September 30, 2009

Some mtDNA links between Europe and Asia

I was planning on writing up a more complete narrative for this post, but I don't think the evidence is -as of yet- strong enough to support very strong speculation. I will simply say that the recent results of Bramanti et al. for a U-dominated older mtDNA stratum in Central/North-eastern Europe can be reasonably extended to cover both North-western Europe and northern Eurasia up to Lake Baikal, the prehistoric limit between Caucasoids and Mongoloids.

This boreal zone of U dominance contrasts with that of the Neolithic and Bronze Age inhabitants, where the familiar mix of ten or so main Caucasoid haplogroups makes its appearance, in various proportions and in various degrees of admixture at the eastern end of its expansion. The eastern Caucasoids were probably derived from both (i) West Asia via the spread of the Neolithic economy to the east wherever it could be ecologically supported, (ii) in the more northern parts, from migrations across the steppe from Central and Eastern Europe.

More ancient DNA research is needed to establish (i) how complete was the U dominance in the pre-Neolithic northern zone, and (ii) when, and where did the other Caucasoid haplogroups break into it.

Anyway, here is the post as it stands:

Ricaut et al. (2004) discovered the presence of mtDNA haplogroup N1a (16147A, 16172C, 16223T, 16248T, and 16355T) in an Iron Age Scytho-Siberian skeleton from the Altai, reporting the presence of haplogroup N1a among Iranians and upper caste Havik Brahmins from India.

The same sequence was detected in a Neolithic Central European (DER1) of the Linearbandkeramik (LBK) culture, with reported modern matches in Egypt and Armenia. The following haplogroups were detected in the Neolithic LBK gene pool: H*, N1a, K, HV, T2, V, J, W, U3.

A later study by Gokcumen et al. (2008) discovered the presence of N1a in modern Kazakhs from the Altai:
The haplotypic variation within the seven N1a samples was relatively high (Table 2), with these haplotypes belonging to both the European and Central Asian branches of this haplogroup, as recently defined by Haak et al. (2005). Thus, the source of N1a haplotypes in Altaian Kazakhs was unclear, although they seemed to have originated west of this part of Central Asia (Gokcumen et al., 2007).
Haplogroup N1a was found to be a genuine signature of the Central European Neolithic by contrasting its high representation in the LBK with the overwhelming presence of haplogroup U (and especially U5 and U4) mtDNA among the Paleolithic and Mesolithic populations of the region.

A separate Neolithic Funnel Beaker (TRB) sample from Scandinavia (Malmström et al. 2009) included only three individuals belonging to haplogroups H, J, and T. Obviously, a sample of 3 is insufficient, but the absence of haplogroup U in it parallels that of the LBK. By contrast, the contemporaneous Mesolithic Pitted Ware culture, represented by 19 samples had single instances of J, and T (which may be due to admixture with the TRB), a single instance of haplogroup V, one of the few ones thought to be European in origin, and a gene pool that was apparently dominated by haplogroups U4 and U5. The picture emerging from the northmost European hunter-gatherers is one of a restricted set of haplogroups where U subclades were dominant (about 3/4).

N1a was also detected in medieval high-status Hungarians:
Commoners show a predominance of mtDNA haplotypes and haplogroups (H, R, T), common in west Eurasia, while high-status individuals, presumably conquering Hungarians, show a more heterogeneous haplogroup distribution, with haplogroups (N1a, X) which are present at very low frequencies in modern worldwide populations and are absent in recent Hungarian and Sekler populations.
While, as we saw, N1a was frequent among Neolithic Central Europeans, its absence in Hungarian commoners suggests that it was re-introduced -in the high status individuals- from Asia.

Interestingly, there has been European and Asian mtDNA evidence that allows us to have a good idea of the mtDNA landscape on which N1a-bearing people migrated from west to east:

The pre-farming foragers of Europe were dominated by mtDNA haplogroup U. The easternmost sample in the aforementioned study was from Samara, in European Russia and consisted of a U5a, and a U5a1 sample. How far to the west and east did the U-dominated population of pre-Neolithic northern Caucasoids extend?

Neolithic Siberians from Lake Baikal, the eastermost anthropologically attested limit of prehistoric Caucasoid populations had only U5a as a Western Caucasoid element in a population dominated by Eastern Eurasian mtDNA. Similarly, the Lokomotiv Siberian burials from Lake Baikal only had U5a in an other Mongoloid mtDNA gene pool. Yu Hong, a Sogdian in China (1,400 years ago) also belonged to haplogroup U5.

U5a was not limited to the territory of Central Europe to China in ancient times. It was the haplogroup of Cheddar Man, a Paleolithic Briton, and U5a1 or U5a1a has also been detected in a Mycenaean from Bronze Age Greece. Interestingly, U5a1 seems to have decreased in frequency in Britain from the 4th c. to the present.

Is it possible that negative selection is affecting mtDNA frequencies in Europe? U-haplogroup turns up in many ancient DNA samples, but the discovery that it was absent (or non-detectible) in Neolithic farmers raises the possibility that its reduced frequency may be due to demography, i.e., the overwhelming of Paleolithic foragers by Neolithic (and later) intruders.

We know that in the Bronze and subsequent ages, Siberians from Krasnoyarsk belonged to a rich assortment of Caucasoid haplogroups. It seems that newcomers from the West joined the U-dominated earliest settlers:
Twenty samples were found to belong to west Eurasian haplogroups (U2, U4,
U5a1, T1, T3, T4, H5a, H6, HV, K, and I
), whereas the 6 remaining samples were attributed to east Eurasian haplogroups (Z, G2a, C, F1b and N9a).
At the other end of the Eurasiatic steppe, in the Bronze Age site of Eulau in Germany, the gene pool was also quite different from that of the Paleolithic inhabitants, with haplogroups K1b, U5b, I, H, X2, K1a2 detected.

Haplogroup X2 represents another link between the west and Siberia according to Reidla et al. (2003):
Overall, it appears that the populations of the Near East, the Caucasus, and Mediterranean Europe harbor subhaplogroup X2 at higher frequencies than those of northern and northeastern Europe (P less than .05) and that X2 is rare in Eastern European as well as Central Asian, Siberian, and Indian populations and is virtually absent in the Finno-Ugric and Turkic-speaking people of the Volga-Ural region. [...] the few Altaian (Derenko et al. 2001) and Siberian haplogroup X lineages are not related to the Native American cluster, and they are more likely explained by recent gene flow from Europe or from West Asia.
The Tubalar, Altaic speakers from the northeastern Altai showed a mixed Caucasoid-Mongoloid mtDNA gene pool, with the western component consisting of haplogroups H8, U4b, U5a1, and X2e:
Specifically, northeastern Altai appears to be a good candidate for the ancestral homeland of the haplogroup U4b, which is apparently ancient European. For some haplogroups, such as X2e, the relatively recent arrival to the Altai region is more likely.
Derenko et al. (2002) discovered a rich assortment of Caucasoid haplogroups in several populations from the Altai, including all aforementioned ones (H, HV1, J*, J1, J1b1, T1, T4, U1a, U2, U3, U4, U5a1, I, X and N1a):
The applied approach permitted identification of 60% of mtDNA types the majority of which had southern Caucasoid origin. Less than 10% of mtDNA types were of eastern European origin.
Derenko et al. (2003) also studied several populations from South Siberia where the Caucasoid component was much diminished (17%) with the following haplogroups present: H, U, J, T, I, N1a, X.

