLG is associated with cancer in other organisms). But it illustrates one of the possible consequences of rapid evolutionary change due to human migration out of Africa: deleterious side effects because of pleiotropy. In other words, as you tinker with the genomic architecture of a population you are going to have to accept tradeoffs as you are optimizing one aspect of function. Genes don’t have just one consequence, but are embedded in myriad pathways. Over time evolutionary theory predicts a slow re-balancing, as modifier genes arise to mask the deleterious side effects. But until then, we will bear the burdens of adaptation as best as we can.

Citation: Zeron-Medina, Jorge, et al. “A Polymorphic p53 Response Element in KIT Ligand Influences Cancer Risk and Has Undergone Natural Selection.” Cell 155.2 (2013): 410-422.

(Republished from Discover/GNXP by permission of author or representative)
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Credit: Aviok

“Think not that I am come to send peace on earth: I came not to send peace, but a sword.” -Matthew 10:34

“There were giants in the earth in those days…when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.” -Genesis 6:4

Seven years ago I wrote a short post, Why patriarchy?, which attempted to present a concise explanation for the ubiquity of what we might term patriarchy in complex societies (i.e., not “small-scale societies”). Broadly speaking my conjecture is that social and political dominance of small groups of males (proportionally) over the past several thousand years is an example of “evoked culture”. The higher population densities in agricultural societies produced a relative surfeit of accessible marginal surplus, which could be given over to supporting non-peasant classes who specialized in trade, religion, and war, all of which were connected. This new economic and cultural context served to trigger a reorganization the typical distribution of power relations of human societies because of the responses of the basic cognitive architecture of our species inherited from Paleolithic humans. Agon, or intra-specific competition, has always been part of the game on human socialization. The scaling up and channeling of this instinct in bands of males totally transformed human societies (another dynamic is elaboration of cooperative structures, though this often manifests as agonistic competition between coalitions of humans).

To get a sense of what I mean when I say transforming, consider this section of an article in The Wall Street Journal which profiles the wife of one of the 2012 New Delhi gang rape:

Some people blame the December gang rape and similar attacks in part on a collision of traditional social expectations—commonplace in rural areas—and the modernity of India’s cities, where rural migrant workers encounter the values of urbanites living by a different set of rules. During the brutal Delhi assault, for instance, the attackers accosted the woman and the young man she was with, asking why they were out together in the evening, the young man told the court.

Speaking about the events of that night, Ms. Devi says she doesn’t understand how a woman could be out for the evening with a man who wasn’t her husband.

The normalcy of this sort of ‘mate guarding’ is taken for granted in many ‘traditional’ societies. You see it reflected in the 1995 film First Knight, where King Arthur tries Lancelot and Guinevere for treason based on a kiss (dishonor to the realm). I won’t go into excessive psychoanalysis, but end by saying that the emergence of radical inequality and stratification with complex societies transformed instincts shaped in small-scale bands where petty conflicts were no doubt the norm. To my knowledge the literature from small-scale societies tends to imply a relatively more relaxed, even modern, attitude toward sexuality than one can see in world of the Eurasian Ecumene.

At this point you might be curious as to the point of reviewing this conjecture. Perhaps I will bring to the fore historical and archaeological evidence which might support this model? No. Rather, I contend that the evidence of this radical reshaping of human power structures, which led to the emergence of patriarchy as we understand it, is reflected in the phlyogenetic history of our species. Two papers illustrate the differing patterns which one sees in the maternal lineage, mtDNA, and the paternal lineage, Y chromosomes.

First, Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers:

Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-recombining region (NRY), discovered >4,000 new SNPs, and identified many new clades. The relative divergence dates can be estimated much more precisely using molecular clock. We found that all the Paleolithic divergences were binary; however, three strong star-like Neolithic expansions at ~6 kya (thousand years ago) (assuming a constant substitution rate of 1e-9/bp/year) indicates that ~40% of modern Chinese are patrilineal descendants of only three super-grandfathers at that time. This observation suggests that the main patrilineal expansion in China occurred in the Neolithic Era and might be related to the development of agriculture.

Second, Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines:

Cambodia harbours a variety of aboriginal (and presumably ancient) populations that have largely been ignored in studies of genetic diversity. Here we investigate the matrilineal gene pool of 1,054 Cambodians from 14 geographic populations. Using mitochondrial whole-genome sequencing, we identify eight new mitochondrial DNA haplogroups, all of which are either newly defined basal haplogroups or basal sub-branches. Most of the new basal haplogroups have very old coalescence ages, ranging from ~55,000 to ~68,000 years, suggesting that present-day Cambodian aborigines still carry ancient genetic polymorphisms in their maternal lineages, and most of the common Cambodian haplogroups probably originated locally before expanding to the surrounding areas during prehistory. Moreover, we observe a relatively close relationship between Cambodians and populations from the Indian subcontinent, supporting the earliest costal route of migration of modern humans from Africa into mainland Southeast Asia by way of the Indian subcontinent some 60,000 years ago.

The scientific methods here are straightforward, or at least tried and tested. The main gains here are in terms of raw numbers and sequencing. Basically this is the extension of phylogeographic work which goes back 20 years, but on steroids. As such one should be cautious. The old phylogeography literature has turned out to be wrong on many of the details. But that’s OK, there’s still gold there, you just have to look.

The broad scale implication of the paper on Chinese Y chromosomal diversity is obvious. Like the Genghis Khan modal haplotype these are lineages which exhibit a ‘star-like phylogeny.’ They explode out of a common ancestor in short order, with few mutational steps. This explosion is simply a reflection of very rapid population growth. The skewed distribution of Y lineages here (i.e., three lineages representing nearly half the population) indicates to me a pattern where elite males tend to be much more fit in reproductive terms than the average male. Rapid population growth may have been correlated with a high rate of extinction of Y lineages due to “elite turnover“.


Citation: Zhang, Xiaoming, et al. “Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines.” Nature Communications 4 (2013).

The second paper looks at mtDNA, the maternal line. There are some specific results which are interesting. In line with Joe Pickrell’s TreeMix results it does look like Cambodians and Indians share deep ancestry dating to the Paleolithic. The PCA to the left shows the relationships of populations in relation to their haplogroups, and one clear finding is that Cambodians tend to cluster with Indians, and not Northeast Asians. This result is not unsurprising. As I’ve noted before on mtDNA lineages South Asians are closer to East Eurasians than they are to West Eurasians. The result for the Y chromosomes is inverted, while autosomes are somewhere in the middle. In addition the results above show that South Chinese Han mtDNA tend to occupy the same part of the plot as the Dai, who are related to the Thai people of Southeast Asia. In contrast the few North Chinese Han tend to cluster with Tibetans and Altaics. Could Sinicization have been male mediated? There’s been circumstantial ethnographic evidence which points to this (e.g., some Cantonese marriage practices may reflect assimilation of Dai women).

The big picture result to me is that it illustrates the discordance between migration patterns of males and females over the past 10,000 years due to the rise of agriculture and its offspring, patriarchy. I hold that there was no hunter-gatherer Genghis Khan. Such a reproductively prolific male, worthy of an elephant seal, is only feasible with the cultural and technological accoutrements of civilization. ~20,000 years ago Temujin may have had to be satisfied with being the big man in a small clan. Thanks to various ideological and military advancements by the year 1200 AD you saw the rise to power of a man who could realistically assert that he was a ‘world conqueror.’


Credit: Brocken Inaglory

Of course I do not believe that the world before agriculture was static. On the contrary the Chinese Y chromosomal paper reports an inferred pattern of lineage extinction which is regular and consistent. But civilization escalated the magnitude of genocide, and in particular androcide of the losers in the games of power. The relative continuity of mtDNA across vast swaths of southern Eurasia is a testament to the fact that the lineages of the ‘first women’ still persists down among the settled agricultural peoples, whose genomes have been reshaped by untold sequences of conquests and assimilations. While female mediated gene flow can be imagined to be constant, continuous, and localized, I believe that male mediated gene flow has a more punctuated pattern. It explodes due to cultural and social innovations, such as the horse or Islam, and long standing Y chromosomal variation which has emerged since the last wave of conquerors is wiped away in a single fell swoop. Obviously this has an effect on the total genome, and I suspect that in some cases repeated male mediated expansions have resulted in striking discordances between the autosomal and mtDNA lineages. You see this in Argentina, where Native American mtDNA seems to persist to a higher degree than autosomal ancestry because of male skew of European migration. And it looks to be the case in Cambodia, where non-North East Asian autosomal ancestry seems to be present a lower fraction than the equivalent mtDNA.

With the rise of ubiquitous genomic typing and sequencing the geographical coverage will be fine grained enough the broad patterns, and specific details, will become clear. Then we will finally be able to understand if the societies fueled by grain truly ushered in the age of the domination of the many by the few. How easily does a scythe become a sword?

(Republished from Discover/GNXP by permission of author or representative)
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Dienekes has a post up highlighting a preprint out of Pontus Skoglund’s group. It is titled Ancient genomes mirror mode of subsistence rather than geography in prehistoric Europe. It doesn’t seem to be online (fingers crossed that it shows up linked at Haldane’s Sieve soon). In any case I am not surprised by the broad outlines of the thesis. And, it is not as if Skoglund’s group is the only one working in this area, I have suspicions that others are finding something very similar. These results out of Europe are probably reflective of the fact that much of the model in Peter Bellwood’s First Farmers is generally correct, the emergence of an agriculture revolution in a few select world societies produced a cultural and demographic revolution.

