Ancient mtDNA from Santimamiñe Cave

I see press releases and news stories on this cave from time to time, but I haven't actually located any published studies. If anyone is aware of more information, feel free to leave a comment.

Genetic research reveals that current population of Urdaibai probably descended from cave dwellers at Santimamiñe

The comparison of DNA extracted from a Homo sapiens who inhabited the Santimamine Cave (in the Basque province of Biscay) some 4,000 years ago, and from 6 other bone remains found in the same cave, with the DNA of 158 persons currently living in the surrounding Urdaibai region, has shown that current individuals have maternal lineages very similar to the archaeological remains. The findings enable putting forward the hypothesis that the current population is descended from the ancient denizens of the Santimamine Cave. 

... 

The research received funding from the Department of Culture of the Provincial Government of Bizkaia, as well as from the Urdaibai District Authority. Once the research in Urdabai is concluded, it is hoped that, shortly, it will be extended to other regions of the Basque Country, using new studies of funerary sites from the same period and from other eras (the Copper Age, the Bronze Age, etc.) thus enabling extending the knowledge we currently have on the special characteristics of the Basque population. This populational group has sparked enormous scientific interest for its distinctive characteristics regarding the preservation of its pre-Indo-European language and its relative isolation from the influence of other peoples and cultures.

Efficient moment-based inference of admixture parameters and sources of gene flow (Lipson et al. 2012)

My reading list keeps getting longer as another paper referenced by Loh et al. has now appeared on the arXiv, a day after the new Moorjani et al. paper on Romani origins. A number of papers from many of the same co-authors have appeared over the span of a couple of months, all of them containing interesting technical discussion on admixture parameter estimation, so perhaps this is a good place to make a list of them for easy reference:

• Patterson et al. (ADMIXTOOLS paper)
• Loh et al. (ALDER paper)
• Moorjani et al. (updates to rolloff)
• Lipson et al. (this one)

This series of papers builds on earlier work, which can be found in the following:

• Reich et al. (2009) (Indian Cline; introduction of f-statistics)
• Green et al. (2010) (Neandertal genome; introduction of D-statistics)
• Durand et al. (2011) (elaboration on D-statistics)
• Meyer et al. (2012) (high coverage Denisova; enhanced D-statistics)
• Pickrell et al. (2012) (Khoisan origins; use of admixture LD with 1-ref)
• Reich et al. (2012) (Native American origins; multiple waves of admixture)

The software introduced in the current paper (Lipson et al. 2012) can be found in the MixMapper page, and according to its description it is similar in spirit to the TreeMix software. Hopefully I'll be able to try it out for myself.

The most interesting thing about the current paper is, of course, its detection, to a lesser extent of the same "North Eurasian" ancestry found in northern Europeans by Patterson et al. also in Sardinians and Basques.

Sardinians did not appear to have such ancestry on the basis of the f3-statistic, but this might have been a consequence of the fact that they were the "least unadmixed" of the Europeans, so any application of f3(Sardinian; X, Amerindian) would not have given a negative result, because there does not exist any X less mixed with this Amerindian-like "North Eurasian" element than Sardinians.

Also, the ALDER paper seems not to have been able to date this type of admixture because of its antiquity. I have tried myself using a 1-ref approach on Sardinians (using Sardinians and various other "eastern" populations as possible contributors) but without success. So, it will be interesting to read how this type of ancestry was detected in the current paper. Any further comments will be posted in this space as updates.

UPDATE I: On the left you can see the model proposed for Europe. A first observation is the absence of a primate outgroup, or indeed of representatives of African hunter-gatherers. This makes sense in the context of this paper, since all African hunter-gatherers have been shown now to have admixture from African farmers, so they cannot be used for the "scaffold" tree, as they are not unadmixed.

However, their type of admixture differs from the admixture found in all other populations. For example, Europeans are a mixture of "Ancient Western Eurasians" and a group related to "Ancient Northern Eurasians". African hunter-gatherers, on the other hand, are a mixture between a group related to the Mandenka-Yoruba clade, and (potentially diverse) sets of "Palaeoafricans". The latter are an outgroup to the rest of mankind, and as such admixture with them cannot be represented in this model; consequently Yoruba assume by default a position of unadmixed outgroup to the rest of mankind, a position which -for reasons mentioned before in this blog- I believe is not correct. What effect this might have on the rest of the tree is not yet clear to me.

arXiv:1212.2555 [q-bio.PE]

Efficient moment-based inference of admixture parameters and sources of gene flow

Mark Lipson, Po-Ru Loh, Alex Levin, David Reich, Nick Patterson, Bonnie Berger

(Submitted on 11 Dec 2012)

The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the tree, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for HGDP individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations---including previously undetected admixture in Sardinians and Basques---involving a proportion of 20-40% ancient northern Eurasian ancestry.

Link

West Asian and North European admixture in Basques and Indo-Europeans

In a previous post I showed that Basques are lacking in the West Asian admixture present in all their West European Indo-European neighbors, consistent with my theory of a late Indo-European invasion of Europe whose ultimate source was the highlands of West Asia.

But, there are alternative theories, one of which purports that the Proto-Indo-Europeans were northern Europeoid pastoralists from the eastern European steppe. Since the North_European ancestral component is lacking in the Tyrolean Iceman and Gok4, the TRB Swede, it is conceivable that North_European bearing populations introduced this component during the Indo-European invasion.

Of course, there is absolutely no archaeological evidence for a massive migration out of the steppe into Europe, as even the main proponents of the steppe hypothesis accept, and as physical anthropology makes clear. And, we don't have to invoke an eastern European invasion to explain the North_European component, since it was present among pre-Indo-European hunter-gatherers from both Gotland and Iberia, as two ancient DNA studies have shown.

In any case, I took the HGDP and 1000Genomes European populations, together with the West_Asian and North_European Dodecad components, and calculated f3 statistics of the form:

f3(IE; Basque, Dodecad Component)

where Basque is either HGDP French_Basque or 1000 Genomes Pais_Vasco_1KG, and Dodecad Component is either West_Asian or North_European.

All the results can be found in the spreadsheet.

Again, there is evidence of West Asian+Basque admixture in all Indo-Europeans (|Z| less than -3) except the islanders from Canarias and Orkney, and the Russians; in the latter case, Basques are probably a poor stand-in for their pre-Indo-European ancestry. So, 32 of 38 comparisons are significant.

One would expect such negative f3 statistics to also apply in the North European+Basque case. After all, there are historically known migrations of Northern Europeoids into Western Europe (both Celts as well as Germanics) which did not affect Basques linguistically; moreover, Basques are southern Europeans, and many of the tested populations are northern Europeans, who are expected to turn up as mixtures of North European+Basque. However, a total of 16 of 38 comparisons are significant, involving, as expected mostly northern European populations.

It thus appears that geography and recent history is sufficient to explain the excess of North_European in some populations. Despite having a dataset with an excess of Iberian and North European populations, not many significant f3 statistics appear, and these are mostly as expected.

In conclusion, by comparing Basques vs. Indo-Europeans there appears no good evidence for the theory that Indo-European languages were brought into western Europe by a massive migration of northern Europeoids from eastern Europe. Basques do not appear distinctive in terms of the North_European component, but they do appear distinctive in terms of the West_Asian one.

