Ancient European DNA and some debatable conclusions

There is a rather interesting paper still in preparation available online and causing some debate.

Iosif Lazaridis, Nick Patterson, Alissa Mittnik, et al., Ancient human genomes suggest three ancestral populations for present-day Europeans. BioArxiv 2013 (preprint). Freely accessible → LINK [doi:10.1101/001552]

Abstract

Analysis of ancient DNA can reveal historical events that are difficult to discern through study of present-day individuals. To investigate European population history around the time of the agricultural transition, we sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany and an ~8,000 year old hunter-gatherer from the Loschbour rock shelter in Luxembourg. We also generated data from seven ~8,000 year old hunter-gatherers from Motala in Sweden. We compared these genomes and published ancient DNA to new data from 2,196 samples from 185 diverse populations to show that at least three ancestral groups contributed to present-day Europeans. The first are Ancient North Eurasians (ANE), who are more closely related to Upper Paleolithic Siberians than to any present-day population. The second are West European Hunter-Gatherers (WHG), related to the Loschbour individual, who contributed to all Europeans but not to Near Easterners. The third are Early European Farmers (EEF), related to the Stuttgart individual, who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model the deep relationships of these populations and show that about ~44% of the ancestry of EEF derived from a basal Eurasian lineage that split prior to the separation of other non-Africans.

Haploid DNA

The Lochsbour skull.
The prominent browridge
is very unusual for
Paleolithic Europeans.

The new European hunter-gatherer samples carried all Y-DNA I and mtDNA U5a and U2e.

More specifically, the hunter-gatherer mtDNA lineages are:

• Lochsbour (Luxembourg): U5b1a
• Motala (Sweden):
• Motala 1 & 3: U5b1a
• Motala 2 & 12: U2e1
• Motala 4 & 6: U5a2d
• Motala 9: U5a2

Additionally the Stuttgart Linear Pottery farmer (female) carried the mtDNA lineage T2c1d1.

The Y-DNA lineages are:

• Lochsbour: I2a1b*(xI2a1b1, I2a1b2, I2a1b3)
• Motala 2: I*(xI1, I2a2,I2a1b3)
• Motala 3: I2*(xI2a1a, I2a2, I2b)
• Motala 6: uncertain (L55+ would make it Q1a2a but L232- forces it out of Q1)
• Motala 9: I*(xI1)
• Motala 12: I2a1b*(xI2a1b1, I2a1b3)

These are with certainty the oldest Y-DNA sequences of Europe so far and the fact that all them fall within haplogroup I(xI1) supports the notion of this lineage being once common in the subcontinent, at least in some areas. Today I2 is most common in Sardinia, the NW Balcans (Croatia, Bosnia, Montenegro), North Germany and areas around Moldavia.

I2a1b (which may well be all them) is currently found (often in large frequencies) in the Balcans and Eastern Europe with some presence also in the eastern areas of Central Europe. It's relative I2a1a is most common in Sardinia with some presence in SW Europe, especially around the Pyrenees. I2a1 (probably I2a1a but not tested for the relevant SNPs) was also found, together with G2a, in a Chalcolithic population of the Treilles group (Languedoc) and seems to be somehow associated to Cardium Pottery Neolithic.

If you want my opinion, I'd think that I2a before Neolithic was dominant, like mtDNA U5 (and satellites U4 and U2e), in much of Central and Eastern Europe but probably not in SW Europe, where mtDNA U5 seems not so much hyper-dominant either, being instead quite secondary to haplogroup H (at least in Western Iberia). But we'll have to wait until geneticists manage to sequence Y-DNA in several SW European Paleolithic remains to be sure.

Autosomal DNA and derived speculations

Most of the study (incl. the must-read supplemental materials) deals however with the autosomal DNA of these and other hunter-gatherers, as well as of some Neolithic farmers from Central Europe and Italy (Ötzi) and their comparison with modern Europeans. 

To begin with, they generated a PCA plot of West Eurasians (with way too many pointless Bedouins and Jews, it must be said) and projected the ancient Europeans, as well as a whole bunch of Circum-Pacific peoples on it:

The result is a bit weird because, as you can see, the East Asians, Native Americans and Melanesians appear to fall way too close to the peoples of the Caucasus and Anatolia. This seems to be a distorting effect of the "projection" method, which forces the projected samples to align relative to a set of already defined parameters, in this case the West Eurasian (modern) PCA. 

So the projection basically formulates the question: if East Asians, etc. must be forcibly to be defined in West Eurasian (WEA) terms, what would they be? And then answers it as follows: Caucasian/Anatolian/Iranian peoples more or less (whatever the hidden reasons, which are not too clear).

Similarly, it is possible (but uncertain) that the ancient European and Siberian sequences show some of this kind of distortion. However I have found experimentally that the PCA's dimension 1 (but not the dimension 2, which corresponds largely to the Asian-specific distinctions) still correlates quite well with the results of other formal tests that the authors develop in the study and is therefore a valuable tool for visualization.

But this later. By the moment the PCA is asking and answering three or four questions by projecting ancient European and Siberian samples in the West Eurasian plot:

• If ancient Siberians are forced to be defined in modern WEA terms, what would they be? Answer: roughly Mordvins (Afontova Gora 2) or intermediate between these and North Caucasus peoples (Mal'ta 1).
• If ancient Scandinavian hunter-gatherers are forced in modern WEA terms, what would they be? Answer: extreme but closest (Skoglund) to Northern European peoples like Icelanders or Lithuanians.
• If ancient Western European hunter-gatherers are forced in modern WEA terms, what would they be? Answer: extreme too but closest (La Braña 2) to SW European peoples like Basques and Southern French.
• If ancient Neolithic/Chalcolithic farmers from around the Alps and Sweden are forced in modern WEA terms, what would they be? Answer: Canarians (next close: Sardinians, then Spaniards).

Whatever the case, there seems to be quite a bit of autosomal diversity among ancient Western hunter-gatherers, at the very least when compared with modern peoples. This makes some good sense because Europe was a big place already in Paleolithic times and must have harbored some notable diversity. Diversity that we may well find to grasp if we only sample people from the same areas once and again.

On the other hand, they seem to cluster in the same extreme periphery of the European cluster, opposed to the position of West Asians, and therefore suggesting that there has been some West Asian genetic flow into Europe since then (something we all assume, of course). 

Using Lochsbour as proxy for the WHG (Western hunter-gatherer) component, Mal'ta 1 as proxy for the ANE (ancient north Eurasian) one and Stuttgart as proxy for the EEF (early European farmer) one, they produce the following graph (to which I added an important note in gray):

The note in gray is mine: highlighting the contradictory position where the other Western hunter-gatherers may fall in because of assuming Lochsbour as valid proxy, when it is clearly very extreme. This was not tested in the study so it is inferred from the PC1, which seems to best approach the results of their formal tests in the WHG vs EEF axis, as well as those of the WHG vs Near East comparisons.

