Genetic discontinuities between Etruscans and modern Tuscans

It is great that such a large medieval sample was assembled for this study, and hopefully it will be possible to type it for either Y chromosome or autosomal markers to determine whether continuity between medieval and modern Tuscans was only matrilineal.

I am not very surprised by the inferred genetic discontinuity. Gene pools maintain their separateness if their bearers have some sort of distinction (linguistic, political, religious, or cultural) from their neighbors. For Etruscans, such distinctions were rapidly dissolved when they were annexed by the Romans. In Imperial times, their language was still known by some, but this, too, passed into oblivion.

As distinctions disappear, so do impediments to bidirectional gene flow. The genetic characteristics of the original people do not so much disappear (genetic genealogists will surely soon scour the databases for ancient Etruscan matches, if they haven't done it already), but are diffused in the larger pool of now undifferentiated neighbors, who, in their turn, diffuse into the territory of the old ethnic entity.

The "Etruscans" label of this post points to many studies in this unfolding story of Etruscan origins. Etruscans remain, until now, the only ancient Mediterranean population for which a substantial mtDNA characterization exists.

PS: Interestingly, the conference abstract which I pointed to earlier seemed to suggest that the genetic discontinuity occurred after 1,500AD rather than before 1,000AD, as the published paper does.

(More on the details of the study to follow after I read the paper)

UPDATE I (Jul 2)

From my reading of Table 2, the medieval Tuscan sequences are:

10 of CRS
2 of 16311C
2 of 16294T 16296T 16304C

and 1 of the following:

16224C 16311C 16355T
16274A
16126C 16193T
16126C 16193T 16294T 16296T 16304C
16114A
16174T
16304C
16318T
16126C 16294T 16296T 16304C
16223T
16189C
16261T
16126C

which seems to indicate a mix of haplogroups H, HV, T, and K in the population according to the Genographic project tool.

UPDATE II (Jul 2)

From the paper:

Analyses of mtDNA diversity in the British Isles (Töpf et al. 2007), and Iceland (Helgason et al. 2009), also showed sharp differences between historical and current populations. In addition, a large fraction (up to 80%, depending on the region considered) of the Dutch surnames were displaced from the areas in which their frequency was highest three centuries ago (Manni et al. 2005). Nobody can tell whether the Netherlands represent an exception or the rule, until similar studies are carried out elsewhere, and there is no comparable information on previous centuries. However, the point here is that a genetic discontinuity between present and past populations seems rather common in the few European countries studied so far. Deep demographic changes in the last two millennia are both suggested by the analysis of ancient DNA in Tuscany, Iceland and Britain, and empirically demonstrated in the Netherlands. Our failure to reproduce by simulation the observed haplotype number of the contemporary Tuscan samples may mean that such changes involved multiple immigration processes, too complex to model at present.

The paper by Töpf et al. in turn points to this study of ancient British mtDNA which I had forgotten about. That study shows an increase of haplogroup H (as most of the OTHER probably is) in modern times compared to the past, and the drastic reduction of some haplogroups as U5a1 and U5a1a. Other cases of apparent drastic change over time, involves the Central Europeans (reduced haplogroup N1a) compared to early Central European farmers., and medieval vs. modern Danes (reduced haplogroup I).

So, the picture does seem to suggest substantial changes in mtDNA gene pools over time across many parts of Europe and time frames. Whether this reflects population movements or selection, remains to be seen. In the paper on the Netherlands, for examples (Manni et al.) cited in this paper shows that the original surnames in a region can be rapidly replaced over a genealogical time frame.

Studies such as these put into question the widely held assumption that modern gene pools reflect prehistorical events, such as the repopulation of Europe after the glacial age, or the advent of farming. If genetic change is so substantial over 100 generations, we are rather foolish, I believe, to attempt prehistoric reconstructions about events that took place 300 or even 600 generations ago.

Molecular Biology and Evolution, doi:10.1093/molbev/msp126

Genealogical discontinuities among Etruscan, Medieval and contemporary Tuscans

Silvia Guimaraes et al.