This confirms previous ADMIXTURE analyses that Basques occupy an "intermediate" position along the north-south axis of variation in Europe, and an absolutely terminal one in terms of the West Asian component.

It is very interesting that ancient DNA research has provided clues about a very "uneven" landscape of prehistoric Europe, with Sardinian-like farmers in Sweden and Northern European-like hunter-gatherers in Iberia and very little in-betweens. But, these two elements eventually did mix, and, with the addition of a new group of people emanating from the highlands of West Asia, acquired their Indo-European speech, and went on to become the living nations of Europe.

Much remains to be discovered: the first ancient DNA traces of the constituent elements must be identified in space and time, and the history of their intermixture must be tracked.

IE-speaking West Europeans are West Asian-admixed relative to Non-IE speaking Basques

Previous ADMIXTURE experiments have shown that the Basques differ from the Indo-European speaking Europeans primarily due to a lack of a "West Asian" genetic component most strongly represented on the highlands of West Asia, from Anatolia and the Caucasus through Iran to Baluchistan. The same component is "missing" from ancient European DNA prior to 5kya, making it a good candidate for an element present in the elusive Proto-Indo-Europeans.

I wanted to test the admixture of IE-speaking populations formally, so I used threepop as implemented in TreeMix which performs a formal f3 test of admixture. According to Patterson et al. (2012):

An important feature of this test is that it definitively shows that the history of mixture occurred in population C; a complex history for A or B cannot produce negative F3(C; A,B).

A negative Z-score of the f3 test is unambiguous evidence of admixture, but a zero or positive one does not exclude it.

I report f3 statistics of the following form:

f3(A; B, West_Asian)

where West_Asian consists of 50 random individuals drawn from the K7b West_Asian component.

The full list of populations used in this experiment can be seen below. They include two sources of Basques (from the HGDP and 1000Genomes Project, from France and Spain), as well as 22 Indo-European speaking populations from Western Europe

I set A as each of the 24 populations, and calculate f3-statistics of the form f3(A; B, West_Asian) where B is any one of the remaining 23 populations. Thus, there are 24*23 = 552 f3-statistics in total, of which  2*22 = 44 are of the form f3(IE; non-IE, West_Asian).

If my conjecture is correct, then I expect:

1. the IE-speaking Europeans to show significantly negative f3(IE; non-IE, West_Asian) statistics
2. the non-IE speaking Basques to show non-negative f3(non-IE; IE, West_Asian) statistics
3. the remaining f3(IE1; IE2, West_Asian) statistics to be either negative or not, depending on different levels of West_Asian-related admixture in different IE populations associated with either the Indo-Europeans or other, later, population movements emanating from West Asia.

My expectation is confirmed by the evidence. You can see all f3 statistics in the spreadsheet. I note that:

(1) Here is a histogram of the 44 f3(IE; non-IE, West_Asian) comparisons:

42 of 44 Z-scores are negative and significant, suggesting that most  IE-speaking West European populations are West Asian-admixed relative to non-IE Basques. The two that are not, involve A='Orkney_1KG', which is a drifted island population. According to Patterson et al. (2012):

As mentioned earlier, the only case where the f3-statistic for a population that is truly admixed fails to be negative is when the population has experienced a high degree of population-specific genetic drift after the admixture occurred.

(2) All f3(non-IE; IE, West_Asian) statistics are positive. With the caveat about drift in mind, there does not seem to be any evidence that Basques are more West Asian-admixed than any other population.

(3) Here is a histogram of the 462 f3(IE1; IE2, West_Asian) statistics:

This shows evidence in differences in West_Asian admixture in some but not other IE populations. 55 of the 462 comparisons show significant evidence of admixture. These mostly involve German, French, and Italian populations vs. Iberian and British Isles ones. As mentioned above, this may reflect either the diminution of Indo-European-related West Asian ancestry across Europe, or it may be due to post-IE population movements.

Discussion

It is becoming increasingly apparent that modern Europeans are the descendants of both early Neolithic farmers, presumably from the Levant or Anatolia, as well as the indigenous Mesolithic hunter-gatherers. Neolithic ancestry has persisted most strongly in southern Europe, and in Sardinia above all. Mesolithic ancestry has persisted most strongly in northern Europe, and especially in the Baltic area; however, it is everywhere in the minority, as evidenced by the ~10-fold diminution of mtDNA haplogroup U related lineages from near 100% in the earliest samples until today.

In all probability there do not exist unmixed descendants of either early Neolithic or Mesolithic Euroeans. Intriguingly, one population that may be most strongly descended from the Mesolithic Europeans are the Saami, who possess very high levels of mtDNA haplogroup U5b. But even in their case, there is evidence of more recent influences, such as Y-haplogroup N1c.

The Saami have always been somewhat of a puzzle for prehistorians, with some attributing their physical appearance to survival of cold-adapted Paleolithic northern Europeans, while others attributing it to more recent movements from Siberia. As it is so often the case, both may have been partially right: it is now revealed that the Saami are not unique in possessing affinities with northeast Asians and Amerindians, so they are descended both from the Mesolithic northern European substratum (as evidenced by mtDNA haplogroup U5b) and from more recent Siberian peoples, and are thus positioned between east and west for more than one reason.

In the rest of Europe things were not any simpler. Both analysis of modern populations, as well as the mounting ancient DNA evidence ought to have convinced us by now that "there's something about Sardinians." It does seem to appear that this island population represents has preserved most faithfully the early Neolithic European gene pool, which, as it turns out, took its time mixing with the indigenous Mesolithic populations, since it is still evident down to the Iron Age. But, all things come to an end, and so did the domination of ancient Europe by Sardinian-like people.

In continental, and especially, northern Europe, the Neolithic inhabitants, resembling modern southern Europeans, eventually admixed with the Mesolithic foragers. A legacy of this event, as well as, possibly further incursions from the east, combined to give modern northern Europeans a greater affiliation with the east of Eurasia. But, it turns out, things were not much simpler in southern and western Europe.

The modern Basques share the East Eurasian-like admixture of continental Europeans, albeit to a smaller degree than people living in the north. They, like other Europeans are a mix of Mesolithic and Neolithic peoples. But, one thing stands out in their case: their language is not Indo-European and they live surrounded by Romance Indo-European speakers. In older times, their neighbors were Indo-European Celts, some of which have survived in places like Ireland. Further away, live Germanic peoples, some of which ventured into Iberia, without much affecting the local population. One thing is certain: the Basques can no longer be seen as unmixed descendants of Cro-Magnon man. But, if they have not continued as living fossils of Paleolithic man, then, what is to account for their linguistic peculiarity?

In the current post I make one such suggestion in the framework of my theory on the Indo-Europeanization of Europe. I showed that Basques differ from all their Romance, Celtic, and Germanic fellow West Europeans in lacking a "West_Asian" influence. I have previously investigated segments of such influence in two northern Europeans. In the future, with new instruments, such as ADMIXTOOLS, we may be able to figure out exactly when other European populations were affected by this influence. For peoples living close to West Asia (e.g., Greeks or Italians), the pattern may be obscured by recent historical contacts. But, the same will probably not be true for populations living in far Western Europe (e.g., Iberians or Irish).

