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.

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

Abstract

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.

Link

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.

Link

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.

Abstract

Background

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.

Results

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).

Conclusions

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.

Link

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 :

Η θέση μου για τις βουλευτικές εκλογές της 4ης Οκτωβρίου 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.

UPDATE II:

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."

Related:

• Ancient mtDNA from Iceland
• Roman Age, Viking Age, and Eskomo mtDNA
• Ancient Viking mtDNA from Denmark
• Ancient British mtDNA
• Y chromosomes and mtDNA from Eulau
• Central European farmers not descended from local hunter-gatherers

Current Biology doi:10.1016/j.cub.2009.09.017

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

Helena Malmström et al.

Abstract

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.

Link

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:

Herodotus of Halicarnassus, Histories, Book 7:

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.

Arrian, Anabasis, Book 8:

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.

Abstract

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.

Link

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

Abstract

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.

Link

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.

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).

Link

Climate influence on morphological differentiation of humans

Related:

• Cranial morphology and population history
• Cranial anatomy and population history or climate adaptation
• Drift more important than selection in shaping the human skull
• Reduction of human cranial diversity and distance from Africa

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.

Link

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.

Link

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.

Link

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

THE ETHNIC HISTORY OF MEDIEVAL NOVGOROD (BASED ON CRANIOMETRIC DATA)

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.

Link

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_2 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:

• On the mtDNA molecular clock (Endicott et al. 2009)
• Time-dependency of the human mtDNA evolutionary mutation rate

UPDATE:

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.

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.

Link

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.

Link

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:

• mtDNA time depth of humanity more recent than previously thought
• Time-dependency of the human mtDNA evolutionary mutation rate
• Purifying selection and the mtDNA clock (Soares et al. 2009)

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

Abstract

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.

Link

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.

Link

"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."

Paleolithic flax fibres from Georgia (Kvavadze et al. 2009)

From BBC News:

A Georgian cave has yielded what scientists say are the earliest examples of humans making cords.

The microscopic fibres, discovered accidentally while scientists were searching for pollen samples, are around 30,000 years old.

A team reports in the journal Science that ancient humans probably used the plant fibres to carry tools, weave baskets or make garments.

Some of the fibres are coloured and appear to have been dyed.

Science Vol. 325. no. 5946, p. 1359 DOI: 10.1126/science.1175404

30,000-Year-Old Wild Flax Fibers

Eliso Kvavadze et al.

A unique finding of wild flax fibers from a series of Upper Paleolithic layers at Dzudzuana Cave, located in the foothills of the Caucasus, Georgia, indicates that prehistoric hunter-gatherers were making cords for hafting stone tools, weaving baskets, or sewing garments. Radiocarbon dates demonstrate that the cave was inhabited intermittently during several periods dated to 32 to 26 thousand years before the present (kyr B.P.), 23 to 19 kyr B.P., and 13 to 11 kyr B.P. Spun, dyed, and knotted flax fibers are common. Apparently, climatic fluctuations recorded in the cave’s deposits did not affect the growth of the plants because a certain level of humidity was sustained.

Link

Warfare rather than agriculture as a cause of fires in the Neolithic of northern Vietnam

PNAS doi:10.1073/pnas.0813258106

Warfare rather than agriculture as a critical influence on fires in the late Holocene, inferred from northern Vietnam

Zhen Li et al.

Fire has played an essential role in the development of human civilization. Most previous research suggests that frequent-fire regimes in the late Holocene were associated with intensification of human activities, especially agriculture development. Here, we analyze fire regimes recorded in the Song Hong delta area of Vietnam over the past 5,000 years. In the prehistoric period, 2 long-term, low-charcoal abundance periods have been linked to periods of low humidity and cool climate, and 5 short-term fire regimes of 100–150 years in duration occurred at regular intervals of ≈700 years. However, over the last 1,500 years, the number, frequency, and intensity of fire regimes clearly increased. Six intensified-fire regime periods in northern Vietnam during this time coincided with changes of Vietnamese dynasties and associated warfare and unrest. In contrast, agricultural development supported by rulers of stable societies at this time does not show a positive correlation with intensified-fire regime periods. Thus, warfare rather than agriculture appears to have been a critical factor contributing to fire regimes in northern Vietnam during the late Holocene.

Link

Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico (Gravlee et al. 2009)

I had posted when this appeared in AAPA 2008, and now the full paper has been published.

Figure 1 shows the relationship between "color" and genetic ancestry. As can be seen, the "color" categories overlap in terms of genetic ancestry, even though their averages are in the right order:

The paper is a powerful reminder that social race is not the same as genomic ancestry, and that racial disparities in an observable trait do not necessarily reflect differential genetic proclivities.

PLoS ONE 4(9): e6821. doi:10.1371/journal.pone.0006821

Genetic Ancestry, Social Classification, and Racial Inequalities in Blood Pressure in Southeastern Puerto Rico

Clarence C. Gravlee et al.

Abstract

Background

The role of race in human genetics and biomedical research is among the most contested issues in science. Much debate centers on the relative importance of genetic versus sociocultural factors in explaining racial inequalities in health. However, few studies integrate genetic and sociocultural data to test competing explanations directly.

Methodology/Principal Findings

We draw on ethnographic, epidemiologic, and genetic data collected in southeastern Puerto Rico to isolate two distinct variables for which race is often used as a proxy: genetic ancestry versus social classification. We show that color, an aspect of social classification based on the culturally defined meaning of race in Puerto Rico, better predicts blood pressure than does a genetic-based estimate of continental ancestry. We also find that incorporating sociocultural variables reveals a new and significant association between a candidate gene polymorphism for hypertension (α2C adrenergic receptor deletion) and blood pressure.

Conclusions/Significance

This study addresses the recognized need to measure both genetic and sociocultural factors in research on racial inequalities in health. Our preliminary results provide the most direct evidence to date that previously reported associations between genetic ancestry and health may be attributable to sociocultural factors related to race and racism, rather than to functional genetic differences between racially defined groups. Our results also imply that including sociocultural variables in future research may improve our ability to detect significant allele-phenotype associations. Thus, measuring sociocultural factors related to race may both empower future genetic association studies and help to clarify the biological consequences of social inequalities.

Link

Reduced fecundity of fat women

J Womens Health (Larchmt). 2009 May;18(5):633-6.

The relationship between obesity and fecundity.

Yilmaz N, Kilic S, Kanat-Pektas M, Gulerman C, Mollamahmutoglu L.

OBJECTIVE: Obesity is an important factor that might reduce fecundity. In order to determine the underlying physiological mechanisms and risk factors, the obesity-fecundity association is investigated in relation to parity, menstrual cycle regularity, smoking habits, and age. METHODS: This was a retrospective cohort study of 22,840 women who gave birth between January 2006 and January 2007 in the Dr Zekai Tahir Burak Women's Health Research and Education Hospital. Age, parity, prepregnancy body mass index (BMI) values, time to pregnancy data related to smoking, and reproductive, medical, and gynecological history were obtained from the medical records. RESULTS: Fecundity was reduced for overweight and obese women compared with optimal weight women, and this reduction was more evident for obese primiparous women. Fecundity remained reduced for overweight and obese women with normal menstrual cycles. Obese and overweight women were found to smoke significantly more than the optimal weight group. CONCLUSIONS: Obesity was found to be associated with reduced fecundity for all weight-adjusted groups of women and persisted for women with regular cycles. Weight loss should be encouraged initially during the treatment of infertile overweight and obese women.

Link

Ancient mtDNA from Yayoi period Doigahama (Japan)

Journal of Human Genetics doi: 10.1038/jhg.2009.81

Mitochondrial DNA analysis of Yayoi period human skeletal remains from the Doigahama site

Kazunari Igawa et al.

We analyzed the mitochondrial DNA extracted from 14 human skeletal remains from the Doigahama site in Japan to clarify the genetic structure of the Doigahama Yayoi population and the relationship between burial style and kinship among individuals. The sequence types obtained in this study were compared with those of the modern Japanese, northern Kyushu Yayoi and ancient Chinese populations. We found that the northern Kyushu Yayoi populations belonged to the groups that include most of the modern Japanese population. In contrast, most of the Doigahama Yayoi population belonged to the group that includes a small number of the modern Japanese population. These results suggest that the Doigahama Yayoi population might have contributed less to the formation of the modern Japanese population than the northern Kyushu Yayoi populations. Moreover, when we examined the kinship between individuals in the Doigahama site, we found that the vicinal burial of adult skeletons indicated a maternal kinship, although that of juvenile skeletons did not. The vicinal burial style might have been influenced by many factors, such as paternal lineages, periods and geographical regions, as well as maternal lineages. In addition, skeletons considered to be those of shamans or leaders had the same sequence types. Their crucial social roles may have been inherited through maternal lineage.

Link

European admixture and obesity traits in African Americans

Obesity (Silver Spring). doi:10.1038/oby.2009.282

Admixture Mapping of Obesity-related Traits in African Americans: The Atherosclerosis Risk in Communities (ARIC) Study.

Cheng CY, Reich D, Coresh J, Boerwinkle E, Patterson N, Li M, North KE, Tandon A, Bailey-Wilson JE, Wilson JG, Kao WH.

Obesity is an important cause of morbidity and mortality worldwide. In the United States, the prevalence of obesity is higher in African Americans than whites, even after adjustment for socioeconomic status (SES). This leads to the hypothesis that differences in genetic background may contribute to racial/ethnic differences in obesity-related traits. We tested this hypothesis by conducting a genome-wide admixture mapping scan using 1,350 ancestry-informative single-nucleotide polymorphisms (SNPs) in 3,531 self-identified blacks from the Atherosclerosis Risk in Communities (ARIC) study. We used these markers to estimate the overall proportions of European ancestry (PEAs) for each individual and then scanned for the association between PEA and obesity-related traits (both continuous and dichotomous) at each locus. The median (interquartile range) PEA was 0.151 (0.115). PEA was inversely correlated with continuous BMI, weight, and subscapular skinfold thickness, even after adjusting for socioeconomic factors. In contrast, PEA was positively correlated with BMI-adjusted waist circumference. Using admixture mapping on dichotomized traits, we identified a locus on 2p23.3 to be suggestively associated with BMI (locus-specific lod = 4.11) and weight (locus-specific lod = 4.07). After adjusting for global PEA, each additional copy of a European ancestral allele at the 2p23.3 peak was associated with a BMI decrease of ~0.92 kg/m(2) (P = 2.9 x 10(-5)). Further mapping in this region on chromosome 2 may be able to uncover causative variants underlying obesity, which may offer insights into the control of energy homeostasis.

Link

Colin Renfrew video on the "Renfrew hypothesis" of Indo-European origin

A two-part video interview of Colin Renfrew; the discussion of Indo-European spans roughly 22:20 to 40:40 in the second part.

Part I



Part II

More ASHG 2009 abstracts

For the first part, see here.

See Part I for another study on Ashkenazi Jews. We will have to look at the details of the study when it comes out, but the fact that Ashkenazi Jews are (a) between southern Europeans and Near Easterners, and (b) form a distinct cluster of their own at K=3 seems to support my theory that most of the European ancestry in Jews is of ancient origin in southern Europe rather than due to recent admixture with Central/Eastern Europeans: at K=2 the ancestral components are identified, but these components mixed a relatively long time ago, so that after a subsequent period of relative isolation, a distinctive pattern was formed out of the mixture which is identified at K=3.

Genome-wide SNP analysis of Ashkenazi Jews reveals unique population substructure

The Ashkenazi Jews (AJ) are a genetic isolate that has been widely utilized in genetic studies of both mendelian and complex disorders. However, the genetic variation and population structure of the AJ have been previously investigated with relatively few individuals and few genetic markers. We have now genotyped a large AJ cohort with the Affymetrix 6.0 genome-wide SNP array. After strict quality control filters, genotype data at 775K SNPs in 466 unrelated AJ individuals were available for analysis. To investigate the genetic structure of the AJ relative to other populations we used principle components analysis (PCA) as well as the frappe clustering algorithm. When merged with the worldwide Human Genome Diversity Project dataset, PCA shows the AJ are distinct from all other groups, including both European and Middle-Eastern populations. Further PCA using AJ genotypes combined with a large European dataset again validates the separation of AJ from European populations. Interestingly, principle component one seems to largely separate European and Middle-Eastern populations geographically according to latitude with the AJ fitting South of Europe and North of the Middle-East. Additional analysis using the frappe population clustering algorithm is consistent with a unique population signature for the AJ. Limiting the frappe clustering to only two population groups, specifying k=2, reveals that AJ cluster more closely to Europeans than Middle-Eastern populations but when allowing three populations, k=3, AJ form a group distinct from both the Middle-East and Europe. Compared to European populations, AJ also show an increase in genome-wide linkage disequilibrium, consistent with possible founder effects. These findings will aid in the design and use of AJ in case-control and association studies and clearly demonstrate the genetic separation of AJ from other populations.