The available mitochondrial DNA (mtDNA) data do not point to clear genetic relationships between current Tuscans and the Bronze-Age inhabitants of Tuscany, the Etruscans. To understand how and when such a genetic discontinuity may have arisen, we extracted and typed the mtDNAs of 27 medieval Tuscans from an initial sample of 61, spanning a period between the 10th and 15th centuries A.D.. We then tested by serial coalescent simulation various models describing the genealogical relationships among past and current inhabitants of Tuscany, the latter including three samples (from Murlo, Volterra, Casentino) which were recently claimed to be of Etruscan descent. Etruscans and medieval Tuscans share three mitochondrial haplotypes, but fall in distinct branches of the mitochondrial genealogy in the only model that proved compatible with the data. Under that model, contemporary people of Tuscany show clear genetic relationships with Medieval people, but not with the Etruscans, along the female lines. No evidence of excess mutation was found in the Etruscan DNAs by a Bayesian test, and so there is no reason to suspect that these results be biased by systematic contamination of the ancient sequences or laboratory artefacts. Extensive demographic changes before 1000 A.D. are thus the simplest explanation for the differences between the contemporary and the Bronze-Age mitochondrial DNAs of Tuscany. Accordingly, genealogical continuity between ancient and modern populations of the same area does not seem a safe general assumption, but rather a hypothesis that, when possible, should be tested using ancient DNA analysis.

Link

Common variants and schizophrenia

Until now, the hunt for the genetic etiology of psychiatric disorders didn't go very well. Three new papers in Nature make some progress by noting that a combination of many genes, especially of the Major Histocompatibility Complex is predictive of schizophrenia and bipolar disorder risk. From the NIH news release:

Three schizophrenia genetics research consortia, each funded in part by NIMH, report separately on their genome-wide association studies online July 1, 2009, in the journal Nature. However, the SGENE, International Schizophrenia (ISC) and Molecular Genetics of Schizophrenia (MGS) consortia shared their results – making possible meta-analyses of a combined sample totaling 8,014 cases and 19,090 controls.

All three studies implicate an area of Chromosome 6 (6p22.1), which is known to harbor genes involved in immunity and controlling how and when genes turn on and off. This hotspot of association might help to explain how environmental factors affect risk for schizophrenia. For example, there are hints of autoimmune involvement in schizophrenia, such as evidence that offspring of mothers with influenza while pregnant have a higher risk of developing the illness.

From news.com.au:

As well as pinpointing key immune system mutations, complementary discoveries from each consortium showed clearly that many small genetic variations combine in different ways to increase a person's risk of developing schizophrenia.

"If you look at any individual with schizophrenia no single gene is really strong, but put these genes together and you get a meaningful influence," Dr Cairns said.

From the deCODE news release:

"Genetics offers a unique window for better understanding diseases like schizophrenia because the brain and cognition are so little understood and so difficult to study. Discoveries such as these are crucial for teasing out the biology of the disease and making it possible for us to begin to develop drugs targeting the underlying causes and not just the symptoms of the disease. One of the reasons this study was so successful is its unprecendented size. Pooling our resources has yielded spectacular results, which is what the participants from three continents hoped for. At the same time, this study underscores the fact that rare variants may well carry a significant part of the genetic risk of schizophrenia, so our next task is to use the ever more affordable sequencing technologies to find more of them," said Kari Stefansson, CEO of deCODE and corresponding author on the paper.

In the first phase of the study, the deCODE-led SGENE consortium conducted a genome-wide scan of more than 300,000 SNPs in a total of 17,000 patients and controls from England, Finland, Germany, Iceland, Italy and Scotland. The 1500 SNPs with the best signal were then analyzed in 11,000 patients and controls from the International Schizophrenia Consortium (ISC) and the European-American portion of the Molecular Genetics of Schizophrenia studies (MGS). Twenty-five SNPs with strong suggestive correlation were then followed up in more than 20,000 patients and controls from the Netherlands, Denmark, Germany, Hungary, Norway, Russia, Finland and Spain. Bringing together the results of different consortia established he association between the the total of seven markers on chromosomes 6, 11, and 18 with increased risk of schizophrenia.

So, while these three studies are a vindication of sorts for common variants, the greater part of the risk remains to be found in rare variants that are not captured by the 300K SNPs or so that were genotyped. But, by any means, this is a significant victory in the search for the hidden heritability.