I tried to figure out how these formal tests are reflected, if at all in the PCA, mostly because the PCA is a much easier tool for comprehension, being so visual. Eventually I found that the dimension 1 (horizontal axis) is very close to the genetic distances measured by the formal tests (excepted those for the ANE component, obviously), allowing a visualization of some of the possible problems caused by their use of Lochsbour as only reference, without any control. Let's see it:

The same PCA as above with a few annotations in magenta and green

While not exactly, the slashed vertical magenta line (median in the dimension 1 between Lochsbour and Stuttgart) approximates quite well the WHG vs EEF values measured in the formal tests. Similarly, the slashed green axis (median in PC1 between Lochsbour and an good looking Bedouin) approximates to a great extent the less precise results of the formal tests the authors applied to guesstimate the West Asian and WHG ancestry of EEFs, which ranged between 60% and almost 100% West Asian (my line is much closer to the 60% value, which seems more reasonable). 

When I tried to find an alternative median WHG/West Asian line, using Braña 2 and the first non-Euro-drifted Turk I could spot (Anatolia is much more likely to be the direct source of West Asian ancestry in Europe than Bedouins), I got exactly the same result, so no need to plot any second option (two wrongs sometimes do make one right, it seems). But when I did the same with La Braña 2 and Stuttgart I got a genuine good-looking alternative median line, which is the slash-and-dot magenta axis.

This alternative line is probably a much more reasonable 50% WHG-EEF approximation in fact and goes right through Spain, what makes good sense for all I know.

Of course the ideal solution would be that someone performed good formal tests, similar to those done in the study, with Braña 2 and/or Skoglund, which should be more similar to the actual WHG ancestry of modern Europeans than the extremely divergent Lochsbour sequence. An obvious problem is that La Braña produced only very poor sequences but, well, use Skoglund instead or sample some Franco-Cantabrian or Iberian other Paleolithic remains.

Whatever the solution, I think that we do have a problem with the use of Lochsbour as only WHG proxy and that it demands some counter-testing. 

What about the ANE component? I do not dare to give any alternative opinion because I lack tools to counter-analyze it. What seems clear is that its influence on modern Europeans seems almost uniformly weak and that it can be ignored for the biggest part. As happens with the WHG, it's quite possible that the ANE would be enhanced if the sequence from Afontova Gora is used instead of that of Mal'ta but I can't foresee how much. 

Finally some speculative food-for-thought. Again using the visual tool of the PCA, I spotted some curiosities:

Speculative annotations on the PCA

Most notably it is apparent that the two WHG populations (Western and Scandinavian) are aligned in natural axes, which seem to act as clusters. Extending both (dotted lines) they converge at a point closest to some French, notably the only "French" that tends towards "Southern France" and Basques. So I wonder: is it possible that these two WHG cluster-lines represent derived ancient branches from an original population of SW France. We know that since the LGM, the area of Dordogne (Perigord) was like the megapolis of Paleolithic Europe, with population densities that must have been several times those of other areas. We know that this region was at the origin of both Solutrean and Magdalenian cultures and probably still played an important role in the Epipaleolithic period. 

So I do wonder: is that "knot" a mere artifact of a mediocre representation or is it something much more real? Only with due research in the Franco-Cantabrian region we will find out. 

Neanderthals, Denisovans and everything else

A recent analysis of the nuclear DNA of a Neanderthal toe from Altai has caused widespread interest.

Kay Prüffer et al., The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2013. Pay per view → LINK [doi:10.1038/nature12886]

The story of a finger and a toe

Both the Denisovan and Neanderthal DNA sequences discussed in this paper come from small bones found at the same location: Denisova cave, Altai Republic. The Denisovan sequence that revolutionized human paleogenetics a few years ago corresponds to a finger phalanx bone of some 50,000 years ago. The less notorious Neanderthal sequence discussed in this study corresponds to a toe imal phalanx, which was found in a lower layer in the same gallery of the same cave, and hence should be older.

This is very interesting to underscore because it seems to imply that Neanderthals were in Altai and specifically in Denisova cave very early, at dates similar to those we find in West Asia (Tabun excepted) and they may even be older than Denisovans in the very cave that gave them their name.

The toe sequence was found in a previous study to have Neanderthal mtDNA, closely related to the lineages of European Neanderthals of various dates and sites. Instead the finger mtDNA (Denisovan) was derived from a more ancient branch of humankind than the very point of split between Neanderthals and modern humans (H. sapiens) and has been recently shown to be related to European H. heidelbergensis from Atapuerca. 

Notes in red are mine.

This study focuses on the autosomal DNA of both Neanderthals and Denisovans. Unlike mtDNA, whose phylogenetic position is simple and quite straightforward, autosomal or nuclear DNA (nDNA) is extremely much more complex to understand because of its recombining nature, requiring of statistical approaches, which may get extremely complex and potentially subject to premise biases. When comparing two individuals this gets largely simplified but it is a lot more complex when doing the same with larger samples.

And that is precisely what this study does: comparing one Denisovan, several Neanderthals and also several modern humans. Therefore it is a very complex paper and the authors necessarily assume some evaluation risks, which nevertheless are discussed in depth in the supplemental material, a methodology of the Pääbo team that we can't but greatly appreciate.

Age estimates

The study makes two age estimates, one based on a very conservative and truly unbelievable Pan-Homo split date of 6.5 Ma BP and the other based on observed per generation mutation rates, which happens to be perfectly coincident with a Pan-Homo split of 13 Ma BP, the oldest extreme of Langergraber's estimate. This coincidence alone is of enough relevance for all molecular clock approaches, because it effectively demands the doubling of all age estimates based on the ridiculously short 6.5 Ma Pan-Homo split supposition. 

Red outlines are mine. Click to enlarge.

It also produces a semi-reasonable San-West African age estimate of c. 86-130 Ka, although I would think it a bit older in fact or at the very least at the top end. This highlights the severe difficulties of such molecular clock estimates, because a 4 Ma divergence between the alleged introgressing mystery archaic in the Denisovan genome, seems out of the question according on the archaeological and paleontological record, which only documents Homo species since c. 2 Ma ago, half that time (within the estimate but clearly very far from the top end).

Altai Neanderthal inbreeding

An important finding of this study is that the studied individual was extremely inbred, with parents in effective relationship comparable to that of grandparent and grandchild or half siblings. This inbreeding tendency, even if extreme, is not so strange in populations that have experienced founder effect bottlenecks and small population sizes. The Denisovan and the modern human Karitiana people are not so extreme but range in the lower end of double first cousins level of genetic relationship between the parents. Other Native Americans like the Mixe are close to that range, while the other compared populations, Papuans and Sardinians, show much lower levels of inbreeding.

Whatever we may think of Altai Neanderthal inbreeding, their drift parameter is still very low when compared with European Neanderthals. This is not discussed in the paper but such extreme drift also seems to imply extreme inbreeding issues in European Neanderthals, even if these may have other causes such as an extremely strong founder effect or whatever.

Bonobo-specific segments were removed, so the bonobo position is not realistic.