Another paper on the topic, albeit one which uses HLA haplotypes to infer admixture and is limited to Jewish/Central European admixture.

Admixture between Ashkenazi Jews and Central Europeans

When distinct populations inhabit the same geographic space, culture often acts to restrict random mating in our species, while at the same preventing complete genetic privacy. The residency across Central Europe by the Ashkenazi Jews over the last thousand years is such a case. HLA typing from bone marrow donor registries in Israel, Poland and Germany were utilized to measure admixture between central European host populations and Ashkenazim. Inferred high resolution HLA A-B-DRB1 haplotype frequencies were generated from each population. A total of 1,676 Polishorigin- Ashkenazim and 13,556 Polish haplotypes were analyzed, along with a similar sample of ~5 million German haplotypes. The informativeness of HLA haplotypes is shown by the A-B-DRB1 haplotype 0101-0801-0301, the most common haplotype found in northern Europe. HLA B*0801 bearing haplotypes are present in the Near East, but those B*0801 haplotypes carry the HLA C allele Cw*0702 instead of the Cw*0701 found in 0101-0801- 0301. The 100 most common haplotypes constituted 53% of the total Ashkenazi, and 45% of the Polish, and 43% of the German samples, reflecting the sizeable total fraction of very rare haplotypes familiar in population samples of the diverse HLA system. The most common Ashkenazi haplotype had a frequency of 6.14% (n = 102.9) and the 100th haplotype was present at 0.29% (n = 4.86). Comparable values for the Polish sample were 5.83% (n = 790.3) and 0.13% (n = 17.6), respectively. Haplotypes from one population compared to those haplotypes in a second could be classified into three categories: less frequent, statistically identical or more frequent. In the graph of the ordered 100 Polish haplotypes, the less frequent Ashkenazi haplotypes supply a possible signature of admixture from the Poles into the Polish Ashkenazim, while the haplotypes more frequent in Ashkenazim than Poles are candidates for movement of genes from the Ashkenazim to the Poles. The averaged frequency differences between these categories give an indication of population admixture. The analysis showed that 1.8% of Polish haplotypes may be of Ashkenazi origin and 0.6% of Ashkenazi of Polish origin. The sample from Germany, in which the initial generations of Polish- Ashkenazi history was spent, was useful in demonstrating consistency of haplotype frequencies by rank order. The results show clear evidence of admixture occurring in both directions between two largely HLA-distinct populations.

The following study demonstrates a point I have argued several times before with Afrocentrists, namely the intermediate genetic position of Ethiopians between Caucasoids and Sub-Saharan Africans. It also underscores the difference between social and biological classifications: Ethiopians are undoubtedly "socially" black in most other societies, but intermediate between Negroids and Caucasoids anthropologically. This reality was recognized even by early anthropologists who coined the term of Ethiopids to describe them as a separate intermediate category between Caucasoids and Negroids.

The distribution of sex-specific human genetic variation in Ethiopia.

Ethiopia has been proposed as a candidate location for the emergence of anatomically modern humans, and the source region for the expansion out of Africa. It is also a region of substantial cultural diversity as expressed in languages (Nilo-Saharan, Cushitic, Semitic, and Omotic language families), religions (Christians, Jews, Moslems and Animists), ethnic identities (over 80 groups) as well as many marginalised groups socially excluded on grounds of caste-like occupation, supposed origin, or both. The demographic history of Ethiopia over the past several thousand years has involved both sustained migration of Semitic speakers from the Arabian Peninsula as well as internal conquests of lands in the south. To investigate the demographic histories of ethnic groups we analysed a battery of SNPs and microsatellites on the non-recombining portion of the Y chromosome (NRY) and sequence variation in the Hypervariable Segment 1 (HVS1) of mtDNA (5756 samples from 45 ethnic groups). Commonly used summary statistics (gene diversity h, genetic distance Fst) were analysed within the context of non Ethiopian data e.g. West Africa (Igbo, Nigeria) and Europeans. We present preliminary results reporting a wide range of genetic diversity values within ethnic groups (h: NRY = 0.743 - 0.972, HVS1 = 0.962 - 0.996) and pairwise genetic distance values between groups (Fst: NRY = 0.000 - 0.294, HVS1 = 0.000 - 0.035). A clustering of Ethiopian groups was observed when using principal coordinate analyses with genetic distances, appearing midway between a West African Niger-Congo speaking group (Igbo of Nigeria) and an Indo- European speaking group (Greek Cypriots). Some south-western groups (e.g. Anuak) showed greater similarity to West-Africans while the culturally influential Amhara were more similar to Europeans. Gene flow between dominant Dawuro agriculturalists and excluded members of the Manja was sex-biased, with many more NRY haplotypes common to the two groups than mtDNA haplotypes, relative to the distribution of the two systems across all the ethnic groups. The marginalised group had a particularly low level of mtDNA HVS1 diversity (h = 0.705). Of particular interest is the extensive sharing of discriminating NRY and mtDNA haplotypes across many ethnic groups, suggesting either a) the creation or preservation of cultural diversity despite substantial inter-group gene flow or b) recent ethnogenesis of the currently extant groups.

Yet another study of differences between ancient and modern mtDNA gene pools. I hope the 2012 crowd doesn't follow up on this for its own bizarre purposes...

Genetic Diversity of the Ancient People in Mesoamerica

DNAs were extracted from the human remains buried in the Moon Pyramidat archaeological Teotihuacan site in Mexico. Nucleotide sequences of theirmitochondrial D-loop and SNP sites were determined by the PCR-directsequencing. To reveal the genealogy of mitochondrial DNA sequences ofthe individuals buried in the Moon Pyramid and assess their positions amongNative Americans, we first constructed a network of the mitochondrial DNAfrom the contemporary Native Americans; the northern Native Americans(Haida, Bella Coola, and Nuu Chah Nulth), the central Native Americans(Huetar, Kuna, and Ngöbé), and the southern Native Americans (Yanomami,Zoro, Gavião, and Xavante), and compared them with those of the individualsfrom the Moon Pyramid. All of the mitochondrial DNA types from the MoonPyramid individuals were unique, and clear genetic affinities were notobserved between the Moon Pyramid individuals and any of the 10 NativeAmerican populations. To investigate genetic diversity among the contemporarycentral Native American populations, we constructed a phylogenetictree of their mitochondrial DNA sequences using the neighbor-joiningmethod. There was a major mitochondrial DNA sequence common to thesethree central Native American populations. However, there were a relativelysmall number of mitochondrial DNA types in each population, most of whichwere, moreover, unique to each Native American population. Next we comparedthe mitochondrial DNA sequences of the Moon Pyramid individualswith those of the ancient Mesoamerican people, ancient Maya people fromthe classic Copán site. We also used Huetar people as a reference for thecontemporary central Native Americans. The distribution of the mitochondrialDNA types found in the ancient Native Americans is greatly different fromthat found in the contemporary Native Americans. These results show thatgenetic diversity in the ancient Native Americans was not as low as that inthe contemporary Native Americans, suggesting an occurrence of bottleneckin the past.

This will be of great interest to Y chromosome enthusiasts.

Improved resolution of the human Y-chromosomal phylogeny using
targeted next-generation sequencing

The non-recombining part of the Y chromosome provides unique insights into male-specific aspects of human genetics and history. We are using next-generation Illumina sequencing to fully re-sequence targeted regions of the Y and resolve the Y-chromosomal phylogeny by characterization of additional single nucleotide polymorphisms (SNPs) on lineages of interest. Initially ~6 Mb of Y sequence (NCBI36:Y-chromosome: 12,308,579- 18,230,132) is being generated for an African haplogroup A male. The strategy involves sequence enrichment by long template PCR of genomic DNA (10-20 ng/reaction) using overlapping fragments of 5.5 - 6.5 kbp. Currently ~70% of primer pairs work using a standard touchdown PCR protocol. Fragments obtained from a single individual are pooled and used for library preparation and IIlumina sequencing. Re-sequencing generates accurate high coverage data; SNP calling and their subsequent validation will be presented. Most SNPs are expected to be rare but some are likely to resolve deep divisions within African populations. Subsequently, we aim to (1) determine the time depth of the human Y phylogeny, (2) resolve multifurcations in the major lineages by discovering additional SNPs on the relevant and (3) discover SNPs that mark any lineage of particular interest. In addition, we will be able to provide a subset of all primers that work well with this protocol to investigators who are interested in Y-chromosomal phylogenies so that comparable standard datasets can be generated for use by the community.

Female to male breeding ratio in the history of modern humans

Was the genetic contribution of men and women to successive generations the same? As a population, did we have fewer fathers than mothers? Was polygyny present among hominid lineages to influence relative divergence rates of autosomes and sex chromosomes? Students of genetic variation of the uniparentally inherited mitochondrial and Y-chromosome DNA confronted these questions, fewer addressed it by looking at the DNA diversity of autosomes and sex chromosomes (Hammer et al. 2009, Keinan et al. 2009) with equivocal results. Our approach is different: we analyzed the ratio of the population recombination rate, ρ, between autosomes and the X chromosome. The chromosome X recombines only in the female meiosis whereas autosomes undergo cross-overs in both male and female germ lines such that their relative ρ reflects changes in the breeding ratio, β. The estimate of β is calculated from the observed chromosomal ρ’s, obtained by InfRec (Lefebvre and Labuda 2008), after their calibration with the average chromosomal recombination rates known from pedigree data. We have tested our approach using coalescent simulations under different input parameters’ values and various demographic scenarios. For the HapMap populations we obtained β of 1.4 in Yoruba from West Africa, 1.2 in European and 1.0 in East Asian samples. This suggests that in the history of modern humans the reproductive variance between men and women did not drastically differ, thus consistent with the prevalence of monogamy or mild polygyny in the human lineage. Known incidences of polygyny may be of recent origin, related to raise of agriculture and shift from hunter-gathering to food producing economies, and therefore not sufficiently common to leave a strong genetic signature in the recombinational record. (Supported by GenomeQuebec/Genome Canada and Canadian Institutes of Health Research).

Accurate inference of individual ancestry geographic coordinates
within Europe using small panels of genetic markers

The study of genomewide datasets of thousands of individuals of European ancestry supports the close correspondence between genetic distances and geographic coordinates within Europe, especially when information from hundreds of thousands of genetic markers is used. In fact, Principal Components Analysis (PCA), summarizing genetic variation over the top two principal components (PCs), results in plots that are surprisingly reminiscent of geographic maps of Europe. We set out to discover those markers that are most closely correlated with geographic origin, seeking to predict individual ancestry at a fine level, and even for closely spaced populations. To this end we analyzed a previously described subset of the Population Reference Sample (POPRES). We focused on 12 populations and 1224 individuals for which geographic coordinates (longitude and latitude) of individual origin are given for at least 20 individuals per population. First, we performed a complete leave-one-out crossvalidation experiment using 447,212 SNPs, and a simple nearest neighbors approach to infer geographic coordinates. This resulted in extremely high accuracy, placing individuals within an average longitudinal error of 2.2 degrees, and an average latitudinal error of 0.88 degrees. Next, we applied an algorithm that we have previously described to select the top 5,000 SNPs that correlate well with population structure as captured by PCA. We then filtered highly correlated SNPs using standard linear algebraic algorithms for the column subset selection problem. We thus selected 500 maximally uncorrelated markers, which have a Pearson correlation coefficient of 0.92 with PC 1, and 0.83 with PC 2. We extensively validated the effectiveness of such SNP panels for genetic ancestry testing by once more performing a complete leave-one-out crossvalidation experiment on the 1224 studied individuals (approx. two weeks of CPU time in commodity hardware). Using 500 carefully selected SNPs we can place individuals within a few hundred kilometers of their reported origin (average longitudinal and latitudinal error of 4.7 and 1.9 degrees respectively). Finally, we crossvalidated our best panel of 500 SNPs on the HapMap CEPH European individuals, placing them accurately on the Northwestern corner of Europe. Not surprisingly, our SNP panel includes markers that are either within genes reported to be under selective pressure in Europeans, or in high LD with such genes.