From the Stanford release:

Using commercially available "SNP chips" designed to detect those more-common variants, the investigators looked for differences between the DNA of people with schizophrenia versus the DNA of those without the disease. The scientists required that such differences achieve "genome-wide statistical significance." Here's why: If you flip a million coins, one at a time, you're going to see all kinds of seemingly miraculous events — say, 15 heads in a row — that may seem significant but are typical when you toss even a perfectly balanced coin so many times.

Shi's job was to devise analytical techniques to determine whether the "finding" of a SNP's greater likelihood among schizophrenics was real or spurious. The genomic region on chromosome 6 survived this rigorous statistical test.

"These findings show that our genetic methods are working, and that the genetic underpinnings of schizophrenia can be understood," said Levinson. "Similar methods have produced critical new discoveries in many other common diseases, once very large numbers of people could be studied. Now we see that the same approach works for psychiatric disorders like schizophrenia."

The three papers (in no particular order):

Nature doi:10.1038/nature08185

Common polygenic variation contributes to risk of schizophrenia and bipolar disorder

The International Schizophrenia Consortium

Abstract

Schizophrenia is a severe mental disorder with a lifetime risk of about 1%, characterized by hallucinations, delusions and cognitive deficits, with heritability estimated at up to 80%1, 2. We performed a genome-wide association study of 3,322 European individuals with schizophrenia and 3,587 controls. Here we show, using two analytic approaches, the extent to which common genetic variation underlies the risk of schizophrenia. First, we implicate the major histocompatibility complex. Second, we provide molecular genetic evidence for a substantial polygenic component to the risk of schizophrenia involving thousands of common alleles of very small effect. We show that this component also contributes to the risk of bipolar disorder, but not to several non-psychiatric diseases.

Link

Nature doi:10.1038/nature08186

Common variants conferring risk of schizophrenia

Hreinn Stefansson et al.

Abstract

Schizophrenia is a complex disorder, caused by both genetic and environmental factors and their interactions. Research on pathogenesis has traditionally focused on neurotransmitter systems in the brain, particularly those involving dopamine. Schizophrenia has been considered a separate disease for over a century, but in the absence of clear biological markers, diagnosis has historically been based on signs and symptoms. A fundamental message emerging from genome-wide association studies of copy number variations (CNVs) associated with the disease is that its genetic basis does not necessarily conform to classical nosological disease boundaries. Certain CNVs confer not only high relative risk of schizophrenia but also of other psychiatric disorders1, 2, 3. The structural variations associated with schizophrenia can involve several genes and the phenotypic syndromes, or the 'genomic disorders', have not yet been characterized4. Single nucleotide polymorphism (SNP)-based genome-wide association studies with the potential to implicate individual genes in complex diseases may reveal underlying biological pathways. Here we combined SNP data from several large genome-wide scans and followed up the most significant association signals. We found significant association with several markers spanning the major histocompatibility complex (MHC) region on chromosome 6p21.3-22.1, a marker located upstream of the neurogranin gene (NRGN) on 11q24.2 and a marker in intron four of transcription factor 4 (TCF4) on 18q21.2. Our findings implicating the MHC region are consistent with an immune component to schizophrenia risk, whereas the association with NRGN and TCF4 points to perturbation of pathways involved in brain development, memory and cognition.

Link

Nature doi:10.1038/nature08192

Common variants on chromosome 6p22.1 are associated with schizophrenia

Jianxin Shi et al.

Abstract

Schizophrenia, a devastating psychiatric disorder, has a prevalence of 0.5–1%, with high heritability (80–85%) and complex transmission1. Recent studies implicate rare, large, high-penetrance copy number variants in some cases2, but the genes or biological mechanisms that underlie susceptibility are not known. Here we show that schizophrenia is significantly associated with single nucleotide polymorphisms (SNPs) in the extended major histocompatibility complex region on chromosome 6. We carried out a genome-wide association study of common SNPs in the Molecular Genetics of Schizophrenia (MGS) case-control sample, and then a meta-analysis of data from the MGS, International Schizophrenia Consortium and SGENE data sets. No MGS finding achieved genome-wide statistical significance. In the meta-analysis of European-ancestry subjects (8,008 cases, 19,077 controls), significant association with schizophrenia was observed in a region of linkage disequilibrium on chromosome 6p22.1 (P = 9.54 times 10-9). This region includes a histone gene cluster and several immunity-related genes—possibly implicating aetiological mechanisms involving chromatin modification, transcriptional regulation, autoimmunity and/or infection. These results demonstrate that common schizophrenia susceptibility alleles can be detected. The characterization of these signals will suggest important directions for research on susceptibility mechanisms.

