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.

bioRxiv http://dx.doi.org/10.1101/010512

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.