Thursday, 28 March 2013

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.

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.

Wednesday, 27 March 2013

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.


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.


Monday, 25 March 2013

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.
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.


Long live the 25th March 1821


Friday, 22 March 2013

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.


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.
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.
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.
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.

Tuesday, 19 March 2013

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.


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.

Monday, 18 March 2013

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.

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:


  • 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.

Friday, 15 March 2013

Admixture in Southern Africa (Petersen et al. 2013)


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.

Monday, 11 March 2013

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


  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.

Sunday, 10 March 2013

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.

Thursday, 7 March 2013

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.

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.

Wednesday, 6 March 2013

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.

Tuesday, 5 March 2013

Late Middle Pleistocene teeth from South China (Liu et al. 2013)

From the paper:

The Panxian Dadong P3 falls in the upper left quadrant, an area that, with the exception of two out of the nine Atapuerca-SH specimens and S7-34, is exclusively occupied by recent humans. Thus this geometric morphometric analysis indicates that the general crown conformation of the Panxian Dadong P3 resembles some European Middle Pleistocene hominins, Chinese Upper Pleistocene hominins, and particularly the recent human specimens. 
According to the above comparisons, the Panxian Dadong P3 preserves some primitive and highly polymorphic traits, but in general its conformation is derived. Its occlusal morphology is simple, and the contour is symmetrical with a lingual cusp that is narrower than the buccal one. All these features make the Panxian Dadong P3 most similar to Upper Pleistocene hominins and recent humans in our comparative samples.
I suspect that the age of these teeth will render them useless for ancient DNA work.
Journal of Human Evolution doi:10.1016/j.jhevol.2012.10.012
Late Middle Pleistocene hominin teeth from Panxian Dadong, South China
Wu Liu et al.
The hominin teeth and evidence of hominin activities recovered from 1991 to 2005 at the Panxian Dadong site in South China are dated to the late Middle Pleistocene (MIS 8–6 or ca. 130–300 ka), a period for which very little is known about the morphology of Asian populations. The present study provides the first detailed morphometric description and comparisons of four hominin teeth (I1, C1, P3 and P3) from this site. Our study shows that the Panxian Dadong teeth combine archaic and derived features that align them with Middle and Upper Pleistocene fossils from East and West Asia and Europe. These teeth do not display any typical Neanderthal features and they are generally more derived than other contemporaneous populations from Asia and Africa. However, the derived traits are not diagnostic enough to specifically link the Panxian Dadong teeth to Homo sapiens, a common problem when analyzing the Middle Pleistocene dental record from Africa and Asia. These findings are contextualized in the discussion of the evolutionary course of Asian Middle Pleistocene hominins, and they highlight the necessity of incorporating the Asian fossil record in the still open debate about the origin of H. sapiens.

Our rabbit-hunting ancestors (Fa et al. 2013)

From the paper:

Relative to other mammal groups, rabbit bone abundance was always significantly higher during the Upper Palaeolithic (76%) and Mesolithic (59%) than during the Middle Palaeolithic (Fig. 4). The difference between the average rabbit remains and that of cervids, the second most abundant prey item, were less than 10% during the Mousterian. In contrast, during the Upper Palaeolithic and Mesolithic, the difference between the rabbit and the second-most important prey items was over 60% and 20%, respectively. After the rabbit, large ungulates (caprids, cervids and equids) were relatively important during the Middle and Upper Palaeolithic, while caprids, cervids and suids took that place during the Mesolithic (Fig. 4).
Our evidence indicates that hominin diets may have changed from one dependent on large mammals during the Middle Palaeolithic to diets dominated by smaller species in the Upper Palaeolithic, in particular by the wild rabbit. The explanation for this transition is either that climate change negatively impacted large mammal populations, forcing prehistoric people to incorporate smaller vertebrate species into their diets, or that people themselves negatively impacted large mammal populations, which in turn forced foragers to add smaller species to their diets.