Link

Uyghurs as an admixed not source population (Xu et al. 2009)

This paper is interesting not so much because it estimates admixture in Uyghurs (click on the post label for previous studies on the topic), but because it explicitly rejects the hypothesis that they are a source ("donor") population.

If a population has substantial genetic variation which overlaps with that of two other groups, then there are two possible interpretations:

1. It represents the population from which the other two groups sprang, or at least contributed genes to both of them
2. It represents a mixture of the two other groups
   

What this paper does, is to show that Uyghurs are best explained as a mixture of Caucasoids and Mongoloids (#2) rather than #1.

Molecular Biology and Evolution, doi:10.1093/molbev/msp130

Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors

Shuhua Xu et al.

Abstract

The Uyghur are a group of people primarily residing in Xinjiang of China which is geographically located in Central Asia, from where modern humans were presumably spread in all directions reaching Europe, east and northeast Asia about 40 kya. A recent study suggested that the Uyghur are ancestry donors of the East Asian gene pool. However, an alternative hypothesis, i.e. the Uyghur is an admixture population with both East Asian (EAS) and European (EUR) ancestries is also supported by our previous studies. To test the two competing hypotheses, here we conducted a haplotype sharing analysis based on empirical and simulated data of high density single nucleotide polymorphisms (SNPs). Our results showed that more than 95% of Uyghur (UIG) haplotypes could be found in either East Asian (EAS) or European (EUR) populations, which contradicts the expectation of the null models assuming that UIG are donors. Simulation studies further indicated that the proportion of UIG private haplotypes observed in empirical data is only expected in alternative models assuming that UIG is an admixture population. Interestingly, the estimated ancestry contribution of 44%:56% (EAS:EUR) based on haplotype sharing analysis is consistent with our previous estimation with STRUCTURE analysis. Although the history of Uyghurs could be complex, our method is explicit and conservative in rejecting the null hypothesis. We concluded that the gene pool of modern Uyghurs is more likely a sole recipient with contribution from both EAS and EUR.

Link

Humans capable of (but not good at) assessing relatedness from faces

Proceedings of the Royal Society B doi: 10.1098/rspb.2009.0677

Human ability to detect kinship in strangers' faces: effects of the degree of relatedness

Gwenaël Kaminski et al.

Abstract

The resemblance between human faces has been shown to be a possible cue in recognizing the relatedness between parents and children, and more recently, between siblings. However, the general inclusive fitness theory proposes that kin-selective behaviours are also relevant to more distant relatives, which requires the detection of larger kinship bonds. We conducted an experiment to explore the use of facial clues by ‘strangers’, i.e. evaluators from a different family, to associate humans of varying degrees of relatedness. We hypothesized that the visual capacity to detect relatedness should be weaker with lower degrees of relatedness. We showed that human adults are capable of (although not very efficient at) assessing the relatedness of unrelated individuals from photographs and that visible facial cues vary according to the degree of relatedness. This sensitivity exists even for kin pair members that are more than a generation apart and have never lived together. Collectively, our findings are in agreement with emerging knowledge on the role played by facial resemblance as a kinship cue. But we have progressed further to show how the capacity to distinguish between related and non-related pairs applies to situations relevant to indirect fitness.

Link

A colorful view of the potency of skulls and the reality of race

(updated June 30)

I used distruct to create a graphical display of the clusters revealed by my 2004 model-based clustering of 2,504 human skulls on 57 metrical variates. As mentioned in the original article, these traits are enough to distinguish some human races (e.g., Caucasoids=Norse, Zalavar, Berg, Egyptian), or even individual populations (e.g., Eskimo, Buriat, or Bushmen).

