April 30, 2012

Another look at Neolithic inhabitants of Sweden, using 'euro7'

After my initial analysis of the new Swedish Neolithic data, I decided -like with the Iceman-  to assess them with the euro7 calculator. Check the spreadsheet for comparative values in modern populations.

Of the hunter-gatherers: Ajv70 turns out to be 100% "Northeastern" in this analysis; Ajv52 is 75.1% "Northeastern", 21.8% "Northwestern", 2.9% "Far_Asian", and 0.3% "African". The "Northeastern" component is modal in the Baltic area.

Gok4, the Megalithic farmer was 61.5% "Northwestern", 21.4% "Southeastern", and 17.1% "Southwestern". The "Northwestern" component is modal in Atlantic Europe.

Modern Scandinavians have very little "Southeastern" and "Southwestern" by comparison, and this is probably what accounts for the clear southern origin of Gok4. But, Gok4 does seem to share the major "Northwestern" component with modern Scandinavians.

Two additional 'euro7' components occur in modern Scandinavians, "Caucasus" (~5%) and "Northeastern" (~20-25%). These components also occur in modern populations of the British Isles: the "Caucasus" one at similar or higher frequencies, the "Northeastern" one at lower ones than is the case in Scandinavia.

The fact that these two 'euro7' components are also missing in Oetzi strongly suggests to me that there was a late-Neolithic or post-Neolithic east-to-west migration into Europe from an eastern source area. Given the absence of "Caucasus" in Neolithic Gotland hunter-gatherers, it is a reasonable assumption that this migration may have originated from further south and east, where the "Caucasus" component occurs in modern populations.

There have been several indications linking Northwestern Europe with the Northeast Caucasus region. The latter exhibits high levels of Y-haplogroup R1b, the main Northwest European lineage. It also exhibits unexpectedly high levels of the "Northwest" component. I have little doubt that these twin facts constrain our understanding of the peopling of Western Europe by anchoring it -in some manner- to the Caspian and its environs.

If I had to guess I would propose the following scenario:
  • The "Northwestern" component represents the pre-Megalithic first farmers of Northwestern Europe, consisting of Linearbandkeramik farmers emanating from Central Europe and admixing with pre-farming Atlantic hunter-gatherers.
  • The "Megalithic" phase of the Neolithic saw the infusion of a new wave of maritime colonists originating in the eastern Mediterranean ("Southeastern") via Iberia ("Southwestern") and reaching their terminus in Scandinavia.
  • The last major population movement into Northwestern Europe involved the arrival of a population element from the northern parts of the Near East via the Caucasus, probably originating in the north Iran/Armenia/Azerbaijan/Dagestan "short arc" west and south of the Caspian where there is a local maximum of R1b frequency.
Thankfully, there is ongoing ancient DNA work on both the European steppe and the Balkans/Anatolia, i.e., the two possible conduits through which any additional "players" in the peopling of Europe must have passed through. Together with ancient DNA study of other archaeological cultures in continental Europe itself, (e.g., Corded Ware/Bell Beaker) our picture of prehistoric events is bound to become ever sharper in coming years.And, hopefully, once the actors in the drama are revealed, we can move on to the late Bronze and Iron Ages, to see how they interacted to form the historical peoples of West Eurasia.

Tracing the origin of language in Africa (again)

A recent paper on the origin of language in Africa was subjected to heavy criticism not long after its publication. Now, the African origin of language hypothesis is championed by a new pair of authors who also base their claim on phonemic diversity of African languages.

I am sure that there will be a new round of criticism by linguists shortly, but for my part, I will simply note a couple of things:

First, the paper assumes rather than prove a tree-like divergence of human languages. It is not at all clear to me that language does have a common origin in humans. For one thing, research on Neandertal anatomy has suggested that they had the ability to vocalize, and Neandertals diverged from other humans long before the emergence of H. sapiens or even H. helmei in the African Middle Stone Age.

It could very well be that the ability to talk may have been invented twice or even more times, evolving perhaps from a simpler communication system available to species such as H. heidelbergensis. If that is the case, then a tree model of the accumulation of phonemic diversity need not only involve Out of Africa migration, but also contact with other human groups with languages of their own, possessing separate phonemic inventories.

A second point that needs to be made is that I do not really understand the inference of law-like accumulation of phonemic diversity on which the paper is based. It could well be argued, for example, that migration creates separate language communities that undergo different processes of phonemic evolution, some of them retaining ancestral phonemes, some of them developing new ones. Indo-European is a case in point, where languages such as Greek and German have added fricatives, and dispensed with aspirated stops while Hindi has not. The totality of the phonemic inventory in Indo-European languages today may be greater than it was in PIE.

But, there is also a process of simplification within languages leading to a loss of phonemes (e.g., the simplification of the Greek vowel system and the loss of initial aspiration). It is not clear to me whether simplification or diversification wins out in the end: perhaps our ancestors had a much richer phonemic diversity in the past which was reduced as people started becoming part of larger social units than the ancestral hunting tribe. In such units people might get rid of their ancestral way of speaking and accumulate into a new and simpler way, in the same manner that e.g., the phonemic inventory of the entire world is reduced after a couple generations into the sounds of American English by people who become part of the American social unit.

Finally, the paper assumes Out-of-Africa 60-70ky ago. I have been a vocal critic of that idea for quite some time now, and a bird tells me (or should I say tweets me?) that a new synthesis will soon be published that takes into account some recent and exciting archaeological discoveries, that point to a pre-100ky event and apparently exclude a post-70ky one. But, more on that when it sees the light of day and I read it for myself.

 PLoS ONE 7(4): e35289. doi:10.1371/journal.pone.0035289

Dating the Origin of Language Using Phonemic Diversity

Charles Perreault, Sarah Mathew


Language is a key adaptation of our species, yet we do not know when it evolved. Here, we use data on language phonemic diversity to estimate a minimum date for the origin of language. We take advantage of the fact that phonemic diversity evolves slowly and use it as a clock to calculate how long the oldest African languages would have to have been around in order to accumulate the number of phonemes they possess today. We use a natural experiment, the colonization of Southeast Asia and Andaman Islands, to estimate the rate at which phonemic diversity increases through time. Using this rate, we estimate that present-day languages date back to the Middle Stone Age in Africa. Our analysis is consistent with the archaeological evidence suggesting that complex human behavior evolved during the Middle Stone Age in Africa, and does not support the view that language is a recent adaptation that has sparked the dispersal of humans out of Africa. While some of our assumptions require testing and our results rely at present on a single case-study, our analysis constitutes the first estimate of when language evolved that is directly based on linguistic data.


April 28, 2012

A first look at the DNA of Neolithic inhabitants from Sweden

I was eager to get my hands on the ancient DNA from ancient Swedish Neolithic people, as soon as I became aware of it a few months ago. I was finally able to extract SNPs from the data, and I decided to test the samples with my K7b and K12b calculators from the Dodecad Project, as I had also recently done for the Tyrolean Iceman. You can skip to the Results section if you want.