I am not sure how modern hunter-gatherers hunt rabbits, but I would think that trapping, or some type of slingshot or blowdart would be ideal for this small and fast-moving animal. Did Neandertals simply lack efficient technology to capture rabbit, or is there some other reason why they underutilized the species?
Journal of Human Evolution DOI: 10.1016/j.jhevol.2013.01.002
Rabbits and hominin survival in Iberia
John E. Fa et al.
High dependence on the hunting and consumption of large mammals by some hominins may have limited their survival once their preferred quarry became scarce or disappeared. Adaptation to smaller residual prey would have been essential after the many large-bodied species decreased in numbers. We focus on the use of a superabundant species, the rabbit, to demonstrate the importance of this taxon in Iberia as fundamental to predators. We show that the use of the rabbit over time has increased, and that there could have been differential consumption by Neanderthals and Anatomically Modern Humans (AMH). Analysis of bone remains from excavations throughout Iberia show that this lagomorph was a crucial part of the diet of AMH but was relatively unutilised during the Mousterian, when Neanderthals were present. We first present changes in mammalian biomass and mean body mass of mammals over 50,000 years, to illustrate the dramatic loss of large mammalian fauna and to show how the rabbit may have contributed a consistently high proportion of the available game biomass throughout that period. Unlike the Italian Peninsula and other parts of Europe, in Iberia the rabbit has provided a food resource of great importance for predators including hominins. We suggest that hunters that could shift focus to rabbits and other smaller residual fauna, once larger-bodied species decreased in numbers, would have been able to persist. From the evidence presented here, we postulate that Neanderthals may have been less capable of prey-shifting and hence use the high-biomass prey resource provided by the rabbit, to the extent AMH did.

Monday, 4 March 2013

Y chromosomes of pastoralists and farmers from the Sahel

Am J Phys Anthropol DOI: 10.1002/ajpa.22236
Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel
Jana Bučková et al.
The African Sahel is conducive to studies of divergence/admixture genetic events as a result of its population history being so closely related with past climatic changes. Today, it is a place of the co-existence of two differing food-producing subsistence systems, i.e., that of sedentary farmers and nomadic pastoralists, whose populations have likely been formed from several dispersed indigenous hunter-gatherer groups. Using new methodology, we show here that the male gene pool of the extant populations of the African Sahel harbors signatures of multiple and differentiated contributions from different genetic sources. We also show that even if the Fulani pastoralists and their neighboring farmers share high frequencies of four Y chromosome subhaplogroups of E, they have drawn on molecularly differentiated subgroups at different times. These findings, based on combinations of SNP and STR polymorphisms, add to our previous knowledge and highlight the role of differences in the demographic history and displacements of the Sahelian populations as a major factor in the segregation of the Y chromosome lineages in Africa. Interestingly, within the Fulani pastoralist population as a whole, a differentiation of the groups from Niger is characterized by their high presence of R1b-M343 and E1b1b1-M35. Moreover, the R1b-M343 is represented in our dataset exclusively in the Fulani group and our analyses infer a north-to-south African migration route during a recent past.

Friday, 1 March 2013

Genomewide diversity in the Levant (Haber et al. 2013)

Razib points me to a new paper (and its associated data, consisting of Christian, Druze, and Muslim Lebanese).
Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture
Marc Haber et al.
The Levant is a region in the Near East with an impressive record of continuous human existence and major cultural developments since the Paleolithic period. Genetic and archeological studies present solid evidence placing the Middle East and the Arabian Peninsula as the first stepping-stone outside Africa. There is, however, little understanding of demographic changes in the Middle East, particularly the Levant, after the first Out-of-Africa expansion and how the Levantine peoples relate genetically to each other and to their neighbors. In this study we analyze more than 500,000 genome-wide SNPs in 1,341 new samples from the Levant and compare them to samples from 48 populations worldwide. Our results show recent genetic stratifications in the Levant are driven by the religious affiliations of the populations within the region. Cultural changes within the last two millennia appear to have facilitated/maintained admixture between culturally similar populations from the Levant, Arabian Peninsula, and Africa. The same cultural changes seem to have resulted in genetic isolation of other groups by limiting admixture with culturally different neighboring populations. Consequently, Levant populations today fall into two main groups: one sharing more genetic characteristics with modern-day Europeans and Central Asians, and the other with closer genetic affinities to other Middle Easterners and Africans. Finally, we identify a putative Levantine ancestral component that diverged from other Middle Easterners ~23,700–15,500 years ago during the last glacial period, and diverged from Europeans ~15,900–9,100 years ago between the last glacial warming and the start of the Neolithic.

Doubt cast on Tam Pa Ling age

For reference, see the post on the original article:
  • Tam Pa Ling: modern humans in Southeast Asia at 63-46ka

From a criticism of the original paper:

Hence, contrary to the authors' assertion that TPL1 has a “minimum secured age of 46 ka and a maximum age of ∼63 ka”, the published stratigraphy, if correct, indicates that the TPL1 specimen is no older than 46 ka. TPL1’s status as “the earliest well-dated modern human fossil east of the Jordan Valley” also appears weak compared with the Liujiang specimen dated to ∼153 ka (3), the Callao Cave fossil in the Philippines dated to 67 ka (4), and, above all, the ∼100 ka modern fossil from Zhirendong (5), discovered only 484 km northeast of Tam Pa Ling in Southern China.

