Greece and Asia Minor in the Late Bronze Age: The Historical Background of Homer's Iliad

 

An interesting recent talk by Wolf-Dietrich Niemeier.

Morphological and mtDNA analysis of Mezzena mandible

 

I've written about late Neandertals becoming more AMH-like, and a new study on an Italian specimen that postdates the arrival of AMH in Europe lends some further support to that idea.
The Mezzena jaw has Neandertal mtDNA and shares a number of morphological traits with other Neandertals, but its overall shape places it within the cluster of modern humans  (triangles; figure on the left). Notice also that Qafzeh 9 (Q9) and Shkul V (SV) are also within the cluster of modern humans, and Spy 1 (a Neandertal) is actually closer to modern humans than to other Neandertals.
From the paper:

The position on the scatter plot of our specimen of interest, Mezzena, has been calculated a posteriori. Unsurprisingly, the Mezzena mandible does not present any particular affinities with mid-Pleistocene specimens. It is most similar to AMHs being positioned within the H. sapiens cloud of points and the DFA classifies the specimen with modern humans (Table S7). Especially its shape is similar to that of Ohalo II and to a lesser extent to the recent modern human specimen China5. However, it should be noted that its position also indicates affinities with some Neanderthal specimens: the late Neanderthal Spy 1 and Saint-Césaire, the Near-East specimens Tabūn II and Amud 1, and to a lesser extent the classic Neanderthals La Ferrassie 1 and Guattari III (Figure 2).

According to the authors:

In this light, we can interpret the position of the Mezzena mandible which stands within the modern human shape space, while presenting strong shape similarities with some Neanderthal specimens. Such a conflicting taxonomical position is not surprising, considering the geological age of the mandible [30]. Indeed, numerous late Neanderthals such as Spy 1, Saint Césaire and the Near-East mandibles Amud 1 and Tabun II possess hints of a chin (i.e. tuber symphyseo) though not a true modern human morphology [37], [51]. Late Neanderthals lived in area where AMHs might have been already present [2], [23], [52], while the Levantine fossils are displaying a less derived Neanderthal morphology [35], [36]. 

Therefore, in our view, this change in morphology of the mandibular chin among the fossils of Mezzena and other late Neanderthals could have been the result of a small degree of interbreeding with AMHs.

It would be interesting to sequence Mezzena to confirm the existence of AMH admixture.
PLoS ONE 8(3): e59781. doi:10.1371/journal.pone.0059781
Possible Interbreeding in Late Italian Neanderthals? New Data from the Mezzena Jaw (Monti Lessini, Verona, Italy)
Silvana Condemi et al.
In this article we examine the mandible of Riparo Mezzena a Middle Paleolithic rockshelter in the Monti Lessini (NE Italy, Verona) found in 1957 in association with Charentian Mousterian lithic assemblages. Mitochondrial DNA analysis performed on this jaw and on other cranial fragments found at the same stratigraphic level has led to the identification of the only genetically typed Neanderthal of the Italian peninsula and has confirmed through direct dating that it belongs to a late Neanderthal. Our aim here is to re-evaluate the taxonomic affinities of the Mezzena mandible in a wide comparative framework using both comparative morphology and geometric morphometrics. The comparative sample includes mid-Pleistocene fossils, Neanderthals and anatomically modern humans. This study of the Mezzena jaw shows that the chin region is similar to that of other late Neanderthals which display a much more modern morphology with an incipient mental trigone (e.g. Spy 1, La Ferrassie, Saint-Césaire). In our view, this change in morphology among late Neanderthals supports the hypothesis of anatomical change of late Neanderthals and the hypothesis of a certain degree of interbreeding with AMHs that, as the dating shows, was already present in the European territory. Our observations on the chin of the Mezzena mandible lead us to support a non abrupt phylogenetic transition for this period in Europe.
Link

Refined IBD in Beagle 4

 

The Beagle page doesn't show version 4 yet, but I'm sure it will eventually turn up there since this paper has just been published.
Genetics doi: 10.1534/genetics.113.150029