Genetic relationships among the ancient Chinese populations viewed
from discrete cranial traits

The discrete cranial traits are informative in revealing the genetic relationship of human populations. Given little available knowledge on these traits, especially their underlying genetic determinants, the primary aim of this study is to select a small number of traits that are sufficiently informative to represent genetic differentiation among East Asian populations. We studied overall 51 traits for 1,578 skulls from 19 necropolises, and found that 5 traits could capture the largest variation in East Asian populations studied. They are accessory mandibular foramen, palatine torus, mandibular torus, mastoid foramen extra-sutural, and infraorbital suture. The analysis on these 5 traits resulted in similar population relationships to that using all 51 traits. The study on discrete cranial traits could not only facilitate exploration of the genetic relationship of populations, and could also allow identification of the genes underlying these anthropological traits.

Admixed ancestry and stratification of regional gene pools of Quebec

In Quebec, studies of different molecular polymorphisms have shown that the French Canadian gene pool is as diverse as its source European populations and, contrary to what was previously anticipated, does not display more homogeneity. To better understand the genetic structure of the contemporary population, we analyzed the origins and contribution of 7,798 immigrant founders identified in the genealogical ascendance of a sample of 2,221 subjects representative of the French Canadian population of Quebec. As expected, French founders are the most important in number (n=5,326) in all Quebec regions. They contribute for about 90% of the regional gene pools, except for regions located in the easternmost part of the province (76%), which are characterized by more diverse origins. Although this study supports the French founders’ importance, it also puts in the balance arguments in favor of the heterogeneity of the founding pool. The majority of immigrants landed as single member of their family, originating from all the regions of France. In addition, nearly all subjects have mixed origins, including French and non-French. Taken together, these results put into perspective the idea of the homogeneity of the origins of the French Canadians and of a pan-Quebec founder effect. The differential descent and genetic contribution of immigrant founders across regions points to the stratification of the French Canadian population of Quebec, showing a east-west gradient of diversity. These results will contribute to optimize study design in gene mapping studies relying on the founder effect in the French Canadian population of Quebec.

A nonsynonymous SNP in EDAR is associated with tooth shoveling

Teeth display variations among individuals in the size and the shape of cusps, ridges, grooves, and roots. In addition, there are certain dental characteristics which are predominant in certain human groups, such as tooth shoveling of upper incisors that is major in Asian populations but rare or absent in African and European populations. The common characteristics of dental morphology are thought to be determined mainly by genetic factors. However, genetic polymorphisms associated with dental morphology have not been elucidated yet. In humans, the ectodysplasin A receptor gene (EDAR) as well as the ectodysplasin A gene (EDA) is know to be responsible for hypohidrotic ectodermal dysplasia, a genetic disorder causing abnormal morphogenesis of teeth, hair, and eccrine sweat glands. Human genome diversity data have revealed that the derived allele of a nonsynonymous single nucleotide polymorphism (SNP), rs3827760 that is also called EDAR T1540C, is predominant in East Asian populations but absent in populations of African and European origins. It has recently been reported that the 1540C allele is associated with Asian-specific hair thickness. The aim of this study is to clarify whether the nonsynonymous polymorphism in EDAR is also associated with dental morphology in humans or not. For this purpose, we measured crown diameters and tooth shoveling grades, genotyped EDAR T1540C, and analyzed the correlations between them in Japanese populations. To comprehend individual patterns of dental morphology, we applied a principal component analysis (PCA) to individual-level metric data, the result of which implies that multiple types of factors affect the tooth size. This study clearly demonstrated that the number of the Asian-specific EDAR 1540C allele is strongly correlated with the tooth shoveling grade. The SNP significantly affected PC1 and PC2 in PCA, which denotes overall tooth size and the ratio of mesiodistal diameter to buccolingual diameter, respectively. Our study revealed a main genetic determinant of tooth shoveling that has classically received great attention from dental anthropologists. Further studies using powerful DNA technology will lead to clearer understanding about genetic factors for phenotypic variations in tooth morphology such as Carabelli’s tubercle, the numbers of cusps and roots, and the size balances shown in metric measurements.

Direct estimation of the microsatellite mutation rate

Characterizing the behavior of mutations is fundamental to our understanding of genetic variation. Attempts to directly observe DNA mutations arising from germline transmissions are confronted by two challenges: The large amount of DNA sequence that needs to be collected in order to observe a mutation (since the mutation rate in humans is estimated to be ~2x10-8 per generation), and a poor signal-to-noise ratio, due to the fact that any modern genotyping technology has an error rate far exceeding the mutation rate. Using deCODE Genetics’ database of over 95,000 Icelanders genotyped at over 3,000 microsatellite loci, we directly observed mutations in germline transmissions from pedigrees. Microsatellites are thought to have mutations rates as high as 10-3 per locus per generation. To overcome the genotyping error rate, which was estimated in this data set to be ≤10-2 per allele call after appropriate filtering, we carried out two independent analyses: (1) We restricted our analysis to mother-father-child trios, and required the mutated allele to be genotyped at least twice in both the child and in the transmitting parent to confirm mutant transmissions. This identified 2,124 mutant events from 5.62 million instances of parent-child transmissions, yielding a mutation rate estimate of 3.78x10-4 averaged across the markers that we analyzed. (2)Wetraced the haplotype affected by the mutation through local pedigrees, requiring that the mutant haplotype is observed in the affected proband’s children, and simultaneously, that the wildtype haplotype is observed in the affected proband’s siblings. This identified 788 mutant events from 1.59 million instances of parent-child transmissions, yielding a mutation rate of 4.96x10-4. Our collection of mutant events is significantly larger than previous studies. This allows for categorical analyses of microsatellite mutation rates partitioned based on the gender and age of the individual transmitting the allele, as well as the repeat type and cytogenetic position.

Eastern European ancestry in New Hampshire

There have been a bunch of studies on Hispanic Americans, Native Americans, African Americans, but very little work on European Americans (if we exclude the perennial fascination of the genetics community with Ashkenazi Jews and some studies which included European Americans of known European parentage).

This is one of the first studies I've seen where the objective was to look at a geographically definite population of European Americans and study its diverse origins in Europe itself. While there are many European Americans whose ancestry is no mystery at all (because their ancestors arrived within memory), there are also large numbers of them with much older ancestry, and these should sometime become the object of study, both for their own sake, but also because they may represent a separate evolutionary road of their ancestral European gene pool.

The STRUCTURE result, beautified by CLUMPP, is really fascinating. Unlike most studies where sub-population labels of clustered individuals are put on the chart, in this case individuals do not necessary report a single ancestry, so cannot be put on a single population label. Yet it is really evident that "European Americans from New Hampshire" can be broken down to several groups with a distinctive ancestry.

From the paper:

Bayesian clustering conducted using the structure software revealed distinct subpopulations, with the highest and most reliable probabilities between a K of 5 and 7. The bar plots are shown for K = 2 to K = 8 from the CLUMPP software (aligns multiple runs of structure) from 10 runs at each K (Figure 1a). As expected, individuals in the sample appear highly admixed; however distinct populations are discernible. The FST's increase consistently as K increases, with the average FST's for K = 4 to K = 7 around the level of “little genetic differentiation” as defined by Wright (approx. 0.05) (Figure 1c,d) [22]. The admixture values increase for lower K's, but begin to drop at K = 6 to values between 0.6–0.7 (Table S2). In selecting the most correct K, parsimony is an important consideration, i.e. that the simpler answer tends to be correct. Though there may be some validity to further subdividing the groups, the most statistically consistent and the most parsimonious K based on the structure output is K = 6. Further analysis using the ancestral data is used to describe the groupings and lends support to our selection of K = 6.

...

These results suggest that genetic population structure is detectable in a highly admixed US population and that this structure correlates with self-reported ancestry. To our knowledge, this is the first time such an investigation has uncovered a strong link between structure and ancestry in what would otherwise be assumed to be a homogeneous US state where most individuals are of European ancestry. Our data indicate that that admixture has not eliminated the genetic structure found within Europe, and descendants of the Russian, Polish and Lithuanian immigrants remain genetically distinct from the rest of the population and are closely related to one another.

...

Exploratory analysis revealed that among the ancestries, those reported by at least five individuals were: American Indian (n = 32), Austria (n = 5), Belgium (n = 5), Canadian Indian (n = 14), Canada (n = 113), Czech Republic (n = 5), England (n = 355), Finland (n = 7), French-Canadian (n = 54), France (n = 173), Germanic (countries where Germanic languages spoken) (n = 5), Germany (n = 110), Greece (n = 9), Ireland (n = 218), Italy (n = 41), Jewish (n = 6), Lithuania (n = 12), Canadian Maritime Provinces (n = 6), Netherlands (n = 25), Poland (n = 44), Russia (n = 13), Scotland (n = 157), Sweden (n = 24), Switzerland (n = 7), UK (n = 11), US (n = 42), Wales (n = 24).

PLoS ONE doi:10.1371/journal.pone.0006928

Genetic Population Structure Analysis in New Hampshire Reveals Eastern European Ancestry


Chantel D. Sloan et al.

Abstract

Genetic structure due to ancestry has been well documented among many divergent human populations. However, the ability to associate ancestry with genetic substructure without using supervised clustering has not been explored in more presumably homogeneous and admixed US populations. The goal of this study was to determine if genetic structure could be detected in a United States population from a single state where the individuals have mixed European ancestry. Using Bayesian clustering with a set of 960 single nucleotide polymorphisms (SNPs) we found evidence of population stratification in 864 individuals from New Hampshire that can be used to differentiate the population into six distinct genetic subgroups. We then correlated self-reported ancestry of the individuals with the Bayesian clustering results. Finnish and Russian/Polish/Lithuanian ancestries were most notably found to be associated with genetic substructure. The ancestral results were further explained and substantiated using New Hampshire census data from 1870 to 1930 when the largest waves of European immigrants came to the area. We also discerned distinct patterns of linkage disequilibrium (LD) between the genetic groups in the growth hormone receptor gene (GHR). To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population.

Link

ASHG 2009 abstracts

It's that time of year again. Here is a list of abstracts from ASHG 2009 that caught my attention in three broad areas. It will be very interesting to see these when they become full papers, but if you are one of the lucky ones that goes to Hawaii this October and want to drop me a line about any of them, feel free to do so!

Population Genetics

Haplogroup H of mitochondrial DNA, a far echo of the West in the heart of Central Asia

Through the millennia, Inner Asia played a pivotal role in shaping the history that greatly added to the cultural, ethnic, and genetic diversity observed throughout present Eurasia. Perhaps the two most significant phenomena witnessed in this part of the world were the ambitious expansion strategy employed by Mongolia’s most prominent personality, Genghis Khan and the complex network known as the Silk Road that for nearly 3,000 years contributed to the exchange of goods and the transmission of philosophy, art, and science that laid the foundation for the great civilizations of China, India, Egypt, Persia, Arabia, and Rome, and in several respects to the modern world. Over the last few years, through an international collaborative effort, researchers at the Sorenson Molecular Genealogy Foundation were able to collect 2,727 DNA samples, informed consents, and genealogical data in Mongolia, Kyrgyzstan, and Kazakhstan. All the samples were sequenced for the three hypervariable segments of the mitochondrial DNA (mtDNA) control region to assess the genetic composition of the modern population of these countries. We identified ~600 different haplotypes that could be ascribed to more than 30 haplogroups and sub-haplogroups. As expected, most haplogroups are typical of modern East Asian populations, but intriguingly, many different Western Eurasian clades were also identified, with a particular high incidence of H (~8.0%), the most common haplogroup in Europe. This feature cannot be attributed to genetic drift since different H sub-lineages have also been identified, each of them represented by several different haplotypes. The mtDNA distribution profile in the heart of Central Asia suggests a direct link between this area and Western Eurasia that could be explained by ancient migrations or by more recent historical events, such as Genghis Khan’s conquering efforts and trade or cultural exchanges along the Silk Route. To discriminate between these two possible scenarios, we are now analyzing a subset of these samples at the highest possible level of resolution - that of complete mtDNA sequences - focusing particularly on those H mtDNAs that seem to be the most informative considering their control-region haplotypes. Our preliminary data seems to be in favor of rather ancient genetic inputs from the West in shaping the peculiar mtDNA gene pool of Inner Asia’s present-day populations.

The following study seems to do precisely what I recently asked for:

However, as the PCA analysis shows, Ashkenazi Jews are distinct from both Europeans and non-Jewish Middle Eastern populations and cannot be viewed as a simple mix of the two; their distinctiveness must be -in part- due to the specific features of the small founder population of that community after it became effectively reproductively semi-isolated from gentiles after Roman times. It would be interesting to see different Jewish communities studied in the context of a broad variety of European and Middle Eastern populations, to determine whether Ashkenazi distinctiveness is specifically Ashkenazi or more generally Jewish distinctiveness; I would bet on a combination of the two.

