December 09, 2014

"Ancient DNA: the first three decades" meeting papers

A bucketload of papers here. Some titles of interest:

  1. Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles
  2. Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach
  3. The ancient Yakuts: a population genetic enigma
  4. Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process
  5. Mitochondrial DNA variation in the Viking age population of Norway
  6. Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction
  7. Screening ancient tuberculosis with qPCR: challenges and opportunities
  8. Parallel detection of ancient pathogens via array-based DNA capture
  9. Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania
  10. Ancient genomics
  11. Ancient population genomics and the study of evolution

December 06, 2014

African Genome Variation project paper

A choice quote:
To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6). This markedly reduced population differentiation, as measured by a decline in mean pairwise FST from 0.021 to 0.015 (Supplementary Note 6), suggests that Eurasian ancestry has a substantial impact on differentiation among SSA populations. We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise FST = 0.027) may be a remnant of East African diversity pre-dating the Bantu expansion10.
I think this should be highlighted for a couple of reasons.

1. In too many papers to count, decreasing genetic diversity from East Africa was taken as evidence of an origin of H. sapiens in that locality and its expansion from there to Eurasia. This "East Africa=cradle of mankind" theory has, as far as I can tell, nothing really to stand on. Granted, the oldest anatomically modern human remains have been found in East Africa 200-150 thousand years ago. But, the fact that old sapiens have been found in East Africa and not elsewhere is easily explained by the excellent conditions for preservation (as opposed, e.g., deserts or rainforests of Africa or elsewhere), and by the extraordinary effort by palaeoanthropologists in that area. One also needs to overlook a century of physical anthropology that concluded that East Africa was a contact zone between Caucasoids and Sub-Saharan Africans. We now know that there is no deep lineage of humans in modern east Africans. Take out the Eurasian ancestry and only a paltry Fst=0.027 remains with other Sub-Saharan Africans, a fraction of the Fst between, say, Europeans and East Asians.

2. There has been enormous literature about phenotypic variation in Africans. The ultra-migrationism of old was replaced by ultra-selectionism that sought to explain every phenotypic marker of Eurasian admixture in Africa not as evidence of such admixture, but as a parallel process of evolution whereby some Africans tended to resemble some Eurasians not because of admixture but because of adaptation to similar environmental conditions.

This suggests that a large proportion of differentiation observed among African populations could be due to Eurasian admixture, rather than adaptation to selective forces (Supplementary Note 6).
This study also confirms the presence of Eurasian admixture in the Yoruba
Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period13, 14.

Nature (2014) doi:10.1038/nature13997

The African Genome Variation Project shapes medical genetics in Africa

Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, et al.

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.


December 02, 2014

Remains of Richard III identified

From the paper:
Four of the modern relatives were found to belong to Y-haplogroup R1b-U152 (x L2, Z36, Z56, M160, M126 and Z192)13, 14 with STR haplotypes being consistent with them comprising a single patrilinear group. One individual (Somerset 3) was found to belong to haplogroup I-M170 (x M253, M223) and therefore could not be a patrilinear relative of the other four within the time span considered, indicating that a false-paternity event had occurred within the last four generations. 
In contrast to the Y-haplotypes of the putative modern relatives, Skeleton 1 belongs to haplogroup G-P287, with a corresponding Y-STR haplotype. Thus, the putative modern patrilinear relatives of Richard III are not genetically related to Skeleton 1 through the male line over the time period considered. However, this is not surprising, given an estimated average false-paternity rate of ~1–2% (refs 12, 17, 18). The putative modern relatives and Richard III are related through a male relative (Edward III) four generations up from Richard III (Fig. 1a and Supplementary Fig. 2), and a false-paternity event could have happened in any of the 19 generations separating Richard III and the 5th Duke of Beaufort, on either branch of the genealogy descending from Edward III. Indeed, even with a conservative false-paternity rate18 (see Supplementary Methods) the chance of a false-paternity occuring in this number of generations is 16%.

Nature Communications 5, Article number: 5631 doi:10.1038/ncomms6631

Identification of the remains of King Richard III

Turi E. King et al.