If my theory is correct, then this signal will postdate the 5kya mark. By how much? It is not clear how long the Indo-Europeans of western Europe maintained themselves separately, perhaps as I have speculated, as a trading/military elite centered around metallurgy and its products. Ancient DNA research has the potential of resolving this issue by first identifying the earliest arrival of the West Asian influence, and, subsequently, detecting the first emergence of something akin to the modern population. One way or another, the cat is out of the bag, and in a the coming years many of these issues will be resolved.

East Eurasian-like ancestry in Northern Europe (part 3)

(This is the third part of the series. See part 1 and part 2.)

In the first two parts of the series, I showed that northern European populations show hints of East Eurasian ancestry when compared against Sardinians. I used Dai, Han, and Karitiana as reference populations for East Eurasia. In the current post, I extend this analysis by using HGDP Papuans and the Onge (Reich et al. 2009) from the Andaman Islands.

The f4 statistics using Karitiana, Papuan, and Onge populations can be found in this spreadsheet.

Below, you can see that they are all near perfectly correlated with each other.

The visual appraisal is confirmed when we calculate the correlation coefficients:

The fact that all three populations track the same signal is strong evidence for the direction of gene flow: from Asia into northern Europe. If the signal was present in only one of the three populations, then it could conceivably be an artefact of gene flow in the opposite direction (from northern Europeans to the affected population). But, the fact that all three populations show the same pattern would require northern European-like admixture in the Andaman Islands, Papuan New Guinea and South America, which does not appear very parsimonious.

While the signals from the three populations are correlated, their intensity varies. The Z-scores provide a measure of this intensity. The mean Z-scores using a Karitiana, Papuan, and Onge reference across all populations are respectively -17.7, -8.0, and -6.0.

While I did not include the Han reference of part 1 in this analysis, inspection of the f4 statistics (which can be obtained at the bottom of that part), suggests that the Z-scores become more significant when using an Onge, Papuan, Han, and Karitiana reference in that order. For example, for the Finnish_D population, they are: -10.037, -13.2949, -23.9305, and -27.764 respectively.

It thus appears that the element contributing East Eurasian-like ancestry in northern Europeans was derived from the northern spectrum of East Eurasians; the Karitiana may live in South America today, but they trace their ancestors to northern Eurasia, having entered the Americas c. 15ka.

In my opinion, the signal has been formed by a superposition of a few factors:

1. The fact that Y-haplogroup R, the main lineage in modern northern Europeans has a common origin (Y-haplogroup P) with haplogroup Q, the main lineage in modern Amerindians, and many Siberians. We can hypothesize that the population that brought R into Europe was intermediate genetically across the Caucasoid-Mongoloid spectrum. In West Eurasia, this population admixed with the Palaeo-West Eurasians (Y-haplogroups IJ, G, and possibly LT), and contributed their DNA primarily to the northern Europeoids.
2. Other population movements of more regional impact, such as Y-haplogroup N, which affected mainly Uralic, Baltic, and East Slavic populations, as well as elements from the mixed West/East Eurasian mtDNA contact zone that ancient DNA analysis has revealed in Eastern Europe and Siberia.

The raw dumps of fourpop output for Papuan and Onge reference can be found here.

East Eurasian-like admixture in Northern Europe (part 2)

This is a continuation of my earlier post. Please refer to it for the methodology. A new part 3 can be found here.

I have repeated the experiment with a much larger set of populations:

English_D, British_D, Ukranians_Y,  Karitiana, Spaniards, Sardinian,  Serb_D, Mordovians_Y, Irish_D,  French, Finnish_D, Chuvashs_16,  Romanian_D, N_Italian_D, French_Basque,  Austrian_D, Russian_D, Hungarians_19,  Kent_1KG, German_D, Belorussian,  Tuscan, Lithuanian_D, Orkney_1KG,  Dutch_D, TSI30, Ukrainian_D,  Bulgarians_Y, Bulgarian_D, Russian,  Swedish_D, Pais_Vasco_1KG, French_D,  Castilla_Y_Leon_1KG, Lithuanians, San,  Polish_D, Romanians_14, Orcadian,  Cornwall_1KG, Valencia_1KG, North_Italian,  FIN30, Norwegian_D, CEU30

I used Sardinians as the Caucasoid reference population, Karitiana for Mongoloids, and San for Africans. The latter two were chosen because they live at maximally opposite corners of the Earth (South America vs. South Africa).

A first plot of the f4 statistics used for f4 regression ancestry estimation is seen below:

Clearly, some evidence of a cline is present, but several populations appear to deviate from it. In order to get the cleanest possible cline, I carried out the following greedy procedure: I calculate the correlation coefficient of this set, and iteratively remove one population that leads to the maximum improvement of the correlation, until no further improvement takes place. The following populations were removed with this procedure:

Spaniards, Serb_D, Romanian_D, N_Italian_D, Tuscan, TSI30, Bulgarians_Y, Bulgarian_D, Castilla_Y_Leon_1KG, Romanians_14, Valencia_1KG

This seems to make sense, as all these are southern European populations. Note that their removal does not mean that they do not partake in the same phenomenon as northern Europeans: they also exhibit Karitiana-shift relative to the Sardinians, but there are probably other confounding factors that make them fall "off-cline". Including them would diminish the clarity of the cline for Northern European populations. The regression of the remaining populations can be seen on the right:

f4 regression ancestry estimation results are shown on the left. These appear to be much higher than was the case with the Han and Dai in the previous experiment.

I can't say that I've made any obvious mistakes, but these admixture proportions are substantial, and call for an explanation. Whatever their true levels, I am fairly confident on at least a few points:

First, it is evident that northern Europeans have higher levels of this element than southern Europeans; the latter are not altogether deficient in it, but they fall "off-cline", making estimation of their admixture proportions more difficult.

Second, within northern Europe, there is a fairly clear east-west cline of diminishing Amerasian-like admixture. The minimum occurs in Sardinians and secondarily in Southwest Europe. Romance, Celtic, and Germanic populations all have less of it than Balto-Slavic and Uralic ones. And, some populations of northeastern Europe seem to have a noticeable excess of it.

The groups with the most Amerasian-like admixture possess Y-haplogroup N, a clear trace of eastern ancestry that is not shared by most Europeans. The arrival of this haplogroup, either with Comb Ceramic of the Baltic Neolithic or later with Seima Turbino Bronze Age expansions is probably responsible for the local excess in Northeastern Europe. The Chuvash are, of course, a Turkic population but of Finno-Ugrian genetic origin.

But, the presence of this element even in Western Europe cannot be explained on the basis of typically Mongoloid elements which are almost completely lacking there. If Mesolithic Europeans were themselves Asian-shifted, then this would account for the presence of the element, but not necessarily for its clinal manifestation. The double (north-south and east-west) cline indicates every sign of an intrusive element. So, for the time being, I will propose that this is associated with late (e.g., Copper and Bronze Age) phenomena, such as the northern stream of the Bronze Age Indo-European invasion of Europe.

This may be due to the

• (i) northern Indo-European groups picking up some native east European or Siberian elements as they made their way into Europe, 
• or (ii), more likely, in my opinion, that the Y-haplogroup R1 group of people, whose closest relatives are in Central/South Asia (R2) , and whose more distant relatives (Q) are in Siberia and the Americas, were from the beginning an "intermediate population" between West and East Eurasia. The R1 group of people in its R1b and R1a varieties first appear in Europe during the Copper Age, and they are lacking in early Neolithic sites.