Irreconcilable differences between stratigraphy and direct dating cast doubts upon the status of Tam Pa Ling fossil

Alain Pierret et al.


... and from a reply to the criticism by the authors:

They question the validity of the dating because of an apparent “reverse stratigraphy” (Fig. 1), whereby “older” dates are located higher in the section [i.e., 51.4 (14C) at 2.1 m] and “younger” dates are at the bottom of the section [i.e., 48 ka (optically stimulated luminescence [OSL]) and >49.2 ka (14C) at 4.3 m] (2). This criticism ignores the presented SEs (table 2 and table S1 in ref. 1), which make the results statistically equivalent (Table 1). More importantly, they ignore that the radiocarbon results are well beyond the accepted radiocarbon barrier of ∼40 ka (3), indicating that the charcoal has a minimum age of ∼40 ka. Bearing in mind these problems, we have conservatively estimated the burial age to be ∼46 ka according to the luminescence dating of the sediments. As the luminescence results are stratigraphically consistent, we perceive no irreconcilable differences between the stratigraphy and dating.
Finally, we interpret TPL1 as the earliest human fossil that is both well-dated and fully modern in morphology. Zhirendong demonstrates a mixture of archaic and modern traits, making it significant but not fully modern in appearance (4). Similarly, the metatarsal from Callao Cave is only diagnostic to the genus Homo given that it falls within “the morphological and size ranges of Homo habilis and H. floresiensis” (ref. 5, p. 123). Although the modernity of the Liujiang fossil is not questioned, it has no direct date and no secure stratigraphic provenance. It has been variably dated to ca. 20 ka, ca. 67 ka, 111 to 139 ka, and >153 ka (6), and this uncertain stratigraphic context has prevented many scholars from accepting any of the dates currently attributed to it (6).

Reply to Pierret et al.: Stratigraphic and dating consistency reinforces the status of Tam Pa Ling fossil

Fabrice Demeter et al.


Extremely old (237–581 kya) root of human Y-chromosome phylogeny

I had mentioned this research before, and now it has officially been published. There are three things to be excited about this new paper:
First, it forces us to consider the possibility of either (i) archaic admixture in Africa, or (ii) a much more ancient time depth of modern humans than the first fossils from Ethiopia dated to about ~200 thousand years ago.
Second, it underscores the importance of collaboration between academia and regular folk, since it was the combined contributions of academics, genetic genealogists, and the owners of the new A00 basal Y-chromosomes that made this new discovery possible.
And, third, it shows that the extraordinary can be discovered without contacting isolated tribes or seeking human bones in remote regions, but rather through careful scrutiny of large volumes of data for the proverbial needle in the haystack.
The paper developed a model of Y-chromosome mutation based on the estimate of Kong et al. Significantly, though:
If we were to use the higher mutation rate (1.0x10^-9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39x10^-9  -   7.07x10^- 9), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ~39 kya6 (i.e., versus ~63 kya for the mutation rate used here).
A 39kya common ancestor for Eurasian Y-chromosomes makes no sense, since we now know for sure that by that time, the differentiation of Eurasians was already well on its way and modern humans in remote parts of the Old World have been documented much earlier than that time.
A ~63kya common ancestor, on the other hand, fits nicely with my "two deserts" theory of modern human origins, according to which the ancestors of Eurasians faced an ecological crisis in Arabia when it became much drier post-70kya; that seems like a most opportune time for the major Eurasian bottleneck and the corresponding coalescence of Eurasian Y-chromosomes to a single man. And, while there is no a priori reason for Y chromosomes and mtDNA to behave similarly, the age of the "older" Eurasian ur-mother, haplogroup N at 59 thousand years, with presumably an older ancestor within mtDNA haplogroup L3 founding the Eurasian population.
Also, if modern human-Neandertal admixture had occurred  "most likely 47,000–65,000 years ago", then the expansion of modern Proto-Eurasians within a 70-60kya timeframe north Out-of-Arabia would have brought them in contact with their northern Neandertal neighbors. On the other hand, it would be incredible if modern humans experienced admixture with Neandertals but were still much later a very small population (to allow for the coalescence of their Y-chromosomes to one man ~39kya).
So, in summary, the mutation rate used by the authors seems consistent with what we know about an important calibration point of the human story.
But, who were the people in Africa responsible for the introgression of A00 chromosomes? Mendez et al. used the haplotype of the African American A00 individual and discovered his patrilineal kin among theMbo of Cameroon, who are Bantu farmers.
I have observed before that Pygmies and Bushmen represent only a tiny fraction of pre-existing African genetic diversity, the part that had not yet been absorbed into the farmers' expanding population by the time that Africa came to the attention of of modern science. We see traces of Pygmy and Bushman ancestry in some African farmers, and there were probably other groups, no longer extant as distinct ethno-cultural entities, but, nonetheless, surviving as genetic fragments in the genomes of the farmers.
Thus, while it still makes sense to study the surviving hunter-gatherers of Africa who make up perhaps a percent or less of the population of Africa, it may be equally important to study different groups of African farmers who may possess a much richer treasure trove (albeit diluted) of such "Palaeoafrican" ancestry.
Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes.40,41,43,44 This could take the form of long-standing population structure among AMH populations45 or archaic introgression from an archaic form into the ancestors of AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.47 Further surveys in sub- Saharan Africa and in the African Diaspora might uncover more diverged basal lineages, which will help to disentangle some of the complex evolutionary processes that shape patterns of Y chromosome diversity.