Inferred population history

Both populations leading to the Altai Neanderthal and Denisovans, but not modern humans, appear to have gone through a strong decline in population size since hundreds of millennia ago. The Denisovan decline seems to begin c. 800 Ka ago while the Neanderthal one may have begun c. 500 Ka ago. While this is coincident with a general expansion of the H. sapiens branch (still undifferentiated in Africa), peaking around c. 250 Ka ago before differentiation and relative decline. In their words:

All genomes analysed show evidence of a reduction in population size that occurred sometime before 1.0 million years ago. Subsequently, the population ancestral to present-day humans increased in size,whereas the Altai and Denisovan ancestral populations decreased further in size. It is thus clear that the demographic histories of both archaic populations differ substantially from that of present-day humans.

Neanderthal and Denisovan admixture in modern humans

The new tests confirm in essence the previous findings: there is significant Neanderthal introgression in modern humans descending from the migrants out of Africa and there is also significant Denisovan one among Australasian populations.

Additionally and with some caution, the authors think that much lesser Denisovan introgression (of around 0.2%) is found among East Asians and that these, as well as Native Americans, show slightly more Neanderthal admixture than West Eurasians. In my understanding this may be caused by minor African flow to West Eurasia after the admixture event (and/or residual "First Arabian" persistence) and I would think that measuring South Asians would help to clarify this issue (because African admixture is negligible in the subcontinent but they are also distinct from East Asians).

These measurements are so weak that the authors agree to all kind of cautions about them in any case.

In addition to all this, the supplemental material (section 13) also detects tiny, almost homeopathic, amounts of Neanderthal gene flow to Yorubas (~0.02%), obviously mediated by H. sapiens backflow from Asia and Europe into parts of Africa, which eventually influenced other African populations. An even more diluted amount may also be present among the Mbuti Pygmies.



Altai Neanderthal admixture in Denisovans

This issue is not really explained in the paper as such, and we have to reach out to the Supplemental Information chapter 15 in order to grasp it.

It is clear that the Altai Neanderthals are closer to Denisovans than other Neanderthals are by approx. the following fractions (directly deduced from the raw affinities listed in fig. S6a.2):

• 2% more than Mezhmaiskaya
• 7% more than Vindija (avg.)
• 9% more than El Sidrón

Feldhofer appears closer instead but this sequence was not used by the authors in most tests because it has too dubious quality.

In section 15 of the supplementary material, using complex methodology and lamenting the lack of a second Denisovan sample which would be most useful, they estimate a minimal 0.5% (Altai) Neanderthal introgression in Denisovans, with strong warnings that this could well be quite higher. I don't know why they are not even considering a more direct approach, but I would dare to guesstimate the introgression to be close to 8% from the above raw data, assuming that there are no further complexities at play, such as other Heidelbergensis introgression in European Neanderthals, etc. The drift parameter (see above) does not seem to be one such complexity because Mezhmaiskaya is almost as drifted as Vindija yet it is consistently much closer, as it seems to correspond to its specific relatedness to Altai Neanderthals in mtDNA (and possibly also in nDNA if it is admixture what causes their pseudo-tree positioning closer to the root, what would be typical).

Note in blue is mine.

Mystery archaic genetic flow into Denisovans

The authors find that some 0.5-8% of the Denisovan genome appears to come from another hominin, which split from the human trunk even earlier.

We caution that these analyses make several simplifying assumptions. Despite these limitations, we show that the Denisova genome harbors a component that derives from a population that lived before the separation of Neanderthals, Denisovans and modern humans. This component may be present due to gene flow, or to a more complex population history such as ancient population structure maintaining a larger proportion of ancestral alleles in the ancestors of Denisovans over hundreds of thousands of years.

Later in the discussion section they ponder further the implications of this finding:

The evidence suggestive of gene flow into Denisovans from an unknown hominin is interesting. The estimated age of 0.9 to 4 million years for the population split of this unknown hominin from the modern human lineage is compatible with a model where this unknown hominin contributed its mtDNA to Denisovans since the Denisovan mtDNA diverged from the mtDNA of the other hominins about 0.7–1.3 million years ago⁴¹. The estimated population split time is also compatible with the possibility that this unknown hominin was what is known from the fossil record as Homo erectus. This group started to spread out of Africa around 1.8 million years ago⁴², but Asian and African H. erectus populations may have become finally separated only about one million years ago⁴³. However, further work is necessary to establish if and how this gene flow event occurred.

Going to the detail of the matter (i.e. supplemental material sections 16a and 16b), one of the key details is that present-day Africans share more derived alleles with Neanderthals than with Denisovans. This can only be explained because Denisovans have other archaic ancestry prior to their apparent divergence from Neanderthals or (what is about the same) because Denisovans diverged themselves prior to the Neanderthal-Sapiens split, what is what the mtDNA (unlike the nDNA) suggests. However the difference, even if consistent across comparisons, is too small (a few percentage points) to be attributed to the later scenario.

This means that Denisovans appear to be at nDNA level some sort of an independent branch of proto-Neanderthals with some other but minor archaic admixture. Instead at mtDNA level they appear to be unrelated to Neanderthals and related instead to H. heidelbergensis (a detail not discussed in this paper because it is a too recent independent discovery).

There are still many details to explore but, in principle, it would seem that the Denisovan branch appears to be a divergent proto-Neanderthal one (maybe related to the Hathnora hominin, which looks very much Neanderthal) with lesser other archaic (H. heidelbergensis?) admixture, which nevertheless remained prominent in their mtDNA for whatever accidental reason.

Whether the H. heidelbergensis population of Atapuerca responds to this same profile (i.e. they were Denisovans too) or belongs instead to the "other archaic" population which introgressed in the Denisovan genome remains to be solved. So far we only know the mitochondrial lineage and this one may be misleading, as seems to be the case with the Denisova hominin.

Note in red is mine

Modern human genetic evolution

Benefiting from the high quality of the archaic genomes of Altai, the authors cataloged a long list of simple mutations exclusive to our species: 31,389 single nucleotide substitutions and 4,113 short insertions and deletions (indels). Additionally they found other 105,757 substitutions and 3,900 indels shared by 90% of their modern human sample of 1094 individuals.

They suggest some lines for future research in this regard, maybe focusing on genes known to influence brain development or regions that could show signs of positive selection. These preliminary lines of research are explored in SI-20, noticing potential selection in genes that affect the ventricular zone of the brain and cell proliferation in fetal brain development.

Machiavellism, social dominance orientation and authoritarianism are tightly related (and subclinically psycopathic)

Depending on one's ideology this may seem either obvious or counterintuitive but that is what a powerful set of five successive studies has found.