Of course, some skulls don't fall in the right cluster, but this is to be expected both due to the state of the original collections (*) and due to the plasticity of the human skull that may create false associations.

But, on the whole, the clusters emerge as distinct and unmistakable entities; this level of resolution at a global scale is only possible -if at all- with hundreds of thousands of genetic markers, yet 57 linear measurements pretty much do the same trick.

One can only imagine what would be possible if someone takes a 3D scanner around the world to visit the same museum collections that Howells did several decades ago. But, perhaps, physical anthropologists have better things to do these days than discovering differences between human populations...

(*) For example, W.W. Howells noted in his work that one of the American skulls obviously belonged to a white settler.

UPDATE (June 30)

Please consult the original article for details on the populations and the methodology used. Note that K=14 is the number of clusters which maximizes the Bayes Information Criterion, but it is by no means the end of the story. For even higher K, some populations can be further separated, although some of them (e.g., Europeans) never split into fairly "clean" clusters with these 57 variables.

Below are all the results for K=2 to K=14. As with Rosenberg et al. (2002) and the work that followed it, the first split contrasts East Asians with Eurafricans. It is important to note that the pattern of successive splits should not be interpreted as a phylogeny of human populations, i.e., a history of human subdivisions.

Predomestication grain deposits in Jordan

See also: Crop domestication didn't happen overnight or in one place

Proc Natl Acad Sci U S A. 2009 Jun 22.

Evidence for food storage and predomestication granaries 11,000 years ago in the Jordan Valley.

Kuijt I, Finlayson B.

Food storage is a vital component in the economic and social package that comprises the Neolithic, contributing to plant domestication, increasingly sedentary lifestyles, and new social organizations. Recent excavations at Dhra' near the Dead Sea in Jordan provide strong evidence for sophisticated, purpose-built granaries in a predomestication context approximately 11,300-11,175 cal B.P., which support recent arguments for the deliberate cultivation of wild cereals at this time. Designed with suspended floors for air circulation and protection from rodents, they are located between residential structures that contain plant-processing instillations. The granaries represent a critical evolutionary shift in the relationship between people and plant foods, which precedes the emergence of domestication and large-scale sedentary communities by at least 1,000 years.

Link

Quantifying the effect of different aspects of the Mediterranean diet: the EPIC study

BMJ. 2009 Jun 23;338:b2337. doi: 10.1136/bmj.b2337.

Anatomy of health effects of Mediterranean diet: Greek EPIC prospective cohort study.

Trichopoulou A, Bamia C, Trichopoulos D.

OBJECTIVE: To investigate the relative importance of the individual components of the Mediterranean diet in generating the inverse association of increased adherence to this diet and overall mortality. DESIGN: Prospective cohort study. SETTING: Greek segment of the European Prospective Investigation into Cancer and nutrition (EPIC). PARTICIPANTS: 23 349 men and women, not previously diagnosed with cancer, coronary heart disease, or diabetes, with documented survival status until June 2008 and complete information on nutritional variables and important covariates at enrolment. MAIN OUTCOME MEASURE: All cause mortality. RESULTS: After a mean follow-up of 8.5 years, 652 deaths from any cause had occurred among 12 694 participants with Mediterranean diet scores 0-4 and 423 among 10 655 participants with scores of 5 or more. Controlling for potential confounders, higher adherence to a Mediterranean diet was associated with a statistically significant reduction in total mortality (adjusted mortality ratio per two unit increase in score 0.864, 95% confidence interval 0.802 to 0.932). The contributions of the individual components of the Mediterranean diet to this association were moderate ethanol consumption 23.5%, low consumption of meat and meat products 16.6%, high vegetable consumption 16.2%, high fruit and nut consumption 11.2%, high monounsaturated to saturated lipid ratio 10.6%, and high legume consumption 9.7%. The contributions of high cereal consumption and low dairy consumption were minimal, whereas high fish and seafood consumption was associated with a non-significant increase in mortality ratio. CONCLUSION: The dominant components of the Mediterranean diet score as a predictor of lower mortality are moderate consumption of ethanol, low consumption of meat and meat products, and high consumption of vegetables, fruits and nuts, olive oil, and legumes. Minimal contributions were found for cereals and dairy products, possibly because they are heterogeneous categories of foods with differential health effects, and for fish and seafood, the intake of which is low in this population.