But one can take things too far, and I think Bellwood did. The results above, and elsewhere, also confirm that there was not total demographic replacement. In many regions the agriculturalists absorbed the hunter-gatherers. Using light coverage of whole genomes Skoglund’s group inferred that the farmers who arrived in prehistoric Europe from the Middle East seem to have contributed most of the ancestry of Southern Europeans, and also match nearly perfectly the genetic profiles of farming populations in Scandinavia. In contrast, ancient hunter-gatherers in Scandinavia and prehistoric Spain resemble contemporary Baltic groups (e.g., Lithuanians, Finns, and Scanadinavians). Finally, they conclude that modern Scandinavians are slightly more close to ancient hunter-gatherers than the farmers. This implies substantial farmer admixture in demographic terms. The group notes that previous inferences of Middle Eastern admixture were compromised by the fact that modern groups often exhibit African admixture. When you look only at the non-African portion, they are a much better proxy. One reason I am curious about the preprint in full is that I believe that even removing African admixture, one might be biased by selection of ‘reference’ populations. It seems likely that there were major eruptions from Arabia in antiquity and the medieval period (inferred by comparing religious isolates such as Arab Christians with their Muslim neighbors).

Setting aside that a two-way admixture seems unlikely to be the whole story*, it does offer up a way to explore an interesting question: on what sort of genes do hunter-gatherers and farmers differ? Specifically I’m wondering about utilizing admixture mapping. In Scandinavian populations regions of the genome where there are adaptations for farming are localized should be enriched for farmer ancestry, and vice versa for hunter-gathering. In the case of Northern Europeans farmers moved up latitudinal clines, and adapted to local conditions only halting. This explains in part that it seems Iberia and parts of Western Europe have more farmer ancestry than regions of Northeast Europe which are closer to the original zone of expansion as the crow flies. Not only did the hunter-gatherers have some cultural traits which conferred benefits in the deep north, but likely there were particular adaptations in these climes which aided their survival.

I understand that admixture mapping for populations which have mixed (and frankly were not that genetically different in the first place) may be difficult. But linkage disequilibrium based methods have been pushed much further back than I could have imagined, and it has been done with South Asians in regards to “Ancestral Northern Indian” vs. “Ancestral South Indian” ancestry and genetic functionality (specifically disease risk alleles).

* In addition, I am more skeptical of a simple demic diffusion model than I was in the past. I think there may have been multiple demographic pulses, followed by equilibration phases.

(Republished from Discover/GNXP by permission of author or representative)
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Credit: PartnerHund

It’s an exciting time for those interested in the evolutionary genomics of the dog. In 2010 a big SNP-array paper came out, Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Today we’re going whole genome, which is important because many of the SNP-arrays are ascertained on domestic dogs (i.e., they are designed to pick up dog variation, and so may distort our perception of the variation in wolves). Recently I talked about an analysis of the evolutionary genomics of the dog, The genomics of selection in dogs and the parallel evolution between dogs and humans. The main interesting result of that group was to push the divergence of the dog and wolf lineages further back in time, ~30,000 years, in line with some archaeological and mtDNA finds. I did not find their arguments for the origin of the dog in East Asian convincing. Now a new preprint on arXiv, Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs, pushes this even further.

First, after reading the paper I recommend the comments at Haldane’s Sieve, where the authors engage in some back and forth. Second, one of the authors put the supplementary information on a Dropbox, so you can get that too. I highly recommend this in particular, because it has detailed methods, code, and also concise but useful explanation of concepts such as D-statistics. Overall the paper breaks down into two broad themes, the phylogenetics and analysis of adaptation and selection. There was many X coverage of an Israeli, Croatian, and Chinese wolf, and a Basenji, Boxer, and Dingo. For the primary analysis the sample sizes were N = 1, but that is not a major issue as they had extremely accurate and precise estimates as to the polymorphism across these individuals because of the repeated coerage.

A major takeaway in terms of demographics for this paper is that it’s complicated. The authors inferred that domestic dogs went through a population bottleneck in the past on the order of one to two magnitudes. Second, wolves also went through a population bottleneck, albeit milder. On the first read through I was surprised by the second finding, but after talking to a canine geneticist I was told that this wolf bottleneck had long been known. The genomics confirmed prior expectations rather than smoking out novel inferences.

Perhaps a more surprising finding is that the ancestor of dogs, and yes, there was one ancestral population, not many, derives from an extinct wolf lineage. Their inference was derived from the fact that the three wolves, sampled from putative regions of dog domestication, all exhibit equal genetic distance from the dogs. Previous work had suggested that dogs may have derived from Near Eastern wolves, while other researchers argued for an East Asian origin. The results here support the proposition that these suggestions are misinterpreting genuine gene flow between local populations of wolves and dogs. The authors detected gene flow between West Eurasian wolves and the western dogs (Basenji and Boxer) and East Eurasian wolves and eastern dogs (the Dingo).

On a minor note, these results also confirm a pre-agricultural origin for the dog, with a divergence of ~11-16 thousand years B.P. across the 95% confidence interval. This is at some discrepancy with the Chinese group, but this may just be an artifact of a different mutation rate parameter. The take home either way is that dogs pre-date agriculture.

But that doesn’t mean agriculture is irrelevant. As far as the adaptation goes there’s a lot here, and I’m not sure that this paper has anything revolutionary in that dimension. First, they confirm that just as in humans there is variation among canids in terms of copy number in the amylase gene conditional on lifestyle. Dingos and Alaskan huskies have very few copies, while ancient West Asian dogs have many. Also, the authors find normal variation in wolves for this trait, implying that amylase polymorphism is part of standing genetic variations.

I will leave it to you to survey the veritable alphabet soup of genes which have been buffeted by natural selection by evolutionary process when it comes to dogs. I’m more curious about variation within dog at this point, as there should be heritable variation there too.

Cite: arXiv:1305.7390v2 [q-bio.GN]

(Republished from Discover/GNXP by permission of author or representative)
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German woman, product of Mid-Neolithic?
Source: Siebbi

Yesterday I pointed to a paper which was interesting enough, but didn’t pass the smell test in relation to other evidence we have (at least in my opinion!). A primary concern was the fact that uniparental (male and female lineages) show a peculiar distribution of variation in comparison to autosomal genetic variation (i.e., the vast majority of the genome) in the case of Europe (genome-wide analysis suggest more of Europe’s variation is partitioned north-south, but Y and mtDNA results often imply an east-west split). But a secondary concern I had was that I felt the models were a bit too stylized. In particular following Cavalli-Sforza and Ammerman the authors concluded that demic diffusion better fits their results of genetic variation in Europe (as opposed to continuity of Paleolithic hunter-gatherers). This is likely correct, but these are not the only two models.

A paper out in Nature Communications, using analysis of the phylogenetics of whole ancient mitchondrial genomes, outlines my primary concern when it comes to the models being tested, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans:

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

In other words, the mitochondrial genomic landscape of Europeans not only exhibits discontinuity with Paleolithic populations (though ~10% of Europeans, including my father-in-law, carry the U5 mtDNA haplogroup, which does seem to date to the Ice Age), but also with the “First Farmers.” In the case of this paper the focus is on Central Europe and Germany, and haplogroup H, which is modal across Europe (my wife and daughter are H1). That’s because they’ve already done work on this region and these mtDNA genotypes (see: Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities).

Probably the most arresting figure is the panel to the left. Here you have the authors perform a Procrustes analysis where they compared genetic variation of populations to geographic variation. For Europe what is striking (but unsurprising) is the correspondence between the two dimensions. What is noteworthy are the exceptions. The LBK, Germany’s first farming society (ergo, by definition early Neolithic), and the BBC, a late Neolithic culture with putative origins in Spain (this is disputed) do not align with Central Europe. Rather, LBK is shifted toward the Near East, and BBC toward Spain. The former result recapitulates what they discovered earlier. But, The “Middle Neolithic” samples are overlain upon Central Europe! This is why the authors argue that there was a disruption between the LBK and Middle Neolithic cultures (Rossen [4625–4250 BC], Schoningen [4100–3950 BC], Baalberge [3950–3400 BC] and Salzmunde [3400–3025 BC]).

Of course that’s not the end of the story. BBC arrived in the late Neolithic, presumably from Southwest Europe, and also made contributions. The mitochondrial genomic landscape of Central Europe did not freeze in the Middle Neolithic, but, it can be argued that this was a major “phase transition,” just as the shift between the Paleolithic and Neolithic was a major disruption. This is a radical change from the orthodoxy of the early 2000s. Then it was common to assert that the extant haplogroups in the Old World achieved their current distributions between the Last Glacial Maximum and the expansion in the wake of the Holocene warming. These data, along with many other points of evidence imply that in fact contemporary genomic variation is more a function of dynamics particular to the Holocene, the last 10,000 years, rather than the Ice Age.

Going back to the title of the post my contention here is that a stylized demic diffusion scneario with a wave-of-advance as one population expands into another does not model what has occurred in Europe over the past ~10,000 years. Before 2010 the argument was between those who argued that the diffusion was modest in its genetic impact, and those who argued that it wasn’t modest. But ultimately they were arguing over the margins. These results imply that diffusionary processes are not sufficient to characterize the nature of demographic turnover. Rather, there were repeated eruptions, replacements, and admixtures. It is cliche to refer to phyologeographic and archaeogenetic excavations as pealing back a palimpsest, but this actually gets to the reality that the elements of the object under study are more discrete than one might assume.

Let us posit for example an imaginary history which might explain these data.

1 – The “First Farmers” (LBK) establish nucleated settlements isolated from the hunter-gatherers, who recede and are marginalized

2 – A later culture of “Second Farmers” organized around military principles overturns the ascendancy of the “First Farmers.” Additionally, this second wave is a hybrid population, which emerged out of the synthesis of the nucleated first wave and the hunter-gatherer substrate.

3 – Finally, a subsequent series of prehistoric populations interject themselves onto the historical scene, though only inflecting the genomic landscape characterized by step 2. Like the second group these are themselves populations with diverse origins in prehistory, a syntheses of various geographical and tribal strands.