Laura Niemi & Liane Young, Caring across Boundaries versus Keeping Boundaries Intact: Links between Moral Values and Interpersonal Orientations. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0081605]

Abstract

Prior work has established robust diversity in the extent to which different moral values are endorsed. Some people focus on values related to caring and fairness, whereas others assign additional moral weight to ingroup loyalty, respect for authority and established hierarchies, and purity concerns. Five studies explore associations between endorsement of distinct moral values and a suite of interpersonal orientations: Machiavellianism, prosocial resource distribution, Social Dominance Orientation, and reported likelihood of helping and not helping kin and close friends versus acquaintances and neighbors. We found that Machiavellianism (Studies 1, 3, 4, 5) (e.g., amorality, controlling and status-seeking behaviors) and Social Dominance Orientation (Study 4) were negatively associated with caring values, and positively associated with valuation of authority. Those higher in caring values were more likely to choose prosocial resource distributions (Studies 2, 3, 4) and to report reduced likelihood of failing to help kin/close friends or acquaintances (Study 4). Finally, greater likelihood of helping acquaintances was positively associated with all moral values tested except authority values (Study 4). The current work offers a novel approach to characterizing moral values and reveals a striking divergence between two kinds of moral values in particular: caring values and authority values. Caring values were positively linked with prosociality and negatively associated with Machiavellianism, whereas authority values were positively associated with Machiavellianism and Social Dominance Orientation.

A synthesis of the results of the five studies is presented in figure 2:

Figure 2. Summary of correlations observed across all studies.
Each square represents an observation of a significant partial correlation (politics, religion, and gender controlled). Each circle represents an observation of a significant zero-order correlation. Study (#) indicated on each circle/square. Moral values are color-coded.

"Mach" means Machiavellianism and "SDO" means social dominance orientation, which are clearly and positively correlated among them, via the same set of "group values" (ingroup loyalty, authority and purity). Instead helping those close to oneself and prosocial distribution are very positively correlated among them and associated with the "humanist values" or caring and fairness.

This is very much counterintuitive, especially as the authors use the term "individualizing" for the caring and fairness values, which makes absolutely no sense to me, as individualism means selfishness and aloofness, even misanthropy. Hence I replaced that term for "humanist" although I also pondered "personalist" (as the person can be something more whole and socially connected than the individual).

The produce of the two sets of values is even more at odds with the concept individualism. In fact it is the group (or "binding and dividing") value people who actually strive for social dominance and favor Machiavellianism. This is because they do not think in the group as extensive but as intensive and almost certainly as tool for their own individualist selfish goals. 

Interestingly:

Most interpersonal behavior requires individuals to balance selfish motivation with prosocial motivation – to be a positive social partner who helps other people. These orientations are not mutually exclusive – care for the self is at times necessary to enable care for others. However, for some individuals, a motivation to dominate or exploit the group for selfish aims, measureable as Machiavellianism [20] or Social Dominance Orientation [21], may take precedence. Individuals high in Machiavellianism (“Machs”) admit to employing manipulation and deception to achieve power, status, control, and financial success [20]. These goals require successful management of group relations, which may in turn shed light on the paradoxical nature of Machiavellianism. Machs are often described as socially skilled, well-liked, popular, and excellent at building alliances [22], but they are also subclinically psychopathic [23] and exploitative of others' trust [24], [25]. Machiavellian negotiation of relationships and social structures for personal gain may benefit from a moral stance that elevates values like loyalty and deference to authority. More specifically, these values are critical for the preservation of existing social order but largely insensitive to concerns about caring and fairness. Moralization of these values – alongside relative indifference to caring and fairness values – could facilitate strategic hierarchy management while freeing the individual to feel morally justified in engaging in manipulative or exploitative behavior.

Subclinically psychopathic is a most revealing concept. I have often though of this as a real social problem of first order. The subclinicality may only be because psychiatry has established a boundary not to touch the powerful, what would be playing with fire. But, as we will see below, there is more to it.

What happens with social dominance orientation?

Relatedly, Social Dominance Orientation (SDO) is characterized by a desire for inequality and a tendency to categorize people along a hierarchical “superior-inferior dimension” [21]. SDO, like Machiavellianism, has been found to predict various antisocial outcomes, including explicit racism and sexism as well as reduced empathy and concern for others [21], [26], [27]. While SDO has previously been identified as negatively correlated with individualizing values and positively correlated with binding values [2], SDO has not yet received attention for its potential positive connection with binding values when political orientation is controlled. Since an orientation towards social dominance requires a strict hierarchical worldview, a positive correlation between SDO and authority values, regardless of political orientation, would be predicted [2].

Later in the discussion they turn back to "Machs":

What could account for the positive relationship between respect for authority and Machiavellianism, an antisocial interpersonal style associated with strategic manipulation? Indeed, Machs have been shown to lie more convincingly [35], steal more readily [36], and rationalize deeds with callous unemotionality [37]. To provide the foundation for two potential explanations for this surprising relationship, we first describe two relevant aspects of Machiavellianism: (1) Machiavellianism and psychopathy are distinct in relation to social norm processing, and (2) Machs are likely to be dominant individuals in positions of authority. Next, we propose two potential explanations for the positive relationships between moral valuation of respect for authority and Machiavellianism: (1) Machiavellianism may entail moralization of respect for authority for a variety of strategic reasons, and (2) authority values may license Machiavellian behavior.

Discussing the subtle differences between Machiavellianism and outright psychopathy:

Although Machiavellianism is characterized by selfishness and shares some overlap with psychopathy [23], Machs are not necessarily aloof and unconcerned with social norms. Instead, the ability to manipulate others may actually benefit from a keen sensitivity to norms that govern social structure.

Instead most clinical psychopaths tend to be aloof. 

Another key difference is that Machs are highly sensitive to punishment, while again true psychopaths may be somewhat indifferent to this social corrector, so Machs retreat and even give away profusely in order to avoid this outcome.

Machiavellianism is also clearly related to dominance and control and, therefore to respect for authority:

In addition to being hyper-attuned to social structure, Machs are also likely to reside at the top of those structures in positions of authority. Machiavellian-style social climbing tactics (e.g., manipulation and deception) are more likely to be used by individuals high in dominance and well-equipped to assume authority over others [38]. Likewise, Machiavellian supervisors in a range of business sectors have been described by subordinates as employing authoritarian work habits involving strict control over a hierarchical workplace structure [46]. As individuals who recognize they can personally benefit from “working the system” from a position of authority – rather than attempting to make the system work for all – Machs may be more likely to identify respect for authority as relevant or even central to their concepts of “right and wrong”.

Ironically Machiavellianism finds in authoritarianism a self-serving morality. Being able to play the game and climb to the top, Machs clearly benefit from such respect to authority themselves and will spread the word among their subordinates. It also helps themselves to self-regulate their behavior in ways that are within the boundaries of the game, yet still selfish. Accepting others' authority acts as self-protection and gives them a moral varnish, internalizing these values allows them more easily to perform their flattery and igratiation climbing tactics (otherwise probably perceived as humiliation).

The authoritarian ethics seem also useful in order to condone otherwise anti-social behaviors such as cheating, graft or torture. Other recent studies have shown that individuals primed to feel high in power – that is, closer to “authority figure” status – were more likely to endorse unethical and antisocial behavior [55], [56].

Something I really miss in this study is the proportion of tendencies among the studied group, which could reflect general distribution in society. While the statistical correlations are systematically produced the proportion and intensity of the values of the actual human sample is not shown.

The authors assume that the prosocial values are generally desirable but in reality what I have found way too often is that many people, especially those in intermediate command positions or with a career to develop, experience serious contradictions between the "official" prosocial or humanist ethics and the "unofficial" but very real Machiavellian one. I would even say that they often feel emotionally broken by this contradiction. And this "they" at least sometimes becomes "we" and "I", so painfully.