Abraham's children in the genome era: Major Jewish Diaspora populations comprise distinct genetic clusters with shared Middle Eastern ancestry

Despite residence all over the world, Jewish populations have maintained continuous genetic, cultural, and religious tradition over 4,000 years. The unique ethnic makeup and social practices provide an invaluable opportunity to understand their genetic origins and migrations and to elucidate the genetic basis of complex disorders. To generate a comprehensive HapMap of ethnically diverse, healthy Jewish populations, we used the Affymetrix array 6.0 to genotype 381 samples recruited from 7 Jewish communities with different geographic origins: Eastern European Ashkenazim; Italian, Greek and Turkish Sephardim; Iranian, Iraqi, and Syrian Mizrahim (Middle Easterners). Here, we present population structure results from compiled datasets after merging with the Human Genome Diversity Project and the Population Reference Sample studies, which consisted of 146 non-Jewish Middle Easterners (Druze, Bedouin and Palestinian), 30 northern Africans (Mozabite from Algeria), 1547 Europeans, and 653 individuals from other African, Asian, Latin American, and Oceanian populations. Both principal component analyses and multi-dimensional scaling analysis of pairwise Fst distance show that Jewish populations form a cluster clearly distinct from all major continental populations. The results also reveal a finer population substructure in which each of 7 Jewish populations studied here form distinctive clusters - in each instance within group Fst was smaller than between group, although some groups (Iranian, Iraqi) demonstrated greater within group diversity and even sub-clusters, based on village of origin. By pairwise Fst analysis, the Jewish groups are closest to Southern Europeans (i.e. Tuscan Italians) and to Druze, Bedouins, Palestinians. Interestingly, the distance to the closest Southern European population follows the order from proximal to distal: Ashkenazi, Sephardic, Syrian, Iraqi, and Iranian, which reflects historical admixture with local communities. STRUCTURE results show that the Jewish Diaspora groups all demonstrated Middle Eastern ancestry, but varied significantly in the extent of European admixture. There is almost no European ancestry in Iranian and Iraqi Jews, whereas Syrian, Sephardic, and Ashkenazi Jews have European admixture ranging from 30%~60%. Analysis of identity-by-descent provides further insight on recent and distinct history of such populations. These results demonstrate the shared and distinctive genetic heritage of Jewish Diaspora groups.

So, it seems that there will soon be real genomic data on the source and extent of admixture in Jews. The absence of Greek and Anatolian samples may be problematic in finding the sources of such admixture, but the presence of Tuscans, who are reasonably close to them in a pan-European context should do well to serve as a substitute. In a recent sutdy (in which Anatolians were not included), the closest populations to Ashkenazi Jews were Italians of mostly southern provenance (Fst=0.0040) and Greeks (Fst=0.0042) and fairly close to Tuscans (Fst=0.0066)

The following study seems to demonstrate my recent suggestion of archaic admixture in Africa itself:

It does not, however, tell us that this is because of archaic introgression in Europeans. The culprit could equally well be long-term population structure in Africa, i.e., the presence of "modern" and "archaic" populations in Africa itself.

Deep population structure in sub-Saharan African populations

We analyzed ~500 Kb of resequencing data from 91 different intergenic regions in samples from three sub-Saharan African populations: Mandenka from Senegal, Biaka pygmies from the Central African Republic and San from Namibia. We employed novel methodology to estimate the split times and migration rates between populations. We found strong evidence for split times that predate the exodus of modern humans out of Africa (e.g., > 100 Kya). In addition, we also found evidence of ancient admixture (with unknown ‘archaic’ human groups) in the recent history of both the Biaka and the San.

Analysis of Genomic Admixture in Costa Rica Population

Costa Rica (CR) population is a unique population representing a typical admixture of major continental ancestral populations. 1,301 samples collected from participants in a population-based study conducted in the Guanacaste region of CR were genotyped on a custom Illumina iSelect chip harboring 27,635 SNPs. The SNPs on the chip were selected based on multi-ethnic tagging strategy for three HapMap populations: CEU, YRI and JPT+CHB and cover 1,000 candidate genes/regions for a range of cancers. This data set was sufficiently large for the investigation of population substructure in our CR study and the examination of linkage disequilibrium (LD) patterns. Three HapMap major continental populations and a Native American population from the Illumina iControl DB were used as the reference populations for these analyses. Our preliminary results indicate that the Guanacaste CR population was formed mainly by a three-way admixture with 42.5%, 38.3% and 15.2% Native Indian, European, and African respectively. In addition, 4.0% residual genetic component derived from Asians was observed in our CR samples. Both model based STRUCTURE program and Principal Component Analysis (PCA) revealed consistent substructure pattern for the CR population. The magnitude of LD in the CR population seems to be smaller than all the reference populations except YRI. A more detailed knowledge of the underlying genetic structure of the CR population would be informative to assess its population genetic history and to assist in the interpretation of investigations of complex diseases in the CR or a comparably admixed population.

Analysis of Genetic Substructure of Han Chinese Using Genome-Wide SNP Arrays: Implication for Association Studies.

China will start this year a $30 million effort of genome-wide association studies (GWAS) of common diseases in Chinese populations which have been largely underrepresented in the similar effort worldwide. A general concern is population stratification (ancestry differences) among subpopulations which can cause false positive associations. Han Chinese is the largest ethnic group in the world, however, its population substructures are often expected and yet well characterized. In this study, we examined population substructures in a diverse set of >1,700 Han Chinese samples collected from 26 regions, each genotyped with at least 160K single nucleotide polymorphisms (SNPs). Our results showed that: (a) Han Chinese population is complicatedly substructured, with the main observed clusters roughly corresponding to northern Han, central Han and southern Han; (b) Han Chinese samples collected from large cities, such as Shanghai, Beijing and Guangzhou, show diverse source of ancestries including three aforementioned clusters; (c) HapMap samples (CHB & CHD) and HGDP samples (Han & Han-NChina) deliver a limited representation of Han Chinese people. Building on the above insights, we investigated false positive rates and statistical power in various study designs using both empirical and simulated data. We further explored sample collection strategies and public data usage for future association studies.

It will be interesting to see if the authors of the following study estimated gene flow in non-southern European populations as controls, to see what is the excess of Sub-Saharan admixture detected in the three southern European samples, and exactly what "methods that can infer admixture proportions in the absence of accurate ancestral populations" they used. Hopefully they will also extend their linkage disequilibrium analysis for the other populations besides Spaniards.

Characterizing the history of sub-Saharan African gene flow into southern Europe

Recent analyses of whole-genomeSNP data sets have suggested a history of sub-Saharan African ancestral contribution into southern Europe but not in northern Europe, consistent with previous analyses based on the Ychromosome and mitochondrial DNA. However, there has been no characterization of the proportion of African admixture in southern Europe, or of its date. Here we analyze data from ~450,000 autosomal SNPs in the Population Reference Sample, ~650,000 SNPs from the Human Genome Diversity Panel, and ~1.5 million SNPs from the HapMap Phase 3 Project, and studied patterns of correlation in allele frequencies across populations to confirm the evidence of African ancestry in many southern European populations but not in northern Europeans. Using methods that can infer admixture proportions in the absence of accurate ancestral populations, we estimated that the proportion of sub-Saharan African ancestry in Spain is 2.4 +/- 0.3%, in Tuscany 1.5 +/- 0.3%, and in Greece 1.9 +/- 0.7% (1 standard error). We also studied the decay of admixture linkage disequilibrium with genetic distance, which provided a preliminary estimate of the date of African gene flow into Spain of roughly 60 generations ago, or about 1,700 years ago assuming 28 years per generation. This date is consistent with the historically known movement of individuals of North African ancestry into Spain, although it is possible that this estimate also reflects a wider range of mixture times.

Genome-wide patterns of population structure and admixture among Hispanic/Latino populations

In order to document genome-wide patterns of variation in Hispanics/ Latinos (HL’s) we genotyped individuals from five distinct populations recruited in the US: Mexico, Colombia, Ecuador, Dominican Republic and Puerto Rico. We present population structure results from an extensive genome-wide SNP dataset compiled by merging Affymetrix 500K and Illumina 650K data from these populations together with the Human Genome Diversity Panel, HapMap, Mao et al (2005), and POPRES studies. We apply Principal Component Analysis (PCA) and a clustering method, frappe, to infer admixture and genetic relationships of 262 HL individuals with 467 Africans, 715 Europeans, and 210 Native Americans comprising a total of 88 populations. We observe substructure within Native Americans, and, as expected, find that the admixed HL populations show Native American ancestry derived from local Native American populations. We find striking differences in estimated population-wide mean African, European and Native American ancestry proportions which are consistent with historical admixture and proximity to slave trade routes. The Dominican Republic and Puerto Rico, located on islands along slave trade routes, show high levels of African Ancestry (means 41.7% and 23.6% respectively) with less Native American Ancestry (11.5% and 18.9%). Colombians show a wide range of both African and Native American ancestry, though they have an overall mean of slightly higher Native American ancestry (36.3%) and lower African ancestry (11.7%) than the highly-African Dominicans and Puerto Ricans. Ecuadorians show the highest Native American mean ancestry (54.0%) with low estimated mean African Ancestry (7.3%). Mexico shows the largest range of Native American ancestry (11.0% - 79.0%) with an overall mean of 50.1% Native American ancestry and the lowest African ancestry (5.6%). Our study shows a broad range in admixture proportions across different HL individuals as well as different admixture patterns across populations. We also compare this genotype data with mtDNA and Y chromosome genotypes and use simulations to estimate ancient male and female sex ratios in each HL population. Lastly, we discuss implications of population structure for genome-wide association studies in admixed populations such as HL’s, especially when recruited in the United States.

A new statistical method to infer population admixture events using genetic variation data

We present a novel statistical method that uses densely-spaced Single- Nucleotide-Polymorphism (SNP) data to identify the major admixture events occurring throughout a population’s history. The model has several advantages over leading available analytical approaches in this area, such as principal-components-analysis and STRUCTURE. In particular it can simultaneously (i) take advantage of the information inherent in patterns of linkage disequilibrium, i.e. non-random associations amongst neighbouring SNPs along a chromosome, (ii) efficiently analyse hundreds of individuals at hundreds of thousands of SNPs genome-wide, and (iii) allow for relatively straight-forward interpretation and direct inference of key historical parameters, such as the proportions and times of major admixture events. Using simulated data matched to currently available human datasets, we show that our model can identify and accurately date admixture events that have occurred between 7 and 150 generations ago. As our technique exploits the rich information in genetic data to infer details of a population’s admixture history, it marks a powerful complement to anthropological research and can help to resolve a number of existing controversies. We present results from applications of our model to two datasets: (1) SNP data from 22 distinct genetic regions for individuals from three chimpanzee populations in Africa; (2) genome-wide 650K SNP data for individuals from 53 world-wide populations of the Human Genome Diversity Panel (Science 319, 1100-1104). We highlight a number of intriguing new insights from these analyses. For example, the chimpanzee analysis showcases the model’s ability to infer the relative divergence among populations. The human analysis identifies several important admixture events, some of which are historically wellestablished (e.g. identification of recent European genetic influx into the Maya Native American population), others that can be placed into a clear historical context (e.g. an East Asian genetic influx into several Central and South Asian populations dated precisely to the era of the Mongol empire), and some that are to our knowledge novel (e.g. admixture in the Cambodian population between a Central/South Asian source and an East Asian source dated to around the period of the Cambodian Empire).

Bayesian methods of estimating ancestry using whole-genome SNP data

Estimation of the genetic ancestry of an individual is useful for association studies, disease risk prediction, population genetic analyses and is of inherent interest for the individual themselves. We have investigated methods of estimating ancestry using whole-genome SNP data on each individual. We focus on the scenario where the goal is to determine ancestry in relation to a set of genotype or haplotype data that is available from a set of distinct source populations, for example, the HapMap 2, HapMap 3 or 1000 Genomes datasets. Inference in this setting can focus either on the estimation of global ancestry, in which an overall estimate of the proportion of ancestry from the source populations is needed, or local ancestry, which aims to partition an individual genome into distinct segments of ancestry from the source populations. We have compared 2 models based on the estimated allele frequencies in the source populations at a set of unlinked SNPs. Model 1 only models global admixture, whereas Model 2 models both global and local admixture. Using simulated individuals with differing proportions of CEU and YRI admixture (based on HapMap3 data) we find that there is a relatively small difference in the mean square error of the estimates of global admixture from the 2 methods (1.16 10-4 and 8.88 10- 5 respectively). Since Model 1 is much faster to fit that Model 2 these results suggest that Model 1 can be used to estimate the level of global ancestry, or at the very least will be useful as an initial estimate for use in Model 2. Further investigation is required to see how these results hold for more genetically similar source populations. In contrast, the mean square error for the estimates of local admixture from the 2 methods is 0.298 and 0.0861 respectively, suggesting that an explicit model of local ancestry is needed to carry out this level of inference. We are also investigating the utility and practicality of using linked SNP data to estimate global and local admixture.

