Helicobacter pylori in the Iceman

Science 8 January 2016:
Vol. 351 no. 6269 pp. 162-165

The 5300-year-old Helicobacter pylori genome of the Iceman
Frank Maixner1,*,†, Ben Krause-Kyora2,†, Dmitrij Turaev3,†, Alexander Herbig4,5, et al.

The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The “Iceman” H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.

Link

Bronze Age mixing of multiple populations => Armenians (?)

As far as I can tell, the hypothesis of "several mixtures" comes from looking at many pairs of populations and seeing that different types of pairs seem like they mixed to make Armenians. Possibility (1) is that Armenians have multiple mixtures, and possibility (2) is that none of the sources work very well.

Hellenthal et al. did not find mixture in Armenians, but they worked with a different methodology and smaller sample size. Either, the N=173 sample size enabled detection of this admixture, or differences in methodology account for differences in conclusions. If true, the admixture dates in this paper would be some of the earliest discovered by looking at modern populations (without the help of ancient DNA).

The TreeMix analysis (Figure 4) is inconclusive about admixture from a population best represented by Neolithic Europeans. There is no plot of residuals in this figure, so this model with one migration event may not be adequate. Prior knowledge suggests that it isn't, as Pakistani and European populations have no admixture in Figure 4.

It's great that the authors will share their data!
ftp://ngs.sanger.ac.uk/scratch/project/team19/Armenian
As of this writing, the data is not "live"; it might appear when the paper is published.

bioRxiv doi: http://dx.doi.org/10.1101/015396

Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations

Marc Haber et al.

The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain underrepresented in genetic studies and have a complex history including a major geographic displacement during World War One. Here, we analyse genome-wide variation in 173 Armenians and compare them to 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3,000 and ~2,000 BCE, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1,200 BCE when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans.

Link

Ancient DNA from the Balkans (Iron Age Thrace)

A new paper in PLoS Genetics presents new data from two Iron Age Thracian individuals and puts the Sardinian-ness of Oetzi in new context. The authors write:

The results of the analyses including additional ancient genomes provide mounting evidence that the Iceman's genetic affinity with Sardinians reflects an ancestry component that was widespread in Europe during the Neolithic. Despite their different geographic origins, both the Swedish farmer gok4 and the Thracian P192-1 closely resemble the Iceman in their relationship with Sardinians, making it unlikely that all three individuals were recent migrants from Sardinia. Furthermore, P192-1 is an Iron Age individual from well after the arrival of the first farmers in Southeastern Europe (more than 2,000 years after the Iceman and gok4), perhaps indicating genetic continuity with the early farmers in this region. The only non-HG individual not following this pattern is K8 from Bulgaria. Interestingly, this individual was excavated from an aristocratic inhumation burial containing rich grave goods, indicating a high social standing, as opposed to the other individual, who was found in a pit [15]. However, the DNA damage pattern of this individual does not appear to be typical of ancient samples (Table S4 in [15]), indicating a potentially higher level of modern DNA contamination. On the other hand, the Swedish and the Iberian hunter-gatherers show congruent patterns of relatedness to the modern populations of Northern Europe, which is consistent with the previous results using those samples.

Also of interest, given previous suggestions that the Iceman had more Neandertal ancestry than modern Europeans:

However, all D-tests involving another non-African population do not significantly deviate from zero, suggesting that the Iceman genome contains levels of archaic ancestry that are comparable to that of other non-African populations.

A model of European history is seen on the left. Some details are probably incorrect (e.g., Sardinian Neolithic probably followed the Cardial/Mediterranean route rather the one shown in C). There are no good ancient DNA from Cardial Neolithic farmers, so the fact that Sardinians are similar to the Iron Age Bulgarian, the Stuttgart LBK German, and the Swedish TRB farmers may mean that the Mediterranean/Cardial farmers were related to the ones that went into Europe following the inland route from the Balkans.

In any case, the fact that there are now data from Bulgaria is great, because it means that southern Europe is not hopeless for ancient DNA preservation and hopefully more is on its way.