It would certainly be interesting to study this contradictory social and psychological reality, even cross-culturally. 

In any case this study does produce some very interesting data that should be most valuable for future and more comprehensive research. It also produces very important information for our meditations on our social and personal reality, and certainly it also applies to past realities, at least since society became complex and hierarchical.

Siberian haploid DNA

A new study is available with plenty of data on the haploid genetics of Siberian populations with focus on Tungusic peoples.

Anna T. Duggan et al., Investigating the Prehistory of Tungusic Peoples of Siberia and the Amur-Ussuri Region with Complete mtDNA Genome Sequences and Y-chromosomal Markers. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0081605]

Maybe the most informative graphic is fig. 1, which shows the scatter of mitochondrial DNA:

Figure 1. Map of Siberia showing approximate locations of sampled populations and their basic haplogroup composition.

For the meaning of abbreviations, check table 1.

Typical NE Asian haplogroups like C and D are quite widely distributed, up to the point of becoming difficult to say much about them. Instead A is more concentrated (Nyukhza, Iengra, both of them Evenks, and Koryaks particularly), while Z does appear to show a similar pattern (but with presence among Kamchatka instead of Koryaks and a relevant distributon in NE Siberia (Berezovka and some Yakuts). 

Haplogroup B is rare instead, only showing up in Southern Yakuts. It must be mentioned in any case because of its relevance in the original peopling of America. 

G is not too common, with the partial exception of G1, which shows an Eastern Siberian concentration.

Y is concentrated among Nivkhs (no surprises here), while F seems most important in Yakutia (like B, it is not a typical Northern lineage but its bulk distribution lays further South).

West Eurasian lineages, marked in Brown are concentrated in the Evens of Nyukhza, as well as among some Yakuts. Their presence among Yakuts is easy to understand considering their partial Turkic ancestry but the Nyukhza even larger apportion seems to me derived of some other kind of contact with Altai and the steppe, although the authors seem to favor Yakut admixture instead.

Premonitory FAQ: 

Which is the difference between "M_N" and "Other"? 

No idea: ask the authors. But I'm quite positive that "Other" cannot mean L(xM,N) but rather "other M and N". Speculatively, it could indicate the difference between some M and N sublineages they have tested for and others which they did not. It's sloppy nomenclature in any case.

Y-DNA

[Important post-script note: excepted the basal SNP markers for C and N, which were tested for, all the haplogroups are defined based on STR markers, what may be wrong].

Table 4 lists the Y-DNA haplogroups for Evenks, Evens, Yakuts and Yukaghirs only. C3c1 is very dominant in the Tungusic populations: 87/127 among Evenks, 43/89 among Evens, but all the opposite among Yakuts (1/184) and rather weak also among Yukaghirs (2/13).

Yakuts are dominated by N1c (173/184), lineage that has also some presence among the other sampled populations: Evenks: 18/127 (Nyukhza and Iengra groups), Evens: 30/89 (particularly Sakkyryyr and Sebjan groups), Yukaghir: 4/13.

Q1 is found mostly among Yukaghirs (4/13) with a single Yakut other case.

N1b is also of some importance among Tungusic peoples: 18/127 among Evenks (Taimyr and Stony Tunguska) and 13/89 among Evens (essentially in Tompo).

C3* is found mostly among Nyukhza Evens (13/78), who also harbor most of the Western lineage I detected in the area (4/78). 

The other meaningful Western lineage spotted is, of course, R1a, which is found in two variants: R1a(xR1a1) is concentrated among Taimyr Evenks (3/18) with only another sample among Stony Tunguska Evenks (1/40). R1a1 instead is concentrated among Yakuts (4/184).

There are also erratics (isolated single-individual samples) of C*, J2, O and F*.

There is also other interesting material in the study but I can only extend myself so much. I strongly recommend reading it for everyone with interest in Siberian and related populations, be these Uralics, Native Americans or generally East and Central Asians.

Poverty directly damages brain development

Children that at early ages have similar or even greater gray matter than their wealthier peers, get stuck in a weaker development as they grow just for being poor. That is what a new study has found:

Jamie L. Hanson et al., Family Poverty Affects the Rate of Human Infant Brain Growth. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0080954]

Abstract

Living in poverty places children at very high risk for problems across a variety of domains, including schooling, behavioral regulation, and health. Aspects of cognitive functioning, such as information processing, may underlie these kinds of problems. How might poverty affect the brain functions underlying these cognitive processes? Here, we address this question by observing and analyzing repeated measures of brain development of young children between five months and four years of age from economically diverse backgrounds (n = 77). In doing so, we have the opportunity to observe changes in brain growth as children begin to experience the effects of poverty. These children underwent MRI scanning, with subjects completing between 1 and 7 scans longitudinally. Two hundred and three MRI scans were divided into different tissue types using a novel image processing algorithm specifically designed to analyze brain data from young infants. Total gray, white, and cerebral (summation of total gray and white matter) volumes were examined along with volumes of the frontal, parietal, temporal, and occipital lobes. Infants from low-income families had lower volumes of gray matter, tissue critical for processing of information and execution of actions. These differences were found for both the frontal and parietal lobes. No differences were detected in white matter, temporal lobe volumes, or occipital lobe volumes. In addition, differences in brain growth were found to vary with socioeconomic status (SES), with children from lower-income households having slower trajectories of growth during infancy and early childhood. Volumetric differences were associated with the emergence of disruptive behavioral problems.

Figure 2. This figure shows total gray matter volume for group by age.

The data is clear (for details of the localized frontal and parietal evolution see figs. 3 and 4). The question is: why does this happen? The paper attempts also to discuss that:

These results extend a consistent literature in rodents, non-human primates, and humans suggesting that early environments marked by stress or deprivation negatively influence brain development [65]–[69]. This emerging body of research has found differences in brain structure in portions of the frontal lobe, which fits well with the analysis presented here [68]. These findings suggest that aspects of low SES environments have important functional implications for children's health and adaptation [70], perhaps by influencing key features of central nervous system development. In regards to neurobiological mechanisms, the differences in volume we find are likely due to neuronal remodeling, rather than birth of new neurons (or neurogenesis) [27], [71], [72].

(...)

Candidate factors might include the effects of household resources, environmental stimulation, crowding, exposure to pathogens and noise, parental stress, and nutrition. It is also possible that pre-natal experiences affect brain development and reflect other disadvantages and risks related to poverty. Because humans are able to adapt to a range of environmental conditions, we must understand more about the level at which impoverished environments become toxic for children.

And quite suggestively in the introduction they mention as well that:

Conditions such as the variety and complexity of the stimuli in an animal's cage can influence different aspects of brain structure, including the number of neurons, glial cells, myelination, dendrites, synapses, and neurogenesis (for review, see Ref. [23]–[24]). 

The specific causes can be many but I'd dare say that "caging", i.e. the limitation of stimuli for living in smaller, impoverished, artificial habitats (including of course whatever limitations that the adults around them may have, such as low culture or emotional instability) is likely to be a key negative environmental factor for brain development.