AJHG 10.1016/j.ajhg.2013.02.002
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree
Fernando L. Mendez et al.
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Wednesday, 27 February 2013

Y chromosomes of Corded Ware at Wroclaw-Jagodno (SW Poland)

From the paper:
Two teeth coming from fossil human skeletons were examined in the Molecular Technology Institute of Forensic Medicine Department, Wroclaw Medical University. It was stated that both teeth came from two men on the basis of the gene of amelogenin variants study. Determining polymorphisms of SNP type from chromosome Y resulted in categorizing skeleton from grave no. 1 with very high probability into haplogroup G, whereas skeleton from grave no. 2 with very high probability into one of three haplogroups J, I or E*.
Table 2:

It appears that dots represent identity with the reference sequence, so for example M201 has a dot for skeleton 1 which indicates a T at position 15,027,529 (GRCh37) which is the position where this mutation has occurred. So, the attribution of skeleton 1 to haplogroup G seems reasonable, and suggests continuity between the Neolithic population of Europe (where G is over-represented) and this CW individual.
It's not clear to me how skeleton 2 is attributed to J or I or E* on the basis of these SNPs. If anyone can figure it out, post in the comments.

Journal of Archaeological Science doi:10.1016/j.jas.2013.02.002
Assessment of late Neolithic pastoralist's life conditions from the Wroclaw-Jagodno site (SW Poland) on the basis of physiological stress markers
Bohdan Gworys et al.
So-called physiological stress markers are extremely valuable in assessing life conditions of old human populations. They constitute effects of adverse environmental conditions, which leave traces on skeleton. Those traces allow for partial assessment of life conditions not only in environmental and social but also cultural aspects for prehistoric populations. The aim of this study is to estimate the influence of general environmental conditions on human organism at the final stage of the Neolithic period – in the Corded Ware culture. Two skeletons discovered in a tumulus on the outskirts of Wroclaw in the Jagodno district have been subjected to assessment. Their age at the moment of death has been determined in both cases on the basis of multi-feature analysis of changes occurring in formation of particular morphologic features of skeleton and teeth. Attention has been paid to the obliteration degree of skull sutures and the surface state of chewing tooth crowns. A comprehensive DNA analysis has been conducted determining sex of the remains. Also bacteriological analysis of the research material has been conducted. Measurements of all available metric features of the skeletons have been performed with the use of the Martin method. Inventory and basic description of the finds accompanying skeleton remains have been carried out as well. Intensity of the following physiological stress markers have been defined and evaluated: Harris lines; cribra orbitalia; cribra cranii. Skull morphology, degree of suture obliteration, surface state of chewing tooth crowns and estimation of degree of bone development of postcranial skeleton indicate that both skeletons detailed age was about 16 – 18 years. Harris lines on the femur were formed in the 2nd and the 3rd year of life and on both tibias – in the 2nd year of life. Obtained results indicate that those people were expose to stress connected with food deficit when they were very young. Poor porotic changes on the skull and isotopic data suggest that their life quality increased at later age.