A detailed phylogeography of mtDNA haplogroup C1d: another piece in the Native American puzzle

Recent studies based on complete mitochondrial DNA (mtDNA) sequences revealed that two almost concomitant paths of migration from Beringia led to the dispersal of the first Americans (Paleo-Indians) approximately 15-17 thousand years ago (kya). This first expansion was followed by later more restricted diffusion events from the same dynamically changing Beringian source. Thus, five pan-American (A2, B2, C1, D1, and D4h3a) and four geographically confined (D2, D3, X2a, and C4c) mtDNA haplogroups represent the current female legacy of the ancient migratory events that gave rise to the native populations of the double continent. Regarding haplogroup C1, all its members appear to belong to one of three branches: C1b (characterized by the control-region transition at np 493), C1c, and C1d (with the control-region transition at np 16051). These three sub-haplogroups are found throughout the Americas, thus supporting the scenario that they most likely differentiated at the early stages of the Paleo-Indian southward migration. If considered as three separate founders, C1b, C1c, and C1d would bring the currently known number of native pan-American lineages to seven. As a whole, the C1 haplogroup has an estimated age of 17.0- 19.6 ky, while the three individual branches are dated 16.5-17.0 ky, 17.2- 17.6 ky, and 7.6-9.7 ky, respectively. The extremely young age estimate of C1d has been attributed, at least for the moment, to a major underrepresentation of C1d mtDNAs (only nine complete sequences published to date) in the current Native American mtDNA phylogeny. We have addressed this issue in the current study by completely sequencing more than 60 novel mtDNAs belonging to haplogroup C1d, which were carefully selected on the basis of both control-region variation and geographic/ethnic origin. Phylogeographic analyses have provided not only an accurate evaluation of the expansion time of C1d in the Americas, but also a detailed picture of its current distribution in both general mixed and indigenous populations.

Genetic diversity of European population isolates in the context of their geographic neighbors

Mapping traits in population isolates provides an opportunity to simplify the challenges of complex trait mapping because such populations likely have enhanced levels of linkage disequilibrium and reduced genetic heterogeneity for the underlying traits. Here we analyze high-throughput SNP genotyping data to compare genomic-scale patterns of variation in several European population isolates (Adygei, Basque, Orcadian, Roma from Slovakia, Sardinians, and Sorbs) and contrast their patterns of variation to geographical proximal populations. Our results reveal insights for the demographic history of each of these unique populations, suggest substantial variation among these population isolates in patterns of diversity, and highlight the importance of population selection in genome-wide association mapping.

Incompatibility of current Finnish mitochondrial diversity with simulations of assumed settlement history

Traditionally, geneticists studying Finnish population history have assumed a model where Northern and Eastern Finland were mostly uninhabited until the 16th Century A.D. and were then settled by small family groups from South-Western Finland. The reduced genetic diversity and the distinct Finnish disease heritage are seen as consequences of these founder effects. Y-chromosomal diversity is indeed reduced in the present population, especially in the eastern parts of the country. However, mitochondrial diversity is not heavily reduced compared to South-Western Finnish or other European populations. This discrepancy has been explained with the higher mitochondrial mutation rate having restored mitochondrial diversity in these populations since the founder effects.

In our view it seems unlikely that even with high mitochondrial mutation rates mtDNA diversity could be restored over a mere 17 generations after the alleged tight bottlenecks. Archaeological evidence also suggests a different settlement history, e.g. settlement beginning in South-Eastern instead of South-Western Finland.

In this study we use simuPOP, a state-of-the-art forward simulation tool, to simulate datasets corresponding to Finnish mitochondrial diversity under the traditional model and compare them with actual present-day Finnish data. We show that current mitochondrial variation is unlikely under this model, increasing the credibility of alternative hypotheses.

On the borderline between the east and the west: the maternal genetic background of Karelians

Introduction: The frontier between Finland and Russia represents one of the most conspicuous socioeconomic gaps in the world. Based on the mean gross national product, there is a ten-fold difference between Russian Karelian Republic and Finnish Karelia. Otherwise these populations share the same geophysical environment. For these reasons, Karelia has been a very interesting field of research for multifactorial disease studies. However, this area has undergone many demographic incidents, such as wars and famine, which may cause local differences in the gene pool. In this study, we wanted to elucidate the maternal genetic background of Karelians. Materials: Blood samples were collected from healthy unrelated individuals without known foreign background from four Karelian districts; Aunus(n=218), Viena(n= 87), Tver(n=61) and Finnish Karelia (n=70), The sample collection was performed according to the Basic Principles of the Declaration of Helsinki. Methods: The entire mitochondrial DNA was sequenced in 32 reactions per sample with the BigDye® Terminator v3.1 Cycle Sequencing Kit in the Applied Biosystem’s 3730 Genetic Analyzer sequencing machine. Sequence alignments were made by the SeqScape® Software, Version 2.5 (Applied Biosystem). Results: Haplogroup H was very common in all populations. However, H1a is almost absent in Finnish Karelia. Also U and its subhaplogroups were common. Specially U5b1b1 reached over 16% in Viena Karelians. U4 was most common among Tver Karelians. Conclusions: The maternal genetic background seem to be complex in this area. There is clear regional differences. Also there is solid evidence of gene flow from various sources. Representation of the clearly Asian haplogroups is strikingly low.

Genetic Landscape of Eurasia Viewed from Large Allele Frequency Differences.

The diversification leading to modern human populations in Eurasia is one of the most important topics in the study of human expansions after leaving Africa. Most studies of Eurasia populations have used either limited markers or involved insufficient population coverage. We chose 68 markers based on large allele frequency differences among a few Eurasian populations and then typed them on 1766 individuals from 34 populations representing all subdivisions of Eurasia. Analyses using the STRUCTURE program showed a clinal east-west division when K=2, with a median border dividing Central Asia along the Ob River, the Kazakh highland, the western side of Pamir Mountains, and the southwestern side of the Himalayas. We fit curves to the STRUCTURE loadings using distances of the population coordinates from the median border. The genetic structure changed dramatically only within 2000km on each side of the border. At higher values of K the western populations of East Asia are the first to be distinguished (at K=3): Mongols, Tibetans, Qiang, and Baima, are most distinct from the more eastern populations. At K=4 Southwest and South Asians are distinguished from the Europeans; At K=5 Southeast Asians and at K=6 Central Asians are successively distinguished from eastern East Asians. Several more isolated populations such as Samaritans, Atayals, or Micronesians were distinguished in different independent runs when K=7 providing no clear anthropological information. South Asians were always clustered with Southwest Asians with pronounced similarity to Central Asians. The failure to distinguish South Asians maybe due to the selection of the markers with large allele frequency differences specifically between Europeans and East Asians. We also tested for statistical differences in the allele frequencies for all pairs of clusters when K=6. The results showed significant borders (P less than 0.0001) including those between western East Asians and eastern East Asians or Central Asians; however, insignificant borders were observed between Southwest Asians and Southeast Asians or western East Asians, neither was between Central Asians and eastern East Asians. This indicates substantial gene flow in North Asia between eastern East Asians and Central Asians, and in South Asia between South Asians and Southeast Asians. Using increased population and marker coverage, this study helps to understand the details of genetic diversity and landscape of Eurasians.

Anthropometry

Dairy intake associates with the IGF2 rs680 polymorphism to height variation in Greek children. The GENDAI study

Objective: Height is a classic polygenic trait with a number of genes underlyingits variation. We evaluated the prospect of gene to diet interactions ina children cohort for the IGF2 rs680 polymorphism and height variation.Methods: We screened 795 peri-adolescent children (424 females) aged10-11 years old from the (Gene and Diet Attica Investigation; GENDAI)paediatric cohort for the IGF2 rs680 polymorphism. Results: Children homozygousfor common allele (GG) were taller (148.9 ± 7.9 cm) comparing tothose with the A allele (148.1 ± 7.9 cm), after adjusting for age, sex, anddairy intake (β±SE: 2.1± 0.95, p=0.026). A trend for interaction for theIgfrs680xdairy intake is also revealed (p=0.09). Stratification by IGF2 rs680genotype revealed a positive association between dairy products intakeand height only in A allele carriers, adjusted for the same confounders(standardized β=0.111, p=0.014). When dairy intake was classified, basedon the median value, into two equal groups of low (1.9 ± 0.7 servings/day)and high dairy products intake (4.4 ± 1.5 servings/day), it was found thatin A allele children high dairy eaters were significantly taller (p=0.05) comparedwith low dairy eaters (148.8 ± 7.9 cm vs 147.4 ± 7.7 cm respectively,adjusted for age and sex). Conclusion: A higher consumption of dairy productsassociated with increased height depending on the rs680 IGF2 genotype.Thus, exploring height variants and elucidating possible interactionswith environmental factors like diet could help us to design

A Non-synonymous HNF4A Variant is Associated with Glycemia During Pregnancy and Offspring Head Circumference in Populations of European Ancestry in the HAPO Study

The Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study is a multicenter, international study, which examined the association of maternal glucose levels with fetal growth and outcome in 25,000 pregnant women from multiple ethnic groups to demonstrate a continuous relationship between maternal glucose measures and birth size throughout the range of glucose concentrations. We hypothesize genetic factors contribute to these phenotypes, and examined 1536 fetal and maternal SNPs in 79 candidate loci previously implicated in insulin secretion or sensitivity to determine associations with maternal glycemia and insulin secretion (fasting glucose and Cpeptide and 1-hr glucose from the OGTT) at ~28 weeks gestation and/or offspring size at birth (birth weight, length, head circumference, and sum of skinfolds) for HAPO mothers of European (Belfast and Manchester, UK, and Brisbane and Newcastle, Australia; N=3828) and Asian (Bangkok, Thailand; N=1813) ancestry and their offspring. Associations were assessed through linear regressions with the single trait/outcome under an additive genetic model adjusting for known confounders. Among our strongest signals was rs1800961G>A, which encodes a Thr>Ile amino acid change in exon 4 of HNF4A, recently identified in a GWAS meta-analysis as a variant associated with decreased HDL levels. In the HAPO study, this SNP was strongly associated with increased fetal head circumference (0.5cm [95%CI: 0.3-0.7] per maternal minor allele; P=1.2x10-7) in those of European descent. The maternal minor allele was also weakly associated with 1-hour glucose (4.3mg/dL [95%CI: 0.5-7.9]; P=0.03), birth length (0.7cm [95%CI: 0.2-1.1]; P=0.003), birth weight (52.6g [95%CI: -8.0-113.3]; P=0.09), and sum of skinfolds (0.3cm [95%CI: -0.1-0.6]; P=0.13). This same minor allele in the fetal genome was weakly associated with cord C-peptide (0.1ug/dL [95%CI: 0.01-0.22]; P=0.03), and head circumference (0.2cm [95%CI: -0.1-0.4]; P= 0.08). The same trends were observed among the Thai, although not significantly probably due to a reduction in power from the low risk allele frequency (<2%).>

Selection

In a recent study, Heyer used germline mutation rates to estimate time depth, so I am more inclined to take her dates at face value than in papers which used "evolutionary" rates. It will be interesting to see which Y-chromosome types the authors associates with the both the older and recent expansions.

Super Y-chromosomes in Eurasia and the impact of social selection and Neolithic transition

Some Y-chromosomal haplotypes have been found at unusually high frequenciesin Asian and European human populations. The massive spreadof these lineages has been explained by the impact of social selection i.e.the high reproductive success of some males and their relative/descendantsdue to their high social status. The most well-known examples are the “Khanhaplotype” and the “Manchou haplotype” in Asia, and the U’Neill haplotypein Ireland. But are these frequent haplotypes always associated with recentevents of social selection, or could they be linked to much older processes?To address this question, we have surveyed ~ 3500 males in 97 populationsfrom Turkey to Japan. We have focused on the 12 most frequently representedhaplotypes in Eurasia and tested whether their expansions are linkedto a specific factor such as language or subsistence methods. Our resultsshow that both recent and ancient processes are responsible for the expansionsof these lineages. The recent expansions (2000-3000 years) likely tobe linked to social selection are prevalent in Altaic-speaking and pastoralpopulations. This might indicate a recent cultural change in the social organizationof these populations. The ancient expansions (8000-10000 years)are over-represented in Indo-European speaking and sedentary farmer populations,and are likely to be the result of the Neolithic transition.