I extracted the following number of SNPs from the different individuals, that were in common with my main HGDP reference:

  • 15,734 SNPs: Gok4 (TRB / farmer)
  • 15,385 SNPs: Ajv52 (PWC / hunter-gatherer)
  • 25,108 SNPs: Ajv70 (PWC / hunter-gatherer)
I did have some trouble with my code for extracting data from the third hunter-gatherer individual, Ire8. This also happens to have the lower number of SNPs as reported by Skoglund et al. so its non-inclusion is probably not a great loss.

K7b and K12b are based on a set of 166,770 SNPs, so I intersected the SNPs of the ancient individuals with them, resulting in:

  • 4,054 SNPs: Gok4
  • 4,077 SNPs: Ajv52
  • 6,631 SNPs: Ajv70
This is, of course, a small number of SNPs, and if we tried to infer structure within West Eurasia with them, we might fail. Nonetheless, by exploiting the structure inferred by the larger number of SNPs in modern populations, and using these to test the ancestry of the ancient ones, we get results that appear to agree fairly well with Skoglund et al. (2012).

A problem with comparing against extant populations, rather than ancestral components is that relationships are averaged: for example, Turks in Skoglund et al. appear quite distant to both Neolithic groups, but we cannot know to what extent this is due to their small levels of central/east Eurasian ancestry and to what extent this is due to their native Anatolian ancestry.

We now have two ancient autosomal DNA sampling locations, and both turned up unexpected results. The Iceman, a Copper Age inhabitant of the Alps resembled modern Sardinians. A Megalithic Swedish farmer resembled Southern Europeans, while his hunter-gatherer contemporaries were outside the range of modern variation. These results should give us caution about the identity of past populations elsewhere. 

As I have argued elsewhere, the past seems to have been much more dynamic than many had suspected, and the people that walked and rowed to the ends of the Earth during the Upper Paleolithic did not suddenly grow fetters or decided to stay put during the Neolithic as many "Paleolithic continuity" adepts had proposed.

A couple more caveats:

  1. Irrespective of their actual origin, these individuals would still be inferred to be some admixture of the ancestral components adding up to 100%. This hints at their affiliations, but does not -in itself- supply evidence of their absolute proximity to the ancestral components.
  2. As more and more ancient individuals are sampled, we will be able to generate genuine ancient populations that are ancestral to modern ones. When that happens, we can directly test modern individuals against panels of ancient ones. For the time being, we have to make do with the reverse, i.e., test ancient individuals against panels of modern ones.


In all comparisons with other K7b results, you should take into account the much smaller number of SNPs used on the Neolithic remains from Sweden.

The K7b results are below. Consult the spreadsheet for comparative values in modern populations.

The K12b results are below. Consult the spreadsheet for comparative values in modern populations.

The raw percentages can be seen below; I have also added the results previously calculated for Oetzi, the Tyrolean Iceman:


The results for the two hunter-gatherer samples are as expected predominantly "Atlantic_Baltic" at K=7 and "North_European" at K=12. Since these two samples are outside modern variation, it is expected that their mapping may have added noise; see this post about the dangers lurking at the edges of variation.

Nonetheless, the results can be interpreted as reflecting the fact that the "Atlantic_Baltic" and "North_European" components partially reflect the pre-farming population of Europe. At K=12 it is noteworthy that there is a minor "Atlantic_Mediterranean" admixture in the two hunter-gatherer samples. In my opinion, this may reflect either some level of admixture with the incoming farmers and/or the pre-farming component (but of Western European rather than Baltic type) that may also exist in these foragers. On balance, however, the "North_European" component far outweighs the "Atlantic_Mediterranean" one, which is also consistent with their location (Gotland) which ties them to the Baltic rather than Atlantic Europe.

The farmer sample is remarkable in that, like the Tyrolean Iceman, she seems to be made up entirely of "Atlantic_Baltic" and "Southern" at K=7. There is a hint that the order of the two components are reversed in Gok4 relative to Oetzi, which probably makes sense. The third major West Eurasian component at this level of resolution, the "West Asian" one is conspicuously absent. This component -bimodal in the Caucasus and Balochistan, and strongly represented in the highlands of West Asia in between the two- does occur at ~10% in modern Northern Europeans, so its absence in all Neolithic samples so far hints at its later introduction into at least parts of Europe.

The result at K=12 is fascinating, since Gok4 turns out to be 81% "Atlantic_Mediterranean", and, like Oetzi, with a noticeable "Southwest_Asian" strain. The "Atlantic_Mediterranean" component is bimodal in modern Sardinians and Basques, while the "Southwest_Asian" radiates from southern parts of the Near East into Mediterranean Europe.

Gok4 appears to be "even more Atlantic_Mediterranean" than any modern population. As I mention in the original post, the inhabitants of megalithic monuments  of North-Western Europe were believed by Coon to belong to a "Long Barrow type" which he considered ancestral to the modern "Atlanto-Mediterranean" type. Here is his description:
Toward the end of the Neolithic period, the western Mediterranean countries were invaded by seafarers of a tall, exceptionally long-headed Mediterranean variety; some of these invaders passed through the Straits of Gibraltar, whence they also invaded the British Isles and Scandinavia. 
I would say that the evidence is not incompatible with this scenario. We must probably wait to see whether Gok4 was descended from seafarers from the eastern Mediterranean (where the "Southern" component is modal), following the Mediterranean and then Atlantic coasts up to Scandinavia, or whether they are descended from a different group of people who followed the plains and river valleys of the Balkans and Central Europe and arrived to the north via the inland route. The strong Atlantic_Mediterranean result, coupled with high levels of allele sharing in Cyprus, Greece, France, and the Netherlands, but not particularly in the northern Balkans leads me to prefer the maritime colonization scenario, at least for now. Ancient DNA from more European regions will hopefully help us better understand "what really happened in prehistory."

April 27, 2012

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.


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.


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.


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.


April 26, 2012

Ancient DNA from Neolithic Sweden (Skoglund et al. 2012)

A new paper in Science solidifies the case for migration as the cause for the diffusion of agriculture in Europe. Discontinuity between early Neolithic farmers and Mesolithic foragers in Central Europe had provided strong hints about this discontinuity, and these were confirmed by other ancient European DNA, e.g., from Treilles, or the Tyrolean Iceman. The case now appears irrefutable, that people not ideas were involved in the spread farming to the northern fringes of Europe.

If we were to ever find signs of acculturation, the north-eastern corner of Europe may be best place to look for it. Agriculture arrived late to Scandinavia and the Baltic, so there was maximum opportunity for Neolithic groups in the area to acquire pre-Neolithic genes from acculturated farmers during their ~2ky long journey from the Aegean. Conversely, forager populations persisted here longer than elsewhere in Europe, both due to the remoteness of the area and the relative unsuitability of the Neolithic package brought from more southern latitudes.

During the Neolithic period there still existed foragers in Scandinavia who belonged to the Pitted Ware (PWC) culture. These have been the object of a previous mtDNA study, which found them to be strongly differentiated from contemporaneous Funnel Beaker or Trichterbecherkultur (TRB) farmers. The latter were farmers who were also associated with Megalithic monuments in northern Europe.