UPDATE: Did anyone see a link to the new data? It appears that there are only ~1,000 SNPs in common with the HGDP. [A link to the data will become available at the Bustamante lab website]

PLoS Genet 10(5): e1004353. doi:10.1371/journal.pgen.1004353

Population Genomic Analysis of Ancient and Modern Genomes Yields New Insights into the Genetic Ancestry of the Tyrolean Iceman and the Genetic Structure of Europe

Martin Sikora et al.

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.

Link

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. 

Report on Sardinian-like ancient Europeans from ASHG 2012

Tia Ghose reports from ASHG2012: 

To answer that question, Sikora's team sequenced Ötzi's entire genome and compared it with those from hundreds of modern-day Europeans, as well as the genomes of a Stone Age hunter-gatherer found in Sweden, a farmer from Sweden, a 7,000-year-old hunter-gatherer iceman found in Iberia, and an Iron Age man found in Bulgaria. 

The team confirmed that, of modern people, Sardinians are Ötzi's closest relatives. But among the prehistoric quartet, Ötzi most closely resembled the farmers found in Bulgaria and Sweden, while the Swedish and Iberian hunter-gatherers looked more like present-day Northern Europeans.
...

The findings add to a growing body of evidence showing that farming played a major role in shaping the people of Europe, said Chris Gignoux, a geneticist at the University of California San Francisco, who was not involved in the study.

"I think it's really intriguing," Gignoux said. "The more that people are sequencing these ancient genomes from Europe, that we're really starting to see the impact of farmers moving into Europe."

Any ASHG attendees want to add any interesting details from the presentation? Comment away or e-mail me.

Assessment of ancient European DNA with 'globe13'

Here is my assessment of ancient DNA from Europe using the globe13 calculator:

You can consult the spreadsheet for the distribution of these components in modern populations. As in previous analyses, the main distinction is between Northern European-like Mesolithic population (Ajv52, Ajv70, and Bra1), and Mediterranean-like Neolithic (Oetzi and Gok4) one.

Ancient European DNA assessment with 'globe10'

I had previously assessed the same using globe4. See post on globe10 and associated spreadsheet.

The results appear similar to previous analyses overall, with the main features being the presence of "Southern" in Neolithic farmers (which peaks in the Near East), and its absence in hunter-gatherers. Some of the "Amerindian"-like admixture that was evident in globe4 has been "absorbed" by the Atlantic_Baltic (main European) component, but it is interesting that the Swedish hunter-gatherers (Ajv52/Ajv70) continue to show some Amerindian as well as other eastern (Australasian/South Asian) admixture that is lacking in the other samples. These individuals are outside the range of modern populations, but they overall tend to map to the most similar Atlantic_Baltic component with the addition of some eastern influences.

Also of interest is the fact the Oetzi is the only sample which shows a slice of West Asian (5.7%) admixture in this analysis. This was also the case in the previous one using K7b (1.4%). Gok4, on the other hand, the fellow Neolithic individual from Sweden seems to lack this. The arrangement of the Big Three West Eurasian components (Southern/West Asian/Atlantic_Baltic) has subtly changed in this calculator, but it would be tempting, nonetheless, to see in the little West Asian admixture that Oetzi has but Gok4 and the Mesolithic samples seem to lack, something of the vanguard of the arrival of the West Asian component in Europe. Obviously more samples are needed, including ones from the most interesting regions of the Balkans and Anatolia.

Ancient European DNA assessment with 'globe4'

In a previous experiment, I showed that ADMIXTURE at K=4 tracks the same signal of Amerindian-like admixture detected with f-statistics. I encapsulated that analysis in the globe4 calculator over at the Dodecad Project blog, and decided to use it to assess a few ancient European autosomal samples:

Please note that a very variable number of SNPs was extracted from these various samples. These results should be viewed as indicative of possible patterns that might be confirmed by a more thorough analysis. Also, please consult the globe4 post for more details on the methodology behind it, and the interpretation of the 4 components.