Connections between Indus Valley and Mesopotamia

Of interest from the paper:
Based on this distribution of values, it would appear from our preliminary analysis that almost half of the individuals sampled from the Harappa cemetery have isotope values outside the local baseline (0.7158-0.7189). Most of these individuals have values below the Harappa range. In addition, there are at least three non-local individuals with higher values, including one with an extremely isotope ratio that cannot be from the Harappa region. A more detailed discussion of the Harappa samples will be presented in a future publication on the Harappa cemetery, but it is clear that many of what appear to be local individuals at Harappa are females and they are associated in burial with nearby males who are clearly not local. These preliminary patterns require further testing before major conclusions can be proposed, but it does suggest that they represent a unique population of people from multiple regions of the Indus valley or beyond.

Journal of Archaeological Science
Volume 40, Issue 5, May 2013, Pages 2286–2297
A new approach to tracking connections between the Indus Valley and Mesopotamia: initial results of strontium isotope analyses from Harappa and Ur
J. Mark Kenoyer et al.
Exchange and interaction between early state-level societies in Mesopotamia and the Indus Valley during the 3rd millennium BC has been documented for some time. The study of this interaction has been dominated by the analysis of artifacts such as carnelian beads and marine shell, along with limited textual evidence. With the aid of strontium, carbon, and oxygen isotopes, it is now possible to develop more direct means for determining the presence of non-local people in both regions. This preliminary study of tooth enamel from individuals buried at Harappa and at the Royal Cemetery of Ur, indicates that it should be feasible to identify Harappans in Mesopotamia. It is also possible to examine the mobility of individuals from communities within the greater Indus Valley region.

Tuesday, 26 February 2013

mtDNA of Yumans and Athapaskans

Am J Phys Anthropol DOI: 10.1002/ajpa.22237
Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans

Cara Monroe et al.
A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273–3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458–4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in-situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai.

Stable isotopes and Nubian/Egyptian relationships

Wikipedia on Tombos site:

Tombos in an archaeological site in Northern Sudan. The village of Tombos was located at the third cataract of the Nile, not far from Kerma near the present Karmah. An important granite quarry was located here in the Pharaonic era. Its stone was used mostly to build statues and buildings between the river delta and the southern regions of the kingdom. A statue to the Pharaoh Taharqa, abandoned for over 2700 years, contains inscriptions. About 3000 years ago, there were pyramids dedicated to ten noble Egyptians. 
In 2000, several discoveries were made by the archaeologist, Professor Stuart Tyson Smith of the University of California, Santa Barbara. Smith and his team discovered the remains of a pyramid more than 3,500 years old, and the buried remains of an Egyptian colonial administrator named Siamun and his wife, Wernu. The two mummies were intact, and were buried with Ushabti figurines, a boomerang, and painted Mycenaean terracotta.[1] The burial chamber includes a series of rooms, some plundered by thieves, while others were undisturbed in whole or in part. Also, an epigraphic survey by the British Museum uncovered pharaonic rock-inscriptions.[2]
Might be interesting to look at DNA from remains from the Tombos site, both the ones mentioned in Wikipedia and the likely Egyptian immigrants mentioned in the following article.
Am J Phys Anthropol DOI: 10.1002/ajpa.22235
Strontium isotope (87Sr/86Sr) variability in the Nile Valley: Identifying residential mobility during ancient Egyptian and Nubian sociopolitical changes in the New Kingdom and Napatan periods
Michele R. Buzon, Antonio Simonetti
As a successful technique for identifying residential mobility in other areas, this study investigates the feasibility of using 87Sr/86Sr analysis to track the movements of the ancient peoples of Egypt and Nubia in the Nile Valley, who interacted via trade, warfare, and political occupations over millennia. Dental enamel from faunal remains is used to examine variability in strontium sources in seven regional sites; human enamel samples are analyzed from eight Nile Valley sites in order to trace human movements. The faunal samples show a wide range of 87Sr/86Sr values demonstrating that some animals were raised in a variety of locales. The results of the human samples reveal overlap in 87Sr/86Sr values between Egyptian and Nubian sites; however, Egyptian 87Sr/86Sr values (mean/median [0.70777], sd [0.00027]) are statistically higher than the Nubian 87Sr/86Sr values (mean [0.70762], median [0.70757], sd [0.00036], suggesting that it is possible to identify if immigrant Egyptians were present at Nubian sites. Samples examined from the site of Tombos provide important information regarding the sociopolitical activities during the New Kingdom and Napatan periods. Based on a newly established local 87Sr/86Sr range, human values, and bioarchaeological evidence, this study confirms the preliminary idea that immigrants, likely from Egypt, were present during the Egyptian New Kingdom occupation of Nubia. In the subsequent Napatan period when Nubia ruled Egypt as the 25th Dynasty, 87Sr/86Sr values are statistically different from the New Kingdom component and indicate that only locals were present at Tombos during this developmental time. 