A recent article by Rowley-Conwy (2011), from which the figure on the left is taken, gives some archaeological perspective on the Neolithic of southern Scandinavia:
This farming spread must have been by boat. There were no native aurochs on Zealand (Aaris-Sorensen 1980), so the early cattle at Akonge were definitely imported. Farther north, agriculture was probably carried by boat up the coasts, an easier method of travel than overland (see above). Baltic crossings would require longer open-water voyages than in the Cardial or LBK. Irish curraghs can, however, make substantial voyages and weather considerable seas (Hornell 1938, sec. 5:17–21), and a large one has even crossed the Atlantic (Severin 1978).


The agricultural arrival in southern Scandinavia thus appears sharp. Gradualist views of Late Mesolithic developments can be discounted despite the spread of shoe-last axes beyond the farming frontier. Western Norway presents a similar pattern: axes and ceramics were in circulation for over a millennium beyond the farming boundary.
This was the dusk of the European foragers: whatever their contribution to subsequent European populations, their way of life would soon give way to that of the farmer and shepherd. The Pitted Ware culture can indeed be seen as their "last stand", the last time in prehistory when they could co-exist on fairly equal terms with their farmer neighbors.

Hence, it is very exciting to be able to study DNA from this place and time directly, as Skoglund et al. do in a new paper which reports the successful extraction and analysis of ancient DNA from 3 PWC hunter-gathers and one TRB farmer of about ~5,000 years ago:
The Neolithic farmer sample ('Gok4') was excavated from a megalithic burial structure in Gokhem parish, Sweden, and has been directly 14C-dated to 4,921 ± 50 calibrated years BP (calBP), similar to the age (5,100-4,900 calBP) of the majority of other finds in the area (15). There were no indications from the burial context suggesting that Gok4 was different from other TRB individuals (15, 16), and strontium isotope analyses indicate that Gok4 was born less than 100 km from the megalithic structure, similar to all other analyzed TRB individuals from the area (17). The three Neolithic hunter-gatherer samples were excavated from burial grounds with single inhumation graves on the island of Gotland, Sweden, for which associated remains have been dated to 5300-4400 calBP (16).
We must keep in mind that a limited amount of DNA sequence was extracted, which corresponds to a few tens of thousands of SNPs in common with the best modern SNP set used; this corresponds to ~5% of the genome, with different success rates for the four sampled individuals. We must also not forget that these are farmers and foragers from a single point in space-time, and from the periphery of Europe, so we should be cautious in generalizing about the Neolithic transition in other parts of Europe.

Nonetheless, the new study reveals two important pieces of information:

First, the 3 PWC individuals are strongly differentiated from the single TRB one:
Regardless of the underlying model, our study provides direct genomic evidence of stratification between Neolithic cultural groups separated by less than 400 km, differentiation which encapsulates the extremes of modern-day Europe, and appears to have been largely intact for ~1,000 years after the arrival of agriculture.
So, it appears that these individuals lived at roughly the same time and within a small area of Europe, and yet they are as different from each other as the most distant current European populations are. These were not simply drawn from the same or similar populations, some of them deciding to take up farming while others to practice fishing and hunting. These were different populations who maintained their distinctiveness long after "first contact".

Two models have dominated European prehistory in recent decades: acculturationists claimed that the Neolithic package of domesticated plants and animals was transmitted across the continent while the people largely stayed put, while demic diffusionists claimed that people did move, but -at least in the most popular version of the model- that they gradually intermarried with local hunter-gatherers, forming a genetic cline of ancestry, at the far end of which the farmers were mostly derived from local foragers.

One could very well say that the acculturationist model views prehistoric people as smart folk with no legs, apparently ready to take up a good new idea, but reluctant to leave their birthplace. The demic diffusionist model, on the other hand, viewed them as mindless automata, moving across the landscape with little purpose, marrying who they met, and filling a continent in much the same way that gas molecules end up filling a room into which they are introduced.

Both these models are now revealed to be wrong: rather, it seems that "leapfrog" colonization may be responsible for the spread of agriculture and its associated technologies (such as Megalithism) across Europe. In this model, farmers lept from place to place across the landscape intentionally, preserving their gene pool and largely ignoring the pre-existing foragers of the landscape.

Of course, farmer and hunter eventually did mix, and hunting cultures became extinct. But, this was a process that seems to have been complete after 4,000 years BP. Acculturation did eventually happen, and agriculturalists did eventually diffuse to every corner of Europe. But, these are events that happened after the initial group(s) of pioneers had opened the frontier. In this respect, the colonization of Europe bears some resemblance to the settlement of the Americas by Europeans: it happened by leaps and bounds, and the early waves of explorers and pioneers may have opened the landscape but did not immediately fill it: this happened later as a result of demographic growth and new waves of migration, with the extant populations being differentially descended -in different proportions- from migrants and natives.

The second important point of the new study is the revelation that the single Neolithic individual from northernmost Europe was similar to extant southern Europeans:
To more closely investigate the genetic similarity of extant European populations (22, 24) to Neolithic humans, we determined for each SNP and each extant population the average frequency of the particular allele found in either the Neolithic hunter-gatherers or the Neolithic farmer (16). The Neolithic hunter-gatherers shared most alleles with Northern Europeans, and the lowest allele sharing was with populations from Southeastern Europe (Fig. 3A). In contrast, the Neolithic farmer shared the greatest fraction of alleles with Southeastern European populations (Cypriots and Greeks), and showed a pattern of decreasing genetic similarity for populations from the Northwest and Northeast extremes of Europe (Fig. 3B). Individuals from Turkey stand out by low levels of allele sharing with both Neolithic groups, possibly due to gene flow from outside of Europe, but all other European populations can roughly be represented as a cline where allele sharing with Neolithic hunter-gatherers is negatively correlated with allele sharing with Neolithic farmers (Fig. 3C). 
Panel C from the allele sharing figure (left) suggests why we should be cautious about trying to reconstruct European prehistory on the basis of a simple 2-way model of admixture between farmers and hunters.

It is true that extant European populations do fall on a clear cline between them that is strongly significant (R=-0.58, p=0.0029). This means is that they are different to each other in the same ways that farmers/hunters were different from each other. But, this still leaves about 2/3 of the variance unexplained: this may be partly due to the "noise" added by the small number of SNPs, and partly by the contribution of other ancestral groups to extant variation. One of these groups may be the east Eurasian element which must contribute to the differentiation of Turks from Europeans. But, there were probably other West Eurasian elements not represented by the two Neolithic groups: the Mesolithic Pitted Ware individuals have been previously assigned predominantly to mtDNA haplogroup U, which forms a minority in extant Europeans; and a handful of Neolithic samples (LBK, Oetzi, Treilles) have failed to turn up any signs of the dominant R1 Y-haplogroup of extant Northern Europeans. There must be other actors to be revealed in the unfolding story of European origins.

A strong hint for this can also be found in the quite unexpectedly low "TRB" allele sharing of groups from the Northwestern Balkans. This is quite unexpected, as the area is widely believed to be a conduit through which agriculture spread into Central Europe. It is also an area with world maxima of Y-haplogroup I, a lineage which may be a remnant of Paleolithic Europeans, and correspondingly low levels of haplogroups that appear to have arrived later into Europe.