September 29, 2009

Physical attractiveness and reproductive success

Evolution and Human Behavior
Volume 30, Issue 5, September 2009, Pages 342-350

Physical attractiveness and reproductive success in humans: evidence from the late 20th century United States

Markus Jokela


Physical attractiveness has been associated with mating behavior, but its role in reproductive success of contemporary humans has received surprisingly little attention. In the Wisconsin Longitudinal Study (1244 women, 997 men born between 1937 and 1940), we examined whether attractiveness assessed from photographs taken at age 18 years predicted the number of biological children at age 53–56 years. In women, attractiveness predicted higher reproductive success in a nonlinear fashion, so that attractive (second highest quartile) women had 16% and very attractive (highest quartile) women 6% more children than their less attractive counterparts. In men, there was a threshold effect so that men in the lowest attractiveness quartile had 13% fewer children than others who did not differ from each other in the average number of children. These associations were partly but not completely accounted for by attractive participants' increased marriage probability. A linear regression analysis indicated relatively weak directional selection gradient for attractiveness (β=0.06 in women, β=0.07 in men). These findings indicate that physical attractiveness may be associated with reproductive success in humans living in industrialized settings.


September 28, 2009

Y chromosomes of Teleuts

The arrival of R1b in the east remains a mystery. The few prehistoric samples that have been examined did not belong to it, but rather exclusively to R1a1. While some folks (e.g. Spencer Wells) speak about the arrival of R1b in Europe from Central Asia, I consider this almost certainly false, for a very simple reason: there is absolutely no reason why R1b would head stubbornly west and not east. The complete absence of R1b in East Asia, and its near-complete absence in India, makes a long-term presence of it in Central Asia unbelievable.

Genetika. 2009 Aug;45(8):1132-42.

[Comparative characteristics of the gene pool of Teleuts inferred from Y-chromosomal marker data]

[Article in Russian]

[No authors listed]

The gene pool structure of Teleuts was examined and Y-chromosomal haplogroups composition and frequencies were determined. In the gene pool of Teleuts, five haplogroups, C3xM77, N3a, R1b*, R1b3, and R1a1, were identified. Evaluation of the genetic differentiation of the samples examined using analysis of molecular variance (AMOVA) with two marker systems (frequencies of haplogroups and Y-chromosomal microsatellite haplotypes) showed that Bachat Teleuts were equally distant from Southern and Northern Altaians. In Siberian populations, the frequencies and molecular phylogeny of the YSTR haplotypes within Y-chromosomal haplogroup R1a1 were examined. It was demonstrated that Teleuts and Southern Altaians had very close and overlapping profiles of R1a1 haplotypes. Population cluster analysis of the R1a1 YSTR haplotypes showed that Teleuts and Southern Altaians were closer to one another than to all remaining Siberian ethnic groups. Phylogenetic analysis of N3a haplotypes suggested specificity of Teleut haplotypes and their closeness to those of Tomsk Tatars. Teleuts were characterized by extremely high frequency of haplogroup R1b*, distinguished for highly specific profile of YSTR haplotypes and high haplotype diversity. The results of the comparative analysis suggested that the gene pool of Bachat Teleuts was formed on the basis of at least two heterogeneous genetic components, probably associated with ancient Turkic and Samoyedic ethnic components.


September 27, 2009

Y chromosomes of Saudi Arabia

From the paper:
The recent resolutions of the CDEF-M168 tripartite structure to the bipartite DE-YAP and CF-P143 [16, 31] extends the conversation regarding the early successful colonization of Eurasia. While several scenarios remain potentially possible the most parsimonious model is the most prudent. This model proposes the successful colonization of Eurasia by migration(s) of populations containing precursor Y-chromosome founder macrohaplogroup CDET-M168 and basal mtDNA L3 representatives. Regions near but external to northeast Africa, like the Levant or the southern Arabian Peninsula could have served as an incubator for the early diversification of non-African uniparental haplogroup varieties like Y chromosome DE-YAP*, CF-P143* and mtDNA M and N molecular ancestors. These would have spread globally and diversified over time and space. This model would imply that both CF-P143 and the DEYAP evolved nearby but outside Africa. One DE-YAP* ancestor would have spread to Asia and evolved to haplogroup D while another DE-YAP* returned to northeast Africa and evolved into hg E.

The paper unfortunately uses the faulty "evolutionary mutation rate" for Y-STRs, hence its age estimates are wrong and should be roughly divided by 3.

This correction brings the age of Saudi Arabian J1-M267 to ~2,000BC, which corresponds exactly with the inferred linguistic divergence of the most populous clade of Semitic which includes Ugaritic, Aramaic, Arabic, and Hebrew. I have little doubt that the modality of J1 among Semitic populations such as Arabs or Jews can be traced to the Bronze Age expansion of Semitic populations from southwestern Asia.

Related: Y chromosome population structure in Arabian peninsula

BMC Genetics 2009, 10:59doi:10.1186/1471-2156-10-59

Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions

Khaled K. Abu-Amero et al.



Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J1-M267 lineage was estimated using a set of 17 Y-specific STR loci.


Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n=2) and J-M304* (n=3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J1-M267 haplogroup in Saudi Arabia (11.6 +/- 1.9 ky) is similar to that obtained previously for Yemen (11.3 +/- 2) but significantly older that those estimated for Qatar (7.3 +/- 1.8) and UAE (6.8 +/- 1.5).


The Y-chromosome genetic structure of the Arabian Peninsula seems to be mainly modulated by geography. The data confirm that this area has mainly been a recipient of gene flow from its African and Asian surrounding areas, probably mainly since the last Glacial maximum onwards. Although rare deep rooting lineages for Y-chromosome haplogroups E and J have been detected, the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found.


Η άποψή μου για τις επερχόμενες εκλογές

Έχω αναφερθεί τόσο εδώ όσο και στη Γενετική των Ελλήνων για το ζήτημα της Ελληνικής ιθαγένειας. Το ζήτημα αυτό δεν συζητείται καθόλου εν όψει των εκλογών της 4ης Οκτωβρίου, αν και είναι ορατή η πιθανότητα ανατροπής του ισχύοντος πλαισίου απονομής της ιθαγένειας.

Περισσότερες λεπτομέρειες :

September 24, 2009

Modern Scandinavians descended (maybe) from Neolithic TRB but not Mesolithic Pitted Ware ancestors

Coming shortly after Bramanti et al. (2009) which discovered a discontinuity between Neolithic farmers from Central and Eastern Europe and the pre-existing hunter-gatherers, a new study examines ancient DNA from northern European populations, extending the picture of discontinuity all the way to Scandinavia. This is one more nail in the coffin of the cultural diffusion hypothesis, and in favor for a demic diffusion of agriculture all the way to the northernmost reaches of Europe.

More on this after I read the full paper.

UPDATE (Sep 25):

From the paper:
Although the hunter-gatherers of Denmark and southern Sweden adopted pottery early on, the Neolithization first took real shape with the appearance of the Funnel Beaker Cultural complex (FBC, also known as the Trichterbecher Kultur [TRB]) some 6,000 years BP (the oldest evidence possible dating back some 6,200 years BP [9]). Atthis time domestic cattle and sheep, cereal cultivation, and the characteristic TRB pottery were introduced into most of Denmark and southern parts of Sweden [6]. Nevertheless,the Neolithization process was slow in Scandinavia, and large are as remained populated by hunter-gatherer groups until the end of the 5th millennium BP.

One of these last hunter-gatherer complexes was the Pitted Ware culture (PWC), which can be identified by its single-inhumation graves distributed over the coastal areas of Sweden and the Baltic Sea islands that lie closest to the Swedish coast. Intriguingly, the PWC first appears in the archaeological record of Scandinavia after the arrival of the TRB (some 5,300 yearsBP) and existed in parallel with farmers for more than a millennium before vanishing about 4,000 years BP (Figure 1).
The authors sampled 3 TRB individuals from "one passage tomb, Gokhem, dated to 5,500–4,500 years BP" which were found to belong to haplogroups H, J, and T, and 19 PWC individuals "from three different sites on the Baltic island of Gotland dated to 4,800–4,000 years BP" which were found to belong to haplogroups J, T, V (one each), "Other" (two), U5 and U5a (three each), and U4/H1b (eight samples).