In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false-paternity event occurring in any of the intervening generations. DNA-predicted hair and eye colour are consistent with Richard’s appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming.


November 25, 2014

E-M81 in Morocco

Hum Biol. 2014 May;86(2):105-12.

Phylogeography of e1b1b1b-m81 haplogroup and analysis of its subclades in morocco.

Reguig A, Harich N, Barakat A, Rouba H.


In this study we analyzed 295 unrelated Berber-speaking men from northern, central, and southern Morocco to characterize frequency of the E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183, and E1b1b1b2a-M165. For this purpose, we typed four biallelic polymorphisms: M81, M107, M183, and M165. A large majority of the Berber-speaking male lineages belonged to the Y-chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1% to 98.5% in all localities sampled. E1b1b1b2-M183 was the most dominant subclade in our samples, ranging from 65.1% to 83.1%. In contrast, the E1b1b1b1-M107 and E1b1b1b2a-M165 subclades were not found in our samples. Our results suggest a predominance of the E1b1b1b-M81 haplogroup among Moroccan Berber-speaking males with a decreasing gradient from south to north. The most prevalent subclade in this haplogroup was E1b1b1b2-M183, for which diffferences among these three groups were statistically significant between central and southern groups.


Paternal lineages and languages in the Caucasus

An interesting new study on Y chromosome and languages in the Caucasus. The distribution of haplogroups is on the left. The authors make some associations of haplogroups with language families:

  • R1b: Indo-European
  • R1a: Scytho-Sarmatian
  • J2: Hurro-Urartian
  • G2: Kartvelian

Hum Biol. 2014 May;86(2):113-30.

Human paternal lineages, languages, and environment in the caucasus.

Tarkhnishvili D1, Gavashelishvili A1, Murtskhvaladze M1, Gabelaia M1, Tevzadze G2.


Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible.

Link (pdf)

November 07, 2014

Genome of Kostenki-14, an Upper Paleolithic European (Seguin-Orlando, Korneliussen, Sikora, et al. 2014)

A new paper in Science reports on the genome of Kostenki-14 (K14), an Upper Paleolithic European from Russia. This is now the third oldest Homo sapiens for which we have genetic data, after Ust'-Ishim (Siberia, 45 thousand years), Tianyuan (China, 40 thousand years), and now Kostenki (European part of Russia, 37 thousand years). Of these three genomes, the Ust'-Ishim is both the highest coverage and earliest (Siberia is the gift that keeps on givin'), Tianyuan only has its chromosome 21 known, and K14, a complete 2.42x coverage sequence (and, apparently, good teeth, after all these years; left).

The publication of the Tianyuan genome showed that populations related to East Asians and Oceanians existed in the world 40 thousand years ago. So, models based on modern humans that put the split of East Asians from Europeans to a much more recent time period were basically wrong (more on this a little below). The Ust'-Ishim genome showed that populations basal to both East Asians and Europeans existed in the world 45 thousand years ago. So, either East Asians and Europeans hadn't gone along their different paths yet, or, if they had, Ust'-Ishim happened to be a side branch and not the major East Asian and European lineages.

K14 may not be the older Upper Paleolithic human, but as of this writing it is the only Upper Paleolithic European that has been published so far, the next ones being the Loschbour, Motala, and La Brana Mesolithic Europeans who who have about 1/5 of its age. The new paper shows that K14 was definitely European (or more correctly West Eurasian or Caucasoid), as it was more similar to modern Europeans than to East Asians or other non-West Eurasian populations. Thus, the morphological description of the sample as "Australoid" by some early anthropologists did not reflect its ancestral makeup. Also, this proves that Caucasoids existed 37,000 years ago, which most physical anthropologists would believe, but it is nice to have direct confirmation. This pushes the lower bound from 24,000 years ago (because MA-1 was West Eurasian according to the results of Raghavan et al.). It will be nice to push the lower bound further to the past as there are much older bones (and plenty of teeth) from earlier Upper Paleolithic Europeans.