Another important point is that levels of allele sharing between these Neolithic individuals and modern Europeans is generally lower than between most pairs of modern European populations. This is, in part, expected, since the Neolithic specimens are separated by modern populations by ~5ky of evolution, but may also be due to the contribution of unsampled groups to the ancestry of the latter.

From the paper:
We found that compared to a worldwide set of 1,638 individuals (21-23), all four Neolithic individuals clustered within European variation (Fig. S5). However, when focusing the analysis on 505 individuals of European and Levantine descent, the three Neolithic hunterg atherers appeared largely outside the distribution of the modern sample, but in the vicinity of Finnish and northern European individuals (Fig. 1A). In contrast, the Neolithic farmer clustered with southern Europeans, but was differentiated from Levantine individuals. This general pattern persisted for a geographically broader reference data set of 1,466 extant individuals of European ancestry (22, 24) (Fig. 1B), for a much larger number of markers from 241 individuals in the 1000 genomes project (25) (Fig. 1C), and using model-based clustering (26, 27) (Fig. 1D). Although all Neolithic individuals were excavated in Sweden, neither the Neolithic farmer nor the Neolithic hunter-gatherers appeared to cluster specifically within Swedish variation, a pattern that remained also for a larger sample of 1,525 individuals from across Sweden (28) (Fig. S9, Fig.S21-22).
I will try to perform an analysis of these 4 Neolithic Europeans, as I did with the Iceman, and see how they relate to a larger number of populations: for example, the Mesolithic hunter-gatherers have the highest allele sharing with Poles: do they share even more with Lithuanians and other Baltic peoples? The Neolithic farmer is by far closer to Cypriots: are there any populations of the Near East that are close to it as well?

Hopefully, in the near future we may get our first glimpses of genuine Mesolithic Europeans:
In our genomic analyses, the Scandinavian Neolithic hunter-gatherers (PWC) have a genetic profile that is not fully represented by any sampled contemporary population (Fig. 1), and may thus constitute a gene pool that is no longer intact or that no longer exists. While the origin of the Neolithic hunter-gatherers is contentious, the similar mtDNA haplogroup composition of PWC individuals (8) (Table 1) and Mesolithic- and Paleolithic individuals (7, 29) indicate some continuity with earlier European populations, but resolving this hypothesis will require pre-Neolithic genomic data.
The continuity between Mesolithic and Neolithic hunter-gatherer populations in the Baltic is supported by craniometric analysis from a recent paper (left), but it is definitely worth investigating whether -despite their strong differentiation- the Neolithic farmers and foragers of Sweden may not have already started -at least partially- the process of amalgamation.

Hopefully we can soon extract more DNA from other Neolithic Europeans, as well as pre-contact European foragers. It is probably in the Copper and Bronze Ages that we are to encounter some the remaining players that formed the European genetic landscape and witness how they all combined to form the proto-historical and recent Europeans.

A Postscript:

Until recently, it had become commonplace in archaeology to seek local origins for most archaeological phenomena. Three years ago, I pointed out that new evidence was pointing towards a major migrationism comeback in our understanding of European prehistory. So, it is worth reviewing what was once thought about the people buried in Swedish megalithic monuments. From Carleton Coon's The Races of Europe, (1936) Chapter IV):
In Sweden, out of twenty-four male crania found in passage graves, only one was brachycephalic; for the most part a pure Long Barrow type is represented. (Section 12) 
The Megalithic Long Barrow people must have come by sea, and they probably came from somewhere in the Mediterranean. (Section 10)
The paper is also discussed in the weekly Science podcast. The supplementary materials are freely available.

Science 27 April 2012: Vol. 336 no. 6080 pp. 466-469 DOI: 10.1126/science.1216304

Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe

Pontus Skoglund1,*, Helena Malmström1, Maanasa Raghavan2, Jan Storå3, Per Hall4, Eske Willerslev2, M. Thomas P. Gilbert2, Anders Götherström1,5,*,†, Mattias Jakobsson

The farming way of life originated in the Near East some 11,000 years ago and had reached most of the European continent 5000 years later. However, the impact of the agricultural revolution on demography and patterns of genomic variation in Europe remains unknown. We obtained 249 million base pairs of genomic DNA from ~5000-year-old remains of three hunter-gatherers and one farmer excavated in Scandinavia and find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.


April 25, 2012

Rise of the Planet of the Apes postponed

In Rise of the Planet of the Apes, a young scientist experiments with genetically modified chimpanzees, inadvertently making one exhibit human-like behavior. I thought of the movie as I was listening to the live webcast of Svante Paabo's talk at the Genomes Environments Trait conference (not sure if/when there will be an archival copy of the talks available).

Paabo was discussing how scientists had identified amino acid substitutions in the FOXP2 gene that were fixed in humans and different from chimpanzees, and, more recently -thanks to the availability of the Denisova genome- of differences that were fixed in modern humans and different in our closest genetic relatives (archaic humans).

The question naturally arises: how can we tell what the (modern) human specific mutations actually do.

Paabo said that we could do this if we created transgenic chimps/humans with the human/chimp version of the gene, but then jokingly crossed out the idea since ethics committees would never approve it.

He went on to say that the human version of FOXP2 was input into transgenic mice instead, with some evidence that these mice had different vocalization than regular mice. Even though we cannot actually breed humans with the chimp version of FOXP2, there may actually be some of the 7 billion humans in existence that may harbor back-mutations giving them this version.

Naturally, the question arises: if nature itself mutates human FOXP2 into its chimp version and vice versa, why is it unethical to do so in the lab?

Of course, there are good ethical reasons why we wouldn't want to give human children a chimp gene: we don't exactly know what it will do, but the risk of causing harm to a human person is sufficient reason to act cautiously.

But, why is it unethical to give chimps the human version of the gene? After all, the fact that the human version is fixed (in humans) may mean that is doing something really important and giving us some ability that we shouldn't toy around with. But, what evidence is there that the reverse is also true, and the chimpanzee harboring a human FOXP2 gene would face any problems at all?

This brings me to the topic of a recently introduced bill which would ban chimpanzee research altogether. This would not only subject the issue of chimp research to ethics committees who would probably not approve it, but ban it altogether.

There are substantial benefits in learning more about FOXP2 and other genes in which humans differ from chimpanzees. There is the intellectual benefit of learning what makes us special within nature, and how we differ from apes. There is the practical benefit of potentially easing the suffering of patients with damaged copies of genes that are fixed in the human lineage. Or, of understanding how language ability and cognition emerge, so that we can one day hope to create machines capable of it, freeing mankind from a great deal of toil.

And, there is the infinitesimal potential that we'll end up with an unhappy chimp ready to organize the simian takeover of our planet. Thankfully, Pinky and the Brain do not give rise to the same levels of dread and insecurity, so, for the time being we still have the option of experimentation with mice.

Personally, I'm all for putting human FOXP2 in chimps and seeing what happens. And, I am rather dismayed that the scientific and political culture has become so risk-averse that an experiment that would bring no harm to any humans, that would benefit humans, and that may not, indeed, affect negatively the chimps involved is, nonetheless, rejected out of hand on the basis of the nebulous probability that it might.