Eight years ago, and in a totally different context, I wrote:

Similarly, 9 out of 10 Basques are descended from a man who has also fathered 9 out of 10 Kets from Siberia and 9 out of 10 Maya Indians from America. That man, founder of haplogroup P thus has descendants who belong to two of the major human races (or three, if Amerindians are considered as separate from Asian Mongoloids)   

... 

In conclusion, human continental populations form groups of genetic and phenotypic similarity, and these groups can be considered races in the phenetic sense. However, these groups are not monophyletic, hence in the cladistic sense they should not be considered as valid taxa. Since the principle of common descent is generally applied in modern systematics (or at least it should!), I think it's best not to recognize human subspecies. 

If these data pan out, it may be revealed that the European branch of the Caucasoids is actually a product of admixture too, with at least two of its constituent elements being the "Palaeo-West Eurasians" (Y-haplogroups G, IJ, possibly LT) and the "Neo-NW Eurasians" (Y-haplogroups N1 and R1), with the "Neo-Afrasians" (Y-haplogroup E1b1b) forming a third element.

(A raw dump of fourpop output can be found here).

Ancient mtDNA from hunter-gatherers and farmers of Northern Spain (Hervella et al. 2012)

Having just finished writing my mega-post on the new exciting ancient DNA results from Sweden, a new paper has caught my attention which presents data from Paleolithic-to-Bronze Age inhabitants of northern Spain. Since this is an open-access paper, I'll let you read it, and post my own comments later as an update to this post.

UPDATE: Just three observations on the study:

1. 50% of the hunter-gatherers belonged to haplogroup U subclades, hence confirming for this region as well that this lineage was over-represented in pre-farming populations; the remainder were assigned by the authors to H subclades on the basis of HVR polymorphisms.
2. Haplogroup V that had been proposed as having originated in the Franco-Cantabrian region is again conspicuously absent in the ancient data
3. It now appears that the N1a dominance in LBK samples (and in a French Megalithic) was not shared by all Neolithic groups, with no N1a turning up in the Spanish samples

From the paper:

The Neolithic sample of France (NEO_FR) is closer to present-day populations in the Near East, because it shows similar frequencies for haplogroups TX, W, J, H and U (the ones with the highest correlation for the first axis in the PCA, data not shown). However, the Neolithic populations from the Iberian Peninsula (NEO_CAT and NEO_NAVARRE) are located between the variability of present-day European populations and those in the Near East. Likewise, the Chalcolithic populations in the Basque Country (Longar, SJaPL and Pico Ramos) occupied a similar position to the Neolithic groups of the Iberian Peninsula (Figure 2).

The results from this paper are hence in agreement with lots of other lines of evidence pointing to an exogenous population element in the formation of the Neolithic in Southwest Europe as in Scandinavia.
The authors attribute this to maritime colonization:

Maritime colonization, transporting small and different Neolithic groups from the Near East pool could contribute to explain the difference.

Hopefully, we will be able to obtain autosomal DNA from some of the Neolithic samples as we did in Scandinavia, and I would be much surprised if these Neolithic inhabitants of Iberia were not Oetzi-like and hence intermediate between most modern populations of Southern Europe and the Near East.

PLoS ONE 7(4): e34417. doi:10.1371/journal.pone.0034417

Ancient DNA from Hunter-Gatherer and Farmer Groups from Northern Spain Supports a Random Dispersion Model for the Neolithic Expansion into Europe

Montserrat Hervella et al.

Abstract


Background/Principal Findings

The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe.

Methodology/Significance

Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe.

Conclusion

The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation.

Link

Pre-Roman genetic structure has persisted in modern Basque populations

This is a fairly interesting study that paints a picture of continuity of genetic structure among Basques since pre-Roman times. I am not sufficiently familiar with either Basque history or geography to comment on this in detail, but the central conclusion that Basques differ from their neighbors in being more isolated and less cosmopolitan is something that I have also noticed in my own experiments (see for example the K12b population portraits, contrasting French_Basque and Pais_Vasco_1KG with other Iberian/French populations).

For those who know more, does the following scheme make sense?

Y-haplogroup frequencies, showing a preponderance of R-M269 related lineages and a strong showing of the the I-M26 lineage are shown below. The latter links Basques with Sardinians, as well as probably with Neolithic France.

Codes (from the paper): BIG, Bigorre; BEA, Béarn; CHA, Chalosse; ZMI, Lapurdi/Baztan; NLA,Lapurdi Nafarroa; SOU, Zuberoa; RON, Roncal and Salazar valleys; NCO, CentralWestern Nafarroa; NNO, North Western Nafarroa; GUI, Gipuzkoa; GSO, SouthWestern Gipuzkoa; ALA, Araba; BBA, Bizkaia; BOC, Western Bizkaia; CAN,Cantabria; BUR, Burgos; RIO, La Rioja; NAR, North Aragon.

The picture of continuity is further strengthened by ancient Basque Y-chromosomes, showing the same picture of R1b-majority/I minority as today. What we really need now is to bridge the gap between late antiquity and the Neolithic, and beyond to better understand the temporal sequence of settlement.

Mol Biol Evol (2012)doi: 10.1093/molbev/mss091

Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers

Begoña Martínez-Cruz et al.

Basque people have received considerable attention from anthropologists, geneticists and linguists during the last century due to the singularity of their language and to other cultural and biological characteristics. Despite the multidisciplinary efforts performed to address the questions of the origin, uniqueness and heterogeneity of Basques, the genetic studies performed up to now have suffered from a weak study-design where populations are not analyzed in an adequate geographic and population context. To address the former questions and to overcome these design limitations, we have analyzed the uniparentally inherited markers (Y chromosome and mitochondrial DNA) of ∼900 individuals from 18 populations, including those where Basque is currently spoken and populations from adjacent regions where Basque might have been spoken in historical times. Our results indicate that Basque-speaking populations fall within the genetic Western European gene pool and they are similar to geographically surrounding non-Basque populations, and also that their genetic uniqueness is based on a lower amount of external influences compared to other Iberians and French populations. Our data suggest that the genetic heterogeneity and structure observed in the Basque region results from pre-Roman tribal structure related to geography and might be linked to the increased complexity of emerging societies during the Bronze Age. The rough overlap of the pre-Roman tribe location and the current dialect limits supports the notion that the environmental diversity in the region has played a recurrent role in cultural differentiation and ethnogenesis at different time periods.

Link

Pre-Neolithic Basque mtDNA gene pool (?)

I haven't read the paper, but I'm unconvinced that an 8,000 YBP estimate of separation (even if it were made with the precision of an atomic clock) "clearly supports" genetic continuity with the Paleolithic/Mesolithic settlers of the Franco-Cantabrian region.

Not only because the date in question is within a millennium or two of the arrival of the Neolithic in Iberia, one of those "curious coincidences."

Much more importantly, because the wisdom of Barbujani continues to be ignored when it comes to tying genetic age estimates to archaeology.

The American Journal of Human Genetics, 23 February 2012 doi:10.1016/j.ajhg.2012.01.002

The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times

Doron M. Behar et al.