But there is a slight kink in the story, as K14 also belonged to Y-haplogroup C which is predominantly East Asian/Ocenian/Native American today. So, maybe there is some distant link to these populations in its ancestry. But, there is definitely a link to much more recent Europeans: the tiny percentage of living Europeans who have preserved K14's Y-chromosomal type (some of which were doubtlessly told a few years back that they were descendants of Genghis Khan, before the phylogenetic structure of C was known), the La Brana hunter-gatherer from Mesolithic Spain, as well as Neolithic Europeans from Hungary.

The authors of the current paper also date the date of Neandertal admixture to 54 thousand years. This seems very compatible with the finding of between 50 and 60 thousand years by Fu et al. (2014) based on the Ust'-Ishim genome (which is both earlier and better, so the chunks of Neandertal ancestry in it are probably be longer and more well-defined).

The authors propose the following model for how various populations are related to each other:

This model is not formally tested, but at least it seems to derive Europeans as a 3-way mixture that is basically identical to that of Lazaridis et al., with some relabeling of populations (MHG=WHG and NEOL=EEF).

The model also includes Yeniseian Siberians as a mixture of MHG and East Asians (although it does not include actual East Asians). It's strange that Yeniseians apparently are given no ANE ancestry but only WHG/MHG. Both Raghavan et al. and Lazaridis et al. mentioned that ancestry related to MA-1 in living Siberians is diminished, but none at all?

The major new finding of this paper, however, is that K14 had Basal Eurasian ancestry, which was first proposed for EEF from Germany 7,000 years ago, so now it postulated for Russian hunter-gatherers 37,000 years ago. I don't think many archaeologists would derive European farmers from Russia (Russia is actually one of the last places in Europe that became agricultural). So, maybe the hunter-gatherers from Russia had Basal Eurasian ancestry and this wasn't limited to the ancestors of the EEF? If they did, it's strange that Loschbour, La Brana, MA-1, Ust'-Ishim, Swedish Mesolithic (and maybe KO1?) didn't have it. So, either Kostenki was very unique or there is an alternative explanation for its strangeness.

The evidence for the Basal Eurasian ancestry in K14 is summarized in the figure above in bullet point (b).

  • The statistic D(Mbuti, East Asia; HG, K14) is less than 0. So, there's some link between HG and East Asians. Is this because of Basal Eurasian admixture in K14 or due to some admixture between Caucasoids and Mongoloids after the time of K14? (this might cause the lower dates of European-East Asian splits alluded to above).
  • The statistic D(Mbuti, East Asia; NEOL, K14) is 0. So, East Asians don't "prefer" either Neolithic Europeans (NEOL) or K14. I guess the value of this statistic depends on how much Basal Eurasian the different populations have and what's the relationship between East Asians, K14, and the non-Basal Eurasian part in K14.
  • Finally, "NEOL component for K14 in ADMIXTURE". I think they are referring to the "Middle East" component (right). This may be Basal Eurasian ancestry, or maybe because K14 is so old, it pre-dates the European/Middle Eastern divide and its ancestry isn't attracted to either Europe or the Middle East, so it gets ancestry from both (and many other colors besides).

It is fascinating how many new questions are both answered and raised each time a new genome gets published (and there has been a constant stream of these over the last couple of years).

Science DOI: 10.1126/science.aaa0114

Genomic structure in Europeans dating back at least 36,200 years

Andaine Seguin-Orlando1,*, Thorfinn S. Korneliussen1,*, Martin Sikora1, et al.

The origin of contemporary Europeans remains contentious. We obtain a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. We find that K14 shares a close ancestry with the 24,000-year-old Mal’ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a meta-population that at times stretched from Europe to central Asia.


October 22, 2014

High coverage genome from 45,000-year old Siberian (Ust'-Ishim)

This is the oldest full genome of a modern human published to date and it also comes from a time (45 thousand years ago) that coincides with the Upper Paleolithic revolution in Eurasia.