Lactase Persistence; Multiple causal mutations in sub-Saharan pastoralists

Background Milk is the primary source of nutrition for newborn mammals, including humans. The majority of human adults, estimated at approximately 65%, are unable to digest lactose (the main carbohydrate in milk) effectively since lactase expression is down-regulated after weaning, as it is in other mammals. In some humans however, lactase expression persists into adulthood (lactase persistence, LP) allowing adult consumption of milk from other species, and the frequencies of this trait vary throughout the world. A C-T SNP -13910 bases upstream from the lactase gene (LCT) is associated with LP in Europe. The -13910*T is rare in milk drinking groups in Africa although two other variants (-13915*G, -14010*C) have been shown previously to be significantly associated with LP and in an accompanying abstract (Ingram et al) we confirm a third locus (-13907*G) and present a fourth candidate SNP. However some LP individuals have also been identified who carry none of these alleles. Aims To examine the distribution across Africa of these and other allelic variants; to examine other regulatory regions in population groups in which enhancer alleles are lacking. Results The geographic and ethnic distribution of -13907*G, -13910*T, -13915*G, -14009*G, and -14010*C in 10 different countries and 15 distinct ethnic groups across Africa (n=1221 individuals) is presented here. Several other variants in this enhancer region are also described here for the first time. These tightly clustered enhancer variants are more frequent in pastoralist milk drinking groups than agriculturalist populations and are associated with several different LCT core haplotypes. Two further candidate regulatory regions have been sequenced in the same populations including a 1000bp region immediately upstream from LCT where novel variants have been found. Conclusions The data support the notion that many different mutations do have a functional role in LP, and that the trait has arisen independently several times, being subject to the positive selection conferred by the increased ability to digest milk lactose by people in pastoralist societies.

Extreme Evolutionary Disparities Seen in Positive Selection Across Seven Complex Diseases

Genome-wide association studies (GWASs) have successfully illuminated disease-associated variation. But whether human evolution is heading towards or away from disease susceptibility remains an open question. We analyzed the seven diseases studied by the Wellcome Trust Control Case Consortium (WTCCC), to calculate the relative selective pressure at every significant loci. Results reveal striking differences between the seven studied diseases. We find evidence of recent positive selection in favor of alleles increasing the risk of Type 1 Diabetes (T1D), Crohn’s Disease (CD), Hypertension (HT), Rheumatoid Arthritis (RA), and Bipolar Disorder (BD). Riskassociated alleles (defined as the allele most strongly associated with disease among associated SNPs) for Type 2 Diabetes (T2D) fall largely within the random neutral region, and Coronary Artery Disease (CAD) shows less positive selection than expected by random. When only protective alleles are considered (defined as the allele least strongly associated with disease among associated SNPs), we find that SNPs only associated with T1D, CD, and RA appear to exhibit significant signatures of positive selection. There is significant asymmetry in the 96 SNPs strongly associated with T1D (pvalue ≤0.005) showing strong signs of positive selection, with 79 SNPs selecting for the risky allele, and only 17 SNPs selecting for the protective allele. Furthermore, selection patterns of Coronary Artery Disease (CAD) fall far below the expected levels of random, implying stable allele frequencies. Results reveal the evolutionary trajectories of T1D and CD favor risk alleles, possibly due to their simultaneous role in protection from infectious diseases. These results inform on current understanding of disease etiology, thus aiding efforts to discover novel approaches to disease treatment and prevention.

Detecting Natural Selection in the Human Genome from Pilot1 Data in the 1000 Genomes Project

Identifying signatures of natural selection in the human genome is of fundamental implication for the study of population evolution and for the biomedical research. The distribution of selection in genome will provide important functional information. Natural selection modify the level of variability within and between populations and shapes the pattern of genetic variations in the genome. Genetic variation in genome is the raw data for detection of natural selection. The 1000 Genomes Project produces whole genome sequencing data and offers a unique and great opportunity to scan the genome for signature of natural selection. Five statistics: Tajima’D, Fu and Li’s F, Achaz’s Y, Fay and Wu’s H and Zeng et al.’s E (based on comparing the site frequency spectrum within population) and Fst statistic (based on the measure of population subdivision) were applied to Pilot 1 data in 1,000 genome project to scan the entire genome for detection of selection, where 344 chromosomes from ASI, CEU and YRI were sequenced. A total of more than 20 million of variant sites, 4.8 millions common in three populations were identified. We calculated seven statistics in 10 kb and 100 kb windows across the genome for each population and obtained their empirical distributions. Results show that two kinds of windows analyses lead to the similar distributions. The proportional rank of the test statistic in a particular window compared with the overall empirical genomic distribution was taken as empirical P-value for that window. We identified 3,046 candidate selection regions in ASI population, 2,015 selection regions in CEU, and 2,204 selection regions in YRI at 5% empirical significance level in 10 kb by five statistics based on differences in frequency spectrum. Among 457 candidate genes of selection reported from PubMed, we detected 102 selection genes in ASI, 53 selection genes in CEU, and 101 selection genes in YRI and 11 selection genes common in three populations by familiar Tajima D test. By comparison we obtained 3.9 million SNPs and the whole genome’s fixation index about 0.10~0.11. By compared with the empirical genome-wide distribution of FST, we identified 5, 278 candidate selection regions at an empirical significance level of 2.5% from each of the 22 autosomal chromosomes. Among 581 identified selection regions by FST which were reported from literatures, we found that 294 selection regions overlap our results.

Genomic Landscape of Positive Natural Selection in North European Populations

Analysing genetic variation of human populations to detect loci that have been affected by positive natural selection is important for understanding adaptive history and phenotypic variation in humans. In this study, we analysed recent positive selection in Northern Europe from genome-wide datasets of 250 000 and 500 000 single nucleotide polymorphisms in a total of over 1000 individuals from Great Britain, Northern Germany, Eastern and Western Finland, and Sweden. Coalescent simulations were used to demonstrate that the integrated haplotype score (iHS) and long-range haplotype (LRH) statistics have sufficient power in genome-wide datasets of different sample sizes and SNP densities. Furthermore, the behavior of the FST statistic in closely related populations was characterized by allele frequency simulations. In the analysis of the North European dataset, dozens of regions in the genome showed strong signs of recent positive selection. Most of these regions have not been discovered in previous scans, and many contain genes with interesting functions (e.g. RAB38, INFG, NOS1AP, and APOE). In the putatively selected regions, we observed a statistically significant overrepresentation of genetic association to complex disease, which emphasizes the importance of the analysis of positive selection in understanding the evolution of human disease. Altogether, this study demonstrates the potential of genome-wide datasets to discover loci that lie behind evolutionary adaptation in different human populations.

Evidence of Indigenous American specific selection in skin pigmentation genes

Recent studies of selection in human pigmentation genes have focused on Old World populations, neglecting the evolutionary changes that have occurred in Indigenous American populations since their migration into the Americas. Previous research shows correlations between Indigenous American ancestry and skin pigmentation variation, suggesting a genetic role in the determination of skin pigmentation among these populations. However, few genes contributing to these differences have been described. To identify genes that may have undergone Indigenous American specific changes, this work examines signatures of selection in 82 pigmentation candidate genes by genotyping 88 indigenous individuals from Central and South America using the Affymetrix Genomewide Human SNP Array 6.0. The resulting 906,600 single nucleotide polymorphisms (SNPs) were surveyed for signatures of selection in the Indigenous American populations compared to the HapMap Phase I populations. Evidence of selection was identified using four measures selected for the complementarity of their approaches, including the reduction in heterozygosity (lnRH), Locus-Specific Branch Length (LSBL), Tajima’s D, and by examination of the haplotype block structure. When computing lnRH and LSBL as well as when examining changes in haplotype frequency, the East Asian and European HapMap populations were included because they are the most closely related populations available. These analyses differentiate the selective changes that appear to be shared among East Asian and Indigenous American populations from those that are unique to the Indigenous American populations. For each test, the top5%of the empirical distribution of results was examined and pigmentation genes falling in this tail of the distribution were considered to show statistically significant evidence of selection. Based on these analyses, 12 genes - ADAM17, POMC, AP3B1,OPRM1, SILV, OCA2/HERC, PLDN, MYO5A, RAB27A, CYP1A2, ATRN, and ASIP - show evidence of selection unique to the Indigenous American populations. Many of these genes have known functional roles in melanogenesis and suggest potential pathways responsible for the observed differences in skin pigmentation between Indigenous American and Old World populations.

Patterns of correlation between genetic ancestry and facial features suggest selection on females is driving differentiation.

Human facial features show extensive variation within and among populations. By investigating the relationship between dimorphism in facial features and genetic ancestry in different populations, we can explore the roles of sexual and natural selection on the human face. We measured sexual dimorphism in facial traits while controlling for the effects of overall size differences and then tested for interactions between sex and genetic ancestry. The study sample consists of 254 subjects (n=170 females, n=84 males), ages 18-35, showing West African and European genetic ancestry sampled in the United States and Brazil. Maximum likelihood genetic ancestry estimates were determined from 176 ancestry informative markers (AIMs), which allowed for the proportional estimation of genetic ancestry from four parental populations (West African, European, East Asian, and Native American). Three-dimensional photographs of faces were acquired using the 3dMDface imaging system (Atlanta, GA). 22 standard anthropometric landmarks were placed on each image and XYZ coordinates were collected. All 231 possible pairwise inter-landmark distances were calculated and then log transformed. Using the pairwise distances, we tested whether some distances were larger in one sex than the other, having taken size into account, in a) African Americans sampled in the United States, b) Brazilians sampled in Brazil, and c) the combined African American and Brazilian sample. We found that several pairwise distances differed between the sexes. For example, the distance from the brow to nasal bridge was found to be more than 5% larger in females than males. We then tested for an interaction between sex and genetic ancestry by testing for differences in the slopes of the ancestry association between males and females. Although the pattern differed slightly between samples, after Bonferroni correction many correlations were the found to be same in both sexes. However, females in all three samples had many additional significant correlations that were not seen in males, while males had very few correlations that were not found in females. The results of these analyses suggest that selection on females is driving the differentiation in facial features among populations.

Effect of natural selection on North Asian mitochondrial haplogroup variation

The human mtDNA exhibits striking, region-specific sequence variation. The regional distribution of mtDNA haplogroups have attributed either to genetic drift assisted by purifying selection (Elson et al., 2004; Kivisild et al., 2006; Ingman, Gyllensten, 2007) or to an adaptation to different climates (Mishmar et al., 2003; Ruiz-Pesini et al., 2004). In an attempt to study the mode of selection in mtDNA variation in human populations we sequenced and analyzed 211 complete mtDNA sequences belonging to haplogroups A, C and D accounting in total for 49.3% of mtDNA lineages in North Asia. The North Asian haplogroups A, C and D showed a highly significant deviation from the standard neutral model as well as a bell-shaped distribution of pairwise differences consistent with rapid population expansion. To determine the overall importance of selection in shaping human mtDNA variation we calculated Ka/Ks ratio both for aggregated mtDNAs and for 13 proteinencoding genes within particular haplogroups (A, C and D). We have found a prevalence of Ks over Ka within haplogroups A, C and D indicating the influence of negative selection on mtDNA during evolution. Consistent with some previous reports we have found the Ka/Ks ratio for the ATP6 gene to be the highest among the North Asian sequences suggesting thereby that this gene has been subject to positive selection. We have also observed a set of genes with a somewhat higher Ka/Ks ratio relative to other mitochondrial genes - CO2 for haplogroup A, ND3 and ND4 for haplogroup C. Meanwhile the other approach taking into account the difference in NS/S ratios between the haplogroup-associated and private substitutions (Elson et al., 2004) shows the significant departures from neutrality only for haplogroup D and its subhaplogroup D4. Furthermore single gene analysis reveals the relatively strong influence of negative selection only in CYTb gene within haplogroupD(p=0.011, NI=14.1). In general, our results indicate that there is an evidence for both gene-specific and lineage-specific variation in selection acting on North Asian mtDNAs.