Different lines of evidence point to the resettlement of much of western and central Europe by populations from the Franco-Cantabrian region during the Late Glacial and Postglacial periods. In this context, the study of the genetic diversity of contemporary Basques, a population located at the epicenter of the Franco-Cantabrian region, is particularly useful because they speak a non-Indo-European language that is considered to be a linguistic isolate. In contrast with genome-wide analysis and Y chromosome data, where the problem of poor time estimates remains, a new timescale has been established for the human mtDNA and makes this genome the most informative marker for studying European prehistory. Here, we aim to increase knowledge of the origins of the Basque people and, more generally, of the role of the Franco-Cantabrian refuge in the postglacial repopulation of Europe. We thus characterize the maternal ancestry of 908 Basque and non-Basque individuals from the Basque Country and immediate adjacent regions and, by sequencing 420 complete mtDNA genomes, we focused on haplogroup H. We identified six mtDNA haplogroups, H1j1, H1t1, H2a5a1, H1av1, H3c2a, and H1e1a1, which are autochthonous to the Franco-Cantabrian region and, more specifically, to Basque-speaking populations. We detected signals of the expansion of these haplogroups at ∼4,000 years before present (YBP) and estimated their separation from the pan-European gene pool at ∼8,000 YBP, antedating the Indo-European arrival to the region. Our results clearly support the hypothesis of a partial genetic continuity of contemporary Basques with the preceding Paleolithic/Mesolithic settlers of their homeland.

Link

Lactase persistence in Neolithic Iberia

This is an extremely important study as it establishes the occurrence of lactase persistence in Neolithic Europe. This invalidates the idea proposed by some about a very late (post-Neolithic) introduction of lactase persistence into Europe by a pastoral population from the east, since we now have good evidence about the presence of this trait in a Neolithic sample from Atlantic Europe.

The frequency is higher than in the early Neolithic Linearbandkeramik (where it was absent in the tested samples), and lower than in present-day Basques, although levels of 27% are quite comparable to some modern south European populations. We are unlikely to detect the earliest occurrence of this trait (when it was limited to the original mutant and his descendants, prior to having a substantial advantage for digesting milk), but the new findings represent a new non-zero data point in the time series, which will certainly fill up as more points in space and time are tested.

European Journal of Human Genetics advance online publication 11 January 2012; doi: 10.1038/ejhg.2011.254

Low prevalence of lactase persistence in Neolithic South-West Europe

Theo S Plantinga et al.

The ability of humans to digest the milk component lactose after weaning requires persistent production of the lactose-converting enzyme lactase. Genetic variation in the promoter of the lactase gene (LCT) is known to be associated with lactase production and is therefore a genetic determinant for either lactase deficiency or lactase persistence during adulthood. Large differences in this genetic trait exist between populations in Africa and the Middle-East on the one hand, and European populations on the other; this is thought to be due to evolutionary pressures exerted by consumption of dairy products in Neolithic populations in Europe. In this study, we have investigated lactase persistence of 26 out of 46 individuals from Late Neolithic through analysis of ancient South-West European DNA samples, obtained from two burials in the Basque Country originating from 5000 to 4500 YBP. This investigation revealed that these populations had an average frequency of lactase persistence of 27%, much lower than in the modern Basque population, which is compatible with the concept that Neolithic and post-Neolithic evolutionary pressures by cattle domestication and consumption of dairy products led to high lactase persistence in Southern European populations. Given the heterogeneity in the frequency of the lactase persistence allele in ancient Europe, we suggest that in Southern Europe the selective advantage of lactose assimilation in adulthood most likely took place from standing population variation, after cattle domestication, at a post-Neolithic time when fresh milk consumption was already fully adopted as a consequence of a cultural influence.

Link

Lack of significant population structure in Spain

I took the Iberian Spanish (IBS) regional populations, and ran multidimensional scaling on them (left). Most of the populations form a tight cluster, with Basques and Canary Islanders having averages further removed from the main cluster.

It should be noted that the Canarias sample consists of only two individuals (big red dots): one removed from the main cluster, one in the midst of individuals from Castilla Y Leon (small red dots).

MCLUST analysis using 1 dimension, reveals 2 clusters: one consisting of Pais Vasco individuals (blue dots), the other of everyone else, with one Aragonese and one Cantabrian individual showing mixed probabilities between the two clusters.

The overall impression is that there may be additional population structure here (e.g., for Canarians or Galicians), but the sample sizes are not sufficient to make additional clusters unambiguously evident, except in the case of Basques vs. non-Basques.

First assessment of 1000 Genomes Iberian Spanish (IBS) sub-populations

As promised, I have taken the IBS sample from the latest available 1000 Genomes data and split it into sub-populations. There are at present 147 IBS individuals, and 108 of them have regional information about them:

• Canarias_1KG 2 
• Galicia_1KG 8 
• Aragon_1KG 6 
• Valencia_1KG 12 
• Andalucia_1KG 4 
• Murcia_1KG 8 
• Baleares_1KG 7 
• Cataluna_1KG 9 
• Pais_Vasco_1KG 8 
• Cantabria_1KG 6 
• Extremadura_1KG 8 
• Castilla_La_Mancha_1KG 6 
• Castilla_Y_Leon_1KG 12

I estimated the admixture proportions of these individuals in terms of the K12a calculator. I do not report averages at this time, as I will repeat the analysis that created K12a, but using new reference individuals from the 1000 Genomes project. Nonetheless, the following figure of the ADMIXTURE analysis gives a visual taste of the makeup of the different populations:

The one population that stands out in this set is that of the Basque Country (Pais_Vasco_1KG) which appears, like the HGDP French_Basque population to differ from its neighbors in having near zero of the "Caucasus" component.

I first speculated that some of the IBS sample were of Basque origin during the summer, and it seems that this was indeed the case.

The paucity of the "Caucasus" component in Dodecad, HGDP, and now 1000 Genomes Basques, together with the paucity of the "Caucasus"/"Gedrosia" components in Finns compared to northern Balto-Slavs and Scandinavians respectively is very suggestive, since these are the two major non-Indo-European speaking populations of Europe. (*)

In my opinion, these comparisons add weight to the growing body of evidence that the PIE Urheimat is to be sought in the territory of West Asia, as a secondary movement, about 8,000 years, ago of the broader series of expansions that began from this area 12,000 years ago.

(*) Hungarians are also non-Indo-European, but they seem to have received their language in historical times through a process of elite dominance.

Migration and Argentinean mtDNA

BMC Genetics 2011, 12:77doi:10.1186/1471-2156-12-77

The impact of modern migrations on present-day multi-ethnic Argentina as recorded on the mitochondrial DNA genome

Maria LAURA Catelli et al.

Abstract (provisional)

Background
The genetic background of Argentineans is a mosaic of different continental ancestries. From colonial to present times, the genetic contribution of Europeans and sub-Saharan Africans has superposed to or replaced the indigenous genetic 'stratum'. A sample of 384 individuals representing different Argentinean provinces was collected and genotyped for the first and the second mitochondrial DNA (mtDNA) hypervariable regions, and selectively genotyped for mtDNA SNPs. This data was analyzed together with additional 440 profiles from rural and urban populations plus 304 from Native American Argentineans, all available from the literature. A worldwide database was used for phylogeographic inferences, inter-population comparisons, and admixture analysis. Samples identified as belonging to hg (hg) H2a5 were sequenced for the entire mtDNA genome.