From the paper:
Given our results, it remains possible that the PWC represent remnants of a larger northern European Mesolithic hunter gather complex. However, it appears unlikely that population continuity exists between the PWC and contemporary Scandinavians or Saami. Thus, our findings are in agreement with archaeological theories suggesting Neolithic or post-Neolithic population introgression or replacement in Scandinavia. To what extent this holds true for other parts of Europe requires further direct testing, although morphological [24, 25], ancient [26], and modern [4, 5] genetic data suggest that this is probably the case.
The results indicate that the PWC was dominated by haplogroup U (about three quarters of the mtDNA gene pool). The inability to resolve between U4 and H1b is due to the portion of the mtDNA sampled. Given (i) the absence of other H subgroups in the large sample, (ii) the higher frequency of U4 in modern populations, (iii) the presence of U4 but not H1b in other pre-farming populations of Europe (after Bramanti et al.), (iv) the absence of U4 in Neolithic populations, (v) the higher coalescence age of U4 compared to H1b, suggesting a deeper ancestry, I am inclined to think that most, if not all of the U4/H1b is actually just U4.


Fst between the PWC and modern populations ranged between 0.036 (Latvians) and Saami (0.25). For Swedes and Norwegians they were 0.051 and 0.061. A few conclusions can be drawn from this:
  1. The notion of Saami as unmixed descendants of pre-farming Europeans is debunked.
  2. Latvians and other populations of the eastern Baltic are the closest (although by no means very close) to the PWC.
  3. Swedes and Norwegians are somewhat closer to the pre-farming inhabitants than is the case for Central Europe where Fst=0.086 was estimated by Bramanti et al. (2009)
Traditional physical anthropology held that there were three main elements in northern Europe, which have been given different names, but can be summarized as follows:
  1. Narrow- and high-faced populations, a new element in the region, similar to that of Central Europe
  2. Broad-faced massive Proto-Europoid populations, the aboriginal inhabitants of northern and eastern Europe
  3. Flat-nosed populations with eastern affiliations
To quote Raisa Denisova:
Latvia's most ancient inhabitants tended to be large in size, with large skulls, a distinctly oblong head shape, a broad, high face and a distinctly protruding nose (Denisova 1975). Looking at this data in the context of synchronous populations elsewhere in Europe, we can find specific geographic differentials. This is especially true of the facial width of residents, a factor which has great weight in the specification of race (Denisova 1978). Differences in facial width in Europe became particularly distinctive at the beginning of the Atlantic period, when farming was begun in Europe. At this time, facial width distinctly separated morphological forms in Northern Europe from those in the Mediterranean region -- two distinct geographic regions. Massive, broad-faced morphological forms dominated in northern and northeastern Europe, while gracile, narrow-faced forms are found most often in Middle Europe and the continent's southeastern reaches. During the Atlantic period, narrow-faced populations gradually moved in the northerly and northeasterly direction. They reached the Baltic region only during the Bronze Age. For this reason, during the Mesolithic and Neolithic period, people in the Baltic region (and surrounding regions) had broad faces, a fact which affirms their links to the late Paleolithic populations of Europe.
Modern Scandinavians are more (1) than (2), while modern Balts are more (2) than (1). The mtDNA picture seems fairly consistent with a greater persistence of Proto-Europoid elements among the Balts.

A related public release:
Scandinavians are descended from Stone Age immigrants

Today's Scandinavians are not descended from the people who came to Scandinavia at the conclusion of the last ice age but, apparently, from a population that arrived later, concurrently with the introduction of agriculture. This is one conclusion of a new study straddling the borderline between genetics and archaeology, which involved Swedish researchers and which has now been published in the journal Current Biology.

"The hunter-gatherers who inhabited Scandinavia more than 4,000 years ago had a different gene pool than ours," explains Anders Götherström of the Department of Evolutionary Biology at Uppsala University, who headed the project together with Eske Willerslev of the Centre for GeoGenetics at the University of Copenhagen.

The study, a collaboration among research groups in Sweden, Denmark and the UK, involved using DNA from Stone Age remains to investigate whether the practices of cultivating crops and keeping livestock were spread by immigrants or represented innovations on the part of hunter-gatherers.

"Obtaining reliable results from DNA from such ancient human remains involves very complicated work," says Helena Malmström of the Department of Evolutionary Biology at Uppsala University.

She carried out the initial DNA sequencings of Stone Age material three years ago. Significant time was then required for researchers to confirm that the material really was thousands of years old.

"This is a classic issue within archaeology," says Petra Molnar at the Osteoarchaeological Research Laboratory at Stockholm University. "Our findings show that today's Scandinavians are not the direct descendants of the hunter-gatherers who lived in the region during the Stone Age. This entails the conclusion that some form of migration to Scandinavia took place, probably at the onset of the agricultural Stone Age. The extent of this migration is as of yet impossible to determine."

Current Biology

Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians

Helena Malmström et al.


The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1], [2] and [3]. Of particular interest is whether population replacement or cultural exchange was responsible [3], [4] and [5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7] and [8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7] and [8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.


560K SNP study reveals dual rigin of Indian populations (Reich et al. 2009)

In lieu of a prologue, Herodotus and Arrian on the two groups inhabiting ancient India:

The Indians wore cotton dresses, and carried bows of cane, and arrows also of cane with iron at the point. Such was the equipment of the Indians, and they marched under the command of Pharnazathres the son of Artabates. [...] The eastern Ethiopians- for two nations of this name served in the army- were marshalled with the Indians. They differed in nothing from the other Ethiopians, save in their language, and the character of their hair. For the eastern Ethiopians have straight hair, while they of Libya are more woolly-haired than any other people in the world.

The appearance of the inhabitants, too, is not so far different in India and Ethiopia; the southern Indians resemble the Ethiopians a good deal, and, are black of countenance, and their hair black also, only they are not as snub-nosed or so woolly-haired as the Ethiopians; but the northern Indians are most like the Egyptians in appearance.
The paper establishes a number of different facts, that have been hinted at in previous autosomal studies, and studies based on Y chromosomes and mtDNA:
  1. Modern Indians are derived from two ancestral populations. The first one, termed Ancestral North Indians (ANI) were Caucasoids, the other, Ancestral South Indians (ASI) were distinct from both Caucasoids and Mongoloids in a Eurasian context.
  2. The ASI no longer exist in non-admixed form, but in various degrees of admixtures with ANI; the closest living population to the ASI are the Andaman Islanders.
  3. Upper castes are higher in ANI ancestry than middle and lower castes. ANI percentages of ancestry are correlated with Western Eurasian Y chromosomes (P=0.04) and mtDNA (P=0.08).
  4. Indo-European speakers are higher in ANI ancestry than Dravidian speakers.
This paper does seem to imply that Indians are a mixture of Western Eurasians and indigenous Indians. However, we should not conclude that they are a simple 2-way mix of invading Indo-Aryans and indigenous Dravidians: for example, the ANI component could be a palimpsest of different Caucasoid populations who came to the subcontinent over time. For example, we do know that South Americans are composed of Amerindians, Caucasoids, and Negroids in different proportions of admixture, but this does not mean that there was a simple mix between the three, but rather a continuous process of migration that brought (and continues to bring) people into the New World. It remains to be seen which groups participated in the diffusion of the ANI component in India.

However, the fact that ANI is correlated with caste status and language does suggest that the Indo-Aryan migration who brought Indo-European languages to India has not been totally wiped out genetically. Indo-European populations have maintained a higher degree of ancestry from the ANI component, and upper caste Indo-Europeans have maintained an even higher degree of such ancestry.

The beauty of this study is that it does not consider either a simple mixture model (like STRUCTURE does) in which populations are derived from 2 or more ancestral ones, or a simple branching model, in which populations are derived tree-like from a common root with no admixture between them. Rather, they consider both tree-like divergence of populations followed by admixture. The following figure from the paper illustrates this:
We can see that (i) the relationship between Andaman Islanders and ASI is not particularly close, although they do form a clade in relation to the other populations, (ii) the relationship between CEU and ANI is fairly close (in this context). The authors further determine (in the supplement) that CEU and ANI do form a clade separate from the non-IE speaking Adygei from the Caucasus.