On the other hand I can imagine that certain enrichment (cultural, health even technological, why not?) that has happened to our species in general in the last centuries, may be behind the so-called Flynn effect, which is that the measured IQ has been growing everywhere quite steadily. 

But in any case it is quite worrying that these social differences have such a big effect on the children and emphasizes the need to overcome them and to provide the best possible environment for the development of the future generations.

Ancient East Asian Y-DNA maps

I'm fusing here data from two different and complementary sources:

• Hui Li et al. Y chromosomes of prehistoric people along the Yangtze River. Human Genetics 2007. → LINK (PDF) [doi:10.1007/s00439-007-0407-2]
• A 2012 study integrally in Chinese (so integrally that I don't even know who the authors are → LINK) but whose content was discussed in English (after synthetic translation) at Eurogenes blog. I deals with a variety of ancient Y-DNA from the Northern parts of P.R. China.

Update (Dec 25): much of the Northeastern aDNA is also discussed in an English language study (h/t Kristiina):

Yinqiu Cui et al. Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China. BMC 2013. Open access → LINK [doi:10.1186/1471-2148-13-216]

Combining the data from both sources, I produced the following maps:

Neolithic (before ~4000 BP):

Metal Ages (after ~4000 BP):

Discussion

I find particularly interesting the first map because it outlines what seem to be three distinct ethnic (or at the very least genetic) regions in the Neolithic period:

• A Central-South region dominated by O3
• An Eastern area around modern Shanghai dominated by O1
• A Northern region dominated by N

Later on, in the Metal Ages, a colonization of the North/NE by these O3 peoples seems apparent, followed, probably at a later time, by a colonization of the West (Taojiazhai).

We do not have so ancient data for the West but we can still see a diversity of lineages, notably Q (largely Q1, if not all), C (most likely C3, also in the NE) and N (also in the NE). While the arrival of O3 to this area was probably late, the arrival of R1a1a is quite old, however it is still almost certainly related to the first Indoeuropean migrations eastwards, which founded the Afanasevo culture in the area of Altai.

I find also very interesting the presence, with local dominance often, of N (including an instance of N1c) and Q in the Northern parts of P.R. China, because these lineages are now rather uncommon but are still dominant in Northern Asia, Northeastern Europe and Native America. The fact that they were still so important in the Northern Chinese frontier in the Neolithic and even in the Metal Ages should tell us something about their respective histories and, in the case of N, origins as well.

It is also notable that no D was detected anywhere. However the regions with greatest D frequencies like Tibet, Yunnan or Japan were not studied.

See also: Ancient Jomon mtDNA from Japan.

Rhône-Provence Bell Beaker

Just a brief note on two French language papers from a decade ago that have shown up in my academia.edu alerts.

The most relevant one because of its wider scope is:

Olivier Lemercier, Muriel Pellissier & Yaramila Tchérémissinoff, Campaniforme et sépultures, au-delà du standard. La place du Campaniforme dans l évolution des sépultures du sud-est de la France au 3e millénaire avant notre ère. Proceedings of the International Conference held at the Cantonal Archaeology Museum (Sion, Switzerland), 2001. → available (with free registration) at academia.edu.

Abstract (only part in English)

Where are the famous Bell Beaker individual burials in the south east of France? What is the nature of the burials wherein we actually find Bell Beaker elements ? And what kind of Bell Beaker is it ? And also : where does the Bell Beakers stand in the evolution of the funeral architectures and rites between the end of the Middle Neolithic and the Early Bronze Age? Answering these questions, thanks to the presence of more than a hundred funeral sites in the area, would change our vision of the Bell Beakers fenomenon itself. These questions are also the occasion to present the diversity and the traditions of the funeral practices by the 3rd millenium BC.

I took some time to read it in spite of my limited skills at French (but it's still Romance, so well... any educated Romance speaker can read it with some effort) and the overall conclusions are not too surprising: Bell Beaker is not only a burial thing, Bell Beaker appears in burial contexts of older local tradition, etc. 

The details and nuances are many more, of course. On one side the authors discern (much as it happens overall within European Bell Beaker) three groupings: 

• Corded style in Ardèche
• International style in the left margins of the Rhône
• A local variant in the later period

Notice that the authors argue that both the Corded and International styles are roughly contemporary. I can't judge this but, if real, it may mean a blow against the classical notion of Corded style being older and arriving to SW Europe via the Rhône. 

Another interesting aspect of the paper is that the authors argue for overall continuity of burial styles, which are varied:

• individual burials with roots in early Neolithic
• collective burials of both dolmenic-megalithic and cave typology
• other rarer types, with a handful of examples each

Bell Beaker seems mostly related to collective burials, although in the BB period Megalithism seems to recede somewhat in favor of collective burials in caves, a tradition common in other parts of Europe, especially in the South and SW. This really casts all kind of doubts about BB in this region being able to be explained as some sort of migration from Central Europe (or anywhere else) because, unlike in this Indoeuropeanized area, BB individual burials as such are extremely rare; instead we must talk of BB elements inserted in local traditions of collective or "clannish" nature, just as we can see in Iberia and other Western areas where Indoeuropean influences was still non-existent. 

The other paper is:

Robin Furestier et al., 1974-2004 le site du Fortin-du-Saut (Châteauneuf-les-Martigues, Bouches-du-Rhône) et le Campaniforme 30 ans aprés. Congrès du Centennaire: Un siècle de construction du discours scientifique en Préhistoire → available at academia.edu (registration needed as well).

This is about a particular Bell Beaker site near Marseilles, whose typology seems mostly influenced by the Portuguese VNSP civilizational center. Otherwise there is other non-BB pottery without decoration and what seems locally rooted stone tools and arrow points.

If you are fluent in French and happen to find out any error in my interpretation, please feel free to correct me in comments, thanks in advance.

A note on comments

I'm keeping pre-moderation on comments as some individuals who have been banned keep posting and posting and I want them out (also the occasional spambot but not the main reason). 

However I've realized that I do not always get notice of all comments awaiting moderation (as I should), so some comments sit in limbo for longer than they should (until I notice on my own, what may take days or even weeks). My obligate and truly felt apologies but sadly is something beyond my control (although I'll try to look at the comments awaiting moderation list more often). 

If you find that your comment has not been published (and you and your comment are legit - the usual trolls abstain, of course, but most people and comments are much welcome here) please send me an email and I'll solve that ASAP. My public email can be found in my Blogger profile, although you have to delete the anti-spam protection "DELETETHIS" (it won't work otherwise).

East African mtDNA charts at Ehio Helix

There's a (thankfully) growing interest in African genetics, both because of its importance for the origin of Humankind as a whole and also for its more direct relevance for Africans and people of recent African descent elsewhere. Therefore I can't but emphasize again the great work that Ethio Helix blog is doing in this aspect.

Today Ethio Helix gifts us with a most informative visual synthesis of East African mtDNA in form of bar charts. These are extremely interesting because of the wild array of lineages that this African region has, including quite significant amounts of less frequent lineages like L4, L5 or L6, or also the more extended but still worth studying L0 (and of course L2 and L3, as well as the occasional L1).