Results
Phylogenetic and admixture analyses indicate that only half of the Native American component in urban Argentineans might be attributed to the legacy of extinct ancestral Argentineans and that the Spanish genetic contribution is slightly higher than the Italian one. Entire H2a5 genomes linked these Argentinean mtDNAs to the Basque Country and improved the phylogeny of this Basque autochthonous clade. The fingerprint of African slaves in urban Argentinean mtDNAs was low and it can be phylogeographically attributed predominantly to western African. The European component is significantly more prevalent in the Buenos Aires province, the main gate of entrance for Atlantic immigration to Argentina, while the Native American component is larger in North and South Argentina. AMOVA, Principal Component Analysis and hgs/haplotype patterns in Argentina revealed an important level of genetic sub-structure in the country.

Conclusions
Studies aimed to compare mtDNA frequency profiles from different Argentinean geographical regions (e.g., forensic and case-control studies) should take into account the important genetic heterogeneity of the country in order to prevent false positive claims of association in disease studies or inadequate evaluation of forensic evidence.

Link

Basques (?) in 1000 Genomes IBS (Iberian Spanish) sample

I am looking at the population portraits of the Dodecad v3 results (all of which will be provided as a zip once I finish calculating averages), and I discovered an interesting presence of presumably Basque individuals in the 1000 Genomes IBS sample.

First, here are the Dodecad Spanish:

And, the Behar et al. (2010) Spaniards:

And, the HGDP French Basque:

Notice that they are composed almost entirely of "West European" and "Mediterranean" components.

Here is IBS:

Notice a few individuals that resemble Basques. I haven't found a description of the origin of the IBS individuals, but I would wager that a few Basque individuals are included, that resemble their French co-ethnics.

Genetic structure of West Eurasians

I have decided to generate a new major data dump of ADMIXTURE results. In comparison to previous such experiments:

1. The focus is entirely on West Eurasians (Caucasoids).
2. I have excluded all potential relatives from the source datasets, as well as several populations that tend to create uninformative clusters of their own (e.g., Druze or Ashkenazi Jews); exceptions are populations of great anthropological interest (e.g., Basques).
3. I have included all relevant Dodecad Ancestry Project populations with 5+ participants.
4. I have developed a new way of "framing" the region of interest by choosing appropriate sets of individuals from outside of it.

"Framing" populations

I have, since the beginning of my ADMIXTURE experiments, emphasized the importance of including appropriate population controls designed to squeeze out minor distant admixture in populations of interest, so that it does not confound the inference of region-specific components.

This leads to a problem: there are many possible sources of admixture. For example, we do not know a priori which set of African populations may have contributed to Caucasoid populations, or which set of East Asian ones. We could choose e.g., the Yoruba and the Chinese to represent Sub-Saharans and East Asians, but that might exclude possible sources of variation, and lead to Yoruba- and Chinese- specific clusters rather than more general Sub-Saharan and East Asian ones. If we included more population controls, we would cover more possible sources of variation, but ADMIXTURE would infer components of little interest (e.g., between Pygmies vs. Bushmen or Mongols vs. Chinese)

To avoid this, I propose to create meta-populations consisting of a single individual from many populations, i.e., a Yoruba, a Mandenka, a San, a Mbuti Pygmy, etc. for Sub-Saharan Africa, or a Miaozu, a Han, a Mongol, a She, a Hezhen, etc. for East Asia. That way we are both helping ADMIXTURE infer general components, while at the same time preventing it from inferring non-region specific ones.

Results

The entirety of the results presented here can be downloaded. They include:

1. Population sources
2. ADMIXTURE proportions for populations
3. Fst divergences between components
4. Population portraits showing individual level variation

See spreadsheet and associated bundle (or here).

At K=3, we observe the emergence West Eurasian, Sub-Saharan, and East/South Asian components.

The impact of the Sub-Saharan component is felt most distinctly in North Africa and the Near East, especially among Arabs; the impact of the East/South Asian one in West Asia and Northeastern Europe, especially among Finnic and Turkic speakers.

It is interesting to note that 39.8% of the Indian_D sample is assigned to the E/S Asian component. I had previously estimated in a roundabout way, and in a slightly smaller sample that the Ancestral South Indian component in Project participants was 33.3%, so ADMIXTURE has roughly managed to infer correctly that about 1/3 of this Indian sample's ancestry is more closely related to East Asians than to West Eurasians.

At K=4, the first split within the Caucasoid group appears: a component centered onn Europe, and one on West/South Asia.

Many populations possess both these components in clinal proportions.

The European component shrinks to insignificance in Arabians, such as Saudis and Yemenese.

The West/South Asian component shrinks to insignificance in Northeast Europeans, such as Finns, Lithuanians, north Russians, and Chuvash.

At K=5, a new Mediterranean component emerges. This is highly represented in populations to the North, South, and East of the Mediterranean sea.

This component is noteworthy for its absence in India and Northeastern Europe.

In Northeastern Europe, the Mediterranean component is hardly represented at all, whereas the West/South Asian component, freed of its K=4 Mediterranean associations now makes its appearance.

Conversely, in the West Mediterranean, among Basques, Sardinians, Moroccans, and Mozabites the West/South Asian component vanishes to non-existence.

At K=6, a North African component emerges.

Notice its presence in the Near East and parts of Southern Europe.

The two regions can be contrasted in terms of their African components, with very high North/Sub-Saharan African ratio in Europe vs. much lower in the Near East.

The explanation for this seems straightforward, as Europe was affected by North Africa in prehistoric and historic times, whereas the Near East also shares a border with more southern parts of the African continent, as well as the potential influence of the medieval slave trade that seems to have affected Muslim Near Eastern populations disproportionately.

At K=7, a Southwest Asian component emerges which is highest in Arabia and East Africa. I could've called this Red Sea, but I've reserved this name for a similar component that emerges at higher K.

It is clear that this is the main Caucasoid component present in East Africa.

It vanishes to non-existence in the Northern fringe of Europe, in the British Isles, Scandinavia, and among the Finns and Lithuanians.

Another interesting aspect of its distribution is its presence in Pakistan but not India. Perhaps, in this case, it reflects historical contacts between the Islamic Near East and parts of South Asia.

At K=8, we observe most of the familiar components from the K=10 analysis of the Dodecad Project. However, the use of the framing populations has meant that these components emerge before either Africans or East Eurasians split.

Now, the South Asian component appears, which swallows up most of the E/S Asian component that previously linked South with East Asians. This component extends a great way to the Near East and eastern parts of the Caucasus.

Quite interestingly, the remainder of the Caucasoid component in South Asia that is not absorbed by the new South Asian component seems to be split between the West Asian and North/Central European components, with an absence of the South European component.

It is among the Lezgins of the Caucasus that such a combination occurs, on the western shore of the Caspian Sea. The same combination of Caucasoid components also occurs in Uzbeks and Chuvash.

I conclude from this that the Caucasoids who entered South and Central Asia were probably derived from the eastern fringes of the Caucasoid world where only the West Asian (in the south) and North/Central European (in the north) are in existence. The area around the Caspian Sea seems like an excellent candidate for their origin, as I have speculated before, as that region has two important properties:

1. It is transitional between predominantly N/C European populations to the north and predominantly W Asian populations to the south
2. It is the border of the influence of the S European element, with Georgians possessing some of it, while Lezgins do not.