What is now needed is to calculate the genetic distances between ANI and a wide assortment of Western Eurasian populations. Indeed, as these populations have undergone their own processes of admixture (e.g., Near Eastern populations with Arabs, Turks with Central Asians, Russians with Finns, Central Asian Iranians with Turks and Mongols, and so on), we cannot generally infer that the source population(s) of the ANI component are extant in non-admixed form. Nonetheless, the discovery of a strong relationship of ANI with a West Eurasian population may help us pinpoint the geographical origin of ANI outside India.

The paper does demolish some theories that have been popular in some circles:

There is no evidence of caste as simply social division of labor. This thesis is inconsistent with differential ANI admixture (and distance from Western Eurasians) across the caste hierarchy.

There is no evidence that Indo-Aryan and Dravidian speakers differ only in language. It is now clear that they are different from each other genetically as well, and this difference is not an "internal affair" of India, but is related to populations outside it. Indo-Aryan speakers differ precisely in having a larger ANI component.

There is no evidence that Indo-European languages originated in India. Let us consider what this would entail:
  1. Suppose postulated ancient Indian PIE speakers had a similar genetic makeup as modern Indians (i.e., a mix of ANI and ASI). Then, the absence of the ASI component outside South Asia cannot be explained.
  2. If ancient Indian PIE speakers had a purely ANI makeup, then the absence of the ASI component outside South Asia -as in (1)- can be explained. However, this would entail that sharply differentiated populations (ANI and ASI) co-existed in India without mixing for thousands of years; ANI-like PIEs spread from India with their languages; ANI and ASI admixed afterwards. To say that this scenario is not parsimonious would be charitable.
  3. The only way in which PIE languages may have originated in India would be if they spread without the spread of people. However, before the advent of writing and modern means of transportation and communication, the only way to spread languages was by migration of people.
From a related Nature story:
The researchers also found that Indian populations were much more highly subdivided than European populations. But whereas European ancestry is mostly carved up by geography, Indian segregation was driven largely by caste. "There are populations that have lived in the same town and same village for thousands of years without exchanging genes," says Reich.
The paper has plentiful (and free) supplementary information.

Related posts by Gene Expression and John Hawks.

Nature 461, 489-494 doi:10.1038/nature08365

Reconstructing Indian population history

David Reich et al.


India has been underrepresented in genome-wide surveys of human variation. We analyse 25 diverse groups in India to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the 'Ancestral North Indians' (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the 'Ancestral South Indians' (ASI), is as distinct from ANI and East Asians as they are from each other. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39–71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry. Allele frequency differences between groups in India are larger than in Europe, reflecting strong founder effects whose signatures have been maintained for thousands of years owing to endogamy. We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically.


Is Homo sapiens polytypic?

An interesting paper worth reading, which considers the idea that Homo sapiens can be subdivided to subspecies against two diametrically opposite ideas, namely (i) that there are no human subspecies, and (ii) that human taxonomic differences warrant the rank of species. The author rejects (i) on the grounds that Homo sapiens exhibit higher levels of diversity (in terms of heterozygosity and Fst) compared to species where subspecies are recognized. I had not heard of (ii) argued recently, but Woodley cites Fuerle as a recent supporter, offering the following criticism:
FST reflects the relative amount of total genetic differentiation between populations, however different measures of genetic distance involving mtDNA and autosomal loci are simply inappropriate for the purposes of inter-specific comparison as the different genes involved will have been subject to markedly different selection pressures and are therefore not likely to have diverged at the same time [62]. To illustrate this point, this author listed alternative estimates of the distance between the gorilla species and the common chimpanzee and bonobo, based on various nuclear loci and autosomal DNA. The much higher numbers reflect the extreme variation that can be expected when different genes are considered. Fuerle’s presentation of the data is also problematic for another reason, namely he makes no mention of the current debates surrounding gorilla and chimpanzee/bonobo taxonomy; as new research on these taxa regularly generates novel and in some cases wildly variable estimates of genetic distance between these primates, and there is even some debate over whether the eastern and western gorillas are separate species [60].

Curnoe and Thorne have estimated that periods of around two million years were required for the production of sufficient genetic distances to represent speciation within the human ancestral lineage [56]. This indicates that the genetic distances between the races are too small to warrant differentiation at the level of biological species, as the evolution of racial variation within H. sapiens started to occur only 60,000 years ago, when the ancestors of modern humans first left Africa.
Personally I think that the evidence is clear that human races or subspecies exist, but the discovery that geographic differentiation exists at the level of races, ethnic groups, sub-ethnic groups, and that even villages can be subdivided into geographically distinguishable clusters, make renewed effort into formalizing taxonomy at the sub-species level an especially worthwhile endeavor.

Medical Hypotheses doi:10.1016/j.mehy.2009.07.046

Is Homo sapiens polytypic? Human taxonomic diversity and its implications

Michael A. Woodley


The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (FST) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.


September 23, 2009

Aristotle at Mont Saint-Michel

A fairly good review in English:

The West’s Cultural Continuity: Aristotle at Mont Saint-Michel (reviewed by Thomas F. Bertonneau):
Long before the late Eduard Said invented “Orientalism” to exalt Arab culture and Islamic society at the expense of the West, bien-pensants like Voltaire inclined to express their rebellion against the dwindling vestiges of Christendom by representing Europeans as bigots or clowns and raising up exotic foreigners – Voltaire himself wrote about Turks and Persians of the Muslim fold – to be the fonts of wisdom and models of refined life in their tracts and stories. The sultan and dervish look with amused tolerance on the gaucheries of the European rubes. The rubes swing their elbows and knock over the pottery. It was the Eighteenth-Century philosophes and illuminati who coined the pejorative term Dark Ages to refer to the centuries immediately following the collapse of the Roman imperial administration in the West under pressure of the Gothic assertions of the Fifth Century. Liberal discourse often casually extends the same term to apply it to all of medieval European civilization up to the Renaissance. Specialist historians have, however, long since demonstrated that no such absolute discontinuity as the term Dark Ages insinuates ever existed, which means that the Enlightenment version of history is at least partly wrong. And yet the usual story retains its currency, as an item in a kind of liberal folklore.


In Aristote au Mont Saint-Michel, Gouguenheim points out that a Greek demographic presence linked the culminating period of Late Antiquity with the incipient phase of the Middle Ages in the West; and that presence persisted for centuries. “In the Europe of the High Middle Ages, many regions sheltered knots of ethnic Hellenes: Sicily, Southern Italy, and again Rome.” These communities supported literate elites, who contributed actively to the Latinate majorities among whom they lived, giving rise to such notable figures as Gregory of Agrigento (born 559), who became bishop in his native city later in life; George, Bishop of Syracuse, killed by the Arabs while on a mission to them in 724; Saint Gilsenus (mid-Seventh Century), a Greek-born monk living in a Roman monastery who evangelized in Hainault with Saint Armand; and Simeon of Reichenau, known as “The Achaean,” who belongs to the Tenth Century. In men like Simeon this Byzantine Diaspora reached well beyond Mediterranean Europe into the Rhine and Danube regions. Not only Greek but also Syriac Christians became additional mediators of the classical heritage at this time, driven from their homeland by the Jihad. “Paradoxically,” writes Gouguenheim, “Islam from its beginning transmitted Greek culture to the Occident by provoking the exile of those who refused its domination.”

More aggressively, “Muslim rejection – or indifference – to Greek knowledge manifested itself again through the destruction of the cultural centers that were the monasteries, the Muslims not acting in this way any differently from the Vikings.” One could remark here, however, that the Vikings at least had the decency after two centuries to cease their predatory behavior and settle down as members of Christendom.