Improving the Accuracy and Efficiency of Identity by Descent Detection in Population Data
Brian L. Browning and Sharon R. Browning
Segments of identity by descent (IBD) detected from high-density genetic data are useful for many applications, including long-range phase determination, phasing family data, imputation, IBD mapping and heritability analysis in founder populations. We present Refined IBD, a new method for IBD segment detection. Refined IBD achieves both computational efficiency and highly accurate IBD segment reporting by searching for IBD in two steps. The first step (identification) uses the GERMLINE algorithm to find shared haplotypes exceeding a length threshold. The second step (refinement), evaluates candidate segments with a probabilistic approach to assess the evidence for IBD. Like GERMLINE, Refined IBD allows for IBD reporting on a haplotype level, which facilitates determination of multi-individual IBD and allows for haplotype-based downstream analyses. To investigate the properties of Refined IBD, we simulate SNP data from a model with recent super-exponential population growth that is designed to match UK data. The simulation results show that Refined IBD achieves a better power/accuracy profile than fastIBD or GERMLINE. We find that a single run of Refined IBD achieves greater power than 10 runs of fastIBD. We also apply Refined IBD to SNP data for samples from the UK and from Northern Finland, and describe the IBD sharing in these data sets. Refined IBD is powerful, highly accurate, easy to use, and is implemented in Beagle version 4.
Link

Was Homo floresiensis a cretin?

 

From the paper:

We are therefore disturbed that Brown (2012), though selecting those features that imply to him that LB1 could not be a cretin, does not also cite the many features in those same publications that imply cretinism, nor does he cite the many more features, both observational and quantitative implying cretinism, in Oxnard (2008), Oxnard et al. (2011), and Dennison et al. (2012). What is sorely needed is an independent review of, and free access to, the Liang Bua material.

HOMO - Journal of Comparative Human Biology
Volume 63, Issue 6, December 2012, Pages 407–412
More on the Liang Bua finds and modern human cretins
Charles Oxnard et al.
Brown (2012: LB1 and LB6 Homo floresiensis are not modern human (Homo sapiens) cretins, Journal of Human Evolution) makes errors of fact, omission and interpretation. Brown's comments refer, among others, to (1) delayed growth and development indicated by unfused epiphyses, (2) postcranial limb proportions: limbs to trunk, between limbs, and within limbs, (3) postcranial bone torsions and angles, (4) postcranial robusticity, real and apparent, (5) skull features, and (6) cretinism on Flores. In each of these areas, much information about cretins is incorrect and much information (Oxnard et al., 2010) comparing the Liang Bua remains with cretins is ignored.

Link

Population structure in the Netherlands

 

The three PCs are color-coded in panels b,c,d.
European Journal of Human Genetics , (27 March 2013) | doi:10.1038/ejhg.2013.48
Population structure, migration, and diversifying selection in the Netherlands
Abdel Abdellaoui et al.
Genetic variation in a population can be summarized through principal component analysis (PCA) on genome-wide data. PCs derived from such analyses are valuable for genetic association studies, where they can correct for population stratification. We investigated how to capture the genetic population structure in a well-characterized sample from the Netherlands and in a worldwide data set and examined whether (1) removing long-range linkage disequilibrium (LD) regions and LD-based SNP pruning significantly improves correlations between PCs and geography and (2) whether genetic differentiation may have been influenced by migration and/or selection. In the Netherlands, three PCs showed significant correlations with geography, distinguishing between: (1) North and South; (2) East and West; and (3) the middle-band and the rest of the country. The third PC only emerged with minimized LD, which also significantly increased correlations with geography for the other two PCs. In addition to geography, the Dutch North–South PC showed correlations with genome-wide homozygosity (r=0.245), which may reflect a serial-founder effect due to northwards migration, and also with height (♂: r=0.142, ♀: r=0.153). The divergence between subpopulations identified by PCs is partly driven by selection pressures. The first three PCs showed significant signals for diversifying selection (545 SNPs - the majority within 184 genes). The strongest signal was observed between North and South for the functional SNP in HERC2 that determines human blue/brown eye color. Thus, this study demonstrates how to increase ancestry signals in a relatively homogeneous population and how those signals can reveal evolutionary history.

Link

Admixture and pigmentation in Cape Verde

 

The interesting thing about this paper is that it shows that one can explain skin color in people from Cape Verde better if one uses their proportion of African/European admixture, rather than by looking at individuals' genotypes at loci associated with the trait. This probably means that many loci of minor effect on the trait differentiate Europeans from Africans.
Prediction of skin color based on ancestry is much better than prediction of eye color from the same, which is not surprising since skin color is a highly polygenic trait.
PLoS Genet 9(3): e1003372. doi:10.1371/journal.pgen.1003372
Genetic Architecture of Skin and Eye Color in an African-European Admixed Population
Sandra Beleza et al.
Abstract
Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3×10−62, SLC24A5 P = 9.6×10−9) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4×10−27, TYR P = 1.1×10−9, APBA2[OCA2] P = 1.5×10−8, SLC45A2 P = 6×10−9) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (~44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ~70% of the estimated heritability.