45 thousand years ago is probably close to when Eurasians started diverging from each other as they spread in all directions. So, we expect that a human from that time would be "undifferentiated Eurasian" and indeed this seems to be the case.

First the Y-chromosome:
The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today6 (Supplementary Information section 9).
and mtDNA:
The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’), which occurs today across Eurasia (Supplementary Information section 8).
It is clear that this was a Eurasian individual:
Based on genotyping data for 87 African and 108 non-African individuals (Supplementary Information section 11), the Ust’-Ishim genome shares more alleles with non-Africans than with sub-Saharan Africans (|Z| = 41–89), consistent with the principal component analysis, mtDNA and Y chromosome results.
It was also more like East Asians than Europeans:
Among the non-Africans, the Ust’-Ishim genome shares more derived alleles with present-day people from East Asia than with present-day Europeans (|Z| = 2.1–6.4).
But, when they compared East Asians with La Brana and MA-1 they didn't see a difference:
However, when an ~8,000-year-old genome from western Europe (La Braña)9 or a 24,000-year-old genome from Siberia (Mal’ta 1)10 were analysed, there is no evidence that the Ust’-Ishim genome shares more derived alleles with present-day East Asians than with these prehistoric individuals (|Z| < 2). This suggests that the population to which the Ust’-Ishim individual belonged diverged from the ancestors of present-day West Eurasian and East Eurasian populations before—or simultaneously with—their divergence from each other. The finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000- to 24,000-year-old individuals from western Eurasia, but not to present-day Europeans, is compatible with the hypothesis that present-day Europeans derive some of their ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia11.
So it seems that the Ust'-Ishim individual belonged to the same branch as Asians and WHG/ANE and modern Europeans are less like it because they also have "Basal Eurasian" admixture which they inherited via the EEF in the model of Lazaridis et al.

The authors could also get estimates of the mutation rate because this is a 45,000 year old individual that hasn't experienced 45,000 years worth of mutations:
Assuming that this corresponds to the number of mutations that have accumulated over around 45,000 years, we estimate a mutation rate of 0.43 × 10−9 per site per year (95% CI 0.38 × 10−9 to 0.49 × 10−9) that is consistent across all non-African genomes regardless of their coverage (Supplementary Information section 14). This overall rate, as well as the relative rates inferred for different mutational classes (transversions, non-CpG transitions, and CpG transitions), is similar to the rate observed for de novo estimates from human pedigrees (~0.5 × 10−9 per site per year14, 15) and to the direct estimate of branch shortening (Supplementary Information section 10). As discussed elsewhere14, 16, 17, these rates are slower than those estimated using calibrations based on the fossil record and thus suggest older dates for the splits of modern human and archaic populations.
This is a very direct confirmation of the "slow" autosomal rate of ~1.2x10-8 mutations/generation/bp using a technology much different than those used before to estimate this. The slower mutation rate implies that major splits in human history (such as the Out-of-Africa event) took place much earlier than the Upper Paleolithic revolution and the spread of humans across Eurasia. Modern humans probably established an early presence in the Levant/Arabia (consistent with Out-of-Arabia), and invented the Upper Paleolithic-related tools/behaviors there much later, and only then spread across Eurasia.

The authors write:
we estimate that the admixture between the ancestors of the Ust’-Ishim individual and Neanderthals occurred approximately 50,000 to 60,000 years BP, which is close to the time of the major expansion of modern humans out of Africa and the Middle East.
This clinches the hypothesis of Neandertal introgression in Eurasians, as Ust'-Ishim has longer Neandertal segments than modern humans, as one might expect from an individual who experienced this admixture more recently in its evolutionary past than modern humans did. It's probably in the Middle East that the Levantine/Arabian modern humans that expanded Out-of-Africa more than 100 thousand years ago came into contact with Neandertals, admixed with them and later carried this ancestry to the rest of Eurasia. I tend to think that the AMH "colony" was first limited to Arabia and only later (post-70kya) expanded north as the climate deteriorated there. The authors estimate the common ancestor of non-African Y-chromosomes (including E, which is probably a back-migration to Africa) to around 70 thousand years ago which may coincide with the Arabian Exodus event.