At K=9, we see the emergence of specific Sardinian and Basque components. Normally this is undesirable, but, I believe this breakup serves to divide the previously inferred South European component meaningfully.

What was South European in lower K seems to have an Atlantic vs. Mediterranean dimension, with the Basque/Sardinian ratio being particularly high in the Atlantic facade of Europe. Conversely, this ratio is low in the Mediterranean as we move eastwards: it is already low in Italy and the Balkans and becomes virtually zero in Cypriots, Armenians, and Levantine Arabs.

North Africa is also particularly interesting in having a low Basque/Sardinian rate, even in Morocco. It appears that Sardinians are a much better proxy of European influences in the region than Basques are.

K=10 is particularly exciting because, for the first time, there is clear evidence of structure in the North/Central European component that can now be split, for the first time, into Northwestern and Northeastern ones.

The NW European component is maximized in Orcadians, and people from the British Isles in general, as well as in Scandinavia. These populations have a low NE/NW ratio, as do the French, Iberians, and Italians.

Conversely, Balto-Slavs have a high NE/NW ratio.

Interestingly, Greeks have a balanced NE/NW ratio (1.2), intermediate between Italians and Balto-Slavs. Similar balanced ratios are also found among Lezgins (1.08), Turks, and Iranians. I conclude that Slavic or other Eastern European admixture cannot account for the totality of presence of this component in Greeks.

Indians have a 1.8 NE/NW ratio. In Pakistan this is 6.5, in Uzbeks it is 2.9, and in the North Eurasian_Ra it is 14.2. My conclusion is that a single migration of steppe people from eastern Europe cannot account for the presence of North European-like genes in Asia.

I propose that a palimpsest of population movements has brought such elements into the interior of Asia: the migration of the early Indo-Iranians from West Asia or the Balkans with a balanced NE/NW ratio, and, the migration of steppe people from Eastern Europe with a high NE/NW ratio. The latter, did affect much of Asia, but it is in India, where Iranian groups did not penetrate in great numbers the lower ratio of the Indo-Aryans has been best preserved.

The case of the Finns is also interesting, as there is a surplus of NE over NW European elements. Their position is intermediate between Scandinavians and Lithuanians/Russians but toward the latter. So, Finns appear to (i) have a substratum similar to Balto-Slavs, (ii) to be influenced by Scandinavians, and (iii) with a balance of East Eurasian elements (5.8% at this analysis) preserving the legacy of their linguistic ancestors from the east. At present it is difficult to determine how much of the NE European component in Finns is due to their eastern ancestors who were presumably mixed Caucasoid/Mongoloid long before they arrived in the Baltic, and how much was absorbed in situ.

At K=11 the Ethiopian/East African component emerges, absorbing some of the Red Sea and Sub-Saharan components from the previous K=10 run.

In comparison to the East African component of the Dodecad Project analysis, this component is closer to West Eurasians than to Sub-Saharan Africans, and a residual Sub-Saharan element remains in the two East African (Ethiopian and East_African_D) population samples. Presumably this is due to the more complete sampling of Sub-Saharan genetic diversity using the Sub_Saharan_H "framing" population.

Outside Africa, both E African/Sub-Saharan components are present in the Near East and North Africa with higher E African/Sub-Saharan ratios in the Near East and lower ones in North Africa.

In Europe, there are low such ratios in the few populations where African admixture is present, together with some N African. We can probably conclude that African admixture is mostly due to North Africans, and African-influenced Near Eastern populations, rather than directly from Sub-Saharan Africa.

At K=12 the first uninformative cluster emerged, centered on Iraqi Jews, hence I decided to stop the analysis at this point.

Population Portraits

There is a plethora of population portraits in the download bundle, showing how admixture proportions vary in individuals within populations, and how they vary between successive K.

Here is, for example, the K=11 portrait of Cypriots. A picture of overall homogeneity of this sample emerges, but notice how the NW European and NE European have disjoint presence in the Cypriot individuals, with 5 having some of the former, 6 having some of the latter, and only 1 of these having both.

Compare with Lezgins (right) where these two components occur in all individuals. Whatever this admixture represents, it must be old enough if it is so uniformly distributed in the population.

Here are the Georgians at K=10. Notice that their NE European component is unevenly distributed, and in every case where it occurs it is accompanied by a thin slice of East Asian. This may well indicate partial Russian or other Eastern European ancestry in these individuals.

Side-by-side comparisons are also quite useful. Consider Armenians vs. Lezgins vs. Iranians at K=7

Notice how Lezgins, who live north of the Caucasus mountains possess some of the N/C European component, which the Armenians, who live to the south of them lack. This should come as no surprise, as the Lezgins inhabit parts of the ancient Sarmatia Asiatica. Compare with Iranians, who are differentiated by their Indo-European Armenian neighbors by the presence of a "S Asian" component, which, in turn, ties them to their Indo-Aryan linguistic relatives.

Much more can be said, but I'll let readers explore the data on their own, and draw their own conclusions from them.

AAPA 2011 abstracts

A draft of the abstracts from the 80th meeting of the American Association of Physical Anthropologists is online. Some titles of interest:

Cristian Capelli et al.
Early Y chromosome lineages in Africa: the origin and dispersal of Homo sapiens.

The study of Y chromosome variation in extant populations has provided significant insights into the genetic history of Homo sapiens. Focusing on sub-Saharan Africa, demographic events associated with the spread of languages, agriculture and pastoralism have been targeted but little is known on the early history of the continent. The first two branches of the Y chromosome genealogy, namely haplogroup A and B, are African specific, with average continental frequencies of 14-34%, reaching up to 65% in groups of foragers . Despite the potential of such lineages in revealing signatures of the ancient peopling of the continent, an exhaustive investigation of their distribution and variation is currently missing. Here we show that their systematic dissection provides novel insights into the early history of our species. We highlighted complex pattern of populations’ dynamics among hunter-gatherer communities, evidence for the peopling of western and southern Africa, and showed the retention of the very early human Y chromosome lineages in eastern and central but not southern Africa. These results open new perspectives on the early African history of Homo sapiens, with particular attention to areas of the continent where human fossil remains and archaeological data are scanty.

Aslihan Sen et al.

The genetic history of the Karachays:Insights from mtDNA and Y-chromosome evidence

The Karachay-Malkar population of the northwestern Caucasus Mountains has an interesting but unclear history. Oral traditions indicate that they descended from the Alans, ancient Iranian tribes who entered the region starting in the 1st century BC. However, they now speak a Kipchak Turkic language, which was purportedly brought to the Caucasus by the Kumans from the Minusinsk Basin (Yenisei River-Altai Mountains). They are also allegedly related to the Hun-Bulgars, with the name Malkar/Balkar being evidence for this affiliation. Therefore, to elucidate their genetic past, we characterized genetic variation in 106 Karachay individuals using a combination of HVS1/ HVS2 sequencing and SNP analysis for mtDNAs and SNP and STR analysis for Y-chromosomes. We observed a predominance of mtDNA haplogroups H and U in this population, along with a minority of East Eurasian lineages, and mostly Y-chromosome haplogroups G, I, J and R1. The mtDNA data suggest that the Karachay are most similar to the Adygei, among Caucasus populations, and have affinities with eastern Iranians, supporting the hypothesized link to Scythio-Iranians (Alans), although being quite distant to Turkic speaking indigenous Altaians. By contrast, Y-chromosome data point to genetic links with populations from Anatolia, the Near East and the Balkans, as well as the Volga-Ural region, Central Asia and Siberia, the source area for ancient Turkic populations. Using these data and associated genealogical and linguistic evidence, we attempt to reconstruct the history of the Karachay population and assess its genetic relationships to the diverse ethnolinguistic groups of the Caucasus.