So I strongly recommend you to take a look. If you have any problems with the graphs (Google seems a bit buggy on them, he says), I solved them by mere zooming out (some sort of white layer was obscuring the rightmost part of them).

Update: it does not work well with Chrome (slow on Windows, does not work at all on Ubuntu) but it works perfect with Firefox.

A complementary Y-DNA chart is linked at this older post.

The Denisovans were not alone

H. heidelbergensis from Atapuerca
Cranium 5 "Miguelón"
(CC by José Manuel Benito)

About half an hour ago, somewhat cryptic comments in this blog and my email woke me up, more abruptly than I would have desired maybe, to a new game-breaking finding: researchers have sequenced the mtDNA of a 400,000 years old Homo heidelbergensis from Atapuerca (Iberian Peninsula, Europe) and it was not at all like most would have expected.

Mathhias Mayer et al., A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 2013. Pay per view → LINK [doi:10.1038/nature12788]

Abstract

Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene¹. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils^{2, 3}, consisting of at least 28 individuals⁴ dated to over 300,000 years ago⁵. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits^{6, 7, 8}. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans^{9, 10}, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.

The key figure is this one, which phylogenetically relates the newly sequenced mtDNA with the known Homo ones:

Figure 4: Bayesian phylogenetic tree of hominin mitochondrial relationships based on the Sima de los Huesos mtDNA sequence determined using the inclusive filtering criteria.
All nodes connecting the denoted hominin groups are supported with posterior probability of 1. The tree was rooted using chimpanzee and bonobo mtDNA genomes. The scale bar denotes substitutions per site.

It has been argued by all sides (myself included) that the H. heidelbergensis of Atapuerca and other European locations are ancestral to Neanderthals. Some say that also to H. sapiens, while others argue that ours is a wholly distinct line, derived from H. rhodesiensis, and yet others claim that H. rhodesiensis is not different from H. heidelbergensis in spite of being older and rooted, it seems, in South Africa.

The clear evidence for migrations out of Africa, before our species, is limited to two periods: (1) the c. 1.8 Ma old migration of H. erectus/georgicus with Olduwayan technology (mode 1, "choppers"), and (2) the c. 1 Ma old migration of H. ergaster/antecessor (sometimes also confusingly called H. erectus) with Acheulean technology (mode 2, typically "hand axes"). Archaeological evidence for later migrations does not exist.

See: Late human evolution maps at Leherensuge.

So we could well ask, if H. heidelbergensis is not ancestral to Neanderthals, then where do Neanderthals come from?

It must be answered that we do not know yet if H. heidelbergensis is or not ancestral to Neanderthals or in what degree it is. The mitochodrial (maternal) lineage may well be misleading in this sense. Denisovans themselves were much more related to Neanderthals via autosomal (nuclear) DNA than the mtDNA, so it may also be the case with European Heidelbergensis.

In fact it is still possible that these individuals represent some sort of admixture between older and newer layers of human expansion. But there is no clear answer yet. What is clear is that no Neanderthals have these mitochondrial sequences but others closer to those of H. sapiens - and this is the most puzzling part in fact. 

But one thing is clear: the World is much bigger than just Europe, and that was also the case back in Paleolithic times. Our answer may well lay under the sands of some tropical desert, the waters of the sea or whatever other place in Asia or Africa.

Even if we'd find the "missing link", so to say, we might not be able to discern it as such without genetic sequencing and that is often not even possible at all. However this pioneer research, as well as its precursors on a bear also from Atapuerca and a 700,000 years old horse (the true record of ancient DNA recovery), give us some hope of getting an improved, even if sometimes perplexing, understanding of the complexity of the human adventure.

The Mal'ta aDNA findings

The recent sequencing of ancient DNA from the remains of a Central Siberian young boy, corresponding to the Gravettian site of Mal'ta, West of Lake Baikal, dated to c. 24,000 years calBP, has caught the interest of many anthropology enthusiasts. During my hiatus of more than two months, most people who asked me to retake blogging with an specific request, talked of these findings. Let's see:

Maanasa Raghavan et al., Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 2013. Pay per view → LINK [doi:10.1038/nature12736]

Abstract

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians^{1, 2, 3}, there is no consensus with regard to which specific Old World populations they are closest to^{4, 5, 6, 7, 8}. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia⁹, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers^{10, 11, 12}, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages⁵. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians^{2, 13}. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago¹⁴, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

Haploid lineages

The Mal'ta boy, MA-1, carried distinct yDNA R* and mtDNA U* lineages. While both are clearly related to those dominant in Europe and parts of Asia (West, South) nowadays, they are also distinct from any specific dominant lineage today.

R* (yDNA) is neither R1 nor R2 but another distinct branch of R. This kind of R(xR1, R2) is most rare today and found mostly in and around NW South Asia. Following Wikipedia, this "other R" is found in:

• 10.3% among the Burusho
• 6.8% among the Kalash
• 3.4% among the Gujarati

However I must say that I recall from old discussions that some R(xR1) is also found among Mongols and some North American Natives. I would have to find the relevant studies though (maybe in an update).

U* (mtDNA) is also quite rare today but has been found in Swabian Magdalenian hunter-gatherers, as well as in some Neolithic samples, although it may well be a totally different kind of U* (I could not discern the specific markers in the paper nor the supplementary materials and it must be reminded that the asterisk only means "others").

Autosomal DNA

The study also shows some statistical inferences from the autosomal (or nuclear) DNA of the Mal'ta boy:

Figure 1 [b & c]
b, PCA (PC1 versus PC2) of MA-1 and worldwide human populations for which genomic tracts from recent European admixture in American and Siberian populations have been excluded19.
c, Heat map of the statistic f3(Yoruba; MA-1, X) where X is one of 147 worldwide non-African populations (standard errors shown in Supplementary Fig. 21). The graded heat key represents the magnitude of the computed f3 statistics.

Here we can appreciate that MA-1 is closest to Native Americans but still rather intermediate between them and South and West Eurasians. Interestingly East Asians are quite distant instead, suggesting that MA-1 was still not too much admixed with that continental population, unlike what happens with Native Americans, who are essentially East Asian in the autosomal and mtDNA aspects. So this kid appears to be some sort of a "missing link" in the Paleolithic ethnogenesis of Native Americans.

Figure 2 | Admixture graph for MA-1 and 16 complete genomes. An admixture graph with two migration edges (depicted by arrows) was fitted using TreeMix21 to relate MA-1 to 11 modern genomes from worldwide populations22, 4 modern genomes produced in this study (Avar, Mari, Indian and Tajik), and the Denisova genome22. Trees without migration, graphs with different number of migration edges, and residual matrices are shown in Supplementary Information, section 11. The drift parameter is proportional to 2Ne generations, whereNe is the effective population size. The migration weight represents the fraction of ancestry derived from the migration edge. The scale bar shows ten times the average standard error (s.e.) of the entries in the sample covariance matrix. Note that the length of the branch leading toMA-1 is affected by this ancient genome being represented by haploid genotypes.