April 23, 2012

Ancient DNA from pre-Columbian Andean community

BMC Genetics 2012, 13:30 doi:10.1186/1471-2156-13-30

Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community

Mateusz Baca et al.

Abstract (provisional)


A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves.


The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y-chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave.


Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities.


April 21, 2012

Bearers of French surnames in Flanders differ from those bearing Flemish surnames

This certainly appears consistent with my postulated origins of these subgroups within European R-M269. Hopefully the same process could be repeated in others parts of Europe.

We have a hierarchy of tools for uncovering the origins of modern populations: traditional genealogy for relatively recent ancestors, surnames for slightly older ancestors, and finally ancient DNA which could eventually be applied to historical persons and communities.


Heredity , (18 April 2012) | doi:10.1038/hdy.2012.17

In the name of the migrant father—Analysis of surname origins identifies genetic admixture events undetectable from genealogical records

M H D Larmuseau, J Vanoverbeke, G Gielis, N Vanderheyden, H F M Larmuseau and R Decorte


Patrilineal heritable surnames are widely used to select autochthonous participants for studies on small-scale population genetic patterns owing to the unique link between the surname and a genetic marker, the Y-chromosome (Y-chr). Today, the question arises as to whether the surname origin will be informative on top of in-depth genealogical pedigrees. Admixture events that happened in the period after giving heritable surnames but before the start of genealogical records may be informative about the additional value of the surname origin. In this context, an interesting historical event is the demic migration from French-speaking regions in Northern France to the depopulated and Dutch-speaking region Flanders at the end of the sixteenth century. Y-chr subhaplogroups of individuals with a French/Roman surname that could be associated with this migration event were compared with those of a group with autochthonous Flemish surnames. Although these groups could not be differentiated based on in-depth genealogical data, they were significantly genetically different from each other. Moreover, the observed genetic divergence was related to the differences in the distributions of main Y-subhaplogroups between contemporary populations from Northern France and Flanders. Therefore, these results indicate that the surname origin can be an important feature on top of in-depth genealogical results to select autochthonous participants for a regional population genetic study based on Y-chromosomes.


Neandertal admixture vs. Ancient African structure

The case for Neandertal admixture has been made on the basis of the D-statistic. This is a genomewide statistic which quantifies how two modern populations differ from each other at sites where Neandertals carry the derived allele. If population A tends to agree with Neandertals more than population B does, then this is consistent with Neandertal admixture in population A. It is also consistent with admixture in Neandertals from modern humans, and with ancient population structure whereby some humans carry admixture from before the common ancestor of modern humans and Neandertals.

A new paper goes beyond the D-statistic with the goal of trying to decide between two different models: Neandertal admixture in Eurasians or ancient African population structure. It does so by simulating the site frequency spectrum under the two models and comparing the result with the observed shape of the spectrum. From the paper:

Durand et al. (2011) suggested that the ancient structure model results in more variation in gene tree depth than the recent admixture model. Greater variance in tree depth would alter the frequency spectrum but not the D-statistic. Here, we show that the sfs appropriately conditioned can distinguish between recent admixture and ancient structure because it is particularly sensitive to episodes of recent admixture.

This is how Durand et al. (2011) explained this:

However, it is known that ancestral population subdivision result in a higher than expected variance in coalescence times (Wall, Lohmueller & Plagnol 2009). Therefore, ancestral subdivision is likely to result in more variation in gene tree depth when using several samples from the extant population. This in turn will affect the site frequency spectrum of the extant population (Harpending et al. 1998). Designing a statistic to distinguish between the two scenarios will require using more than one sample per population.

Here is how the authors describe their two models, pictured on the left:
[admixture] In this model, we assume that there was a single episode of admixture at time tGF in the past (t = 0 being the present) from Neanderthals to non-Africans after the migration of humans out of Africa (Figure 1a). With probability f, a non-African lineage was derived from a Neanderthal lineage. The parameter f represents the fraction of the non-African genomes of Neanderthal origin. We define the divergence time of non-African and African populations as tH > tGF. We denote by tN > tH the divergence time of Neanderthals and the population ancestral to modern humans.


[structure] We assume in this model that the population ancestral to modern humans and Neanderthals was divided into two randomly mating subpopulations (Figure 1b). We assume that subpopulations exchanged migrants symmetrically at rate m per generation. At time T in the past, subpopulations merged into one panmictic population. A similar model was proposed in Slatkin and Pollack (2008). Green et al. (2010) noted that this model could explain the extra similarity of Neanderthals with non-Africans, and Durand et al. (2011) showed that D-statistics could not distinguish between ancient structure and recent admixture for plausible demographic parameter ranges.
I don't quite understand the ancient population structure model as presented in this paper. It appears that time T (when the populations merged into one panmictic population) precedes the split between modern humans and Neandertals.

This is definitely not what I've had in mind when I've spoken about African population structure before; rather, I think that within the genus Homo there were at least two subpopulations (let's call them A and B) that had long-term reproductive isolation. B gave rise to H. sapiens and H. neanderthalensis but some subpopulations of H. sapiens admixed with A long after the sapiens/Neandertal split. The basis for that model is dual: (i) the late persistence of archaic humans in Africa that no longer exist there and hence may have been absorbed by African sapiens and (ii) the greater genetic variation in extant Africans which is consistent with either an Out-of-Africa bottleneck or an Into-Africa event followed by admixture.

In any case, it is worth giving the investigated parameters of the authors' two models:
In the recent admixture model, tH was set to 4,500 generations ago (112.5 kya, Li and Durbin 2011), and tN was set to 12,000 generations ago (300 kya, Green et al. 2010). The tGF parameter was set to 2,000 generations (50 kya), and f was chosen to be 0.05. 
In the ancient structure model, T was varied between 12,000 to 32,000 generations ago, in steps of 2,000 generations. The intensity of ancient migration m was set to 4Nm = {0,1,…,10}. The non-African and Neanderthal populations split 12,000 generations ago (tN), and tH, the population split time between YRI and the non-African populations, was 4,500 generations ago.
I have a few observations:
  • The population split between YRI and non-Africans is set at 112,500 years ago. This is most certainly inaccurate, since Yoruba possess mtDNA haplogroup L3 in common with Eurasians (age ~70ky), and they are also near completely within Y-haplogroup DE-YAP (which links them with Eurasians within a ~50ky timeframe). A split between YRI and non-Africans at 112,500 years ago is virtually impossible. An apparent split at that time is plausible once we take into account that this number is inflated by admixture in Africa, and the YRI group may be partially descended partially from a West Eurasian-like population admixing with an older African substratum (early AMH or even older Africans).
  • Archaic admixture in Africans has been little studied and there are several new studies in the works which will investigate it. For the time being, an initial admixture study, as well as the late persistence of archaic hominins in Africa appears to be consistent with a very late admixture event, rather than with a long-standing process of admixture between structured African populations.
  • In the recent admixture model, the admixture is taken as both instantaneous (at tGF) and recent (50ky). The former assumption seems justified, but it is hard to believe in a model that would have Eurasians deviating from Africans 112,500 years ago and then waiting for 62,500 years to admix with Neandertals. Neandertals began to be neighbors of modern humans from before 100 thousand years in the Levant, and pre-50ky Neandertals such as Kebara are already modern-like, as is Vindija; the latter's deviation towards modern humans is critical because it highlights the very real possibility that the ancient Neandertal genome as currently reconstructed may be in fact partially modern human.
I really don't see why we the two models should differ qualitatively: a postulated abrupt (instantaneous) admixture event with Neandertals (despite the fact that modern humans and Neandertals were clearly neighbors for close to 100 thousand years) vs. a long-standing process of admixture in Africa.