Selection for blue eyes in Europe and light skin pigmentation in East Asia at OCA2/HERC2

OCA2 and HERC2 are two genes on chromosome 15 separated by lessthan 10 kb. Mutations in this region have been shown to have an effect onpigmentation including causing oculocutaneous albinism type 2. In Europeans,a three SNP haplotype (rs4778138, rs4778241, rs7495174) and threeindividual SNPs (rs12913832, rs916977, rs1667394) have been associatedwith blue eyes. We have labeled the three SNP haplotype BEH1. We foundthat the first individual SNP, rs12913832, was in near complete LD withanother SNP (rs1129038). Wetreat these two SNPs together as a haplotype,BEH2. We also found that the other two individual SNPs were actually innear complete LD with each other and decided to label them BEH3. In EastAsians, a SNP (rs1800414) has been identified that is associated with alight skin pigmentation phenotype. We typed these eight SNPs in 64-70population samples. We then examined worldwide distribution of the fourpigmentation alleles. We saw that the light skin allele was at its highestfrequency in eastern East Asia, at midrange frequencies in Southeast Asia,and at lower frequencies in western East Asia. It is virtually absent from therest of the world. BEH1 and BEH3 show very similar global patterns, lowfrequencies to midrange frequencies in Africa and East Asia, midrangefrequencies in India and Eastern Siberia, and midrange to high frequenciesin Southwest Asia, Europe, Western Siberia, the Pacific Islands, and theAmericas. BEH2 shows a different pattern from the other two. It showslow frequencies in East Africa, India, Eastern Siberia, and the Americas,midrange frequencies in Southwest Asians and Southern Europeans, andhigh frequencies in Eastern and Northwestern Europe and Western Siberia.We then typed additional SNPs and test each pigmentation allele for selectionusing the Relative Extended Haplotype Homozygosity (REHH) test. Wefound that the light skin allele of rs1800414 is under selection in East Asiaand that the blue eye allele of BEH2 is under selection in Europe andSouthwest Asia. We show light skin pigmentation has been selected for inEast Asia. This is likely due to lower UV exposure at the higher latitudes(compared to equatorial Africa) and the need for lighter skin for vitamin Dproduction. We also show that blue eyes are selected for in Europe. Thisis most likely due to sexual selection, though another unknown effect of thisparticular allele could be selected for and the blues eyes are a side effect.

Ancestry variation along the genome in Latin American populations and implications for recent natural selection

Latin American populations stem from the admixture starting about 500 years ago of Europeans, Africans and Native Americans. Extreme deviation in ancestry estimates at certain genome locations (relative to the genomewide average) could reflect the action of recent natural selection. We evaluated the distribution of ancestry estimates along the genome using 678 microsatellite markers in 249 individuals sampled from 13 admixed populations across Latin America. We found a significant deviation in ancestry at two genomic locations with more than four times standard deviations from the genome-wide mean: an excess of European ancestry at 14q32 (Zscore = 4.14), and an excess of African ancestry at 6p22 (Z-score = 4.71). These deviations in ancestry were observed in the analysis of the combined dataset as well as in most of the individual populations examined. We showed that our findings are robust to the Native American ancestry populations used. We discussed the implications for recent natural selection in the context of the unique history of the New World, as well as the possibility of artifacts.

Central European farmers not descended from local hunter-gatherers (Bramanti et al. 2009)

This is the real power of DNA: the topic of whether central European farmers were the result of demic diffusion from the southeast or indigenous hunter-gatherers who adopted the agricultural economy has been endlessly debated in archaeological circles.

We are finally in a position to give an answer to the question, and the answer is in favor of the diffusionist camp and against the idea of acculturation by local hunter-gatherers. Surprisingly, modern Central Europeans do not appear to be a simple hunter-gatherer/farmer mix, suggesting that even later events (post-Neolithic) have shaped their genetic diversity.

This study is also a powerful argument against the idea of genetic continuity across long time spans. Most ancient DNA studies so far have reached a similar conclusion. Thus, it also destroys the supposed justification for continuity from Paleolithic Europe to modern times that early mtDNA work (of the Daughters of Eve variety) has proposed, hand in hand with the hunter acculturation hypothesis.

The paper is covered in National Geographic:

Central and western Europe's first farmers weren't crafty, native hunter-gatherers who gradually gave up their spears for seeds, a new study says.

Instead, they were experienced outsiders who arrived on the scene around 5500 B.C. with animals in tow—and the locals apparently didn't roll out the welcome wagon.

"Within a few generations, all the farmers—probably coming from southeast Europe—moved into central Europe bringing their culture, [livestock], and everything," Joachim Burger, a molecular archaeologist at the University of Mainz in Germany, said via email.

The finding is based on analysis of genetic material in the skeletal remains of ancient hunter-gatherers and early farmers found in Germany, Lithuania, Poland, and Russia—though farming is thought to have reached areas as far west as western France during the period of rapid expansion, about 7,500 years ago.

The study goes against a long-standing idea that Europe's first farmers were former hunter-gatherer populations that had settled the region after the last ice age, about 10,000 years ago.

Perhaps, the thinking went, the hunter-gatherers had observed farming practices during their travels or had learned from neighbors.

Instead, the researchers found, the hunter-gatherers and the early farmers remained segregated, according to the study, to be published tomorrow in the journal Science.

And the press release:

Analysis of ancient DNA from skeletons suggests that Europe's first farmers were not the descendants of the people who settled the area after the retreat of the ice sheets. Instead, the early farmers probably migrated into major areas of central and eastern Europe about 7,500 years ago, bringing domesticated plants and animals with them, says Barbara Bramanti from Mainz University in Germany and colleagues. The researchers analyzed DNA from hunter-gatherer and early farmer burials, and compared those to each other and to the DNA of modern Europeans. They conclude that there is little evidence of a direct genetic link between the hunter-gatherers and the early farmers, and 82 percent of the types of mtDNA found in the hunter-gatherers are relatively rare in central Europeans today.

For more than a century archaeologists, anthropologists, linguists, and more recently, geneticists, have argued about who the ancestors of Europeans living today were. We know that people lived in Europe before and after the last big ice age and managed to survive by hunting and gathering. We also know that farming spread into Europe from the Near East over the last 9,000 years, thereby increasing the amount of food that can be produced by as much as 100-fold. But the extent to which modern Europeans are descended from either of those two groups has eluded scientists despite many attempts to answer this question.

Now, a team from Mainz University in Germany, together with researchers from UCL (University College London) and Cambridge, have found that the first farmers in central and northern Europe could not have been the descendents of the hunter-gatherers that came before them. But what is even more surprising, they also found that modern Europeans couldn't solely be the descendents of either the hunter-gatherer alone, or the first farmers alone, and are unlikely to be a mixture of just those two groups. "This is really odd", said Professor Mark Thomas, a population geneticist at UCL and co-author of the study. "For more than a century the debate has centered around how much we are the descendents of European hunter-gatherers and how much we are the descendents of Europe's early farmers. For the first time we are now able to directly compare the genes of these Stone Age Europeans, and what we find is that some DNA types just aren't there - despite being common in Europeans today."

Humans arrived in Europe 45,000 years ago and replaced the Neandertals. From that period on, European hunter-gatherers experienced lots of climatic changes, including the last Ice Age. After the end of the Ice Age, some 11,000 years ago, the hunter-gatherer lifestyle survived for a couple of thousand years but was then gradually replaced by agriculture. The question was whether this change in lifestyle from hunter-gatherer to farmer was brought to Europe by new people, or whether only the idea of farming spread. The new results from the Mainz-led team seems to solve much of this long standing debate.

"Our analysis shows that there is no direct continuity between hunter-gatherers and farmers in Central Europe," says Prof Joachim Burger. "As the hunter-gatherers were there first, the farmers must have immigrated into the area."

The study identifies the Carpathian Basin as the origin for early Central European farmers. "It seems that farmers of the Linearbandkeramik culture immigrated from what is modern day Hungary around 7,500 years ago into Central Europe, initially without mixing with local hunter gatherers," says Barbara Bramanti, first author of the study. "This is surprising, because there were cultural contacts between the locals and the immigrants, but, it appears, no genetic exchange of women."

The new study confirms what Joachim Burger´s team showed in 2005; that the first farmers were not the direct ancestors of modern European. Burger says "We are still searching for those remaining components of modern European ancestry. European hunter-gatherers and early farmers alone are not enough. But new ancient DNA data from later periods in European prehistory may shed also light on this in the future."

And from archaeology.about.com:

A new study published by Barbara Bramanti and colleagues in Science Express on September 4, 2009, supports what some scholars have suspected all along—that the LBK likely were an in-migration of people from the Balkans, and that they did not, initially anyway, do much mixing at all with the earlier inhabitants of Europe.

Bramanti and her colleagues compared the mitochondrial DNA from 20 central European Upper Paleolithic, Mesolithic and Neolithic hunter-gatherers to that from 25 Neolithic farmers and 484 modern Europeans, spanning an age range from about 13,400 to 2,300 BC. The data shows that the early farmers and hunter-gatherers were from distinctively different populations.

This paper follows up on and to a degree contradicts with the hypothesis of an earlier paper that looked only at mtDA of the Neolithic farmers. That study (Haak et al. 2005) discovered that the farmers had a distinctive difference between the current residents of Europe, and hypothesized that that meant that the hunter-gatherers might have been more like the modern inhabitants, and thus, the LBK would have been only a minor component.

The earlier paper by Haak et al. they refer to.

(More technical details once I read the full paper)

UPDATE:

Pre-farming populations seem to have been dominated by mtDNA haplogroup U:

it is intriguing to note that 82% of our 22 hunter-gatherer individuals carried clade U (fourteen U5, two U4, and two unspecified U-types; table 1).

The hunter-gatherers had no N1a -which was a signature of early farmers in the Haak et al. paper- or of haplogroup H, the most common mtDNA haplogroup in Europeans today. The only non-U types in hunter-gatherers were all from the Ostorf site and included haplogroups T2e, J, and K.

The farmers:

In a previous study, we showed that the early farmers of Central Europe carried mainly N1a, but also H, HV, J, K, T, V, and U3 types (11, 12). We found no U5 or U4 types in that early farmer sample.

UPDATE I:

It is important to note the implications of this study: the most certain conclusion is that Neolithic farmers in Central Europe are very sharply differentiated from the Paleolithic-Mesolithic populations. This is clear evidence in favor of the diffusionist idea, since the acculturation hypothesis predicts that the mtDNA of the early farmers would be roughly that of the pre-farming population that picked up the new technology.

However, the evidence of this paper also contradicts the plain demic diffusion hypothesis. According to this hypothesis, farmer genes are gradually replaced by hunter genes as the farming economy spreads, because in each step there is a mix of farmer-indigenous populations which go on to colonize regions beyond the frontier. This is not what appears to have happened. Rather, it seems the farmers moved across Europe with very little interaction with pre-farmers. A long period of no contact between the LBK and foragers is actually supported by archaeology. I have termed this type of diffusion the "skipping stone":

In the Skipping Stone model, farmers move out in search of new territories before they have started to blend with the local foragers; the genetic impact of the initiators of the movement is preserved.

The great speed of the Linearbandkeramik farmers was also experienced by farmers who spread across the Mediterranean. The spread of agriculture in Europe does not appear to have been a slow process of interaction between farmer and forager, but rather a blitz by the first farmers, followed later, after the spread had already occurred by admixture with some of the foragers that remained.

We must also be certain not to jump into conclusions about the relative contributions of farmer and forager in the modern gene pool. Clearly both the idea of a predominantly "Paleolithic" and a predominantly "Neolithic" gene pool is problematic; such continuity is not really evident. However, the reasons for the discontinuity up to the present may be manifold: e.g., later population movements into Europe, or natural selection changing the gene pool without subsequent change of population.

What we do know is this: first farmers were not local foragers who abandoned the old ways for the new ones. Amalgamation between farmer and forager did not happen quickly as the farming economy spread. Finally it did happen, of course, and either because (i) there were few foragers in the mix, or (ii) their mtDNA was selected against, modern central Europeans have very little mitochondrial descent from the earliest European populations.

PS: Natural selection against forager mtDNA is not very outlandish. For example, a severe reduction of U5a1 and U5b haplogroup in Britain from ancient to modern times has been observed, which could potentially mark another data point in a process of selection against that haplogroup over time.