Though isolation by distance and clinal variation is important in this narrative, these dynamics are actually requilibrations after the exogenous shocks of demographic eruptions (note, a reader of this weblog outlined this model years ago in a more primitive form). Agriculture, and agricultural mass societies, were sociological shocks of a massive order, which resulted in protean shifts in the institutional and cultural fabric of diverse peoples. Like early stage innovation and business growth the “Neolithic sector” may have been characterized by rapid growth and high rates of “firm” extinction. Ultimately a series of consolidations and merges resulted in a new more stable order, as the industry entered a “mature phase.” What we term civilization.

Is that a true story? Perhaps not in the details. But I think it’s a truer story than the tales that were on offer in the early 2000s.

Addendum: It is important to note that discontinuity seems a likely story for the Y chromosomes as well (male lineages).

Citation: doi:10.1038/ncomms2656

(Republished from Discover/GNXP by permission of author or representative)
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Since John Hawks already hit it I don’t have much to add about the dog-starch-adaptation-paper in Nature, The genomic signature of dog domestication reveals adaptation to a starch-rich diet. I’m impressed at the yield from the sample sizes that they had, but as John alludes to this area of study has huge possibilities. The authors suggest that agriculture catalyzed domestication. That’s fair enough, and carefully stated I’d say, because the Amerindians seem to have brought domestic dogs to the New World long before agriculture. In other words, the “domestication” event was probably a multi-layered affair. Looking through the supporting information it’s obvious that the domestics were almost all Western breeds. As the search for adaptive variants expands to other lineages we might be in for surprises in terms of the signatures of selection as they vary across the dogs.

Which brings me to humans. After all the variation in digestive abilities also applies to humans, and there’s a fair amount of evidence of recent human adaptation driven by agriculture. Is Paleolithic man to Holocene man what the wolf is to the dog? Evolutionary psychologists have long spoken of the “Paleolithic mind,” but what if the Holocene indeed has witnessed a major evolutionary change in our species? To go back to the dog analogy, imagine that wolves were extinct, and inferences were made about them based on what we know of the dog. How accurate would those inferences be? George Church might be disavowing the project of resurrecting Neandertals, but the reality is that bringing one of them back would be an incredible test of the inferences that are the bread & butter of the paleoanthropological enterprise.

Image credit: Wikimedia

(Republished from Discover/GNXP by permission of author or representative)
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The above image, and the one to the left, are screenshots from my father’s 23andMe profile. Interestingly, his mtDNA haplogroup is not particularly common among ethnic Bengalis, who are more than ~80% on a branch of M. This reality is clear in the map above which illustrates the Central Asian distribution my father’s mtDNA lineage. In contrast, his whole genome is predominantly South Asianform, as is evident in the estimate that 23andMe provided via their ancestry composition feature, which utilizes the broader genome. The key takeaway here is that the mtDNA is informative, but it should not be considered to be representative, or anything like the last word on one’s ancestry in this day and age.

As a matter of historical record mtDNA looms large in human population genetics and phylogeography for understandable reasons. Mitchondria produce more genetic material than is found in the nucleus, and so were the lowest hanging fruit in the pre-PCR era. Additionally, because mtDNA lineages do not recombine they are well suited to a coalescent framework, where an idealized inverted treelike phylogeny converges upon a common ancestor. Finally, mtDNA was presumed to be neutral, so reflective of demographic events unperturbed by adaptation, and characterized by a high mutation rate, yielding a great amount of variation with which to differentiate the branches of the human family tree.

Many of these assumptions are are now disputable. But that’s not the point of this post. In the age of dense 1 million marker SNP-chips why are we still focusing on the history of one particular genetic region? In a word: myth. Eve, the primal woman. The “mother of us all,” who even makes cameos in science fiction finales!

In 1987 a paper was published which found that Africans harbored the greatest proportion of mtDNA variation among human populations. Additionally, these lineages coalesced back to a common ancestor on the order of 150,000 years ago. Since mtDNA is present in humans, there was a human alive 150,000 years ago who carried this ancestral lineage, from which all modern lineages derive. Mitochondrial DNA is passed from mothers to their offspring, so this individual must have been a woman. In the press she was labeled Eve, for obvious reasons. The scientific publicity resulted in a rather strange popular reaction, culminating in a Newsweek cover where Adam and Eve are depicted as naked extras from Eddie Murphy’s Coming to America film.

The problem is that people routinely believe that mtDNA Eve was the only ancestress of all modern humans from the period in which she lived. Why they believe this is common sense, and requires no great consideration. The reality is that the story being told by science is the story of mtDNA, with inferences about the populations which serve as hosts for mtDNA being incidental. These inferences need to be made cautiously and with care. It is basic logic that a phylogeny will coalesce back to a common ancestor at some point. Genetic lineages over time go extinct, and so most mtDNA lineages from the time of Eve went extinct. There were many woman who were alive during the same time as Eve, who contributed at least as much, perhaps more, to the genetic character of modern humans today. All we can say definitively is that their mtDNA lineage is no longer present. As mtDNA is passed from mother to daughter (males obviously have mtDNA, but we are dead ends, and pass it to no one), all one needs for a woman’s mtDNA lineage to go extinct is for her to have only sons. Though she leaves no imprint on the mtDNA phylogeny, obviously her sons may contribute genes to future generations.

Prior to ancient DNA and the proliferation of dense SNP data sets scholars were a bit too ambitious about what they believed they could infer from mtDNA and Y lineages (e.g., The Real Eve: Modern Man’s Journey Out of Africa). We are in a different time now, inferences made about the past rest on more than one leg. But the legend of Eve of the mtDNA persists, not because of its compelling scientific nature, but because this is a case where science piggy-backs upon prior conceptual furniture. This yields storytelling power, but a story which is based on a thin basis of fact becomes just another tall tale.

All this is on my mind because one of the scientists involved with Britain’s DNA, Jim Wilson, has penned a response to Vincent Plagnol’s Exaggerations and errors in the promotion of genetic ancestry testing (see here for more on this controversy). Overall I don’t find Wilson’s rebuttal too persuasive. It is well written, but it has the air of sophistry and lawyerly precision. I have appreciated Wilson’s science before, so I am not casting aspersions at his professional competence. Rather, some of the more enthusiastic and uninformed spokespersons for his firm have placed him in a delicate and indefensible situation, and he is gamely attempting to salvage the best of a bad hand. Importantly, he does not reassure me in the least that his firm did not use Britain’s atrocious libel laws as a threat to mute forceful criticism of their business model on scientific grounds. A more general issue here is that Wilson is in a situation where he must not damage the prospects of his firm, all the while maintaining his integrity as a scientist. From what I have seen once science becomes a business one must abandon the pretense of being a scientist first and foremost, no matter how profitable that aura of objectivity may be. The nature of marketing is such that the necessary caution and qualification essential for science becomes a major liability in the processing of communicating. It’s about selling, not convincing.

Going back to Eve, Wilson marshals a very strange argument:

“The claim that Adam and Eve really existed, as you suggest, refers to the most recent common ancestors of the mtDNA and non-recombining part of the Y chromosome. I don’t agree that there is nothing special about these individuals: there must have been a reason why mitochondrial Eve was on the front cover of Time magazine in the late 80s!….

A minor quibble, but I suspect he means the Newsweek cover. More seriously, this line of argumentation is bizarre on scientific grounds. Rather, it is a tack which is more rational when aiming toward a general audience which might purchase a kit which they believe might tell them of their relationship to “Eve.”

In the wake of the discussion at Genomes Unzipped I participated in further exchanges with Graham Coop and Aylwyn Scally on Twitter, and decided to spend 20 minutes this afternoon asking people what they thought about mitochondrial Eve. By “people,” I mean individuals who are pursuing graduate educations in fields such as genetics and forensics. My cursory “field research” left me very alarmed. Naturally these were individuals who did not make elementary mistakes in regards to the concept, but there was great confusion. I can only wonder what’s going through the minds of the public.

Analogies, allusions, and equivalences are useful when they leverage categories and concepts which we are solidly rooted in, and transpose them upon a foreign cognitive landscape. By pointing to similarities of structure and relation one can understand more fully the novel ground which one is exploring. Saying that the president of India is analogous to the queen of England is an informative analogy. These are both positions where the individual is a largely ceremonial head of state. In contrast, the president of the United States and the queen of England are very different figures, because the American executive is not ceremonial at all. This is not a useful analogy, even though superficially it sees no lexical shift.

Who was Eve? A plain reading is that she is the ancestor of all humans, and more importantly, the singular ancestress of all humans back to the dawn of time. This is a concept which the public grasps intuitively. Who is mtDNA Eve? A woman who flourished 150,000 years ago, who happened to carry the mtDNA lineage which would drift to fixation in the ancestors of modern humans. I think this is a very different thing indeed. For purposes of poetry and marketing the utilization of the name Eve is justifiable. But on scientific grounds all it does is confuse, obfuscate, and mislead.

The fiasco that Vincent Plagnol stumbled upon is just a symptom of a broader problem. Scientists need to engage in massive conceptual clean up, as catchy phrases such as “mitochondrial Eve” and “Y Adam” permeated the culture over the past generation, and mislead many sincere and engaged seekers of truth. This is of the essence because personal genomics, and the scientific understanding of genealogy, are now moving out of the ghetto of hobbyists, enthusiasts, and researchers. Though I doubt this industry will be massive, it will be ubiquitous, and a seamless part of our information portfolio. If people still have ideas like mitochondrial Eve in their head it is likely to cloud their perception of the utility of the tools at hand, and their broader significance.