Aristote au Mont Saint-Michel celebrates a central figure, Jacques de Venise (Twelfth Century), who, not only metaphorically, brought Aristotle to Mont Saint-Michel. Jacques was a cleric of Venetian origin, as his name tells, who studied in Constantinople before reestablishing himself in France. Jacques, as Gouguenheim phrases it, through his Herculean labor of scholarship and translation, supplies “the missing link in the history of the passage of Aristotelian philosophy from the Greek world to the Latinate world.” It is a matter of colossal importance that Jacques, as Gouguenheim reports, “translated a considerable number of Aristotle’s works directly from Greek to Latin, making him a pioneering figure.” (Emphasis added) According to the story prevalent today, Aristotle in his fullness returned to the ken of Christendom through a complicated chain of transactions, beginning with supposed Arabic translations out of Greek, and then, by way of Moorish generosity, from Arabic back into Latin and over the Pyrenees. But the story does not wash. It is plagued by linguistic problems, which Gouguenheim duly rehearses, but it is flatly demolished by what Gouguenheim has discovered concerning Jacques’ work. Jacques’ manuscripts, which are in almost every case the earliest attested for a given Aristotelian opus, swiftly gained a reputation, well founded, for being the most accurate and idiomatic. Jacques’ translations gained wide currency and formed the basis for an Aristotelian revival all across Western Europe.

As Gouguenheim writes, “The two great names of theological and philosophical reflection in the Thirteenth Century, Albertus Magnus and Thomas Aquinas, utilized [Jacques’] Greco-Latin translations.” In a manner, Jacques brought his project to too fine a point of perfection, reestablishing the Aristotelian tradition so effectively that his own pioneering status lapsed into oblivion, exactly in proportion as knowledge of The Metaphysics and the Analytics came to be taken for granted. Many of his original manuscripts lay unrecognized in the archives at Mont Saint-Michel until recent decades.
From a NY Times review:
When Sylvain Gouguenheim looks at today's historical vision of the history of the West and Islam, he sees a notion, accepted as fact, that the Muslim world was at the source of the Christian Europe's reawakening from the Middle Ages.

He sees a portrayal of an enlightened Islam, transmitting westward the knowledge of the ancient Greeks through Arab translators and opening the path in Europe to mathematics, medicine, astronomy and philosophy - a gift the West regards with insufficient esteem.

"This thesis has basically nothing scandalous about it, if it were true," Gouguenheim writes. "In spite of the appearances, it has more to do with taking ideological sides than scientific analysis."


In a new book, he is basically canceling, or largely writing off, a debt to "the Arabo-Muslim world" dating from the year 750 - a concept built up by other historians over the past 50 years - that has Europe owing Islam for an essential part of its identity.

"Aristote au Mont Saint-Michel" (Editions du Seuil), while not contending there is an ongoing clash of civilizations, makes the case that Islam was impermeable to much of Greek thought, that the Arab world's initial translations of it to Latin were not so much the work of "Islam" but of Aramaeans and Christian Arabs, and that a wave of translations of Aristotle began at the Mont Saint-Michel monastery in France 50 years before Arab versions of the same texts appeared in Moorish Spain.

Le Monde was even more receptive: "All in all, and contrary to what's been repeated in a crescendo since the 1960s, European culture in its history and development shouldn't be owing a whole lot to Islam. In any case, nothing essential.


Gouguenheim attacks the "thesis of the West's debt" as advanced by the historians Edward Said, Alain de Libera and Mohammed Arkoun. He says it replaces formerly dominant notions of cultural superiority advanced by Western orientalists, with "a new ethnocentrism, oriental this time" that sets off an "enlightened, refined and spiritual Islam" against a brutal West.

Nuggets: Gouguenheim argues that Bayt al-Hikma, or the House of Wisdom, said to be created by the Abassids in the ninth century, was limited to the study of Koranic science, rather than philosophy, physics or mathematics, as understood in the speculative context of Greek thought.

He says that Aristotle's works on ethics, metaphysics and politics were disregarded or unknown to the Muslim world, being basically incompatible with the Koran. Europe, he said, "became aware of the Greek texts because it went hunting for them, not because they were brought to them."

Gouguenheim calls the Mont Saint-Michel monastery, where the texts were translated into Latin, "the missing link in the passage from the Greek to the Latin world of Aristotelian philosophy." Outside of a few thinkers - he lists Al-Farabi, Avicenne, Abu Ma'shar and Averroes - Gougenheim considers that the "masters of the Middle East" retained from Greek teaching only what didn't contradict Koranic doctrine.


Hunke describes a pioneering, civilizing Islam to which "the West owes everything." Gouguenheim replies that, in deforming reality, her work from the 1960s continues as a reference point that unfortunately still "shapes the spirit of the moment."
The publisher's description:

Aristote au mont Saint-Michel : Les racines grecques de l'Europe chrétienne
On considère généralement que l'Occident a découvert le savoir grec au Moyen Âge, grâce aux traductions arabes. Sylvain Gouguenheim bat en brèche une telle idée en montrant que l'Europe a toujours maintenu ses contacts avec le monde grec. Le Mont-Saint-Michel, notamment, constitue le centre d'un actif travail de traduction des textes d'Aristote en particulier, dès le XIIe siècle. On découvre dans le même temps que, de l'autre côté de la Méditerranée, l'hellénisation du monde islamique, plus limitée que ce que l'on croit, fut surtout le fait des Arabes chrétiens. Même le domaine de la philosophie islamique (Avicenne, Averroès) resta en partie étranger à l'esprit grec. Ainsi, il apparaît que l'hellénisation de l'Europe chrétienne fut avant tout le fruit de la volonté des Européens eux-mêmes. Si le terme de "racines" a un sens pour les civilisations, les racines du monde européen sont donc grecques, celles du monde islamique ne le sont pas.

September 22, 2009

mtDNA of Czech population

Hum Biol. 2008 Dec;80(6):669-74.

Mitochondrial DNA haplogroups in the Czech population compared to other European countries.

Vidrová V, Tesarová M, Trefilova E, Honzík T, Magner M, Zeman J.

The analysis of mtDNA haplogroup frequency in various populations is a tool for studying human history and population dynamics. The aim of this study is to map the frequency of major mtDNA haplogroups in 300 maternally unrelated individuals representing the Czech population of the central part of the Czech Republic. Eighteen polymorphic sites in the coding region of mtDNA were screened by PCR-RFLP to determine 11 mtDNA haplogroups and 5 subhaplogroups. The most frequent haplogroups were H (41%) and U (21%). Less frequent haplogroups were J and T, each with a frequency of 8%. Frequencies of other haplogroups (V, K, HV, W, preV, X, and I) did not exceed 5%. The results of our study reveal that the frequency of mtDNA haplogroups in the Czech population is similar to the frequencies obtained in other European countries, especially Poland, Germany, and Russia. On the contrary, significant differences in haplogroup frequency were found between the Czech and Finnish populations (haplogroups U, T, W) and populations from Bulgaria and Turkey (haplogroups H).


September 21, 2009

Climate influence on morphological differentiation of humans


Anat Rec (Hoboken). 2009 Aug 28. [Epub ahead of print]

Climate Signatures in the Morphological Differentiation of Worldwide Modern Human Populations.

Hubbe M, Hanihara T, Harvati K.

The ability of cranial morphology to reflect population/phylogenetic history, and the degree to which it might be influenced by environmental factors and selection pressures have been widely discussed. Recent consensus views cranial morphology as largely indicative of population history in humans, with some anatomical cranial regions/measurements being more informative on population history, while others being under selection pressure. We test earlier findings using the largest and most diverse cranial dataset available as yet: 7,423 male specimens from 135 geographic human population samples represented by 33 standard craniometric linear measurements. We calculated Mahalanobis D(2) for three datasets: complete cranial dataset; facial measurement dataset; and neurocranial measurement dataset; these morphological distance matrices were then compared to matrices of geographic distances as well as of several climatic variables. Additionally, we calculated Fst values for our cranial measurements and compared the results to the expected Fst values for neutral genetic loci. Our findings support the hypothesis that cranial, and especially neurocranial morphology, is phylogenetically informative, and that aspects of the face and cranium are subject to selection related to climatic factors. The Fst analysis suggest that selection to climate is largely restricted to groups living in extremely cold environments, including Northeast Asia, North America, and Northern Europe, though each of these regions appears to have arrived at their morphology through distinct adaptive pathways.