Link

Relationship of cranial robusticity to cranial form, geography and climate

UPDATE (June 30)
This paper investigates the relationship between cranial robusticity and a number of factors said to underlie it, including cranial size and shape, climate, and neutral genetic variation. Genetic similarity between populations was assessed using the well-known Rosenberg et al. dataset from 2002.

From the paper:

If the robusticity traits are the subject of neutral evolutionary processes, then the distance matrix based on these characters will be strongly correlated with that based on the neutral genetic markers (microsatellite data) (e.g., Roseman, 2004).

...

A functional hypothesis that specifically implicates forces associated with mastication would be supported by a stronger correlation between cranial robusticity and the MLS rather than CLS as the former more directly captures morphology associated with mastication, although it is also possible that changes in overall
cranial shape may be related to mastication. A strong relationship between cranial robusticity and the climatic variables would support the influence of the local environment on the development of cranial robusticity.

Note: CLS/MLS=cranial/masticatory landmark set.

First of all, it turns out that Robusticity traits are closely correlated with each other, suggesting that they do indeed capture an overall factor of "Robusticity" rather than being independent from each other. A notable exception is occipital torus, which is not significantly related to other robusticity traits.

Next up, principal components analysis was performed:

In deciding how many PCs to evaluate, we applied the common Guttman-Kaiser criterion (keep all PCs with eigenvalues [1.0; Kaiser, 1961), which results in the retention of the first three components. However, a more conservative criterion, the Scree Plot (Cattell, 1966), suggests that only PC 1 should be retained. Although PC 1 accounted for a proportionally larger percentage of the total variance in cranial robusticity (27%), the second and third components each explain 11% of the variance and may indicate that there is more than one relevantpattern of cranial robusticity (Table 10).

...

The first PC reflects overall levels of robusticity as all 11 traits load positively (Table 10), although the occipital torus has a loading near zero. ... The groups with the highest median (and mean) scores are New Zealand, Australia/Tasmania, North
America, and South America, while the lowest scores belong to Mongolia, East Asia, Inuit, and Khoe-San (see Fig. 3).

...

Males score significantly higher than females on PC 1 within all groups except the East and West Europeans, East and West Africans, and Khoe-San (Table 11), but males scored higher on average than females even in those groups that did not reach statistical significance

Interestingly, in the test for sex differences in PC1, Europeans differed from each other. Southern Europeans (Peloponnesian Greeks and Italians) were most dimorphic, and West Europeans (Austrians and Germans) were least.

From the paper:

The second PC has both high positive (occipital torus, rounding of orbits) and high negative (sagittal keel, anterior mastoid, bregmatic eminence) loadings ... The highest scoring groups on PC 2 are East Asia, Mongolia, Australia/Tasmania, and the Khoe-San, while East Africa, West Africa, and Eastern Europe have low scores (Fig. 3a). Many of the pair-wise contrasts between the highest and lowest scoring groups are significant, particularly those that include East Africa, East Asia, and Mongolia (Table 10). It appears that while the East Asian populations are gracile overall (see above), they do display some characters typically considered as ‘‘robust’’ (e.g., the occipital torus).

...

The third PC also has a mixed pattern of positive and negative loadings. The traits with the highest loadings are sagittal keel, occipital torus, malar tubercle, bregmatic
eminence (all positive), infraglabellar notch and supraorbital torus (both negative). The North American and, to a lesser extent, New Zealand, groups score highest
on PC 3, in contrast to Australia/Tasmania, Southern Europe, Eastern Europe, and East Africa (Fig. 3b).

In PC1, sex and size differences contribute about 36% of the variation, but only 3 and 8% in PC2 an PC3 respectively.

The author calculated distances between populations for Robusticity, CLS, MLS, Climate, and microsatellites, and sees how the inter-population distance based on robusticity correlates with the other four potentially explanatory factors:

The correlation coefficients from the Mantel tests are weak, ranging from -0.115 to 0.387 (Table 12). The null hypothesis of neutral evolution was rejected as the robusticity distances were not significantly correlated with neutral genetic distances.