My personal guess is that both demography and selection may have played a role in the marginalization of hunter-gatherer mtDNA . LBK farmers were already 3 thousand years removed from the earliest agriculturalists of the Near East, so it is conceivable that they had evolved an mtDNA gene pool adapted to the new lifestyle that outcompeted the indigenous European one. But, the long period of isolation from foragers may mean that only farmer mtDNA benefited from the demographic boom associated with the new economy, and by the time relations between the two groups warmed up, the relatively few newcomers already dwarfed the older population demographically.

UPDATE II (Sep 4):

To understand the magnitude of the difference between farmers and hunter-gatherers, the authors calculate their Fst=0.163, which can be compared with a maximum value of 0.0327 among modern Europeans and 0.133 for modern Eurasians from Europe to Australia. Subsequently, the authors test the hypotheses of (a) continuity between hunter-gatherers and farmers, and (b) continuity between hunter-gatherers and modern Central Europeans, rejecting both.

This isn't very surprising in the light of the anthropological evidence in favor of diffusion of farmers from the Near East and against the acculturation hypothesis presented recently by Pinhasi et al. The very close relationship of the LBK skulls and their proximity to samples from Nea Nikomedeia in Greece and Catal Hoyuk in Anatolia contrasts with the Mesolithic populations.

UPDATE III (Sep 21):

Some possible anthropological evidence for post-LBK infusion into Central Europe:

Mesolithic Europeans display considerable variation in humero-clavicular and brachial indices yet none approach the extreme "hyper-polar" morphology of LBK humans from the MESV. In contrast, Late Neolithic and Early Bronze Age peoples display elongated brachial and crural indices reminiscent of terminal Pleistocene and "tropically adapted" recent humans. These marked morphological changes likely reflect exogenous immigration during the terminal Fourth millennium cal BC.

Science doi:10.1126/science.1176869

Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe’s First Farmers

B. Bramanti et al.

Following the domestication of animals and crops in the Near East some 11,000 years ago, farming reached much of Central Europe by 7,500 years before present. The extent to which these early European farmers were immigrants, or descendants of resident hunter-gatherers who had adopted farming, has been widely debated. We compare new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers, and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in Central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into Central Europe at the onset of the Neolithic.

Link

A Single Origin for Dogs South of Yangtze River, less than 16,300 Years Ago (Pang et al. 2009)

Another recent study by Boyko et al. raised some doubts about the strength of the evidence for dog domestication in Asia, by pointing out that including semi-feral village dogs may increase the observed Asian diversity. The advance access manuscript for this paper is free, so anyone interested in the sampling details. The authors do cite the other recent paper:

Notably, in a recent study of African village dogs (Boyko et al. 2009) it was claimed that the reported high diversity for mtDNA in East Asia compared to other parts of the world (Savolainen et al. 2002), was the result of sampling bias. However, in the present study (see “Results”) we show this assertion to be incorrect.

...

Thus, a direct comparison shows that the smaller South Chinese sample has 73% more haplotypes than the African one; the assertion by Boyko et al. (2009) is the result of not adequately compensating for differences in sample size between the relatively small East Asian samples in Savolainen et al. (2002) and the larger African samples. The African sample has also all the other characteristics of the “western” dog populations: The haplotypes fall in the same parts of the MS networks as for other western populations, leaving large parts unique to East Asia (data not shown); and values are high for UT (66.7%) and UTd (90.9%), and number of unique haplotypes low (12) (compare with e.g. South China: UT (42.0%), UTd (53.4%), and number of unique haplotypes (40; i.e. only one less than the total number of haplotypes in the African sample!)). To conclude, the sample of African village dogs in Boyko et al. (2009), like all “western” samples, has considerably lower genetic variation than the populations in ASY.

Molecular Biology and Evolution, doi:10.1093/molbev/msp195

mtDNA Data Indicates a Single Origin for Dogs South of Yangtze River, less than 16,300 Years Ago, from Numerous Wolves

Jun-Feng Pang et al.

Abstract

There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so far studied control region (CR), and inadequate sampling. We therefore analysed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution, and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture of the origins of the dog can for the first time be suggested. We obtained evidence that the dog has a single origin in time and space, and an estimation of the time of origin, number of founders and approximate region, which also gives potential clues about the human culture involved. The analyses showed that dogs universally share a common homogenous gene pool containing 10 major haplogroups. However, the full range of genetic diversity, all 10 haplogroups, was found only in south-eastern Asia south of Yangtze River, and diversity decreased following a gradient across Eurasia, through 7 haplogroups in Central China, and 5 in North China and Southwest Asia, down to only 4 haplogroups in Europe. The mean sequence distance to ancestral haplotypes indicates an origin 5,400-16,300 years ago from at least 51 female wolf founders. These results indicate that the domestic dog originated in southern China less than 16,300 years ago, from several hundred wolves. The place and time coincide approximately with the origin of rice agriculture, suggesting that the dogs may have originated among sedentary hunter-gatherers or early farmers, and the numerous founders indicate that wolf taming was an important culture trait.

Link

Y chromosomes and mtDNA of Central Asian Turkic and Iranian populations

Unfortunately this paper only studied 12 Y-STRs, reduced to 7 to compare them with previous studies. Moreover, as far as I can see, this data is not available in the journal website. ScienceDaily covers the paper with the totally unwarranted title of "No Such Thing As Ethnic Groups, Genetically Speaking, Researchers Say".

What this paper does show, as far as its limited marker set can, that some Turkic ethnic groups are aggregates of populations of unrelated origin, which is not particularly surprising. One has to look at the spread of Turks from Central Asia to Europe to see that the various "Turks" were usually opportunistic alliances of peoples of different stock. Perhaps these Central Asian ethnic groups will eventually be homogenized by continued in-group marriage.

This brings me to an important point of using genetic diversity to assess how long ago ethnic groups were formed. Some ethnic groups begin as homogeneous entities which become differentiated as they expand and undergo separate evolution/differential patterns of admixture in different localities. Other groups begin as heterogeneous groups of unrelated tribes that become united by some factor, e.g., the emergence of a strong king or dynasty around whom diverse peoples aggregate. In the first case, ethnic evolution is one of diversification over time, as the genetic legacy of the homogeneous founders is fragmented; in the latter, it is one of homogenization, as the genetic legacies of the heterogeneous constituents merge to form a single homogeneous group. Thus, one can't generally conclude, by looking at within-group differentiation whether the group is "old" or "recent" in origin; it could be an old group that has fragmented over a long period of time, or a new one that has not had enough time to become one.

UPDATE (Sep 3):

The study is also covered at the Spittoon under the title New Study on Genetics of Ethnic Groups Reveals We May Not Be So Different After All. Unfortunately, the author of the blog post gets the linguistic divisions wrong:

The Turks are largely nomadic herders. They speak Indo-Iranian languages like Azerbaijani, Turkish, and Altay. Their society is organized into clans, or “descent groups,” whose membership is passed down from father to children.

The Tajiks are, conversely, agriculturalists. They speak various dialects of the the Tajik, or Tajik Persian, language that may have arrived with Muslim invaders 1,000 years ago. Their society is largely patrilocal – meaning that when couples marry they put up residence near the husband’s family; and first cousin marriages are encouraged.

It is of course the Turks who speak Turkic languages, and the Tajiks who speak an Indo-Iranian (or more precisely Iranian) language.

As for the title, which, like the ScienceDaily title, seems to burst at the seams with delight that ethnic differences don't exist, a better angle on the topic would be to observe how prevalent ethnic differences are, if they can exist even among populations that are genetically non-differentiated. The pipe dream of some thinkers, that increased inter-ethnic and inter-racial mating will lead to an abolition of ethnic and racial genetic differences, and, thus, to a happy co-existence of people around the world, is refuted by the finding that humans happily self-segregate themselves along ethnic lines, even when there are no underlying genetic differences.

BMC Genetics 2009, 10:49doi:10.1186/1471-2156-10-49

Genetic diversity and the emergence of ethnic groups in Central Asia

Evelyne Heyer et al.

Abstract

Background

In this study, we used genetic data that we collected in Central Asia, in addition to data from the literature, to understand better the origins of Central Asian groups at a fine-grained scale, and to assess how ethnicity influences the shaping of genetic differences in the human species. We assess the levels of genetic differentiation between ethnic groups on one hand and between populations of the same ethnic group on the other hand with mitochondrial and Ychromosomal data from several populations per ethnic group from the two major linguistic groups in Central Asia.

Results

Our results show that there are more differences between populations of the same ethnic group than between ethnic groups for the Y chromosome, whereas the opposite is observed for mtDNA in the Turkic group. This is not the case for Tajik populations belonging to the Indo-Iranian group where the mtDNA like the Y-chomosomal differentiation is also significant between populations within this ethnic group. Further, the Y-chromosomal analysis of genetic differentiation between populations belonging to the same ethnic group gives some estimation of the minimal age of these ethnic groups. This value is significantly higher than what is known from historical records for two of the groups and lends support to Barth's hypothesis by indicating that ethnicity, at least for these two groups, should be seen as a constructed social system maintaining genetic boundaries with other ethnic groups, rather than the outcome of common genetic ancestry

Conclusions

Our analysis of uniparental markers highlights in Central Asia the differences between Turkic and Indo-Iranian populations in their sex-specific differentiation and shows good congruence with anthropological data.

Link

How humans differ from animals in height and mass variation (McKellar & Hendry 2009)

The authors found that humans within populations have more variation in mass than most animals do. In other words, there are many "thin" and "fat" people in human populations. This isn't very surprising to me, because in developing countries, socioeconomic differences may account for these differences (e.g., some people starve), while in developed countries, most people are employed in jobs and perform activities where having an optimal body mass is not that important for your survival and reproduction.

When it comes to height, humans show a very low within-population differentiation. In other words, most humans are around the "average" height, and really short and really tall ones are not that common. My guess is that this has something to do with the extreme socialization of humans; really short and really tall individuals (although the patterns are gender-specific) do have trouble in human society, if we judge from marriage ads where desired height is often specified, or from various pieces of technology (shields, spears, doors, steps, clothes, etc) which are designed for people of a particular height.

However, between-population differentiation in height is substantial. While we are in the 8th/4th percentiles in our within-population differentiation (very uniform), we are in the 47th/51st percentiles in our between-population differentiation. Thus, while in absolute terms between-population differences are average, these contrast greatly with our very low within-population differences: Human populations appear to be very different from each other in terms of their height.

From the paper:

One interesting result was that humans, in comparison to other animals, show a high level of within-population variation in mass considering their within-population variation in height (Figure 1). Specifically, when considering residuals from a regression of within-population CVs for mass on within-population CVs for length, human males and females fell into the 71st and 91st percentiles, respectively, for the entire distribution of animal species.

...

Another interesting result was that humans show low within-population variation in body height in comparison to body length in non-human animals (Figure 2), but the same was not true for human mass relative to animal mass (Figure S1). These differences can be quantified through several different comparisons. First, the mean within-population CVs for male and female human height correspond to the 8th and 4th percentiles, respectively, of the mean within-population CVs for animal length. In contrast, the mean within-population CVs for male and female human mass correspond to the 56th and 60th percentiles, respectively, of the within-population CVs for animal mass.

...

Specifically, the mean among-population CVs for male and female human height correspond to the 47th and 51st percentiles, respectively, of mean among-population CVs for animal length. Illustrated another way, humans show relatively low levels of within-population variation in height given their among-population variation in height (Figure 3).

PLoS ONE 4(9): e6876. doi:10.1371/journal.pone.0006876

How Humans Differ from Other Animals in Their Levels of Morphological Variation

Ann E. McKellar, Andrew P. Hendry

Abstract

Animal species come in many shapes and sizes, as do the individuals and populations that make up each species. To us, humans might seem to show particularly high levels of morphological variation, but perhaps this perception is simply based on enhanced recognition of individual conspecifics relative to individual heterospecifics. We here more objectively ask how humans compare to other animals in terms of body size variation. We quantitatively compare levels of variation in body length (height) and mass within and among 99 human populations and 848 animal populations (210 species). We find that humans show low levels of within-population body height variation in comparison to body length variation in other animals. Humans do not, however, show distinctive levels of within-population body mass variation, nor of among-population body height or mass variation. These results are consistent with the idea that natural and sexual selection have reduced human height variation within populations, while maintaining it among populations. We therefore hypothesize that humans have evolved on a rugged adaptive landscape with strong selection for body height optima that differ among locations.

Link

Coalescent-based serial founder model of migration outward from Africa (DeGiorgio et al. 2009)

Proc Natl Acad Sci U S A. 2009 Aug 17. [Epub ahead of print]

Out of Africa: Modern Human Origins Special Feature: Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa.

Degiorgio M, Jakobsson M, Rosenberg NA.

Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.

Link