September 20, 2009

History of the people of the Hungarian plain in the 1st millennium

Hum Biol. 2008 Dec;80(6):655-67

History of the peoples of the Great Hungarian Plain in the first millennium: a craniometric point of view

Holló G, Szathmáry L, Marcsik A, Barta Z.

We carried out an examination relying on six dimensions of 1,573 crania coming from the Great Hungarian Plain. The crania represent seven archeological periods: Sarmatian age (1-4th century), the period of transition (about 400-420), Hun and Gepidic epochs (about 420-455 and 455-567, respectively), early Avar age (about 568-670), late Avar period (about 670-895), the epoch of the Hungarian conquest and settlement (about 895-1000), and the Arpadian age (about 1000-1301). We were curious about the anatomical background behind cultural changes of the various populations that inhabited this area. After having noticed some discontinuities between the populations, as revealed by univariate analysis of single dimensions, we performed a principal-components analysis to see whether or not the diverse components showed eventual breaks in the sequence of the populations. Knowing that all the dominant populations had Asian roots, except for the Gepids of Germanic origin, we expected a considerable difference between the Gepidic population and all the other inhabitants. We also assumed that a conquest itself with a large-scale assimilation was unlikely to leave breaklike traits in anatomical patterns, except for aggressive conquests. We found that the second principal component (which correlated with cranial breadth and partly with height) showed a remarkable hiatus in both sexes between Gepids and early Avars. Having done a statistical proof (simultaneous tests for general linear hypotheses) of the observed phenomenon, we found that the gap referring to subsequent populations was significant only in males. A possible reason for this result is that the Avar conquest was much more radical than has been thought. In addition, considering that men were more likely to die in wars, women survived and were assimilated into the conquerors' populations with higher probability, so it is not surprising that the results of multicomparison tests are significant only in men.


September 19, 2009

Genetics and environment contributions to craniofacial phenotypes of Belgians

Hum Biol. 2008 Dec;80(6):637-54.

Contribution of genetics and environment to craniofacial anthropometric phenotypes in Belgian nuclear families.

Jelenkovic A, Poveda A, Susanne C, Rebato E.

In this study we estimate relative genetic and environmental influences on head-related anthropometric phenotypes. The subject group consisted of 119 nuclear families living in Brussels, Belgium, and included 238 males and 236 females, ages 17 to 72 years. Two factor analyses with varimax rotation (the first one related to facial measurements and the second one to overall head morphology) were used to analyze 14 craniofacial size traits. The resulting four synthetic traits [HFCF, VFCF, HDF1, and HDF2-horizontal (breadth) and vertical (height) facial factors and two head horizontal (breadth) factors, respectively] were used as summary variables. Maximum heritabilities (H2) were estimated for all studied traits, and variance components analysis was applied to determine the contribution of genetics and environment on the four craniofacial factors. In addition, we examined the covariations between the face (HFCF and VFCF) and head-related factors (HDF1 and HDF2), separately. Quantitative genetic analysis showed that HFCF, VFCF, HDF1, and HDF2 variation was appreciably attributable to additive genetic effects, with heritability (h2) estimates of 67.62%, 54.97%, 70.76%, and 65.05%, respectively. The three variance components reflecting a shared familial environment were nonsignificant for these four phenotypes. Bivariate analysis revealed significant additive and residual correlations for both pair of traits. The results confirm the existence of a significant genetic component determining the four craniofacial synthetic traits, and common genetic and environmental effects shared by the two face-related phenotypes and by the head-related ones.


September 18, 2009

Craniometric evidence for Slavic-Finnic admixture in medieval Novgorod

The two main sources of the Russian population are well known by genetic evidence, but it is nice to see the historical process of admixture between Slavs and Finns visible in the anthropological record as well. The evidence for the presence of a Baltic component is more surprising in the light of genetic evidence, but at present diagnostic markers of Baltic admixture in uniparentally inherited markers do not appear to be available. Certainly, the high-resolution study of variation in the common N1c an R1a1 Y-chromosome haplogroups may reveal whether differences between Slav, Balt, or Finn (a) still exist, (b) do not exist because of a common substratu, (c) do not exist due to gene flow between the three linguistic groups.

From the paper:
Groups from 13th–14th century burials at Slavenka and Konezerie, and from 14th–16th century burials in Pskov are morphologically heterogeneous, and the variation exceeds that seen in non-admixed groups. Certain crania are markedly Caucasoid, displaying large and dolichocranic braincases, a sharp horizontal facial profile, a high face and a sharply protruding nose. Others are gracile, brachycranic, and have flattened low faces and flattened noses. The former are far fewer than the latter; most individuals are intermediate. The correlation coefficients also attest to heterogeneity; some of them, while concerning morphologically independent traits, are highly significant, and the same heterogeneity is revealed by the principal component analysis (Sankina, 2000).


According to the Mahalanobis distance values, Baltic parallels are especially marked for early Novgorodian groups, whereas Finnic parallels are typical of late groups. While the early and the late groups are very different, continuity between them is evidenced by a combination of intercorrelated traits discovered in the late groups from the upper Luga, Pskov, and the Ingrian Plateau. Speaking of the resemblance between the late Novgorodians and the Finns, it should not be overlooked that most of the former either had absorbed the Finnic substratum or were assimilated descendants of the local Finns. This concerns a group from Slantsy district, certain late groups of the Ingrian Plateau, and many others which, judging by archaeological evidence, were influenced by the traditions of the Baltic Finns.

While the presence of the Finnic element, which manifests itself in late Novgorodian groups, which cannot be disputed, the “Baltic” tendency of early Novgorodians is more difficult to explain. Large-scale Baltic presence in the Novgorodian territory during the pre-Slavic period (Early Iron Age) is evidenced by both archaeological and toponymical data. Recent archaeological and linguistic findings suggest that by the time of the Slavic colonization (7th century AD), Balts and Finns lived in the territory of northwestern Russia side by side, and the Balts which were numerically predominant, migrated to this territory several times, both from the east (the Dnieper basin) and from the west (the Vistula basin) (Vasiliev, 2008). Certain Baltic groups were apparently assimilated by the Slavs. Notably, among the fourteen 10th–13th century eastern Slavic groups from other territories, only three resemble the Balts. Another explanation may be that Balts, Slavs and Finns had absorbed the same ancient European substratum, which had been widely distributed in the past.

Of course, some non-Slavic elements may have participated in the population history of medieval Novgorod in more recent times. For instance, it is hardly accidental that the early group from Pskov is similar to populations of southeastern Estonia, which borders on the Pskov region.
Archaeology, Ethnology and Anthropology of Eurasia
Volume 37, Issue 2, June 2009, Pages 119-134


S.L. Sankina

Cranial series from cemeteries on the territory of the medieval Novgorod Republic were subjected to multivariate analysis. Northwestern Russia is the region where important population changes occurred in the early 2nd millennium AD. As a rule, earlier groups (11th – early 13th centuries) are dolichocranic and exhibit a sharp horizontal facial profile. In those series whose lower chronological limit is 11th–12th centuries, diachronic morphological changes can be traced. In later groups (13th–14th centuries), the cranial index is higher than in earlier ones (11th – early 13th centuries), whereas cranial height and nasal protrusion angle decrease, and the orbits become narrower. Series from the 13th– 16th century cemeteries apparently attest to an admixture. A combination of traits, correlated mostly at the between- group level (orbital breadth, nasal height, and nasal prominence angle), points to the presence of two components. This combination separates early and late Novgorod groups, at the same time opposing neighboring non-Slavic populations. While early groups (11th–13th centuries) resemble the 10th–18th century Balts, late ones (late 13th – early 20th centuries) resemble various Finnic groups of the same period.