To conclude, the new study is to be applauded for trying to evaluate different schemes for reaching the same observed D-statistics, but I would not throw the African structure hypothesis out the window quite yet.

Mol Biol Evol (2012) doi: 10.1093/molbev/mss117

Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity

Melinda A. Yang et al.

Neanderthals have been shown to share more genetic variants with present-day non-Africans than Africans. Recent admixture between Neanderthals and modern humans outside of Africa was proposed as the most parsimonious explanation for this observation. However, the hypothesis of ancient population structure within Africa could not be ruled out as an alternative explanation. We use simulations to test whether the site frequency spectrum, conditioned on a derived Neanderthal and an ancestral Yoruba (African) nucleotide (the doubly conditioned site-frequency spectrum, dcfs), can distinguish between models that assume recent admixture or ancient population structure. We compare the simulations to the dcfs calculated from data taken from populations of European, Chinese, and Japanese descent in the Complete Genomics Diversity Panel. Simulations under a variety of plausible demographic parameters were used to examine the shape of the dcfs for both models. The observed shape of the dcfs cannot be explained by any set of parameter values used in the simulations of the ancient structure model. The dcfs simulations for the recent admixture model provide a good fit to the observed dcfs for non-Africans, thereby supporting the hypothesis that recent admixture with Neanderthals accounts for the greater similarity of Neanderthals to non-Africans than Africans.


April 18, 2012

Another look at the Y chromosomes of Afghanistan

Good things come in pairs, so a little after the recent publication of a paper on the Y chromosomes of Afghanistan, there is yet another paper on the same topic. There is some quite useful information in the open access supplementary material, including a table of haplogroup R-M198 and R-M198*(xM458) frequencies in a wide range of human populations.

Unfortunately, this paper too was probably written before the current developments in the R1a world, and did not take advantage of the newer discovered SNPs. Hopefully the DNA samples can be eventually tested  in more phylogenetic detail.

European Journal of Human Genetics advance online publication 18 April 2012; doi: 10.1038/ejhg.2012.59

Afghanistan from a Y-chromosome perspective

Harlette Lacau et al.


Central Asia has served as a corridor for human migrations providing trading routes since ancient times. It has functioned as a conduit connecting Europe and the Middle East with South Asia and far Eastern civilizations. Therefore, the study of populations in this region is essential for a comprehensive understanding of early human dispersal on the Eurasian continent. Although Y- chromosome distributions in Central Asia have been widely surveyed, present-day Afghanistan remains poorly characterized genetically. The present study addresses this lacuna by analyzing 190 Pathan males from Afghanistan using high-resolution Y-chromosome binary markers. In addition, haplotype diversity for its most common lineages (haplogroups R1a1a*-M198 and L3-M357) was estimated using a set of 15 Y-specific STR loci. The observed haplogroup distribution suggests some degree of genetic isolation of the northern population, likely due to the Hindu Kush mountain range separating it from the southern Afghans who have had greater contact with neighboring Pathans from Pakistan and migrations from the Indian subcontinent. Our study demonstrates genetic similarities between Pathans from Afghanistan and Pakistan, both of which are characterized by the predominance of haplogroup R1a1a*-M198 (>50%) and the sharing of the same modal haplotype. Furthermore, the high frequencies of R1a1a-M198 and the presence of G2c-M377 chromosomes in Pathans might represent phylogenetic signals from Khazars, a common link between Pathans and Ashkenazi groups, whereas the absence of E1b1b1a2-V13 lineage does not support their professed Greek ancestry.


April 16, 2012

Atlantis talk by Brian Rose @ Penn

A talk by Brian Rose at the Penn Museum:

I like the fact that the presenter stresses a couple of points which are often neglected in modern treatments of Atlantis:
  1. The story of Altantis is a myth created by Plato and recognized as such during Antiquity; the point of this myth was not to preserve a legacy of the remote past, but to make a philosophical and political point. So, while the search for Atlantis may have spurred some interesting archaeological work, it is largely a futile effort.
  2. The Atlantis described by Plato was not a utopia, or antediluvian paradise on earth, or the source of human high culture, but rather the antagonist (=the bad guys) in a morality tale. This tale had the aim of presenting the Kallipolis of the Republic as having actually existed in the remote past and as having proven the value of its institutions in the conflict with the Atlantean foe.
The presenter, however, makes another point that is rather less believable, namely that the story of ancient Athens vs. ancient Atlantis was a parable for the recent and ongoing -in Plato's time- conflict between the Greeks and the Persians. He argues that the despotism of the kings of Atlantis parallels that of the King of Persia, while the democratic institutions of 4th c. BC Athens parallel those of old Athens.

That, however, presupposes that Plato was a supporter of democracy, and, in particular, its Athenian incarnation. Nothing could be further from the truth: Plato's entire oeuvre is clearly anti-democratic in character; in the Republic, democracy is the second-to-worst political system, one step above tyranny, the worst.

He certainly did not view the conflict between Greece and Persia in political terms: a contrast between freedom and despotism certainly permeated many ancient accounts, but not necessarily the Platonic (*). And, we should not confuse political freedom with democracy: even the writers -such as Herodotus- who presented the Persian Wars along political terms were happy enough to use the oligarchical Spartans as paragons of freedom and its defense, despite their lack of democracy.

(*) If anything, Plato seems to have subscribed to the view that war is "natural" between different descent groups, and is sometimes engendered by economic competition. He would probably have been baffled by the idea that two states, inhabited by people of the same genetic stock, and having no economic quarrels would fight each other because of their differences in constitution.

Should incestuous marriages be allowed?

German incest couple lose European Court case
A brother and sister from Germany who had an incestuous relationship, arguing they had the right to a family life, have lost their European court case.

Patrick Stuebing and Susan Karolewski had four children together, two of whom are described as disabled.

The European Court of Human Rights said Germany was entitled to ban incest.

Stuebing, who was convicted of incest and spent three years in prison, did not meet his natural sister until he tracked down his family as an adult.

He had been adopted as a child and only made contact with his natural relatives in his 20s.

The siblings grew close after their mother died.

Three of their four children are now looked after in care.

The couple insist that their love is no different to any other.
Of course, I applaud the decision of the ECHR, but I take a rather different view on the justification of it.