 Y-DNA G and I (?) from Polish Corded Ware

 These results come from a 2830-2489 BC Corded Ware burial site in Jagodno, Southwestern Poland. I’ll expand on this post later today. For now, here are a couple of quotes from the study:
Two teeth coming from fossil human skeletons were examined in the Molecular Technology
Institute of Forensic Medicine Department, Wroclaw Medical University. It was stated that
both teeth came from two men on

Friday, 22 February 2013

ADMIXTOOLS 1.1 released

A new 1.1 version of ADMIXTOOLS has been released. From the description:
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. It can be downloaded for LINUX (see documentation). The software package also includes Affymetrix Human Origins Curated Dataset. Write to Arti Tandon if you have questions about the software and for scientific questions write to Nick Patterson. The new release fixes a serious bug in qpDstat. 
I've used this software before and posted some D-statistics from it on the blog, so if you find any that look strange, feel free to leave a comment. In any case, I'll be using the new version of qpDstat from now on.

Thursday, 21 February 2013

Indo-Europeans galore

A whole bunch of papers in a journal I hadn't heard of before, but written by some of the best known people in this field. I see lots of "Buy pdf" links to accompany them, so if you want to spare me the expense, feel free to e-mail me a copy.

Anyway, here's a list of titles for reference:

Anthony, David Two IE phylogenies, three PIE migrations, and four kinds of steppe - p. 1-21
Balanovsky, Oleg; Utevska, Olga; Balanovska, Elena Genetics of Indo-European populations: the past, the future - p. 23-35
Blazek, Vaclav Indo-European zoonyms in Afroasiatic perspective - p. 37-54
Burlak, Svetlana Languages, DNA, relationship and contacts - p. 55-67
Dybo, Anna Language and archeology: some methodological problems. 1. Indo-European and Altaic landscapes - p. 69-92
Dybo, Vladimir Dialectal variation of Proto-Indo-European in the light of accentological research - p. 93-108
Gamkrelidze, Tamaz; Ivanov, Vyacheslav Indo-European homeland and migrations: half a century of studies and discussions - p. 109-136
Kullanda, Sergey Early Indo-European social organization and the Indo-European homeland - p. 137-144
Mallory, J.P. Twenty-first century clouds over Indo-European homelands - p. 145-154
Kornienko, Tatiana 'Archaeological Research in Northern Mesopotamia and North Caucasus' [Chronicle] - p. 155-162
Korovina, Eugenia 'Problems of the Indo-European Homeland' [Chronicle] - p. 163-166

UPDATE: Someone sent me the Anthony paper. Here is the main figure which suggests a correspondence between the linguistic phylogeny of Ringe et al. and the archaeological reconstruction of out-of-steppe movements of its author:

One of the weakest points of the steppe model is its treatment of Anatolians. Movement marked #1 perhaps takes some populations in an indistinct way into the east Balkans, but does not take them all the way to Anatolia.

The steppe model must propose some kind of early round-the-Black Sea mechanism to bring the Anatolians to their historical seats. This is not trivial; it might seem like a small jump from Thrace (where the endpoint of the first migration, marked with 1 is placed) to Anatolia, but it is in fact in the southern parts of the peninsula that we first find the Anatolian speakers. And, Anatolian place names are also recorded in Greece and its immediate environs, and not at all in the proposed migration route. Thus, the arrow must take the Anatolians further west (to account for the evidence from the Aegean, and then bring them south and east). I don't find this very plausible.

Algerian Y chromosomes and mtDNA

From the paper:
For the R-M343 subdivision, the Iberian Peninsula reflects a genuine European profile [45] except for the presence of one Sahel R-V88 type. In contrast, all R-M343 detected in W. Saharan-Mauritanian belong to sub-group R-V88, reaching a frequency of 7%, similar to those observed in other Sahel samples [40]. In the Maghreb countries, the frequency of R-V88 drops to around 1%. On the other hand, the presence in this area of representatives of the European sub-groups R-M412, R-S116, R-U152 and R-M529 points to North-South maritime contacts across the Mediterranean
It would be interesting to estimate the depth of common ancestry of the North African "European" Y chromosomes to determine the epoch during which they arrived there, i.e., whether the common ancestry stems from recent historical contacts (Roman Empire, Vandals, etc.) or from the early settlement of both Mediterranean coasts during the arrival of R-M269 into Europe.