Link

Long live the 25th March 1821

 

Y chromosomes and mtDNA from the Maldives

 

Of interest from the paper:

The haplogroup J(M304) Y chromosomes are all in subgroup J2(M172).

...

However, Eaaswarkhanth et al. (2010) report that Muslims and non-Muslims in India largely have the same Y-haplogroup frequency distribution, except that in Muslims low frequencies of Y-E1b1b1a(M78), Y-J(M304)(xJ2(M172)), and Y-G(M201) are found that are absent in non-Muslims (Eaaswarkhanth et al., 2010). In our Maldivian sample, none of those Y-haplogroups were found.

AJPA DOI: 10.1002/ajpa.22256
Indian ocean crossroads: Human genetic origin and population structure in the maldives
Jeroen Pijpe et al.
The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago. Am J Phys Anthropol 000:000–000, 2013. © 2013 Wiley Periodicals, Inc.

Link

Revised timescale of human mtDNA evolution (Fu et al. 2013)

 

An important new paper has just appeared in Current Biology. It is very exciting for a couple of reasons:

• The paper uses the idea of branch shortening to infer dates for the mtDNA phylogeny. Briefly, if one counts differences between a present-day sample P and an ancient sample A, one can get a sense of when their most recent common ancestor X, lived. But PX and PA are not equal: PA is shorter, because A has "missed" a few thousand years of evolution (depending on its age). If we know the age of A (and this can be reliably known by direct dating for many samples), then we can infer the time of X.

Looking at the ages of many haplogroups, I don't see any that immediately strike me as inconsistent with recent published age estimates based on modern mtDNA alone, such as those from the Copernican reassessment paper. In any case, this is an exciting new application of an idea that will yield good dates for haplogroup ages in the future. For example, it could be used to date Y-chromosome lineages as well, when high-quality sequences of ancient human Y-chromosomes become available.

• The paper also presents a number of new and exciting ancient DNA samples:

Please note that the "Cro Magnon" sample is actually revealed to be non-ancient in the study; that is another utility of the "branch shortening" idea, since it can demonstrate that purported very old samples are in fact fairly recent.
Note the important new samples from Dolni Vestonice, Oberkassel, Continenza, all of which are Paleolithic Europeans and all of which belong, without exception to subgroups of haplogroup U. It appears that Europe was indeed dominated by this haplogroup down to Mesolithic times, with a sharp discontinuity with early Neolithic Europeans.
The only outlier in the European context is Paglicci Str. 4b which is assigned to haplogroup H1. However:

Using this criterion, we excluded Paglicci Str. 4b from further analysis as the rate of C to T misincorporation at the 50 end was only 8.8%, thus making an ancient origin for the DNA in this sample uncertain [14].

Personally, I doubt there was any mtDNA haplogroup H in pre-Neolithic Europe, as the first author of this paper has also argued for in a previous one.
There is also a new sample from Boshan; it is probably too early to detect a pattern, but it is nonetheless noteworthy that it also belonged to mtDNA haplogroup B like the much earlier sample from Tianyuan.
Finally, the paper also discusses the issue of the mutation rate, noting that the divergence between Eurasian (M+N) and African (L3) mtDNA is much later than that inferred for autosomal DNA using new and "slow" de novo autosomal mutation rates. In my opinion there are two possible interpretations for this: one that there's something wrong with the slow rates, while another is that the earlier divergence using autosomal DNA may be a consequence of inflation due to admixture events in Africa.
Current Biology doi:10.1016/j.cub.2013.02.044
A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
Qiaomei Fu et al.
Summary
Background
Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought.
Results
Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya.
Conclusions
Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome.
Link

Abnormalities in Pleistocene Homo

 

An excess of congenital defects is certainly compatible with high levels of inbreeding, and the publication of the Denisova genome clearly suggested "extremely low" genetic diversity in that Pleistocene human. It'll be interesting to see if more ancient DNA data will reveal high levels of inbreeding consistent with the abundance of genetic abnormalities evident in the anthropological record.

PLoS ONE 8(3): e59587. doi:10.1371/journal.pone.0059587
An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo

Xiu-Jie Wu et al.