(Republished from Discover/GNXP by permission of author or representative)
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I mentioned this in passing on my post on ASHG 2012, but it seems useful to make explicit. For the past few years there has been word of research pointing to connections between the Khoisan and the Cushitic people of Ethiopia. To a great extent in the paper which is forthcoming there is the likely answer to the question of who lived in East Africa before the Bantu, and before the most recent back-migration of West Eurasians. On one level I’m confused as to why this has to be something of a mystery, because the most recent genetic evidence suggests a admixture on the order of 2-3,000 years before the past.* If the admixture was so recent we should find many of the “first people,” no? As it is, we don’t. I think these groups, and perhaps the Sandawe, are the closest we’ll get.

Publication is imminent at this point (of this, I was assured), so I’m going to just state the likely candidate population (or at least one of them): the Sanye, who speak a Cushitic language with possible Khoisan influences. There really isn’t that much information on these people, which is why when I first heard about the preliminary results a few years back and looked around for Khoisan-like populations in Kenya I wasn’t sure I’d hit upon the right group. But at ASHG I saw some STRUCTURE plots with the correct populations, and the Sanye were one of them. I would have liked to see something like TreeMix, but the STRUCTURE results were of a quality that I could accept that these populations were not being well modeled by the variation which dominated their data set. Though Cushitic in language the Sanye had far less of the West Eurasian element present among other Cushitic speaking populations of the Horn of Africa. Neither were their African ancestral components quite like that of the Nilotic or Bantu populations. The clustering algorithm was having a “hard time” making sense of them (it seemed to wanted to model them as linear combinations of more familiar groups, but was doing a bad job of it).

Here is an interesting article on these groups: Little known tribe that census forgot. Like the Sandawe this is a population which seems to have been hunter-gatherers very recently, and to some extent still engage in this lifestyle. In this way I think they are fundamentally different from Indian tribal populations, who are often held up to be the “first people” of the subcontinent. More and more it seems that the tribes of India are less the descendants of the original inhabitants of the subcontinent, at least when compared to the typical Indian peasant, and more simply those segments of the Indian population which were marginalized and pushed into less productive territory. Over time they naturally diverged culturally because of their isolation, but the difference was not primal. In contrast, groups like the Sanye and Sandawe may have mixed to a great extent with their neighbors (and lost their language like the Pygmies), but evidence of full featured hunting & gathering lifestyles implies a sort of direct cultural continuity with the landscape of eastern Africa before the arrival of farmers and pastoralists from the west and north.

* I understand some readers refuse to accept the likelihood of these results because of other lines of information. I am just relaying the results of the geneticists. I am not interested in re-litigating prior discussions on this. We’ll probably have a resolution soon enough.

(Republished from Discover/GNXP by permission of author or representative)
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A few weeks ago I alluded to the controversy around proposition 37. This was the GMO labeling law proposal. Many life scientists in California opposed this law. One aspect of this issue is that it is an area where the Left may be stated to be “anti-science.” This is why this was highlighted in Science Left Behind. But there’s a problem with this narrative: the survey data for it is weak. There are broad suggestive patterns…but the reality is that the strongest predictor of skepticism of genetically modified organisms is lower socioeconomic status. The GSS has a variable, EATGM. Here are the results by ideology:

Liberal Moderate Conservative
Don’t care whether or not food has been genetically modified 15 16 17
Willing to eat but would prefer unmodified foods 55 53 52
Will not eat genetically modified food 30 30 31


I would caution that the sample size is small. But, if you dig deeper into the survey data you can find evidence that conservatives are more unalloyed in their support of biotech.

And yet with all this said, today I noticed that the California proposition 37 results are rather stark in their geographic distribution. The measure failed statewide, but 2/3 of the people in San Francisco and Santa Cruz counties supported it, as did 60% of the people in Marin (interestingly, only a little over 50% supported it in San Mateo and Santa Clara). I couldn’t find a tabular list with the results by county, but there are interactive maps. If someone was industrious (and had more time than I do) they would go and collect the data from the maps, and do a loess of “support proposition 37” vs. “support Obama.”

The main problem is that from what I can tell a lot of Left-liberals who support anti-GMO policies, explicit or implicit, do so because they believe that that is anti-corporate. My argument is that whatever issues one might have with agribusiness, one should litigate the question of scale in agriculture directly and forthrightly, rather than focus on sidelights like GMO.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Ideology, Science • Tags: Agriculture, Politics 
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I cropped the image above from the paper Inference of Population Structure using Dense Haplotype Data. The main reason was emphasize the distinctiveness of the Sardinian cluster, on the bottom right. As you can see this population exhibits a lot of coancestry across individuals. This isn’t too surprising, Sardinia is an island, and islands are often genetically distinctive. Random genetic drift prevents populations from diverging through gene flow, but water is a major impediment to gradual isolation by distance dynamics. The original Sardinians are naturally going to diverge from mainlanders over time, and begin to share the same set of common ancestors in the recent past, because their space of reasonable mating possibilities is constrained. The other population which is similar in the heat map above are the residents of the Orkneys, off the north coast of Scotland (the Orkneys has a much smaller population than Sardinia, but, it is also much closer to the mainland).

This is on my mind because Dienekes has a long post where he explores the D-statistic results of various European populations, using Sardinians as one of the references. You don’t need to know the details, just that Northern European populations seem to exhibit an affinity to East Asians. Our favorite human genomicsts at Broad highlighted this tendency, and Dienekes went looking (if David Reich et al. were inclined toward mischief they should just posit some crazy scenario, and see if Dienekes assembles the requisite data set!). Which is all fine, and we’ll see more of this in the near future. It isn’t as if others aren’t using Sardinians.

If you play around with model-based clustering packages (e.g., ADMIXTURE, STRUCTURE, etc.) or PCA the distinctiveness of the Sardinians does jump out at you. In short they are the least Asian of the European populations. If there is a cline, they generally define one of the antipodes of the cline (often, along with the Basques). They’re a natural reference. But we need to be cautious. On occasion a reader has casually asserted that understanding the relationships between populations is easy enough, just find appropriate reference groups. Easier said that done.

A few years ago there was a great deal of debate whether the Sardinians were Neolithic “newcomers” or the descendants of Paleolithic populations. The latter is actually somewhat conjectural in regards to archaeology. There is some evidence of Paleolithic habitation, but it is fragmentary, implying perhaps very low population densities, and likely local extinctions over time. The reason the argument roiled for so long is that if Sardinians are the descendants of Paleolithic Europeans you have the perfect reference. But what if they’re not? I think that question is up in the air, especially in light of the fact that Ötzi the Iceman has affinities to the Sardinians. Ötzi was a mainlander, and an agriculturalist. That does not preclude descent from a common Paleolithic Western European population which adopted agriculture, but I think it tilts us more toward some sort of demographic expansion (likely from the Eastern Mediterranean, but perhaps a secondary expansion from somewhere in the Western Mediterranean).

Ten years ago we were looking at a two-factor model. Europeans the Ice Age hunters, or Europeans the Middle Eastern farmers. Today the past is much more crisp, and yet that crispness has unveiled a befuddling complexity. If I had to put money down I would bet that in another ten years we’ll have to add into our understanding both demographic pulses during the Ice Age, and multiple ones which post-date the Neolithic. It may be that the signals of a relationship between Northern Europeans and the First Americans is very old, and dates back to the Gravettian culture, which spanned Western Europe eastward toward the fringes of the Black Sea. With ancient DNA I believe that we’ll get a sense of who the “First Europeans” were, and it may be that their genetic contribution to modern Europeans is in the same range as the Neandertals whom they assimilated and exterminated!

All something to keep in mind in the coming years, when European paleogenetics may be measured by the Sardinian….

Image credit: Wikimedia

(Republished from Discover/GNXP by permission of author or representative)
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There’s a new ancient DNA paper out which examines the maternal lineage and the autosomal background of two individuals extracted from a Spanish site dated to 7,000 years before the present. That is, during the European Mesolithic. In other words, these are the last wave of Iberian hunter-gatherers before agriculture. I have placed the PCA, with some informative labels, to illustrate the peculiarity of these samples. Here’s the abstract:

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic…is poorly understood, both due to the scarcity of human remains from that period…The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

Here’s another PCA showing one individual on a more fine-grained representation of European populations:

Perhaps the most interesting aspect here is something Dienekes pointed out from the supplements: these two individuals are not only outside of the range of extant European populations in their positioning on a global PCA plot, but they are shifted toward East Asians.

The fact that these two individuals, who really come close to being one data point because they are likely rather closely related, are outside of the modern European population distribution isn’t too surprising. 7,000 years is a long time, and we can’t assume that ancient populations can be recomposed as combinations of the variation of modern populations. But, the shift toward East Asians is surprising to me, because they are Iberian individuals. In PCA and model-based (e.g., ADMIXTURE) clustering frameworks modern Iberians, and populations from Southwest Europe in general, are the most distant from East Eurasians of all West Eurasians. Dienekes opines:

It now appears clear that the Mesolithic substratum in Europe was:

1. Well outside the modern range, contributing a little to extant populations
2. Its contribution in northern populations was higher than in southern ones
3. It may be responsible for the pattern of Asian-shift observed for non-Mediterranean European populations

…It seems that this was the composition of the pre-Neolithic population of Europe that was later supplanted first by the “Mediterranean”/”Southern” components during the early Neolithic, and later by the “West_Asian”/”Caucasus”/”Gedrosia” components, perhaps during the Copper Age. We’ll see whether my prediction pans out soon enough.