A few observations on Y-haplogroup frequencies:

  • The ubuquity of haplogroup Q at trace frequencies in most regions except North Africa (only a little in ALG) is interesting and it's high time that someone looked at the relationship between West Eurasian Q-bearers and their much more numerous East Eurasian cousins.
  • I find the paucity of Y-haplogroup I in North Africa noteworthy; given its high levels in most of Western Europe, its relative absence might indicate that the people who brought "European" R-M269 into N Africa were not occasional recent migrants, but rather earlier settlers. 
  • The relative absence of J2 is expected, given that neither of the two main strata of population ("Berber" and "Arab") may have possessed it initially; it has also not been found in a historical sample from the Canary Islands, whereas its J1 counterpart has.
  • The paucity of haplogroup G, which is the European Neolithic lineage par excellence probably argues against the involvement of the people who colonized Europe during the Early Neolithic in similar events on the south shore of the Mediterranean.
  • The further study of F chromosomes could also be further attempted, given their possible involvement in the Upper Paleolithic of Eurasia

The authors highlight that 80% of mtDNA is Eurasian vs. 90% of Y chromosomes. This might point to asymmetric gene flow from Sub-Saharan Africa. Alternatively, it might point to some mtDNA that is characterized as non-Eurasian (because it does not belong to the M, N macro-haplogroups) being in fact so. It is a persistent question whether lineages that have a wide frequency differential in two regions do so because of gene flow (from the high- to low-frequency area), or because of other processes.

PLoS ONE 8(2): e56775. doi:10.1371/journal.pone.0056775

Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape

Asmahan Bekada et al.

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.


Early modern human burials in Eurasia

Early human burials varied widely but most were simple
"We don't know why some of these burials were so ornate, but what's striking is that they postdate the arrival of modern humans in Eurasia by almost 10,000 years," said Julien Riel-Salvatore, Ph.D., assistant professor of anthropology at CU Denver and lead author of the study. "When they appear around 30,000 years ago some are lavish but many aren't and over time the most elaborate ones almost disappear. So, the behavior of humans does not always go from simple to complex; it often waxes and wanes in terms of its complexity depending on the conditions people live under."

The study, which examined 85 burials from the Upper Paleolithic period, found that men were buried more often than women. Infants were buried only sporadically, if at all in later periods, a difference that could be related to changes in subsistence, climate and the ability to keep babies alive, Riel-Salvatore said.

It also showed that a few ornate burials in Russia, Italy and the Czech Republic dating back nearly 30,000 years are anomalies, and not representative of most early Homo sapiens burial practices in Eurasia.

Admixed populations in neighbor-joining trees

Pac Symp Biocomput. 2013:273-84.

The behavior of admixed populations in neighbor-joining inference of population trees.

Kopelman NM, Stone L, Gascuel O, Rosenberg NA.


Neighbor-joining is one of the most widely used methods for constructing evolutionary trees. This approach from phylogenetics is often employed in population genetics, where distance matrices obtained from allele frequencies are used to produce a representation of population relationships in the form of a tree. In phylogenetics, the utility of neighbor-joining derives partly from a result that for a class of distance matrices including those that are additive or tree-like-generated by summing weights over the edges connecting pairs of taxa in a tree to obtain pairwise distances-application of neighbor-joining recovers exactly the underlying tree. For populations within a species, however, migration and admixture can produce distance matrices that reflect more complex processes than those obtained from the bifurcating trees typical in the multispecies context. Admixed populations-populations descended from recent mixture of groups that have long been separated-have been observed to be located centrally in inferred neighbor-joining trees, with short external branches incident to the path connecting their source populations. Here, using a simple model, we explore mathematically the behavior of an admixed population under neighbor-joining. We show that with an additive distance matrix, a population admixed among two source populations necessarily lies on the path between the sources. Relaxing the additivity requirement, we examine the smallest nontrivial case-four populations, one of which is admixed between two of the other three-showing that the two source populations never merge with each other before one of them merges with the admixed population. Furthermore, the distance on the constructed tree between the admixed population and either source population is always smaller than the distance between the source populations, and the external branch for the admixed population is always incident to the path connecting the sources. We define three properties that hold for four taxa and that we hypothesize are satisfied under more general conditions: antecedence of clustering, intermediacy of distances, and intermediacy of path lengths. Our findings can inform interpretations of neighbor-joining trees with admixed groups, and they provide an explanation for patterns observed in trees of human populations.