Nature 514, 445–449 (23 October 2014) doi:10.1038/nature13810

Genome sequence of a 45,000-year-old modern human from western Siberia

Qiaomei Fu et al.

We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.


October 21, 2014

Ancient DNA from prehistoric inhabitants of Hungary

A very interesting new article on Europe describes new data from ancient Hungary from the Neolithic to the Iron Age. It is open access, so go ahead and read it. I will update this entry with some comments after I read the paper myself.

UPDATE I (The petrous bone):

The authors write:
The endogenous DNA yields from the petrous samples exceeded those from the teeth by 4- to 16-fold and those from other bones up to 183-fold. Thus, while other skeletal elements yielded human, non-clonal DNA contents ranging from 0.3 to 20.7%, the levels for petrous bones ranged from 37.4 to 85.4% (Fig. 1).
This seems like a very exciting technical breakthrough that will increase DNA yields in future studies.


The Neolithic Hungarians are close to Sardinians (this has been replicated in study after study, so it's no longer a surprise when you find Neolithic Europeans that look like Sardinians).

What is surprising is that one KO1 Neolithic European is with the hunter-gatherers (top of the plot). At some level you would expect to find some hunter-gatherers in the earliest Neolithic communities in Europe as Europe wasn't empty land when the early farmers showed up. And KO1 appears one of those guys, "caught in the act" of first contact between the two groups.

The two Bronze Age samples are more like modern continental Europeans but not exactly like modern Hungarians. The Iron Age sample is in the no-man's land between Europe and the Caucasus and his "Asian" Y chromosome and mtDNA seems to agree that this is no ordinary European.

UPDATE III (How they looked):

I really like the visualization of hair and eye color predictions of the last two columns of the table on the right. It seems that the ancient Hungarians had mainly brown hair with more variability after 5,000 years ago. They mostly had brown eyes except three individuals.

An interesting thing is that NE7 who seems to have light hair and blue eyes is just like other Sardinian-like farmers of the Neolithic and also has the mtDNA haplogroup N1a1a1a that is ultra-typical for Neolithic people from Europe. So this is a warning not to conflate appearance with ancestry.

UPDATE IV (Y chromosomes):

As always, the supplement has many of the interesting details. Two Neolithic males were C6 which is the same "weird" haplogroup that La Brana hunter-gatherer from Spain had. Two other ones were I2a which is what Loschbour and Swedish hunter-gatherers had. Strangely, no Neolithic males had G which was found before in many Neolithic Europeans.

A new finding is that the Bronze Age individual BR2 belonged to haplogroup J2a1. I think this is the first time this has been found in ancient DNA and it falsifies the Phoenician sea-faring theory of the dispersal of this lineage.

Finally, the Iron Age Hungarian belonged to haplogroup N. I believe this was found in ancient Magyars from Hungary before, but apparently it existed there long before them.

Nature Communications 5, Article number: 5257 doi:10.1038/ncomms6257

Genome flux and stasis in a five millennium transect of European prehistory

Cristina Gamba et al.

The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.


October 20, 2014

Ancestry Composition preprint

This is one of the main ancestry tools of 23andMe so it is nice to see its methodology described in detail.


Ancestry Composition: A Novel, Efficient Pipeline for Ancestry Deconvolution

Eric Y Durand et al.

Ancestry deconvolution, the task of identifying the ancestral origin of chromosomal segments in admixed individuals, has important implications, from mapping disease genes to identifying candidate loci under natural selection. To date, however, most existing methods for ancestry deconvolution are typically limited to two or three ancestral populations, and cannot resolve contributions from populations related at a sub-continental scale. We describe Ancestry Composition, a modular three-stage pipeline that efficiently and accurately identifies the ancestral origin of chromosomal segments in admixed individuals. It assumes the genotype data have been phased. In the first stage, a support vector machine classifier assigns tentative ancestry labels to short local phased genomic regions. In the second stage, an autoregressive pair hidden Markov model simultaneously corrects phasing errors and produces reconciled local ancestry estimates and confidence scores based on the tentative ancestry labels. In the third stage, confidence estimates are recalibrated using isotonic regression. We compiled a reference panel of almost 10,000 individuals of homogeneous ancestry, derived from a combination of several publicly available datasets and over 8,000 individuals reporting four grandparents with the same country-of-origin from the member database of the personal genetics company, 23andMe, Inc., and excluding outliers identified through principal components analysis (PCA). In cross-validation experiments, Ancestry Composition achieves high precision and recall for labeling chromosomal segments across over 25 different populations worldwide.