On the broadest level I think Dienekes model is entirely possible. I’d give it the highest probability of the range of options, though I have a high uncertainty. The question is the weight of the contributions. Let’s rename the various groups A, B, and C, for the three waves in chronology (hunter-gatherers, first wave farmers, and second wave farmers). Then any European population is:

xA + yB + zC, where x + y + z = 1

About 10 years ago B + C would be one class, so B, and you had a pan-European estimate of:

0.75A + 0.25B

Now some scholars are trying to revise that, and reduce the weight for A. I think we need to be very careful, because we’ve already been burned by overly elegant and simplistic models of the settlement of Europe. For example, here are my made-up estimates quantitatively from everything I’d read so far:

Finns = 0.90A + 0.05B + 0.05C

Lithuanians = 0.85 A + 0.05B + 0.10C

Irish = 0.60 A + 0.30B + 0.10C

Germans = 0.60 A + 0.20B + 0.20C

Basques = 0.40 A + 0.60B

North Italians = 0.40 A + 0.30B + 0.30C

The exercise above was not to give you accurate numbers that I’m sure of, but to give you numbers instead of verbal labels which are imprecise. I’m quite willing to “update” my estimate in the future, and expect to. In the paper the authors highlight that the mtDNA lineages that the two individuals carry is modal in the Sami of northern Finland. Genetically the Sami seem more Finnish that the Finns. But, they also clearly have an “eastern” affinity (diminished, but still present in Finns as well). This dovetails with linguistic connections to North-Central Eurasia, and the margins of Western Siberia. What’s going on here? One hypothesis has been that the Finnic languages (and the Sami) are culturally intrusive, and the Siberian genetic affinity is a signal of this ancient core admixed with the local substrate, which resembles that of Scandinavians.

These results make me update my assessment, and increase my own probability that the Finnic people have deep cultural roots in Northeast Europe. This was already my hunch based on model-based clustering which seemed to show that there were “southern” modal elements present in Scandinavians lacking in Finns or Sami. If Finns or Sami were relatively late arrivals, I would have expected to be more diverse in the complement of ancestral elements, not less. Now the set of results form Mesolithic European genomes indicate to me that what we may be seeing in the Siberian affinity of the Sami (and to a lesser extent the Finns) are the echos of a post-Ice Age expansion of Palearctic peoples from the center of Eurasia which ranged west toward the Atlantic and east toward the Sea of Japan. I suspect that this Palearctic population did not move into a totally empty landscape, so the Mesolithic peoples which the West Asian and East Asia farmers displaced or assimilated were not entirely similar. Rather, they were themselves syntheses between hunter-gatherer groups.

Obviously this is an interesting time to moot these questions. The major issue we need to keep in mind is not to move from one enthusiasm to another. A model of preponderant biological continuity between European hunter-gatherers and early agriculturalists is now in serious doubt, especially for southern Europe. But that does not mean that we should move to a model where the hunter-gatherers were replaced in totality by agriculturalists. This does not seem to have happened in northeast Europe, and the model of replacement itself is probably more complex than a single-step transition.

Citation: Current Biology, 28 June 2012 doi: 10.1016/j.cub.2012.06.00

(Republished from Discover/GNXP by permission of author or representative)
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Community differentiation and kinship among Europe’s first farmers (via Dienekes):

Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.

I have already stated on this weblog that we will probably begin to discern a rather strong pattern soon of an interleaved genetic pattern across Eurasia and Africa where we can infer that populations in an expansionary demographic phase absorbed a host of other groups (more, or less). The exact details are to be worked out, but I’m moderately confident in this sort of pattern.

But these results align with another of my expectations, which I have rather stronger confidence in: that in parts of Eurasia the emergence of agriculture was correlated with the rise of powerful patrilineal kinship groups, which served as the cores of pre-historic polities. I no longer believe that demographic expansion due to cultural innovation can be separated from the likely political and social consequences of these changes. No, rather what we saw with the rise of agriculture was another powerful social innovation, collective units of large numbers of males who operated as one in the quest for land, women, and material self-enrichment. I do not mean to imply here that violence began with the Neolithic. Rather, I simply believe that the numbers enabled by agriculture allowed for specialization and scalability to fundamentally change the game. This was a high stakes “winner-take-all” bet.

As these males spread across the landscape, enabled by their culture (agriculture) and propagating their culture (language), in many cases their genetic-demographic signal may have been diluted across the wave of advance. But their cultural cohesion remained, and I believe that the patterns of Y chromsomal patterns evident across the modern world are an echo of their elimination of rivals. A tree of many Abels was pruned, as a few Cains proliferated like weeds.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Agriculture 
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Halford Mackinder’s conceptualization of the world

With the recent publication of the paper on the archaeogenetics of Neolithic Sweden I feel like we’re nearing a precipice. That precipice overlooks lands of great richness, filled with hope. It’s nothing to fear. It is in short a total re-ordering of our conception of the recent human past, at minimum. The “pots not people” paradigm arose in archaeology over the past few generations due to both scholarly and ideological factors. The scholarly ones being that intellectuals of the 19th and early 20th century made assumptions of extremely tight correspondence between material and cultural characteristics, and demographic dynamics, which seem to have been false. Therefore, the rise of an Anglo-Saxon England and the marginalization of Celtic Britain to the western fringes was not just a cultural reality, but also a fundamentally racial one, as Germans replaced Celts in totality. The ideological problem is that this particular framework was take as a given by the Nazis during World War II, lending a bad odor to the

hypotheses of migration which were once so ascendant.

No one could deny that material cultures rise and fall in pulses, and exhibit variation in spatial distribution over the millennia. But by and large scholars large took a very skeptical view of the idea that large scale migrations of populations may have occurred in prehistory, and could have been the underlying causal factors driving the changes in material culture. But a null hypothesis of demographic stasis was in itself a positive statement of beliefs as to the character of the human past. It was no withholding of judgement.

Today the results from ancient DNA, and more powerful inferential methods which extract patterns out of extant variation, simply can not be easily fitted into a “pots not people” framework. Nor can we go back to a race-is-culture and culture-is-race model in the vein of the Victorians. Rather, the new order model must take into account the imperfect, but non-trivial, correlation between cultural and genetic variation, and, the differences between patterns of cultural and genetic variation.

L. L. Cavalli-Sforza first made famous the correlation between language and genes in History and Geography of Human Genes. But over the past generation a lot of human genetics does seem to confirm that the sharp discontinuity between language families is correlated with discontinuity between genes. I say correlated, because though by and large a demarcated population may have one native language to contrast it with its neighbors, these populations are rarely have one “native genotype” to contrast with their neighbors. Though two populations may exhibit genetic differences, if they have been neighbors for any period of time there is usually gene flow across them which reduces between population difference. A classic case of this can be found in Southern Africa. The Xhosa Bantu ethnic group has long been geographic neighbors with Khoisan populations. This shows in their genomes, which are on the order of 10-20% Khoisan. Additionally, the Khoisan themselves show admixture, from the Bantu, and even Europeans! But though the Xhosa language shows some Khoisan influence, it is certainly not “10-20%”, whatever that may be. Similarly, despite the presence of European and Bantu origin ancestry in the Bushmen, they remain culturally distinct.

The reason for this is pretty straightforward: you are 50% genetically derived from each parent, you are not necessarily 50% culturally derived from each parent. If parents differ in language, religion, and norms, the children may select one particular set of cultural values from one parent, usually in line with the majority culture. In this way individuals who migrate between populations may introduce genetic diversity, but not so much cultural diversity. But this is on a relative small scale, that of the clan or band. What about on a larger structural scale?

Over the past 500 years we have seen cultural shifts which had very little to do with genetics. From what I have read Gaelic went from being the majority to the minority language of the Irish Roman Catholic peasantry between 1800 and 1850. Presumably the famine of those years played a role. Whatever the specific historical factors at work, obviously this was a massively significant shift, without much genetic cause. On contrary, previous non-Gaelic speaking transplants either assimilated (e.g., the Old English and the Norse-Gaels), or remained culturally distinct (e.g., the Ulster Scots and the New English). A contrast to this was the Columbian Exchange, which involved either massive cultural and genetic replacement, or substantial cultural replacement and significant genetic amalgamation.
A key point is that massive cultural change does not always correlate with massive genetic change. The reason that “pots not people” became popular is that earlier scholarship was predicated on an assumption of perfect correspondence, rather than correlation of patterns. As an example of what I mean, assume that you are a given a population of predominantly African origin, with a European minority ancestral component. The population speak a Germanic language, and adhere to Protestant Christianity. What region of Europe would you assume that the European ancestral contribution derived from? Of course it would be Northwest Europe, and that is exactly what you see in black Americans, and what you do not see in black Brazilians, who speak a Southwest European language and are predominantly Roman Catholics. Despite the European language and religion of the African Diaspora of the New World, the dominant genetic contribution remains African. But, you can derive from the cultural identity of these groups which European populations amalgamated with them genetically, or inversely, you can make reasonable inferences of cultural state simply by observing the character of European ancestry on a population level! In other words, robust correlations between genes and culture can occur, even if the two do not exhibit the same weight from population to population (i.e., black Americans are mostly European culturally, but genetically mostly African).

Ruminations on these issues are important when taking into account the latest findings of genome bloggers. As has been noted, trying to reconstruct past populations as combinations of present populations is going to miss something. That is, there is no guarantee that the present captures all the variation of the past. Additionally, the analytic tools must always be used judiciously. The model based clustering algorithms return “ancestral components,” but only in some specific cases do they truly return proportions which align with admixtures between real concrete populations. Rather, you get back patterns of variation and relationships which are visualized for you, but must not be taken in a literal fashion. In regards to the hypothesis free method of principal component analysis, the independent dimensions of variation are still conditional upon the variation you put into the algorithm. By this, I mean that if you overload the data set with one particular population, then the largest explanatory dimensions of variation are going to be dictated by that population.

With all due caution entered into the record, it does seem that some “mysteries” are going to solved in the near future, at least to a first approximation. As far back as the mid-2000s it was apparent in the early STRUCTURE analyses using microsatellites that some European populations, the French Basque and Sardinians, lacked an affinity which spanned Central Eurasia, and reached deep into South Asia. Adding Finns into the mix seems to have confirmed that they too seem to lack it. The main “twist” on this picture though seems to be that Lithuanians and Latvians also have very little of it too. But there is also earlier uniparental work which suggests marginal differences between Indo-European and Finnic populations in the northeast Baltic. To-be-published work on Indian genetics does seem to imply that there was significant in-migration of Indo-European populations into the subcontinent within the last 4,000 years. And an earlier publication by the same group confirmed the old intuition that South Asians seem to exhibit significant, though not total, affinity to West Eurasians. That affinity being a product of recent descent in part from West Eurasians, via a hybridization event.