We report here a neurocranial abnormality previously undescribed in Pleistocene human fossils, an enlarged parietal foramen (EPF) in the early Late Pleistocene Xujiayao 11 parietal bones from the Xujiayao (Houjiayao) site, northern China. Xujiayao 11 is a pair of partial posteromedial parietal bones from an adult. It exhibits thick cranial vault bones, arachnoid granulations, a deviated posterior sagittal suture, and a unilateral (right) parietal lacuna with a posteriorly-directed and enlarged endocranial vascular sulcus. Differential diagnosis indicates that the perforation is a congenital defect, an enlarged parietal foramen, commonly associated with cerebral venous and cranial vault anomalies. It was not lethal given the individual’s age-at-death, but it may have been associated with secondary neurological deficiencies. The fossil constitutes the oldest evidence in human evolution of this very rare condition (a single enlarged parietal foramen). In combination with developmental and degenerative abnormalities in other Pleistocene human remains, it suggests demographic and survival patterns among Pleistocene Homo that led to an elevated frequency of conditions unknown or rare among recent humans.

Link

High-quality Neandertal genome online

The Max Planck institute has posted their high-coverage Neandertal genome on their site. The data can be downloaded from here. They had done the same with the high-quality Denisova genome, and it's great that they're making data available ahead of the official scientific publication, as this allows others to start using it much earlier.
From their site:

The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010.  The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).
DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.

It then appears that Neandertals occupied the same cave as the elusive Denisovans. When? I guess we'll have to wait to find out, but the preliminary genetic analysis shown on the figure (top-left) makes it clear that the "Altai" specimen marked in red which is the source of the high-coverage Neandertal genome does indeed group with other Neandertals, while Denisova is more related to Neandertals than to modern humans.
I've highlighted this before, but it bears repeating: divergence between Neandertals and Denisovans --who were in the same place (Denisova cave), perhaps some thousands of years apart-- seems to exceed that found between any two modern human groups which span the entire Earth.

New Neandertal remains from Mani

The age and cave origin of these remains may conceivably make them useful for ancient DNA studies.
Journal of Human Evolution doi:10.1016/j.jhevol.2013.02.002
New Neanderthal remains from Mani peninsula, Southern Greece: The Kalamakia Middle Paleolithic cave site
Katerina Harvati et al.
The Kalamakia cave, a Middle Paleolithic site on the western coast of the Mani peninsula, Greece, was excavated in 1993–2006 by an interdisciplinary team from the Ephoreia of Paleoanthropology and Speleology (Greek Ministry of Culture) and the Muséum national d'Histoire naturelle (Paris). The site is dated to between ca. 100,000 and >39,000 years BP (Before Present) and has yielded Mousterian lithics, a rich fauna, and human remains from several layers. The latter include 10 isolated teeth, a cranial fragment and three postcranial elements. The remains represent at least eight individuals, two of them subadults, and show both carnivore and anthropogenic modifications. They can be identified as Neanderthal on the basis of diagnostic morphology on most specimens. A diet similar to that of Neanderthals from mixed habitat is suggested by our analysis of dental wear (occlusal fingerprint analysis) and microwear (occlusal texture microwear analysis), in agreement with the faunal and palynological analyses of the site. These new fossils significantly expand the Neanderthal sample known from Greece. Together with the human specimens from Lakonis and Apidima, the Kalamakia human remains add to the growing evidence of a strong Neanderthal presence in the Mani region during the Late Pleistocene.
Link

Thesis of Oleg Balonovsky

is available here as pdf. Lots of interesting information, and a few striking maps. Hopefully, the fact that it's all in Russian won't be much of a problem in this day and age.
I will highlight a few pieces of information. First, a distribution of Y-chromosome haplogroups in Russian groups:

Notice:

• N1c-Tat is a general feature of the Russians, but N1b-P43 is only really found at any significant frequency in the northern groups.
• A strong contrast of E-M78 between central (present) and northern (absent) groups, consistent with a late introduction of this haplogroup in easternmost Europe.
• South-Central-North decreasing frequency of R1a; now, it's not clear how R1a came to be in Russians: some of it may be legacy of its initial entry into Europe from the east, other could be of historical import, and may have even arrived during the Slavic expansion from Central Europe. The pattern probably is the reverse of the high frequency of N1, indicating increasing importance of Finno-Ugric substratum in the north.
• Fairly interesting that of the two likely "Balkan" haplogroups E-M78 and I-P37, the former is modal in central region, the latter in southern one. The absence of both in "deep Asia" suggests a late introduction, as mentioned before, but when?