October 10, 2014

Tomb II at Vergina belonged to Philip II and a possible Scythian wife

Remains of Alexander the Great's Father Confirmed Found
A team of Greek researchers has confirmed that bones found in a two-chambered royal tomb at Vergina, a town some 100 miles away from Amphipolis's mysterious burial mound, indeed belong to the Macedonian King Philip II, Alexander the Great's father. 
The anthropological investigation examined 350 bones and fragments found in two larnakes, or caskets, of the tomb. It uncovered pathologies, activity markers and trauma that helped identify the tomb's occupants.

Along with the cremated remains of Philip II, the burial, commonly known as Tomb II, also contained the bones of a woman warrior, possibly the daughter of the Skythian King Athea, Theodore Antikas, head of the Art-Anthropological research team of the Vergina excavation, told Discovery News.

October 09, 2014

~40 thousand year old cave art from Indonesia

The BBC website has some nice pictures of it.

Nature 514, 223–227 (09 October 2014) doi:10.1038/nature13422

Pleistocene cave art from Sulawesi, Indonesia

M. Aubert et al.

Archaeologists have long been puzzled by the appearance in Europe ~40–35 thousand years (kyr) ago of a rich corpus of sophisticated artworks, including parietal art (that is, paintings, drawings and engravings on immobile rock surfaces)1, 2 and portable art (for example, carved figurines)3, 4, and the absence or scarcity of equivalent, well-dated evidence elsewhere, especially along early human migration routes in South Asia and the Far East, including Wallacea and Australia5, 6, 7, 8, where modern humans (Homo sapiens) were established by 50 kyr ago9, 10. Here, using uranium-series dating of coralloid speleothems directly associated with 12 human hand stencils and two figurative animal depictions from seven cave sites in the Maros karsts of Sulawesi, we show that rock art traditions on this Indonesian island are at least compatible in age with the oldest European art11. The earliest dated image from Maros, with a minimum age of 39.9 kyr, is now the oldest known hand stencil in the world. In addition, a painting of a babirusa (‘pig-deer’) made at least 35.4 kyr ago is among the earliest dated figurative depictions worldwide, if not the earliest one. Among the implications, it can now be demonstrated that humans were producing rock art by ~40 kyr ago at opposite ends of the Pleistocene Eurasian world.


September 28, 2014

43,500-year old Aurignacian north of the Alps

PNAS doi: 10.1073/pnas.1412201111

Early modern human settlement of Europe north of the Alps occurred 43,500 years ago in a cold steppe-type environment

Philip R. Nigst et al.

The first settlement of Europe by modern humans is thought to have occurred between 50,000 and 40,000 calendar years ago (cal B.P.). In Europe, modern human remains of this time period are scarce and often are not associated with archaeology or originate from old excavations with no contextual information. Hence, the behavior of the first modern humans in Europe is still unknown. Aurignacian assemblages—demonstrably made by modern humans—are commonly used as proxies for the presence of fully behaviorally and anatomically modern humans. The site of Willendorf II (Austria) is well known for its Early Upper Paleolithic horizons, which are among the oldest in Europe. However, their age and attribution to the Aurignacian remain an issue of debate. Here, we show that archaeological horizon 3 (AH 3) consists of faunal remains and Early Aurignacian lithic artifacts. By using stratigraphic, paleoenvironmental, and chronological data, AH 3 is ascribed to the onset of Greenland Interstadial 11, around 43,500 cal B.P., and thus is older than any other Aurignacian assemblage. Furthermore, the AH 3 assemblage overlaps with the latest directly radiocarbon-dated Neanderthal remains, suggesting that Neanderthal and modern human presence overlapped in Europe for some millennia, possibly at rather close geographical range. Most importantly, for the first time to our knowledge, we have a high-resolution environmental context for an Early Aurignacian site in Central Europe, demonstrating an early appearance of behaviorally modern humans in a medium-cold steppe-type environment with some boreal trees along valleys around 43,500 cal B.P.