But perhaps the biggest general takeaway, as opposed to specific inference, is that the humans who inhabit the southern and western reaches of “Rimland” are syntheses which emerged in the last 10,000 years. Southeast Asians are derived from several pulses of farmers from the fringes of what became southern China, but absorbing an ancient earlier substratum. South Asians are the product of a fusion of West Eurasians and the western elements of that same substratum, a Paleolithic population of South Eurasians who once spanned the Indus to the South China Sea, and extant today in “pure” form only in the Andaman Islands and the Negritos of the Malay peninsula.* At minimum Europe looks be a synthesis of least two pulses from outside or the margins of Europe (i.e., Southwest Asia and West Central Eurasia), as well as possible expansions from within the subcontinent, not to mention assimilation of the deeply rooted populations by an within the newcomers. As far as the Middle East and North Africa, I think there is enough circumstantial evidence that there too there have been significant population movements since the Neolithic. This is perhaps why many of the earlier genetic analyses using particular Southwest Asian populations as “references” for the original Middle Eastern farmers who moved into Europe may have yielded misleading results.

The major lacunae in my model is in East Asia, in particular China. The Han Chinese do not seem to have much West Eurasian admixture at all (in contrast to the Mongolians and the Hui). Additionally, the data do seem to point to some amalgamation of non-Han populations in southern China. But overall I don’t have a good gasp of how the landscape of East Asia came to be be. Both archaeology and genetics point us to the likelihood that phenotype which we associate with East Asians became overwhelmingly dominant only recently. It is here that the strongest instance of the “first farmers” hypothesis may be found.

Sometimes it is good to live in interesting times.

* The Negritos of Malaya are not pure from the samples I have seen. And those of the Philippines seem to be very distinct the more westerly South Eurasians.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Agriculture, Anthropology, Human Genetics 
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A new paper in Science has just been published which in its broad outlines has been described in conference presentations. When examining the autosomal genetic variation of three individuals of the hunter-gatherer Pitted Ware Culture (PWC), and one of the agriculturalist Funnel Beaker Culture (TRB), the authors found that the two groups were sharply differentiated. The number of SNPs was on the order of 10,000 or so if I read the methods correctly. This is rather thin for studying contemporary within European population differences (~100,000 or more seems to be safe), in particular using hypothesis based clustering algorithms (it seems more manageable for PCA). But the findings are strong enough that I think we shouldn’t discount them. The most fascinating aspect of the results is that while the PWC seem to exhibit affinities with Northern and Northeastern Europeans, the TRB individual seems more similar to extant Southern Europeans!

Others have already commented extensively on the results. Keeping in mind the small sample sizes, limitation of comparisons, and the relatively thin marker set, I think the primary result we can take away from these findings is that old models of pure cultural and demographic diffusion are false. By this, I mean that prior debates which culminated in the early aughts on the “Paleolithic vs. Neolithic” contribution to the ancestry of modern Europeans were fundamentally premised on a demographic diffusion dynamic, whereby genes and ideas exhibited a continuous flow across a flat and featureless landscape. On the contrary, the basic outlines we are seeing here is that the human past exhibited spatial and temporal discontinuity. And why should this surprise us? There is no dialect continuum between Spanish and Chinese across Eurasia. Rather, broad language families are sharply differentiated from each other at zones of contact. Though there are theoretical reasons why the variation in genes should be more clinal, the reality remains that cultural parameters are going to shape the outlines of genetic variation, and those parameters are discontinuous.

There are two framing issues which make this paper’s results intelligible. The first is general. Agriculture likely did not spread in Europe simply through the random-walk “bottom up” expansion of small groups of farmers into an empty frontier. Rather, these populations were almost certainly organized on some supra-clan political level, and used their organizational resources to map out appropriate zones of settlement prior to expansion. The result in the early periods was a “leapfrog” point to point migration pattern, focusing on inland river valleys and coastal zones of rich land factor inputs and clement habitation. This sort of interleaving settlement pattern could easily explain sharp genetic distinctions between co-located populations, which only admixed over time as the last hunter-gatherers did acculturate. The second issue is specific to Scandinavia: it seems that because of its ecological conditions agriculture came late to this zone of Europe, and hunter-gatherer populations reliant on marine organisms were demographically particularly robust. The discontinuous expansion and stasis of farming on the ecological frontier was certainly the case in Scandinavia for nearly 1,000 years, as hunter-gatherers persisted as the spread of farming was halted.

Most of the information in the paper is well summarized by figure 1, which I’ve reedited considerably to illustrate the primary finding. Please note the relative affinities of the LBK and PWC individuals. The LBK individual in the PCA is placed near the Basque and Sardinian populations of Southwest Europe, while the PWC individuals are outside of the distribution of the HGDP Northern Europeans. In another PCA they seem to cluster with East Baltic populations, such as the Latvians. This is in line with earlier mtDNA work.

Also observe the pattern in ADMIXTURE: again, a close correspondence with the Sardinian and Basque samples for the LBK. Of particular interest is the relative lack of component yellow (K = 4) in all of the ~5,000 year old samples. The difference in proportion of this is what also distinguishes the French from the French Basque, and the Tuscans from the Sardinians (along with K = 2, the blue component in the case of the latter). I have truncated the Finnish samples, but unfortunately I suspect what we’re seeing here is something similar to the Kalash, a very homogeneous and relatively inbred population throwing up its own component. So I do not believe K = 1, the purple, is particular informative. The most likely model for the ethnogenesis of the Finnic peoples in Northeastern Europe seems to involve an exogenous Siberian element. From reading the supplements I do not see this affinity in the PWC. That may then date the expansion of the Finns as a circum-polar group of ethnicities in Western Eurasia.

In any case, as Dienekes has noted, I suspect that what is missing from the model outlined in the paper are subsequent population movements in Europe after the initial contact between the indigenes of the north and the LBK from the south. This may be why the PWC individuals in some PCA analyses seem to be placed outside of contemporary distributions, just like Otzi the Iceman.

Using a two-way admixture model the authors construct a framework whereby Northwest Europeans are about 50 percent farmer and 50 percent hunter-gatherer; that is, 50 percent LBK and 50 percent PWC. But as Maju cautions we need to be careful about substituting these ancient populations for all ancient populations. Additionally, the two-way admixture model estimates that Sardinians are 95 percent farmer, while Swedes are 40 percent farmer, farmer as understood as the descendants of LBK. I think the problem here, as I have argued before, and Dienekes has also suggested, is that there were almost certainly multiple waves of agriculturalists within Europe. The Sardinians seem to be relatively unadulterated descendants of an early farmer demographic expansion, which has been supplemented across much of Europe. I’ve you with their estimates of Neolithic farmer ancestry:

Image credit: Oskar Karlin

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Agriculture, Anthropology, Europe 
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One model for the spread of the agricultural way of life into Europe is of inexorable “demic diffusion” via a “wave of advance” of farming populations met by a land surplus. Conceptually and analytically it’s an elegant model. It’s also fundamentally methodologically individualistic, and so in keeping with the spirit of the age. There’s no need to appeal to higher order social structure or organization, farmers who have a specific cultural toolkit drive the dynamic through endogenous growth in pre-state cultures through the production of large families. This growth washes over the frontier of the advance, and the original locus of the demographic pulse synthesizes across a transect with the indigenous substrate. In the early aughts historical geneticists Bryan Sykes and L. L. Cavalli-Sforza sparred over whether demic diffusion was useful or not as a conceptual framework. Sykes reported chromosomal results which implied that 75 percent of the ancestry of Europeans derives from Pleistocene hunter-gatherers. Cavalli-Sforza’s riposte was that the original model did not specify a particular Paleolithic-Neolithic ratio, but rather characterized a dynamic which emphasized the necessity of migration as a mediator for cultural changes (the two perspectives are outlined in Seven Daughters of Eve and A Genetic and Cultural Odyssey).


In the end the debate did seem semantic quibbling. And today it also is likely outmoded and irrelevant. There is a high probability that the basic fundamental assumptions of the original diffusionist model, whether cultural or genetic, were pushed too far. It neglected the profound discontinuities introduced into the equation by the protean tendencies of human culture. Empirically there is evidence of this in works such as Lawrence Keeley’s War Before Civilization of this in the European context. As farmers impinged upon the territories of Mesolithic populations which utilized marine resources the advance of agriculture often stalled, and there are archaeological remains which are suggestive of violent conflict across Northern Europe’s maritime fringe. Additionally, when humans advance into “virgin” territory the landscape can often seem “patchy.” Instead of a spatially uniform wave of advance one almost certainly saw farmers race up favorable valleys and avoid zones of decreased fertility. In the United States the Far West was understood to be more amenable to agricultural techniques than the Great Plains in the 19th century, so one notes a “leap frog” to California and Oregon in the decades before the Civil War, leaving the intervening lands to native populations (at least temporarily).

It is with this in mind that we must take in results being published more recently which suggest a more confused and irregular shift of peoples and cultures in Neolithic Europe. For example, at the symposium on Modern Human Genetic Variation Mattias Jakobsson is reporting on results of ancient DNA from ~5,000 year old samples from Scandinavia. The individual who was a farmer resembles Southern Europeans, while the two hunter-gatherers resemble modern Northern Europeans. Jakobsson observes that most modern European populations span the gamut between the two extremes. A few years ago a paper came out which reported that the mtDNA lineages of LBK individuals from Central Europe (the earliest farming culture) resembled Near Easterners more than modern Europeans. A similar discontinuity seems evident in France. At this point I think there are enough data to force us to move past an simple Neolithic demic diffusion wave of advance, and any model which posits pure cultural diffusion or total replacement of the indigenous populations. We should be careful about making grand pronouncements for the next few years, because the outlines will be clear and pegged down within 5 years due to the impending surfeit of ancient DNA studies.