September 17, 2009

Balloux in Heredity on Mitochondrial Phylogeography

Francois Balloux has some scathing criticism on mitochondrial phylogeography as it is currently practiced (doi: 10.1038/hdy.2009.122). I recommend reading the whole thing. The beginning:
Let us assume I gave a seminar. I would tell the audience about my latest results on the population history of the pigmy shrew. My findings would be based on a stretch of DNA comprising several metabolic genes, showing no signs of genetic recombination. Armed with sequences from a large number of individuals sampled over a broad geographical area, I would make some inference on the colonization routes and times. To make life easier, I would restrict my analysis to the mutations I liked best, with nice names having been given to related sequences, rather than relying on dull mathematical quantities. As I reach one of the key conclusions of the lecture, which would go as follows: 'It is obvious from the distribution of haplotypes Amanda, Eugenie* and Hector_2alpha that the Outer Hebrides were colonised about 50,000 years ago, this was followed by considerable population fluctuations, a bottleneck during the last Ice Age, a swift recovery and a dramatic recent expansion over the last 200 years and...'. Imagine that, at that climactic stage I was interrupted by someone in the audience. The impertinent would say, 'Sir, can I just ask you whether this confidence in your conclusions may not be misplaced; your analysis is based on a single genetic marker, which comprises genes with a central role in metabolism and is thus likely to have been affected by natural selection'. An awkward silence may ensue, as I would find it difficult to dismiss this criticism easily.
and the end:
Despite mitochondrial sequence variation covarying with climate in humans (Balloux et al., 2009), there are better ways to measure temperature. And, I would argue there are also better genetic markers than mtDNA to infer past population history. I fully appreciate that mtDNA has given us some of the most fundamental results on human evolution at a time when using mtDNA was the only realistic option at hand. I do not question the value of mtDNA in forensics and pedigree reconstruction. It is also likely to remain a valuable tool for inference at a localized geographical scale, particularly when testing specific hypotheses rather than making quantitative inferences on the age or size of the populations studied. It is convenient to type and analyse, and its use in humans raises no serious ethical or societal issue. But all these qualities do not counterbalance the fact that a single locus likely to be under selection is inappropriate for population inference at large geographical scales (or over long periods of time in the context of ancient DNA analysis). We have reached an era in which publicly available data sets of large numbers of complete human genomes are a tangible prospect, and I believe it is now time to move on from the excessive reliance on uniparental markers. Exploiting these new resources of autosomal variation will present significant challenges, but it will not help overcoming them if a large fraction of the community of human population biologists persists in sticking to mtDNA as the marker of choice.
The utility of mtDNA for studying modern populations is indeed limited now that we can study hundreds of thousands of markers per individual. However, it is still a very useful marker for ancient DNA, both because it is often the only game in town because of the relative ease with which it can be typed due to its large copy count, and also because it has proven itself to be capable of generating interesting results, as in the recently discovered discontinuity between Paleolithic and Neolithic Central Europeans, studying the mtDNA diversity of Neandertals compared to humans, or detecting sex-biased gene flow in relatively recently admixed populations.

See some of my previous criticisms on facile correlations between mtDNA time depth and archaeological-historical correlations:

John Hawks also comments at length on the paper. An excerpt:
So what can we do? Fortunately we have lots of options. We can test the proposed demographic hypotheses against the historical record. When we make observations that show that people 1000 years ago had very different frequencies of common haplotypes, well, we know it was selection. There hasn't been any genetically significant bottleneck in the last 1000 years! When we see small Neolithic population samples dominated by haplotypes that are very rare today, again, no historically possible bottleneck could have caused that.
I am fundamentally in agreement that bottlenecks, so often invoked in the mtDNA literature, are really a non-issue. Consider why this is the case: every mtDNA paper normally takes a random sample of a few tens or hundreds of people from a population that usually numbers in the thousands or millions. The assumption is that such a small random sample generally preserves -within confidence limits- the haplogroup frequencies in the population. But a bottleneck is exactly such a random sample. You can't, at the same time, use a sample of 100 people to infer haplogroup frequencies, and claim that a bottleneck that reduces the population to a 100 people will radically shift haplogroup frequencies. And, of course, there is absolutely no evidence that any major post-Neolithic human population, save for the Andaman Islanders, the Samaritans, or various such populations ever underwent a bottleneck anywhere near that severity.

However, I am in disagreement that a change of haplotype frequencies across 1,000 years is evidence of selection. A different explanation is that of migration, the introduction of a new population element.

Sometimes, migration is easy to infer. For example, we can be fairly certain that modern Europeans are different from Paleolithic Europeans because of Neolithic and post-Neolithic migration into Europe, because there is an introduction of new haplotypes that were absent in the Paleolithic population. One possible explanation is that instead of "absent" we should say "possibly present at very low frequencies". But, once we see that these haplotypes were present on the early Neolithic migrants, it doesn't take much to put 2+2 together and infer that migration is a likelier explanation.

The same process of migration could be inferred for the Neolithic populations of the Lake Baikal district, where a postulated hiatus in occupation, followed by recolonization by immigrants, proposed on archaeological grounds, coincides with the discovery of a sharp difference between pre- and post-hiatus populations in mtDNA haplotype frequencies. Similarly, the absence of Mongoloid mtDNA before the 7th c. BC in Central Asian samples, followed by its introduction after it, can be parsimoniously explained by admixture, since that admixture is evident also in anthropological and autosomal studies.

In other cases, selection may be a more plausible possibility. For example, the reduction in the frequency of haplogroup I in Denmark since the Viking and Iron Age, or changes of frequency in haplogroups in England since the 11th c. AD, such as the reduction of U5a1 and the increase in H may in fact be due to selection. H was present -although not very frequent- in Neolithic farmers from Central Europe, Corded Ware people from Eulau, and its very high present-day frequency in Europeans (roughly 50%) as there is no plausible source or mechanism that would have brought large numbers of it in Europe.

In conclusion, both migration and selection may help explain shifts in haplotype frequencies over time. As we plug in the holes in our knowledge of the mtDNA distribution across space and time, we will be able to decide between the two.

September 16, 2009

Y chromosome and mtDNA of goats in North Africa

Mol Biol Evol. 2009 Sep 3. [Epub ahead of print]

Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa.

Pereira F, Queirós S, Gusmão L, Nijman IJ, Cuppen E, Lenstra JA; the Econogene Consortium, Davis SJ, Nejmeddine F, Amorim A.

Valuable insights into the history of human populations have been obtained by studying the genetic composition of their domesticated species. Here we address some of the long-standing questions about the origin and subsequent movements of goat pastoralism in Northern Africa. We present the first study combining results from mitochondrial DNA (mtDNA) and Y chromosome loci for the genetic characterization of a domestic goat population. Our analyses indicate a remarkably high diversity of maternal and paternal lineages in a sample of indigenous goats from the northwestern fringe of the African continent. Median-joining networks and a multidimensional scaling of ours and almost 2000 published mtDNA sequences revealed a considerable genetic affinity between goat populations from the Maghreb (Northwest Africa) and the Near East. It has been previously shown that goats have a weak phylogeographic structure compatible with high levels of gene flow, as demonstrated by the worldwide dispersal of the predominant mtDNA haplogroup A. In contrast, our results revealed a strong correlation between genetic and geographical distances in 20 populations from different regions of the world. The distribution of Y chromosome haplotypes in Maghrebi goats indicates a common origin for goat patrilines in both Mediterranean coastal regions. Taken together, these results suggest that the colonization and subsequent dispersal of domestic goats in Northern Africa was influenced by the maritime diffusion throughout the Mediterranean Sea and its coastal regions of pastoralist societies whose economy included goat herding. Finally, we also detected traces of gene flow between goat populations from the Maghreb and the Iberian Peninsula corroborating evidence of past cultural and commercial contacts across the Strait of Gibraltar.


September 15, 2009

Variable genetic ancestry in Brazilians

Braz J Med Biol Res. 2009 Sep 11. pii: S0100-879X2009005000026.

DNA tests probe the genomic ancestry of Brazilians.