Regulation of marriage is central to the moral and legal codes of almost all human societies. Different societies limit marriage in diverse ways:
  1. Age (young people are generally disallowed from marrying, and early marriage has become legally and socially more difficult in much of the world)
  2. Sex (people of opposing sex may marry, although recently some societies have allowed same-sex marriage)
  3. Number (some societies demand exclusivity, while others allow for husbands to marry multiple wives, or more commonly for women to take multiple husbands)
  4. Relation (marriage between close relatives are often prohibited, (almost) universally for parent-offspring or sibling marriage; on the other hand cousin or uncle-niece marriage is prohibited in some societies, or encouraged in others)
  5. Race (there were formerly legal prohibitions of inter-racial marriage, and there are societies in which such marriages are often frowned upon still)
  6. Religion (some belief systems do not require that partners be of the same religion, while others do so)
  7. Social status (marriage across class or caste lines was formerly prohibited either legally or socially, and is still often uncommon)
  8. Former marriage status (divorce and re-marriage sometimes prohibited, provisions for widowhood, etc.)
It is clear that society has deemed the institution of marriage to be an important one, and this is why it has imposed so many legal and social rules upon it. In recent years, the trend has been one towards laissez-faire in the regulation of human affairs. This has been most evident in the case of same sex "marriage", whose advocates actively frame the question in terms of the "rights" of consenting persons.

If the matter is that of constitutional or other "rights", then the state oversteps its role in preventing two consenting persons from entering into the institution of marriage. Those who hold to this view, however, often promote the "right" to marriage of their own particular interest group (mostly of the homosexual community), but downplay similar claims to marriage of other groups (e.g., prohibition against polygamy, incest, young marriage, etc.)

There is a different line of thought, which frames the question of marriage in utilitarian terms. Marriage is seen as promoting child-rearing, family stability, engendering close social ties, and promoting the well-being and happiness of individuals. Again, those who hold to this view propose that their particular form of marriage is useful, while opposing certain forms of marriage for its adverse effects (e.g., the costs associated with invalids born of incestuous marriages, or increased expenditure when economic benefits are extended to new forms of marriage).

When the moral compass of a society atrophies, then its most fundamental institutions become the playing ground of lawyers and economists. Of course, this is a perfectly valid point of view -if one thinks that lawyers and economists, rather than ethicists and priests- make the better judges of what is to be allowed.

Proponents of the modern, secular, and democratic way of doing things will argue that it is an improvement for the rules to be made in the context of Constitutional Law, Democratic Choice, and Economic Expediency.

But, we must not forget that their chosen framework of accepted behavior is not as sure-footed as they may think, because what else is Democracy than the idea that the many are right over the few? What else is adherence to a Constitution than the faith in the idea that what men voted for generations ago should guide the behavior of the living? And, what else is Economics, other than the idea that human prosperity revolves around the maximization of some economic quantity?

To conclude: questions such as "should incestuous marriage be allowed?" force us all to think about who decides the "should."

April 13, 2012

Population structure of US Hispanics

Just a quick observation: the "Native American" components at K=4 and K=5 are probably partially Caucasoid. For example, at K=3, Puerto Ricans are 62% Caucasian, and this becomes 18% at K=5. This is due to the fact that the three "Native American" components at K=5 are actually mixes of a Caucasoid with a local Amerindian component.

As I explain here, ADMIXTURE increases the proportion of the "native" component in the absence of pure-blooded representatives of the indigenous inhabitants. Since the Taino are extinct, the "Native American 3" component is actually a hybrid of the Taino aborigines and Europeans.

PLoS Genet 8(4): e1002640. doi:10.1371/journal.pgen.1002640

Population Structure of Hispanics in the United States: The Multi-Ethnic Study of Atherosclerosis

Ani Manichaikul et al.

Using ~60,000 SNPs selected for minimal linkage disequilibrium, we perform population structure analysis of 1,374 unrelated Hispanic individuals from the Multi-Ethnic Study of Atherosclerosis (MESA), with self-identification corresponding to Central America (n = 93), Cuba (n = 50), the Dominican Republic (n = 203), Mexico (n = 708), Puerto Rico (n = 192), and South America (n = 111). By projection of principal components (PCs) of ancestry to samples from the HapMap phase III and the Human Genome Diversity Panel (HGDP), we show the first two PCs quantify the Caucasian, African, and Native American origins, while the third and fourth PCs bring out an axis that aligns with known South-to-North geographic location of HGDP Native American samples and further separates MESA Mexican versus Central/South American samples along the same axis. Using k-means clustering computed from the first four PCs, we define four subgroups of the MESA Hispanic cohort that show close agreement with self-identification, labeling the clusters as primarily Dominican/Cuban, Mexican, Central/South American, and Puerto Rican. To demonstrate our recommendations for genetic analysis in the MESA Hispanic cohort, we present pooled and stratified association analysis of triglycerides for selected SNPs in the LPL and TRIB1 gene regions, previously reported in GWAS of triglycerides in Caucasians but as yet unconfirmed in Hispanic populations. We report statistically significant evidence for genetic association in both genes, and we further demonstrate the importance of considering population substructure and genetic heterogeneity in genetic association studies performed in the United States Hispanic population.


April 11, 2012

ESHG 2012 titles

The abstract text will be available only two weeks prior to the meeting in June, lest us mere mortals receive more hints about recent scientific progress than we deserve.

The presentations/posters at ESHG were probably ready -as relatively mature work- by the beginning of this year, and will find themselves in journals by its end. This is a year's delay from the time when research could have been available to when it will actually  be so.

It is worth reminding ourselves what the whole charade of pre-publication peer review and the conference circuit, a fossil of a time when there was no WWW or webcasting, amounts to little more than a way of  delaying the dissemination of new research. It is a little ironic that journals and conferences were invented to facilitate the flow of scientific information to as wide an audience as possible, and are now used to make it more difficult.

I put in bold some titles of particular interest.

  • T. W. Winkler et al. C06.2. Genome-wide search for gender different genetic loci for human anthropometric traits: Methods and results from genome-wide meta-analyses across 270,000 Individuals
  • O. Delaneau et al. C17.2. Haplotype phasing using next-generation sequencing reads
  • L. M. Huckins et al. Using ancestry-informative markers to identify fine structure across 15 populations of European origin.
  • A. Rodewald et al. Analysis of mitochondrial DNA haplotypes of old human populations from the Bronze and Iron Age from Romania
  • A. Bahmanimehr et al. Complete mitochondrial DNA diversity in Iranians
  • I. Uktverytė et al. mtDNA haplogroups in the population of Lithuania
  • I. Tachmazidou et al. Population isolates from Greece offer potential for powerful disease gene mapping: the HELIC-Pomak and MANOLIS studies
  • C. Stemper et al. Very high frequency of hereditary prosopagnosia among individuals with high intellectual ability
  • S. Karachanak et al. A Y -chromosome portrait of modern Bulgarians as viewed from different spatiotemporal aspects
  • A. Puzuka et al. Ethnogenetic Estimation of Baltic ancestry