Rather, let’s switch back to the question of clines and gradual shifts. The problem here may be the granularity of the archaeological data. It seems likely that the expansion of agriculture was more spatially patchy, and exhibited more starts and stops, then the samples we have allow us to infer with any confidence. The arrival of startlingly distinctive populations genetically and culturally across which likely rapidly traversed territory in a point-to-point fashion, and their subsequent extinction or assimilation into local substrate, is less surprising when we keep in mind the discontinuous nature of much of cultural change.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Agriculture, Anthropology 
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There’s a new paper in AJHG which caught my eye, The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times (ungated). The first thing you need to know about this paper is that it focuses on only the direct maternal lineage of Basques via the mtDNA. In some ways this is weak tea, since it doesn’t give us a total genome estimate. But there are major upsides to mtDNA and Y. First, because of the lack of recombination it is relatively easy to generate a nice phylogenetic tree using a coalescent model. And second, for mtDNA the molecular clock is considered relatively reliable.

In this specific paper they also expanded the scope of their analysis to the whole mtDNA sequence, instead of just the hypervariable region. Not only did they look at whole sequences, but they also had an enormous sample size. They sequenced over 400 mtDNA genomes from the Basque country and neighboring regions. Haplogroup H peaks in frequency among Basques, and drops off among their neighbors (Gascons, Spaniards, etc.). Because the Basque speak a non-Indo-European language they are usually presumed to be indigenous in relation to their neighbors (or at least more indigenous). Until recently there was a strong presupposition that the Basque were ideal representatives of the pre-Neolithic populations of Western Europe. One common method of analysis would be to use the Basque as a pre-Neolithic “reference,” and simply estimate the impact of a Neolithic demographic wave of advance by using a eastern Mediterranean population as a second “reference” within an admixture framework. But more recent work has muddled the idea that the Basque are the descendants of Paleolithic Europeans. Finally, I suspect we’ll also have to acknowledge complexity in demographic histories. To say that the Basque exhibit continuity with Mesolithic Iberians may not contradict a substantial Neolithic contribution. South Asians for example are one numerous modern group which exhibits sharply divergent affinities if you use Y chromosomes (West Eurasian) or mtDNA (not West Eurasian). Why? The details are prehistorical.

The major takeaway from this paper is that the Basque mtDNA exhibit a pattern of demographic expansion ~4,000 years BP, and ~8,000 years BP. But I think it is important to look at the range of outcomes over their confidence intervals, so I’ve reproduced their second table below:

Table 2. Time Estimates of the Six Autochthonous Haplogroups

Haplogroup N Percentage Rho Standard Error Age (in Years) 95% Confidence Interval
Coalescence Age
H1j1 52 12.4% 1.86 0.49 4845 2324 − 7408
H1t1 34 8.1% 1.94 0.97 5057 99 – 10176
H2a5a1 22 5.2% 1.33 0.65 3422 118 – 6800
H1av1 17 4.0% 1.24 0.52 3213 567 – 5906
H3c2a 14 3.3% 1.27 0.37 3291 1403 – 5204
H1e1a1 12 2.9% 1.23 0.72 3187 −464 – 6927
Splitting Age
H1j1 52 12.4% 2.86 1.11 7514 1764 – 13470
H1t1 34 8.1% 2.94 1.39 7730 554 – 15227
H2a5a1 22 5.2% 2.33 1.19 6094 −6 – 12434
H1av1 17 4.0% 2.24 1.13 5854 65 – 11860
H3c2a 14 3.3% 2.27 1.07 5934 443 – 11619
H1e1a1 12 2.9% 5.23 2.13 14011 2729 – 26000

For our purposes the splitting age is important, because it shows when the Basque specific H lineages diverged from other European H lineages. Some of the intervals are huge (look at H1e1a1), so I don’t know what to make of it. I’ll leave further comments to those more well versed in the mtDNA literature, but I would like to say that it is important to remember that we don’t know where the demographic events inferred occurred. It may not have been in the trans-Pyrenees region at all.

More later.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Agriculture, Anthropology, Basque 
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Once Hidden by Forest, Carvings in Land Attest to Amazon’s Lost World:

For some scholars of human history in Amazonia, the geoglyphs in the Brazilian state of Acre and other archaeological sites suggest that the forests of the western Amazon, previously considered uninhabitable for sophisticated societies partly because of the quality of their soils, may not have been as “Edenic” as some environmentalists contend.

Instead of being pristine forests, barely inhabited by people, parts of the Amazon may have been home for centuries to large populations numbering well into the thousands and living in dozens of towns connected by road networks, explains the American writer Charles C. Mann. In fact, according to Mr. Mann, the British explorer Percy Fawcett vanished on his 1925 quest to find the lost “City of Z” in the Xingu, one area with such urban settlements.

In addition to parts of the Amazon being “much more thickly populated than previously thought,” Mr. Mann, the author of “1491,” a groundbreaking book about the Americas before the arrival of Columbus, said, “these people purposefully modified their environment in long-lasting ways.”

If one wants to recreate pre-Columbian Amazonia, most of the forest needs to be removed, with many people and a managed, highly productive landscape replacing it,” said William Woods, a geographer at the University of Kansas who is part of a team studying the Acre geoglyphs.

“I know that this will not sit well with ardent environmentalists,” Mr. Woods said, “but what else can one say?”

There are two descriptive models which have to be interpreted in different normative frames. First, there is the model whereby before the arrival of the Europeans the New World was lightly populated by indigenous groups which had a minimal impact upon the environment. This is the description. Before the 1960s this was viewed by the mainstream culture as a rationale for the justified conquest of the New World by Europeans, who put the land to productive economic usage, whereas before it had been fallow and under-untilized. After the 1960s many, especially in the environmental movement, inverted the moral valence of the description. Instead of being primitive savages, the native peoples were at balance with the environment. Rather than an outmoded way of life to be superseded, they were a potential model for the future.

The second descriptive model is the one that Charles C. Mann outlines in 1491: New Revelations of the Americas Before Columbus. It posits that in fact the New World was much more heavily populated and its environment more impacted by humanity than we had thought previously. Rather, it suggests that the introduction of Old World diseases resulted in massive population crashes, subsequent to which there was a “re-wilding” of much of the Americas. Mann focuses more on the period before the arrival of Europeans, but if you read the scholarship on the arrival of Paleo-Indians there is a fair amount of evidence that even their appearance resulted in a massive change in the suite of fauna which characterized the New World (e.g., the gray wolf and American bison are also Holocene newcomers, just like man).

Some have argued tat Mann has taken a maximalist position (in fact, some readers have lied and stated that Mann argued that the Amazon was as populated as Bangladesh!). But even granting that Mann may be sampling from the more revisionist tail of the scholarship, I think it is creditable that we need to move away from the extreme position of the first descriptive model. There is a fair amount of circumstantial evidence that New World civilizations had not attained the same level of sophistication and complexity as Old World civilizations (see Guns, Germs, and Steel for some of the reasons why). But it is also likely that the Aztecs and Incas were not sui generis aberrations, but rather one point along the spectrum of social complexity which characterized the New World.

This is a subtle point though, because the new model also has normative ramifications. I state above that New World civilizations were not as complex or developed as Old World ones, and that is not a position that many are comfortable with. Rather, they may want to assert that the New World societies were just as complex and sophisticated as the Old World civilizations, that fundamentally all civilizations have equal value and similar character. Therefore, these partisans are particularly enthusiastic about the model which Charles C. Mann popularizes in 1491, as it reverses the narrative of noble simple savages, projecting the indigenous as highly cultured, and only brought down by the biological weapons which Europeans brought.

Where does that put those who wish to construct a plausible model of reality, rather than a mythic history for purposes of ideology? It is lazy to simply pick the position in the middle, but in this case that’s probably the most prudent unless you want to dive into the primary literature yourself. I don’t accept the old model anymore for a variety of reasons, not just having to do with the natural history of the New World. But, I can’t personally assess in detail the magnitude of the numbers that some of the scholars Mann relies upon to revise upward population estimates. So I take the revision with a grain of salt and some caution.

I would conclude that there is one reason I can think of why the Amazon basin might have been more suitable for human habitation that some other wet tropical zones in the Old World: the relative lack of disease. Many wet lowland zones which would otherwise be suitable farmland are lightly populated due to malaria, but this was not an issue in the New World before 1492.

(Republished from Discover/GNXP by permission of author or representative)
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Over at Scientific American Eric Michael Johnson has a very long post up, The Case of the Missing Polygamists. It is a re-post of something he already published at Psychology Today a few years ago. Though provisionally a review of Sex at Dawn, Johnson covers a lot of ground, and also has extensive quotations from Sarah Blaffer Hrdy.

I’m reflecting upon the post for a second time because it is very rich in ideas, and lays out may different general concepts and specific propositions. The bottom line from what I can gather is that Johnson agrees with those thinkers who believe that agriculture and the Neolithic revolution to a great extent reshaped social relations, and give us a skewed perception of “normal” human societies. I’m not going to rehash all of the points in the piece, but will focus on just a few which I think I can extend upon fruitfully.

Long time readers of this weblog know that I tend to accept that something radical shifted during the Neolithic revolution. I’m of the opinion that like most animals humanity’s state was Malthusian during the age of hunter-gatherers, and of farmers. That is, gains in population eventually absorbed productivity increases due to technology (e.g., bow and arrow) or surplus land (e.g., settlement of the New World by humans). But different forms of Malthusianism can obtain different stable states. The rhythm of life of a Chinese peasant and a Bushmen are very different, despite the fact that both may operate on the Malthusian subsistence margin. Malthusianism is a end point, it does not specify the dynamic by which one proceeds toward it.