Pena SD, Bastos-Rodrigues L, Pimenta JR, Bydlowski SP.

We review studies from our laboratories using different molecular tools to characterize the ancestry of Brazilians in reference to their Amerindian, European and African roots. Initially we used uniparental DNA markers to investigate the contribution of distinct Y chromosome and mitochondrial DNA lineages to present-day populations. High levels of genetic admixture and strong directional mating between European males and Amerindian and African females were unraveled. We next analyzed different types of biparental autosomal polymorphisms. Especially useful was a set of 40 insertion-deletion polymorphisms (indels) that when studied worldwide proved exquisitely sensitive in discriminating between Amerindians, Europeans and Sub-Saharan Africans. When applied to the study of Brazilians these markers confirmed extensive genomic admixture, but also demonstrated a strong imprint of the massive European immigration wave in the 19th and 20th centuries. The high individual ancestral variability observed suggests that each Brazilian has a singular proportion of Amerindian, European and African ancestries in his mosaic genome. In Brazil, one cannot predict the color of persons from their genomic ancestry nor the opposite. Brazilians should be assessed on a personal basis, as 190 million human beings, and not as members of color groups.


September 13, 2009

On the mtDNA molecular clock (Endicott et al. 2009)

This is an excellent paper to read on the technicalities and controversies surrounding the human mtDNA clock. The authors argue against over-reliance on the human chimpanzee splitting as a calibration point, both because of uncertainty about the age of that event, and also because of limitations of the ρ statistic which is widely used to associate the accumulation of genetic diversity with time (e.g., its performance under selection). They further argue that existing mtDNA age estimates are largely over-estimates for such events such as sapiens-Neanderthal divergence, and the arrival of modern humans in various parts of the world. Their concluding remarks:
Further research is needed to improve our confidence in
molecular estimates of human evolutionary timescales.
First, the most reliable calibrations within the human tree
need to be identified. For mitochondrial DNA, this depends
on finding well-defined haplogroups that can be precisely
associated with dated palaeoanthropological evidence [17].
Second, the variation in observed rates across different
timescales needs to be accurately quantified [16–18].
Third, these patterns of rate variation need to be investigated
for nuclear data, including the Y-chromosome and
short tandem repeats.
The chief recommendation arising from the current
state of knowledge in the field is for a movement away
from reliance on the human-chimpanzee calibration;
instead, calibrations within the human tree are preferred
(but see [14]). There are several recent examples of estimates
made using archaeological calibrations [15–17,35],
extending the efforts of earlier authors [3,60]. Considering
recent advances in phylogenetic methodology, there is now
a compelling motivation to employ statistical models that
take into account rate heterogeneity among sites and
among lineages, that correct for multiple substitutions
(saturation), and that incorporate directly the uncertainty
in the ages of calibrations used. Some methods also allow
the statistical evaluation of competing demographic
models, which can have an important influence on estimates
of rates and timescales [17,23].
I have my own misgivings about the possibility of archaeologial calibration of the mtDNA clock. Archaeology provides us with evidence that the arrival of modern humans in a part of the world could not have been later than X years ago, the age of the earliest archaeological or osteological finds.

But, it does not really tell us how many of them arrived, or what their own mtDNA time depth was: if a small number of migrants arrive, it is possible that either their own common ancestor lived fairly close to the time of migration, or that only one of them -due to genetic drift in the small population- will leave matrilineal descendants. In other words, if a small number of migrants participates in the early colonization of a region, chances increase that their mtDNA time depth will be close to the time of their arrival; conversely, known time of arrival -from archaeology- calibrates the molecular clock. Indeed, if the population stays small for a long time after arrival, the common matrilineal ancestor may "reset" several times, and the population's antiquity (based on mtDNA diversity) will appear to be much younger than it really is.

However, if the number of migrants is not small, then in all likelihood the common ancestor precedes the migration substantially, and calibration of the molecular clock by the visible migration would lead to an overestimate in the rate in which mtDNA diversity accumulates, and a molecular clock that produces more recent ages than the true ones.

Many existing works make the assumption of neutrality about mtDNA evolution in humans. This means that no mtDNA lineage has an advantage over any other; and subsequently, the fact that we are all descended from a relatively small number of "mothers" (like the "Daughters of Eve") becomes difficult to explain. Massive disappearance of other lineages (besides the few surviving mothers) is only possible under conditions of strong genetic drift in small populations. Hence, the conclusion, reiterated time and again in the literature about humans being reduced to a few hundred or a few thousand individuals, which has sparked the new mythos of a "small band of humans surviving to colonize the entire world".

In reality, our descent from a small number of "mothers" can be reconciled with a large human population under the assumption that mtDNA is under substantial natural selection. If that is the case, the limited number of surviving lineages is not due to drift in a small population, but to selection in a large one.

My personal guess is that the molecular clock won't be calibrated by reliance to archaeology, but by improvements in the affordability of sequencing. At present it is not really affordable to do full mtDNA genome scans in a few thousand mother-daughter pairs to obtain reliable mutation rate estimates, but this is likely to eventually change, leading to better estimates of the splitting times of various mtDNA lineages.

Some previous topics on the question:
Trends in Ecology and Evolution doi:10.1016/j.tree.2009.04.006

Evaluating the mitochondrial timescale of human evolution

Phillip Endicott, Simon Y.W. Ho, Mait Metspalu and Chris Stringer


Different methodologies and modes of calibration have produced disparate, sometimes irreconcilable, reconstructions of the evolutionary and demographic history of our species. We discuss how date estimates are affected by the choice of molecular data and methodology, and evaluate various mitochondrial estimates of the timescale of human evolution in the context of the contemporary palaeontological and archaeological evidence for key stages in human prehistory. We contend that some of the most widely-cited mitochondrial rate estimates have several significant shortcomings, including a reliance on a human-chimpanzee calibration, and highlight the pressing need for revised rate estimates.


September 12, 2009

Independent horse domestication event in China

See also: Origin of ancient Chinese horses from ancient DNA

Anim Genet. doi:10.1111/j.1365-2052.2009.01950.x

Multiple maternal origins of native modern and ancient horse populations in China

Lei CZ, Su R, Bower MA, Edwards CJ, Wang XB, Weining S, Liu L, Xie WM, Li F, Liu RY, Zhang YS, Zhang CM, Chen H.

Summary To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.

Geographic patterning of goats from Greece, Albania, and Italy

BMC Ecol. 2009 Sep 2;9(1):20. [Epub ahead of print]

Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms.

Pariset L, Cuteri A, Ligda C, Ajmone-Marsan P, Valentini A, Consortium E.

ABSTRACT: BACKGROUND: SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. RESULTS: A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. CONCLUSION: Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.


September 11, 2009

"Mother goddess" figurines theory demolished

I can't say I ever bought into the whole "Mother goddess" theory. It reeks of a pacifistic/New Age/feminist mindset, is heavy on theory, interpretation, and "symbolism" and light on objective facts.

Ancient figurines were toys not mother goddess statues, say experts as 9,000-year-old artefacts are discovered
Made by Neolithic farmers thousands of years before the creation of the pyramids or Stonehenge, they depict tiny cattle, crude sheep and flabby people.
In the 1960s, some researchers claimed the more rotund figures were of a mysterious large breasted and big bellied "mother goddess", prompting a feminist tourism industry that thrives today.
But modern day experts disagree.
They say the "mother goddess" figures - which were buried among the rubbish of the Stone Age town - are unlikely to be have been religious icons.
Many of the figures thought to have been women in the 1960s, are just as likely to be men.


Archaeologist Prof Lynn Meskell, of Stanford University, said: "The majority are cattle or sheep and goats. They could be representatives of animals they were dealing with - and they could have been teaching aides.
"All were found in the trash - and they were not in niches or platforms or placed in burials."
Out of the 2,000 figurines dug up at the site, less than five per cent are female, she told the British science Festival in Surrey University, Guildford.
"These are things that were made and used on a daily basis," she said. "People carried them around and discarded them."