Biology of Genomes 2012 titles

Some interesting titles from the upcoming 2012 Biology of Genomes meeting. I put in bold the ones that I'm most looking forward to.
  • Boerwinkle, E. Population genetics analysis of 1000 whole genome sequences—The CHARGE-S Consortium
  • Colonna, V. Genomic regions of exceptionally high or low population differentiation from the 1000 Genomes Phase I data
  • Gronau, I. Studying genome-wide patterns of genetic diversity using individual human genomes and a coalescent-based Bayesian approach
  • Kelso, J.F. Characterizing recent evolutionary changes on the human lineage using the high-coverage Denisovan genome
  • Kidd, J.M. Out-of-Africa migrations and deleterious alleles in diverse human genomes
  • Limborska, S.A. Genomic variations in populations from the Far North East corner of Europe
  • Myers, S.R. Haplotype-based analysis uncovers a detailed history of migration events in humans and other species
  • Paabo, S. A high-coverage archaic human genome
  • Pritchard, J. Inference of population splits and mixtures from genome-wide allele frequency data
  • Quintana-Murci, L. The demographic and adaptive history of African Pygmy populations, inferred from genome-wide SNP and sequencing data
  • Rodriguez-Flores, J.L. Genome sequence analysis of 100 individuals with Bedouin ancestry from Qatar
  • Schuster, S.C. Sequencing genomes of historic persons
  • Tabrizi, S. Characterizing recent positive selection in humans from the 1000 Genomes Project
  • Xing, J. Mobile elements demonstrate that Australopithecus effective population size was twice that of Homo

Admixture in different regions of Argentina

99 AIMs are probably not good enough to obtain accurate admixture estimates, but they are probably sufficient to highlight real differences in the origins of different Argentinean sub-populations.

PLoS ONE 7(4): e34695. doi:10.1371/journal.pone.0034695

Heterogeneity in Genetic Admixture across Different Regions of Argentina

Sergio Avena et al.

The population of Argentina is the result of the intermixing between several groups, including Indigenous American, European and African populations. Despite the commonly held idea that the population of Argentina is of mostly European origin, multiple studies have shown that this process of admixture had an impact in the entire Argentine population. In the present study we characterized the distribution of Indigenous American, European and African ancestry among individuals from different regions of Argentina and evaluated the level of discrepancy between self-reported grandparental origin and genetic ancestry estimates. A set of 99 autosomal ancestry informative markers (AIMs) was genotyped in a sample of 441 Argentine individuals to estimate genetic ancestry. We used non-parametric tests to evaluate statistical significance. The average ancestry for the Argentine sample overall was 65% European (95%CI: 63–68%), 31% Indigenous American (28–33%) and 4% African (3–4%). We observed statistically significant differences in European ancestry across Argentine regions [Buenos Aires province (BA) 76%, 95%CI: 73–79%; Northeast (NEA) 54%, 95%CI: 49–58%; Northwest (NWA) 33%, 95%CI: 21–41%; South 54%, 95%CI: 49–59%; p less than 0.0001] as well as between the capital and immediate suburbs of Buenos Aires city compared to more distant suburbs [80% (95%CI: 75–86%) versus 68% (95%CI: 58–77%), p = 0.01]. European ancestry among individuals that declared all grandparents born in Europe was 91% (95%CI: 88–94%) compared to 54% (95%CI: 51–57%) among those with no European grandparents (p less than 0.001). Our results demonstrate the range of variation in genetic ancestry among Argentine individuals from different regions in the country, highlighting the importance of taking this variation into account in genetic association and admixture mapping studies in this population.


April 10, 2012

Quantifying Yayoi and Jomon ancestry in Japanese

This paper attempts a difficult task: quantifying the relative influence of Yayoi agriculturalists and Jomon hunter gatherers on the population of Japan. While relatives to the early farmers of Japan can be traced to Korea or China, there are no known relatives of the Jomon people. This is different from the case of Latin Americans, where Amerindians have been largely absorbed in the Mestizo population, but populations with minimal European or African admixture persist. It is also different from the case of Indians, where the Ancestral South Indians have also been largely absorbed but their distant relatives in the Andaman Islands still exist.

This is an issue that will come up time and again: in Europe, for example, the hunter-gatherers disappeared thousands of years ago, and the extant population is apparently a mix of the two in proportions that remain to be determined. And, there were probably older, pre-Neolithic, episodes of admixture, as well, when different groups of modern humans expanded across the globa and mixed with older groups of modern humans, or, as it seems increasingly likely, with archaic humans as well.

It is sometimes possible to obtain ancient DNA from pre-contact individuals and determine their contribution to modern populations directly. However, there is still value in trying to extract this signal in the absence of ancient DNA, as was attempted for archaic Africans, and, in the current paper for the pre-agricultural Japanese. Hopefully, the latter can be eventually studied directly, and their genetic makeup can then be compared with their reconstruction in this paper.

The authors link the Jomon to modern Altaic populations of Siberia. There has already been ancient mtDNA work on the Jomon tying them to Siberia. On the other hand, the link to Altaic populations is intriguing, and I am wondering whether the authors' model (which uses Chinese and Koreans as farmer representatives) may not be actually representing as a substratum of the farmers, what may in fact be -at least partially- an Altaic superstratum.

Scientific Reports 2, Article number: 355 doi:10.1038/srep00355

Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data 

Yungang He et al.

The genetic origins of Japanese populations have been controversial. Upper Paleolithic Japanese, i.e. Jomon, developed independently in Japanese islands for more than 10,000 years until the isolation was ended with the influxes of continental immigrants about 2,000 years ago. However, the knowledge of origin of Jomon and its contribution to the genetic pool of contemporary Japanese is still limited, albeit the extensive studies using mtDNA and Y chromosomes. In this report, we aimed to infer the origin of Jomon and to estimate its contribution to Japanese by fitting an admixture model with missing data from Jomon to a genome-wide data from 94 worldwide populations. Our results showed that the genetic contributions of Jomon, the Paleolithic contingent in Japanese, are 54.3∼62.3% in Ryukyuans and 23.1∼39.5% in mainland Japanese, respectively. Utilizing inferred allele frequencies of the Jomon population, we further showed the Paleolithic contingent in Japanese had a Northeast Asia origin.


April 05, 2012

“Copernican” Reassessment of the Human Mitochondrial DNA Tree

The Cambridge Reference Sequence is dead, long live the RSRS! Let's hope for a smooth transition.

The supplement (the paper itself is open access). Table S5 within the supplement is very interesting, as it contains age estimates for the nodes of the new mtDNA phylogeny, and places the common mtDNA ancestor of humans (represented by the new reference sequence) at ~177,000 years.

The age of L3 (~67,000 years) is a useful sanity check of the time depth estimates, and it corresponds with the onset of Marine Isotope Stage 4. Another useful check is for that of haplogroup H (~13,000 years), consistent with a late Paleolithic origin and Neolithic expansion of this haplogroup.

The two main Eurasian macrohaplogroups M (~50,000 years) and N (~59,000 years) also appear appropriately dated on the cusp of the major Paleolithic expansion of humans across Eurasia. The higher age of N may indeed correspond to an earlier split (this haplogroup is shared by all Eurasians), whereas M has a more contained distribution (largely lacking in West Eurasians), and may have spread later. The age of haplogroup U (~47,000 years), which is the oldest West Eurasian lineage also seems to correspond appropriately to the arrival of the earliest modern humans in Europe.

Related: PhyloTree Build 14.

The American Journal of Human Genetics, Volume 90, Issue 4, 675-684, 6 April 2012 doi:10.1016/j.ajhg.2012.03.002

A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root

Doron M. Behar et al.

Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This “Copernican” reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.