Johnson relays the idea that prior to agriculture humanity had a matrifocal and de facto polyamorous bias. For the purposes of my thought here we need to separate the social and biological. In the social sense matrifocality simply means that males move between focal groups, while females remain in their natal groups. Polyamory implies that males and females may have multiple sexual relationships. In a genetic sense matrifocality should imply that Y chromosomes flow between groups (lower Fst), and mitochondrial lineages exhibit greater geographical constraint (higher Fst). In the longer term equitable pure polyamory would not be genetically distinguishable from pure equitable momogamy (because of more combinations in the former case there may be more diverse autosomal haplotypes, but I’m not sure this is very relevant for this discussion).

It isn’t innovative or surprising for someone to assert that agriculture was a major rupture in human history. Major public intellectuals routinely take a shot at characterizing what made it so special, and it’s a lively area of scholarship. Rather, I will reiterate here what I have held for many years: the “traditional” and normative social systems common among civilized societies since the rise of agriculture and the emergence of mass society are cultural adaptations which serve to constrain impulses which are deeply hard-wired within our species. Elite lineages the world over arranged the pair bonds of their offspring for many generations, and yet this often meets resistance, or at least resignation. The tales of adulterous lovers subject to a tragic fate are common literary motifs. This is I suspect an aspect of evoked culture, the inevitable tension between our deep impulses driven by individual preferences, and the social obligations which many have to had fulfill as part of extended kinship networks which had accrued prestige and capital. Both of these are human universals, as are the consequences. The high culture literature records this tension, and elaborates upon it so as to model proper and correct behavior for elites so as to avoid tragedy.

I have no doubt that hunter-gatherer societies had lineages which accrued prestige and capital. The modern hunter-gatherer societies which Eric Michael Johnson highlights are not representative of the human past. They have been relegated to marginal land. In the past hunter-gatherer societies drew upon lands with greater primary productivity, so the chasm between themselves and their farming successors in terms of physical capital and social stratification was often less than we may expect using the modern relics as references. But, agriculture clearly signaled a shift in scale and quantity. Super-male lineages, such as that of Genghis Khan, are possible only due to the contingent conditions of civilization, in particular all the elements necessary for globalism. Agriculture was likely an amplification of a “winner take all” dynamic in the game of social positioning. And not surprisingly these societies also developed complex belief systems and institutions to moderate and dampen these tendencies, likely due to their innate instabilities, as well as a human bias toward egalitarianism (i.e., land redistribution and opposition to inequality is a tendency in many societies at the commanding heights, while world religions all exhibit an anti-Nietzschean bent, for lack of a better term).

The reason that “Western culture” with its individualist ethos is so attractive, and threatening, is that in many ways it is a purer reflection of the impulses which were operative in the ancestral environment. I am not here talking about the most extreme manifestations of Western liberality in sexual mores, such as gay marriage or formal polyamory (most people do not crave homosexual relations). Rather, a modicum of personal choice and sexual egalitarianism, are out of keeping with the norms which were necessary to maintain social order in the period between small-scale hunter-gatherer societies and the rise of the mass consumer society. On the margins of subsistence in a world of farmers individual action may redound very negatively upon the broader kinship group, so personal norms of honor and propriety may be highly developed.

And yet if these cultural norms were so strong why did humans not evolve their way out of their hunter-gatherer ethos? There are two primary reasons for this. First, for much of human history the norms outlined in high culture texts and religions were applicable only to elite lineages. This is history recorded in the texts, but it may not be most of lived human history. For example, religious marriages in much of medieval Europe were obligate for noble families, but may not have been for peasants, who made recourse to common law relationships. Bastardy is less of a concern in scenarios where property divisions are of no consequence. There’s no property to inherit. But, this phenomenon is probably moderated by the fact that over much of history elite lineages may have been more fecund than the masses. Lived history may be more ephemeral than we realize in a genetic sense.

A second explanation though is that the very tendencies which make adherence to traditional norms somewhat discomforting on an individual level are necessary in other contexts. Love is an inconvenience when it comes to arranging marriages for your offspring optimally on a social dimension, but it may be necessary for men and women to invest in their offspring due to the love they feel for them so that they live and flourish. In other words, psychological impulses which were inconvenient in one domain were necessary and adaptive on others. Phenotypically I’m implying that there was functional constraint, and genetically it would manifest as pleiotropy. I suspect that a strong tendency toward developing loving bonds with children is a much more important characteristic in these elite lineages than dampening the initial discomfort that may occur when one is paired off with someone with whom one is not particularly enamoured. In a social and biological evolutionary sense romantic love is less important than we might think in our individualist age. But, romantic love remains hard-wired within us because it is biologically impossible to suppress its manifestation so long as we need the emotion of love more importantly to bind us together with children.

Finally, let’s go back to Johnson’s treatment of the disjunction between idealized polyamory and realized polygyny in the ancient environment (at least to a mild extent). By this, he points to the reality that some of the Y chromosomal data point to a reproductive skew, where a few males tend to give rise to a disproportionate number in the next generation. In extreme polygyny you have a Genghis Khan situation, where males of one narrow lineage have an enormous reproductive advantage. The scenario sketched out in Johnson’s post is that females may have had relationships with several males (and the inverse), but there was a tendency toward favoring reproduction with one focal male or female. This does not seem to negate the reality of jealousy and drama. We see this among common chimpanzees, who have a classic mating system in the extreme sense outlined by Johnson (this species has huge testicles to generate viscous sperm the competition is so extreme). And modern polygamorists who have formal relationships all tell tales of enormous time investments necessary to maintain proper relationship equilibrium. This is I think the reason that elite lineages in mass agricultural societies turned toward simpler relationship networks. The older model was simply not sufficiently stable for the purposes of maintaining the social and cultural systems necessary for the proper functioning of the older Malthusian civilizations. This is evident when conflicts within elite lineages are often rooted in questions of paternity and maternity (half siblings; Charles Martel was the bastard son of his father, who superseded the legitimate line), or accusations of false paternity (the first Chinese Emperor was subject to this rumors due to his bad reputation in later generations).

Where does this lead us? I think it’s complicated. Many social conservatives would argue that you can’t just dispense with the whole cultural toolkit which has organically evolved over the last 10,000 years, and revert back to the more primal state of affairs before agriculture. Social liberals point out that the forms of the past are no longer necessary in the present. But though affluence has removed many necessary social constraints, we have not warped ourselves back to the Paleolithic either. The balance between our instincts, which evolved in small groups thousands of years ago, and our notional cultural mores, which crystallized during the Axial Age, is still a work in progress. I believe that the world religions were version 1.0 in regards to formalizing workable compromises between our basic natures and the realities of the aristocratic world. What we need is a version 2.0, where we balance the needs of the common person on the street, with their basic impulses. The great compromise between our biology and our current social complexity will continue. But it is a dynamic parameter, not a static element.

(Republished from Discover/GNXP by permission of author or representative)
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Dienekes has an important post up, The womb of nations: how West Eurasians came to be. He outlines a scenario where a rapid expansion of a farming population has overlain much of Western Eurasia, atop aboriginal substrata. A few years ago you’d have laughed at such a model, mostly due to the authority of archaeologists and phylogeographers relying on mtDNA lineage distributions. No longer. This is not necessarily an orthodoxy, and the details of the model vary, but here is my verbal rendering of the simplest scenario:

1) ~50 thousand years hybridization between Eurasian hominins and “Out of Africa”

2) ~40-10 thousand years before the present, crystallization of the Paleolithic order of human population structure, derived from groups seeded in the original migration

3) ~10 thousand to a few thousand years before the present, the Paleolithic order is replaced and assimilated by farmers expanding from a few hearths

Below the fold is a stylized tree representation of what I have in mind.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Agriculture, Anthropology, Genetics, Genomics 
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Ancient DNA suggests the leading role played by men in the Neolithic dissemination:

The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a “multimarkers” approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.

Some notes:

- Otzi the Iceman is G2a.

- A continuity of local maternal lineages would not be so surprising. Recall that ~50% of Argentine mtDNA seems to be indigenous, even though they’re ~80% European in total ancestry, and ~95% European in the paternal line.

- This is not limited to Latin America. In South Asia the majority of the maternal lineages are non-West Eurasian, while the majority of paternal lineages are West Eurasian. Autosomal ancestry seems to be about half West Eurasian.

- There are now several instances of Neolithic settlements yielding relatively rare paternal lineages, which are almost certainly intrusive, but left little impact. The authors step forward with the most plausible, and frankly suprising, rationale:

The high frequency of G2a haplogroup in Neolithic specimens, whereas this haplogroup is very rare in current populations, also suggests that men could have played a particularly important role in the Neolithic dissemination that is no longer visible today. This would imply that intra-European migrations related to the metal ages may have strongly affected the modern
gene pool.

In other words, the European paternal lineage landscape may not be determined primarily by the hunter-gatherers or first farmers, but subsequent groups. The relative lack of the two dominant European haplogroups, R1a and R1b, is particularly notable. What’s going on? Perhaps male lineages were “winner-take-all,” and have a tendency to rise to near fixation and then shift toward extinction, more than female lineages? The Genghis Khan haplotype story may be less exceptional than we think. If this is right then we need to be very careful about the historical lessons we draw from mtDNA and Y chromosomes, because they may give us a skewed and unrepresentative picture of the demographics of the past.

(Republished from Discover/GNXP by permission of author or representative)
• Category: Science • Tags: Agriculture, Genetics, Genomics, Human Genetics 
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Razib Khan
About Razib Khan

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