Even if I am not too keen of TreeMix, in this case the results seem consistent.

We can appreciate here that a sample of Native Americans (the Karitiana, maybe not as "pure" as the Xavantes but still very much so) show up in a different branch from MA-1, reflecting their overwhelmingly East Asian ancestry, mostly by the maternal side (mtDNA). MA-1 instead hangs from the South-West Eurasian branch, soon after the split between South Asians and West Eurasians. Both have extremely drifted branches, surely indicating the small size of their founder populations, typical of the Far North. 

In addition to this basic tree, two admixture events are signaled: one is the already known Denisovan (H. erectus?) weak one into Australasian Natives (represented by Papuans) and the other one, quite more intense, is the one hanging from upstream of MA-1 to Native Americans (Karitiana), reflecting the partial South-West Eurasian ancestry of Native Americans (noticeable also in their dominant paternal ancestry: haplogroup Q). 

The fact that the admixture signal stems from quite upstream of MA-1 indicates that this boy (or rather his relatives) were not direct ancestors of Native Americans in any significant way but rather a different branch from the same trunk. Probably proto-Amerindians were already in this period at the North Pacific coasts, not sure if in Beringia or around Okhotsk or what but certainly they had already separated from the Mal'ta population.

What did we know of Native American genesis before this finding?

There are three principal lines of evidence:

1. Y-DNA, which among Native Americans is essentially haplogroup Q (plus some C3, which is from NE Asia). By phylogenetically hierarchical diversity, haplogroup Q must have coalesced in West or Central Asia (or maybe South Asia?), very possibly in or near Iran. The NE Asian and Native American branches are clearly derived, even if more important numerically today.
2. mtDNA, which among Native Americans is essentially from NE Asia (A, C, D), middle East Asia (B) but also in a small amount from West Asia (X2). 
3. Archaeology: we can track, more or less directly, the proto-NAs by means of following the Upper Paleolithic sequence in Siberia and nearby areas. 
1. C. 47,000 years ago (calBP) H. sapiens with Aurignacoid technology (i.e. linked to West Eurasian earliest Upper Paleolithic) reached Altai, displacing the Neanderthals to the Northern fringes of the district.
2. C. 30,000 years ago, Upper Paleolithic ("mode 4") technology with roots in Altai reached other parts of Siberia, Mongolia and North China, from where it expanded eastwards and southwards gradually in a process of, probably, cultural diffusion. 
3. By c. 17,000 years ago they were already in North America and c. 15,000 years ago in South America. In the LGM they were probably in Beringia already (but this is only indirectly attested so far). 

So we already had a good idea about the origins of Native Americans: their ultimate roots, at least patrilineally, seem to be in Altai (where they were part of the wider West Eurasian colonization at the expense of Neanderthals with Aurignacian-like technology and dogs). Then, probably around 30,000 years ago they expanded eastwards through Siberia and maybe nearby areas, entering in intense and intimate contact with the already existent East Asian populations, with whom they admixed once and again, mostly by the female side. 

It would seem therefore that their society was already patrilocal because otherwise their patrilineages would have just got dissolved among the locals and would have never reached Beringia nor America in such dominant position.

Overall this is the quite clear notion that I have on Native American earliest genesis and for me there is no reasonable doubt about this narrative (except maybe in the fine details). However I must reckon that some individuals have reacted very negatively against it. But no matter how much they yell, I fail to see their arguments. 

How does this new finding affects this narrative?

It simply confirms it with further evidence. By 24,000 calBP the proto-NAs were surely already, as I said before, in NE Asia close to the Pacific coasts, so this Mal'ta population is a branch left behind in their migration (plus whatever new inflows from the West, which we can't evaluate). The very low affinity level with East Asians, in spite of its quite Eastern location, shows that early East Asians had not yet reached, at least in significant numbers, so far North. If they had, they probably did only at more eastern longitudes, probably near the sea, where resources were more plentiful.

In other words: the first Central Siberians were of South+West Eurasian stock and the current East Asian genetic and phenotype hegemony in that area reflects post-LGM flows, mostly lead by yDNA N1. 

Early Native Americans were the product of admixture of these earliest Siberians with NE Asians, admixture that surely happened East of Lake Baikal, although the exact details are still unclear. 

What does MA-1 say about the West?

His mtDNA is generally consistent with other common U-derived lineages found in West Eurasian Upper Paleolithic, so not much other than he was somehow related, what is confirmed by autosomal analysis. 

His yDNA is more interesting maybe, nonetheless because it is probably the oldest sequence of this kind but also because it belongs to haplogroup R. It certainly discards whatever "molecular clock" guesstimates for R that are shorter than this site's age but on its own it is not able to set a real age other than a bare minimum. 

So for example Eupedia's estimate of 29 Ka for R as such could still be valid, although I would say that extremely unlikely. 

Indirectly however it does say something by confirming the overall narrative of Native American origins as above and that means that Eupedia's estimate of a mere 24 Ka age for haplogroup Q is almost certainly wrong by a lot. 

Using that tree, we would have to at least double the age of Q in order to fit with the Altai narrative (which begins at c. 47 Ka ago), what, extrapolating, implies an age for R of at least 58 Ka. I have estimated some 48 Ka of age for R1 and 68 Ka for P, so it makes good sense after these so necessary corrections. The exact ages we may never know but the approximate ages should be something like these. 

And that's about all I can say. More in comments (and/or updates) if need be.



Update (Dec 6): R* and P* (and other rare clades) among Central Asians

A reader sent me copy of the study by Wei-Hua Shou et al. (2010) titled Y-chromosome distributions among populations in Northwest China identify significant contribution from Central Asian pastoralists and lesser influence of western Eurasians, published by Nature (doi:10.1038/jhg.2010.30).

While it is not the bit of info I was recalling above, it does add some information about unmistakable R(xR1,R2) and P(xQ,R) among Central Asian populations (from P.R. China territory). In detail:

• R* is found in 5/31 Tayiks, 1/41 Kazakhs and 1/50 Uyghurs.
• P* is found in 1/31 Tayiks and 1/43 Kirgizes. 

Also of interest should be the presence of:

• Q(xQ1) in  8/35 Dongxiang (a Mongol ethnicity), 1/45 Kirgizes and 1/50 Tu (another Mongol ethnicity).
• F(xG,H,I,J,K) in 2/32 Yugu (Yugurs, a distinct Uyghur sub-ethnicity), 2/41 Kazakh, 1/31 Tayiks and 1/50 Tu.
• K(xN,O,P) in  32/533 total (i.e. 6% in Easternmost Central Asia), among which are most notable: 9/50 Uyghurs, 6/23 Uzbeks, 6/27 Bao'an (another small Mongol ethnicity), 3/32 Xibo (a Tungusic ethnicity), 2/32 Yugu and 2/5 Mongols. I guess that it is possible that this is a distinct K subclade, although it can well be either part of MNOPS (NO*?) or also belong to LT (L?).
• R2 in 1/31 Tayiks and 2/27 Bao'an.