Also of interest a haplotype analysis within R1a1a-M198:

My most immediate observation is the set of mainly Indian highly divergent haplotypes on the left. There has been (well-deserved) excitement about recent Y-SNP progress within this haplogroup, but we should not neglect the occurrence of outliers/relics in our reconstruction of a haplogroup's history. I'd love to see those few Indian haplotypes SNP-tested using the currently available SNPs, or even used to develop new SNPs for this important Eurasian haplogroup.

Millet use ~11 thousand years ago in northern China

 

PNAS March 6, 2012 vol. 109 no. 10 3726-3730
Early millet use in northern China
Xiaoyan Yang et al.
It is generally understood that foxtail millet and broomcorn millet were initially domesticated in Northern China where they eventually became the dominant plant food crops. The rarity of older archaeological sites and archaeobotanical work in the region, however, renders both the origins of these plants and their processes of domestication poorly understood. Here we present ancient starch grain assemblages recovered from cultural deposits, including carbonized residues adhering to an early pottery sherd as well as grinding stone tools excavated from the sites of Nanzhuangtou (11.5–11.0 cal kyBP) and Donghulin (11.0–9.5 cal kyBP) in the North China Plain. Our data extend the record of millet use in China by nearly 1,000 y, and the record of foxtail millet in the region by at least two millennia. The patterning of starch residues within the samples allow for the formulation of the hypothesis that foxtail millets were cultivated for an extended period of two millennia, during which this crop plant appears to have been undergoing domestication. Future research in the region will help clarify the processes in place.
Link

Admixture in Southern Africa (Petersen et al. 2013)

Related:

• The genetic prehistory of southern Africa
• Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

PLoS Genet 9(3): e1003309. doi:10.1371/journal.pgen.1003309
Complex Patterns of Genomic Admixture within Southern Africa
Desiree C. Petersen et al.
Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly proportional to geographic distance. The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion) and inter-continental migration (European-driven colonization) have resulted in complex patterns of admixture between ancient geographically isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan representation, we identify the Ju/'hoan (n = 19) as a distinct early diverging human lineage with little to no significant non-Khoesan contribution. In contrast to the Ju/'hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15) and Khoesan !Xun (n = 14), respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan contributions to the Coloured (n = 25) and Baster (n = 30) populations. The latter populations were further impacted by 170 years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation (admixture). The populations of southern Africa provide a unique opportunity to investigate the genomic variability from some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently diverged human lineages.
Link

Genomewide structure of populations from European Russia (Khrunin et al. 2013)

Notice:

1. The intermediate position of Estonians between Balts and Finns
2. The intermediate position of some Russian groups between Komi and the main body of Europeans.

PLoS ONE 8(3): e58552. doi:10.1371/journal.pone.0058552
A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe
Andrey V. Khrunin et al.
Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.
Link

Secrets of the Stonehenge skeletons

Any Britons in my readership are invited to watch this documentary on Sunday:

Ancient bodies lie buried beneath Stonehenge, but what can they tell us about Britain's greatest prehistoric monument? One man has found vital clues to this ancient puzzle.

A related BBC story has the title of Stonehenge builders travelled from far, say researchers:

The researchers believed as many as 4,000 people gathered at the site, at a time when Britain's population was only tens of thousands. 

... 

The academics suggested that Stonehenge was built about 200 years earlier than previously thought, some 4,500 years ago.

And the Guardian:

Stonehenge may have been burial site for Stone Age elite, say archaeologists
Dating cremated bone fragments of men, women and children found at site puts origin of first circle back 500 years to 3,000BC

In the rise and wane of the cremation ritual I have hinted at the possible rise of the cremation ritual as a way of disposing of the dead in a way that would make their remains portable. Not sure what the current research has discovered but "cremated remains" + "builders from far" makes for a good combination.
If you do watch and learn something that might interest blog readers, feel free to leave a comment.

33,000-year old dog from the Altai

From the paper:

In conclusion, our analyses support the hypothesis that the Altai specimen is more closely related to domestic dogs than to extant wolves, but we stress the point that these analyses were limited to a single, maternally inherited locus and more sequence data would be needed to obtain a statistically well supported phylogeny and unambiguously resolve the genetic relationship of the Altai specimen. However, this preliminary analysis affirms the conclusion that the Altai specimen is likely an ancient dog with a shallow divergence from ancient wolves. These results suggest a more ancient history of the dog outside the Middle East or East Asia, previously suggested as centres of dog origin. Additional discoveries of ancient dog-like remains are essential for further narrowing the time and region of origin for the domestic dog [5].