The strongest (and only significant) correlations are between cranial robusticity and cranial (CLS) or masticatory apparatus shape (MLS). Cranial robusticity in the combined male–female sample is significantly correlated with the masticatory shape, and its correlation with overall cranial shape approached significance (Table 12).

On the Southern European masticatory system:

Whereas South Europe is among the lowest scoring groups on both the shape and robusticity vectors, the highest scoring groups on the robusticity vector (e.g., South America and New Zealand) are not the highest scoring groups on the shape vector (specifically Australia/Tasmania). The more gracile groups (e.g., South European) have more anteriorly positioned zygomatic bones (as indicated by the inferior zygomaticotemporal suture and zygomaxillare), more laterally located postglenoid processes and frontotemporale, and relatively larger cheek teeth (in the anteroposterior direction) that are more superiorly positioned.

Finally, a bit on Australian aboriginals who often get singled out as being particularly robust. It turns out that they are, but their pattern of robusticity involves particular traits, while other human groups, such as Native Americans are robust in a different manner:

While Aboriginal Australians have long been the standard bearers for robust cranial morphology, this study reveals that human populations exhibit more than one pattern of cranial robusticity. The results of this study emphasize a primary trend of variability from gracile to robust (except in the occipital torus region), but also highlight secondary patterns of differential cranial trait expression within populations. For example, the Native American group from Grand Gulch, Utah is characterized by robust expression of the sagittal keel, bregmatic eminence, occipital torus, and malar tubercle, but a more gracile supraorbital region in contrast to the pattern seen in Aboriginal Australians.

All in all, this is an excellent data-driven paper, which combines data from skulls, genes, and climate to arrive at a comprehensive study of the phenomenon of modern human cranial robusticity and its etiology.


American Journal of Physical Anthropology doi:10.1002/ajpa.21120

Relationship of cranial robusticity to cranial form, geography and climate in Homo sapiens

Karen L. Baab et al.

Abstract

Variation in cranial robusticity among modern human populations is widely acknowledged but not well-understood. While the use of robust cranial traits in hominin systematics and phylogeny suggests that these characters are strongly heritable, this hypothesis has not been tested. Alternatively, cranial robusticity may be a response to differences in diet/mastication or it may be an adaptation to cold, harsh environments. This study quantifies the distribution of cranial robusticity in 14 geographically widespread human populations, and correlates this variation with climatic variables, neutral genetic distances, cranial size, and cranial shape. With the exception of the occipital torus region, all traits were positively correlated with each other, suggesting that they should not be treated as individual characters. While males are more robust than females within each of the populations, among the independent variables (cranial shape, size, climate, and neutral genetic distances), only shape is significantly correlated with inter-population differences in robusticity. Two-block partial least-squares analysis was used to explore the relationship between cranial shape (captured by three-dimensional landmark data) and robusticity across individuals. Weak support was found for the hypothesis that robusticity was related to mastication as the shape associated with greater robusticity was similar to that described for groups that ate harder-to-process diets. Specifically, crania with more prognathic faces, expanded glabellar and occipital regions, and (slightly) longer skulls were more robust than those with rounder vaults and more orthognathic faces. However, groups with more mechanically demanding diets (hunter-gatherers) were not always more robust than groups practicing some form of agriculture.

Link

More on the insanity that has dominated historical discourse in FYROM

I recently became aware of how insane some of the claims of the present-day FYROM government have become. It is hard to appreciate this for the Slav-less spectator who doesn't really have access to what is discussed in that country.

Thankfully, there are still rational voices in FYROM, and thanks to the efforts of brave citizens of that country such as Vasko Gligorjevic, we get to hear some of them.

Here are a couple of YouTube videos where the former Prime Minsiter of the country Ljubčo Georgievski describes the program of "antiquization" in the country, the adoption of fringe revisionist history as official, the denial of the Slavic element in modern Slavo-Paionians, and the extremely negative sentiments of proponents of "Ancient Macedonians" against those who emphasize the Slavic element in the country's history.