A limited genetic link between Mansi and Hungarians

Mol Genet Genomics. 2014 Sep 26. [Epub ahead of print]

Y-SNP L1034: limited genetic link between Mansi and Hungarian-speaking populations.

Fehér T1, Németh E, Vándor A, Kornienko IV, Csáji LK, Pamjav H.


Genetic studies noted that the Hungarian Y-chromosomal gene pool significantly differs from other Uralic-speaking populations. Hungarians show very limited or no presence of haplogroup N-Tat, which is frequent among other Uralic-speaking populations. We proposed that some genetic links need to be observed between the linguistically related Hungarian and Mansi populations.This is the first attempt to divide haplogroup N-Tat into subhaplogroups by testing new downstream SNP markers L708 and L1034. Sixty Northern Mansi samples were collected in Western Siberia and genotyped for Y-chromosomal haplotypes and haplogroups. We found 14 Mansi and 92 N-Tat samples from 7 populations. Comparative results showed that all N-Tat samples carried the N-L708 mutation. Some Hungarian, Sekler, and Uzbek samples were L1034 SNP positive, while all Mongolians, Buryats, Khanty, Finnish, and Roma samples yielded a negative result for this marker. Based on the above, L1034 marker seems to be a subgroup of N-Tat, which is typical for Mansi and Hungarian-speaking ethnic groups so far. Based on our time to most recent common ancestor data, the L1034 marker arose 2,500 years before present. The overall frequency of the L1034 is very low among the analyzed populations, thus it does not necessarily mean that proto-Hungarians and Mansi descend from common ancestors. It does provide, however, a limited genetic link supporting language contact. Both Hungarians and Mansi have much more complex genetic population history than the traditional tree-based linguistic model would suggest.


Levallois technology in Nor Geghi 1, Armenia

From the paper:
Empirical evidence supports the contention that Levallois technology is an inherent property of the Acheulian that evolves out of the existing, but previously separate technological systems of façonnage and débitage (7, 35), and shows that Acheulian bifacial technology and Levallois technology are homologous, reflecting an ancestor-descendant relationship (36). Rather than a “technical breakthrough” that spread from a single point of origin, Levallois technology resulted from the gradual synthesis of stone knapping behaviors shared among hominins in Africa and those indigenous to the Acheulian dispersal area in Eurasia (Fig. 1). Consequently, the development of Levallois technology within Late Acheulian contexts represents instances of technological convergence.

Science 26 September 2014: Vol. 345 no. 6204 pp. 1609-1613 DOI: 10.1126/science.1256484

Early Levallois technology and the Lower to Middle Paleolithic transition in the Southern Caucasus 

D. S. Adler

ABSTRACT The Lower to Middle Paleolithic transition (~400,000 to 200,000 years ago) is marked by technical, behavioral, and anatomical changes among hominin populations throughout Africa and Eurasia. The replacement of bifacial stone tools, such as handaxes, by tools made on flakes detached from Levallois cores documents the most important conceptual shift in stone tool production strategies since the advent of bifacial technology more than one million years earlier and has been argued to result from the expansion of archaic Homo sapiens out of Africa. Our data from Nor Geghi 1, Armenia, record the earliest synchronic use of bifacial and Levallois technology outside Africa and are consistent with the hypothesis that this transition occurred independently within geographically dispersed, technologically precocious hominin populations with a shared technological ancestry.


September 23, 2014

ESHE 2014 abstracts

The abstracts for the European Society for the study of Human Evolution meeting that just took place are available in this PDF.