Wednesday, 20 February 2013

AAPA 2013 abstracts

The program of the 2013 meeting of the American Association of Physical Anthropologists is now online (pdf). As always, there is plenty of interest here, so I'll just highlight a few titles that caught my eye; feel free to add more in the comments.

Neolithic human mitochondrial haplogroup H genomes and the genetic origins of Europeans.
Haplogroup (hg) H dominates present-day Western European mitochondrial (mt) DNA variability (>40%), yet was less prevalent amongst early Neolithic farmers (~19%) and virtually absent in Mesolithic hunter-gatherers. To investigate this haplogroup’s significance in the maternal population history of Europeans we employed novel techniques such as DNA immortalization and hybridization-enrichment to sequence 39 hg H mt genomes from ancient human remains across a transect through time in Neolithic Central Europe. The results of our population genetic analyses reveal that the current patterns of diversity and distribution of hg H were largely established during the Mid-Neolithic, but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers, which expanded out of Iberia in the Late Neolithic (~2800 BC). Using a strict diachronic approach allowed us to reconcile ‘real-time’ genetic data from the most common European mtDNA hg with cultural changes that took place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. This revealed the Late Neolithic (2800-2200 BC) as a dynamic period that profoundly shaped the genetic landscape of modern-day Europeans. Furthermore, linking ancient hg H genome sequences to specific points in time by using radiocarbon dates as tip calibrations allowed us to reconstruct a precise lineage history of hg H and to calculate a mutation rate 45% higher than traditional estimates based on the human/chimp split.
Preliminary research on hereditary features of Yinxu Population.
... The 37 individuals sampled in this study have been discovered in middle to small size burials, and therefore constitute a representative sample to study Yinxu commoners’ society. Mitochondrial DNA analysis showed that the Yinxu population included the haplogroups D, G, A, C, Z, M10, M*, B, F and N9a. According to the analysis of molecular variance, the distribution frequency and the rare published data, the Yinxu population shows a closest genetic affinity with the populations of Dadianzi and Zhukaigou early Bronze Age sites (Inner Mongolia), but a more distant relation to the historical period populations. The Yinxu population is also very similar to the modern northern Han Chinese. ... 

Investigating lactase persistence in a Medieval German cemetery: A step towards understanding the rise of the European lactase persistence polymorphism (-3910C/T).
Previous ancient DNA-based studies on the Neolithic found that the incidence of LP falls below detection levels in most regions. Our research shows that between the Neolithic and Medieval periods, the frequency of LP rose from near 0% to over 50%. Also, given that the frequency of LP genotypes in modern-day Germany is estimated at 78.5%, our results indicate that rather than being stable by the Medieval period, the lactase persistent genotype has continued to increase in frequency over the last 1000 years. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistent trait and its global cultural implications.
 New Neanderthal remains from Kalamakia cave, Mani peninsula, Southern Greece.

Peeling back the layers: additional evidence for the date of the Petralona skull (Homo heidelbergensis), Greece.
,.. We conclude that there is no white sinter deposited directly on the skull and therefore the initial date of the skull given by Henning et al. and Grun’s revised date of ca. 200 ka are correct.
Analysis of archaic introgression in Ötzi the Tyrolean Iceman, a 5300 year-old prehistoric modern human.
... We carried out a series of comparisons to address these questions. By examining the Neandertal similarity of individuals from the 1000 Genomes Project, we have substantially expanded the sample of Neandertal-human comparisons. We also examined the genome of the Tyrolean Iceman, a European from approximately 5300 years ago. This is the first comparison of Neandertal genomes to the genome of a prehistoric modern human individual.
A quantitative approach for late Pleistocene hominin brain size.
... The results of our study show that Neanderthals have smaller brains than the Pleistocene AMH despite the fact that the latter are smaller in body mass. However, the Holocene AMH (7 populations) have smaller brain sizes than those of Neanderthals. ...
Re-evaluating the functional and adaptive significance of Neandertal nasofacial anatomy.
... Among Middle and Late Pleistocene Homo, there is evidence that nasal morphology varies with climate, albeit within an archaic architectural nasofacial framework. Neandertal internal nasal dimensions are greater in both height and length than archaic humans from sub-Saharan Africa. Furthermore, while other aspects of the nose are relatively broad, superior internal breadth dimensions in Neandertals are narrowed relative to sub-Saharan archaics. These differences parallel those seen in modern humans, indicating that Neandertals had an increased capacity for nasal heat and moisture exchange over their African counterparts and thus exhibit clear evidence for cold-climate adaptation.