In the second clip, Mr. Georgievski asks why the proponents of "Ancient Macedonians" in FYROM seem so unconcerned with determining the Thracian, Illyrian, Dardanian, and Paeonian element in their ancestry, and are so hell-bent on discovering Macedonian ancestors. He also states -correctly- that Ancient Macedonia, including most of Upper Macedonia was in today's Greece, and all the rest (including FYROM) were conquered by the Macedonians, and not part of Macedonia itself.

Paleolithic Flutes from the early Aurignacian in Germany

The Hohle Fels site was in the news recently for the discovery of the "first depiction of the human form".

Nature doi:10.1038/nature08169

New flutes document the earliest musical tradition in southwestern Germany

Nicholas J. Conard et al.

Considerable debate surrounds claims for early evidence of music in the archaeological record. Researchers universally accept the existence of complex musical instruments as an indication of fully modern behaviour and advanced symbolic communication1 but, owing to the scarcity of finds, the archaeological record of the evolution and spread of music remains incomplete. Although arguments have been made for Neanderthal musical traditions and the presence of musical instruments in Middle Palaeolithic assemblages, concrete evidence to support these claims is lacking. Here we report the discovery of bone and ivory flutes from the early Aurignacian period of southwestern Germany. These finds demonstrate the presence of a well-established musical tradition at the time when modern humans colonized Europe, more than 35,000 calendar years ago. Other than the caves of the Swabian Jura, the earliest secure archaeological evidence for music comes from sites in France and Austria and post-date 30,000 years ago

Link

mtDNA of Tyrolean Iceman using a multiplexed Single-Base-Extension assay

From the paper:

In addition, because the Iceman’s sequence matches the rCRS at nps 497, 498, and 5913 (diagnostic of K1a, K1c, and K1b, respectively), we can extend previous suggestions that the Iceman’s genotype does not belong to any of the three known clades of K1, and should be referred to a new (undefined) paraphyletic clade, of K1 [25] (Figure 1).

...

The likelihood of the current results representing the endogenous DNA of the Iceman is substantially increased by the haplotype falling outside of K1a/K1b/K1c, combined with the unique hg K transition C8137T, matching the results of [25].

...

The fallibility of independent replication

Given the absence of 16093C and 16362C amongst the replication results of Handt et al., the only plausible conclusion is that these derived from a second, entirely different, hg K source. These results, combined with a unique haplotype in [25] and the present study, strongly suggests that both laboratories in the original study suffered from hg K contamination. The mtDNA profiles of the staff in the primary laboratory of the first study were not provided [14]; although a subsequent publication of the replicated results [37] disclosed that a member of the secondary laboratory staff was hg K (16224C-16311C), substantially increasing the likelihood for contamination occurring.

[25] refers to Ermini et al. on the Tyrolean Iceman mtDNA sequence, [14] to Handt et al., and [37] to Richards et al.

BMC Genetics doi:10.1186/1471-2156-10-29

Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman

Phillip Endicott et al.

Abstract (provisional)

Background

Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman.

Results

The multiplex assay developed for this study was able to test sufficient polymorphisms in one reaction to unequivocally demonstrate that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups.

Conclusions

The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results.

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Automatic writer identification of ancient greek inscriptions

IEEE Trans Pattern Anal Mach Intell. 2009 Aug;31(8):1404-14.

Automatic writer identification of ancient greek inscriptions

Panagopoulos M, Papaodysseus C, Rousopoulos P, Dafi D, Tracy S.

This paper introduces a novel methodology for the classification of ancient Greek inscriptions according to the writer who carved them. Inscription writer identification is crucial for dating the written content, which in turn is of fundamental importance in the sciences of history and archaeology. To achieve this, we first compute an ideal or "platonic" prototype for the letters of each inscription separately. Next, statistical criteria are introduced to reject the hypothesis that two inscriptions are carved by the same writer. In this way, we can determine the number of distinct writers who carved a given ensemble of inscriptions. Next, maximum likelihood considerations are employed to attribute all inscriptions in the collection to the respective writers. The method has been applied to 24 Ancient Athenian inscriptions and attributed these inscriptions to six different identified hands in full accordance with expert epigraphists' opinions.

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