Jasem Theyab et al.
The genetic structure of the Kuwaiti population: mitochondrial DNA markers.

In the past few decades, researchers using human mitochondrial DNA (mt- DNA) have significantly contributed to our understanding of human evolution and migration. However, little attention has been paid to the Arabian Peninsula which is assumed to be one of the first inhabited regions following the expansion of early Homo sapiens out of Africa. Recently, a number of investigations have started to reconstruct human expansion through the archaeology and the study of the genetic structure of populations of the Arabian Peninsula. Populations of Kuwait, located in the Northeast portion of the Arabian Peninsula, have not been studied from a molecular genetic perspective. This research investigated the mitochondrial DNA (mtDNA) genetic variation in 117 unrelated individuals to determine the genetic structure of the Kuwaiti population and compared the Kuwaiti population to their neighboring populations. Restriction fragment length polymorphism (RFLP) and mt- DNA sequencing analyses were used to reconstruct the genetic structure of Kuwait. The result showed that the Kuwaiti population has a high frequency of haplogroup pre-HV (18%) and U (12%) similar to other Arabian populations. In addition, the African influence was detected through the presence of haplogroup L (1.6%). Furthermore, the MDS plot showed that the Kuwaiti population is clustered with neighboring populations, including Iran and Saudi Arabia, but not Iraq.

Kristin L. Young et al.
Paternal genetic history of the Basque population of Spain.

This study examines the genetic variation in Basque Y chromosome lineages using data on 12 Y-STR loci in a sample of 158 males from four Basque provinces of Spain. In agreement with previous studies, the Basques are characterized by high frequencies of haplogroup R1b (83%). Five additional haplogroups were identified in this sample: E1b1b (6%), J2a (3%), I2 (3%), G2a (2%), and L (1%). Only 8% of haplotypes were found in more than one province, and the AMOVA analysis shows only a small amount of variation (1.71%, p50.0369) is accounted for between provinces, demonstrating the overall homogeneity of this population. Gene and haplotype diversity levels in the Basques are on the low end of the European distribution (gene diversity: 0.4268; haplotype diversity: 0.9421). Other isolated populations in Europe, including the Swedish Saami, the Roma in Portugal, and Albanians in Kosovo, also exhibit low haplotype diversity levels. Comparison of the Garza-Williamson Index for the Basques and 36 additional European populations shows no significant impact of a recent genetic bottleneck on the continent. A bootstrapped neighbor-joining tree (R2 5 0.922) of Shriver’s genetic distances (DSW) clusters Basque populations with other Atlantic Fringe groups (Galicia, Ireland) and the non- Indo-European Saami. Paleolithic and Neolithic contribution to the paternal Basque gene pool was estimated by measuring the proportion of proposed Paleolithic (R1b, I2a2) and Neolithic haplogroups (E1b1b, G2a, J2a). The Basque provinces show varying degrees of post-Neolithic contribution in the paternal lineages, with 10.9% Neolithic lineages in the combined sample.

Timothy D. Weaver
Did a short-term event in the Middle Pleistocene give rise to modern humans?

It is often stated that modern humans originated 250,000-150,000 years ago. This statement implies, at least implicitly, that something ‘‘special’’ happened at this point in the Middle Pleistocene, such as a speciation event that was perhaps triggered by, or resulted in, a bottleneck in human population size. Two pieces of evidence are usually said to support this contention: that living human mitochondrial DNA haplotypes coalesce _200,000 years ago, and that fossil specimens classified as anatomically modern humans begin to appear shortly afterward. Alternatively, modern human origins could have been a lengthy process that lasted from the divergence of the modern human and Neandertal evolutionary lineages _400,000 years ago to the expansion of modern humans out of Africa _50,000 years ago, and nothing particularly ‘‘special’’ happened 250,000-150,000 years ago. Because this alternative model does not posit a discrete origins event, it may be better able to explain why [50,000-year-old fossils are arguably only ‘‘near modern’’ in anatomy. Here I use computer simulations based on theory from population and quantitative genetics to show that the alternative lengthy-process model also is consistent with a _200,000-year-old mitochondrial DNA coalescence time and the appearance shortly afterward of fossil specimens that, at least for some traits, appear to be anatomically modern. I further discuss how these two models differ in their predictions and whether or not it is possible to distinguish between them with current fossil and genetic evidence.

Steven L. Wang

Regional isolation and extinction? The story of mid-Pleistocene hominins in Asia.

Over the past decade, numerous reviews of the Middle Pleistocene record have taken place in light of new fossil discoveries. However, with primary foci on the Euro- African records, much of the rich fossil evidence in Asia was sidelined and overlooked. It is thus unsurprising that in the minds of many, Asia remains terra incognita— and its hominin record exotic. Moreover, the accuracy of the Asian chronology remains problematic, adding another layer of impediment to our understanding of regional evolution and local adaptation. In this context, I bring a synergistic review of the chronology of mid-Pleistocene hominins from East and South Asia, including recent new dates from key sites such as Zhoukoudian Locality 1 and Hathnora. Using 3-D geometric morphometric data, I examine cranial shape changes between H. erectus and mPH (post-erectus, non- Neandertal mid-Pleistocene Homo), as well as both to later Pleistocene hominins. A large number of not-often-discussed specimens are considered (e.g., Hexian, Nanjing 1, Maba, and Ngawi), many of them original fossils. The cranial anatomy from the Asian mid- Pleistocene suggests the existence of at least two distinctive groups in the region. Additionally, a north-south (geographical) shape difference is observed, hinting the presence of paleodemes each evolving in relative isolation. The shape affinity of mPH to extra-Asian fossils is confirmed; however, depending on the fossil in question (Dali or Narmada), the said affinity to Kabwe and Petralona is exclusive. This, coupled with a limited number of good sample, warrants caution against lumping all Asian mPH within the H. heidelbergensis hypodigm.

John Hawks
Deep genealogy, Neandertal ancestors, and our accelerating evolution

Anthropologists have long confused genealogical and behavioral definitions of humanity. At least five out of six living living humans have Neandertal ancestors, which comprise an estimated 1 to 4% of their ancestry. Human genes have divergent genealogical histories, representing multiple "archaic" populations inside and outside of Africa. Late Pleistocene populations show comparable technical and symbolic abilities within and outside of Africa. A humanlike vocal-auditory channel had appeared before 600,000 years ago. Yet humans of the last 40,000 years have evolved extremely rapidly, in some instances diversifying; in others paralleling each other. Using new visualization methods, I examine the genealogical patterns of human genes. The impact of our rapid Holocene evolution simplifies some genealogical relationships while partially obscuring earlier ones. The genetic echoes of Neandertals and other archaic populations emerge against a slim network binding all living people. These networks show the impact of adaptive potential in ancient human populations. A broad view of human cultural and technical records suggests that gene-culture interaction may be a fundamental aspect of Pleistocene human evolution.