An ancient dog with shallow divergence from ancient wolves is probably what we might expect if dogs had been domesticated by some of the first Upper Paleolithic Eurasians a few thousand years prior to the date of this particular specimen.
PLoS ONE 8(3): e57754. doi:10.1371/journal.pone.0057754
Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog
Anna S. Druzhkova et al.
The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.
Link

Y chromosomes of Bulgarians (Karachanak et al. 2013)

Bulgaria had been something of a blank area in studies of uniparental markers, so it's nice to finally see a comprehensive Y-chromosome study of the country.
The dates in the paper are based on the "evolutionary mutation rate". I suspect that ancient DNA will be the final arbiter in this issue, because, for example, a Mesolithic TMRCA of E-V13 in Bulgaria implies that we'll find a lot of it in Neolithic contexts, whereas a Bronze Age one implies that we'll find a little if any of it, and a discontinuity across time.
Of interest is the occurrence of some E*(xM35, M2) in this sample in Burgas, Varna, and Plovdiv. It would be interesting to trace the ancestry of the bearers of these Y-chromosomes. I know that there still exists a minority-within-a-minority of Black Muslims in Greek Thrace, and it's not inconceivable that these Y-chromosomes may represent the legacy of a similar population; in any case, their haplotypes can be found in Table S5 for anyone wanting to investigate.
SNP Diversity within R seems substantial, and as always, it is difficult to say much, since this may be a consequence of either (i) a plausible role of the Balkans as a staging point of the likely invasion of Europe in late prehistory, or (ii) back-migration of derived R-bearers into the Balkans, be them Slavs or Goths or "eastern" folks of various stripes during history. Once again, I suspect that ancient DNA might solve this riddle, or, alternatively, routine high-coverage sequencing of the Y chromosome that might inform us, e.g., about the TMRCA of a Bulgarian and a German R-U152 or a Bulgarian and Polish R-M458.
PLoS ONE 8(3): e56779. doi:10.1371/journal.pone.0056779
Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry
Sena Karachanak et al

To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ~ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.
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Extreme mobility in the late Pleistocene (Shaw and Stock 2013)

The idea of Pleistocene remains having "extremely active and mobile lives" is consistent with the hypothesis that people moved around during prehistory, and did not simply grow roots after their initial colonization of the planet, as some models of "Paleolithic continuity" have affirmed.
Journal of Human Evolutiondoi:10.1016/j.jhevol.2013.01.004
Extreme mobility in the Late Pleistocene? Comparing limb biomechanics among fossil Homo, varsity athletes and Holocene foragers
Colin N. Shaw, Jay T. Stock
Descriptions of Pleistocene activity patterns often derive from comparisons of long bone diaphyseal robusticity across contemporaneous fossilized hominins. The purpose of this study is to augment existing understanding of Pleistocene hominin mobility patterns by interpreting fossil variation through comparisons with a) living human athletes with known activity patterns, and b) Holocene foragers where descriptions of group-level activity patterns are available. Relative tibial rigidity (midshaft tibial rigidity (J)/midshaft humeral rigidity (J)) was compared amongst Levantine and European Neandertals, Levantine and Upper Palaeolithic Homo sapiens, Holocene foragers and living human athletes and controls. Cross-country runners exhibit significantly (p < 0.05) greater relative tibial rigidity compared with swimmers, and higher values compared with controls. In contrast, swimmers displayed significantly (p < 0.05) lower relative tibial rigidity than both runners and controls. While variation exists among all Holocene H. sapiens, highly terrestrially mobile Later Stone Age (LSA) southern Africans and cross-country runners display the highest relative tibial rigidity, while maritime Andaman Islanders and swimmers display the lowest, with controls falling between. All fossil hominins displayed relative tibial rigidity that exceeded, or was similar to, the highly terrestrially mobile Later Stone Age southern Africans and modern human cross-country runners. The more extreme skeletal structure of most Neandertals and Levantine H. sapiens, as well as the odd Upper Palaeolithic individual, appears to reflect adaptation to intense and/or highly repetitive lower limb (relative to upper limb) loading. This loading may have been associated with bipedal travel, and appears to have been more strenuous than that encountered by even university varsity runners, and Holocene foragers with hunting grounds 2000–3000 square miles in size. Skeletal variation among the athletes and foraging groups is consistent with known or inferred activity profiles, which support the position that the Pleistocene remains reflect adaptation to extremely active and mobile lives.
Link