With these various caveats, I would say that these results seem to make some sense and to be fairly consistent with the scenario of Patterson et al. (2012):

• Oetzi and Gok4, the "farmers" seem to lack the Amerindian component
• Ajv52, and Ajv70, the northern hunter-gatherers seem to possess it
• Bra1, the Mesolithic Iberian seems to lack it as well

Bra1 also happens to be the most limited sample in terms of available SNPs. Nonetheless, this would appear broadly consistent with the idea that the "Amerindian"-like admixture in Europeans emanated from north-eastern Europe. Today, all continental Europeans seem to possess some of it, but this can be explained by migration of Ajv-like individuals and their mixtures into Western and Southern Europe from central or northern Europe for which there is ample historical and archaeological evidence (e.g., Italo-Celts, Germans, and Slavs, in addition to other, earlier phenomena).

A broader context

The absence of the Amerindian-like admixture in South Indian Brahmins and Armenians, and its paucity Kurds and Iranians might indicate that this type of ancestry was not represented in ancient Armenians and Indo-Iranians. Indeed, all these populations possess less of this admixture than those of the North Caucasus. Cypriots possess none of it as well, where the Greek_D sample, a small 2.5% portion. In a previous analysis, I estimated a historical-era estimate of North European admixture in Greeks, and this admixture presumably incorporates the signal of Amerindian-like admixture. Additionally, an Iron Age individual from Bulgaria will soon be announced as being Sardinian-like.

The sum of these factors leads me to believe that the signal of Amerindian-like admixture did not play an important role in the formation of the Graeco-Phrygians (and their Armenian relatives) and the Indo-Iranians, or at least did so to an insignificant degree. As the former expanded westward from the PIE homeland, and the latter eastward, they would have had little opportunity to encounter this type of admixture; rather, they would have admixed with Sardinian-like individuals in the west, and Ancestral South Indian (ASI)-like or East Asian individuals in the east.

On the other hand, as Indo-European groups expanded into eastern Europe, setting off a chain of events that would eventually transform most of the northern part of the continent, and, in historical times, much of the rest of it, they would have met with Ajv-like individuals carrying the signal of Amerindian-like admixture, as well as the Oetzi/Sardinian-like farmers that had spread all the way to Scandinavia by the late Neolithic. The population formed by this mixture would have carried with it the signal of Amerindian-like ancestry, and would then transpose it across the continent. The signal would become increasingly muted westward and southward, and indeed this is what we observe.

UPDATE: It is interesting to see that South Indian Brahmins (both the Metspalu et al. sample, and my Iyer_D and Iyengar_D samples) lack this admixture, while Uttar Pradesh Brahmins do not, given the rolloff evidence for a more recent admixture of the latter. This is consistent with a historical admixture event, after the migration of Brahmin groups southwards, as described in that post.

West Asian and North European admixture in Basques and Indo-Europeans

In a previous post I showed that Basques are lacking in the West Asian admixture present in all their West European Indo-European neighbors, consistent with my theory of a late Indo-European invasion of Europe whose ultimate source was the highlands of West Asia.

But, there are alternative theories, one of which purports that the Proto-Indo-Europeans were northern Europeoid pastoralists from the eastern European steppe. Since the North_European ancestral component is lacking in the Tyrolean Iceman and Gok4, the TRB Swede, it is conceivable that North_European bearing populations introduced this component during the Indo-European invasion.

Of course, there is absolutely no archaeological evidence for a massive migration out of the steppe into Europe, as even the main proponents of the steppe hypothesis accept, and as physical anthropology makes clear. And, we don't have to invoke an eastern European invasion to explain the North_European component, since it was present among pre-Indo-European hunter-gatherers from both Gotland and Iberia, as two ancient DNA studies have shown.

In any case, I took the HGDP and 1000Genomes European populations, together with the West_Asian and North_European Dodecad components, and calculated f3 statistics of the form:

f3(IE; Basque, Dodecad Component)

where Basque is either HGDP French_Basque or 1000 Genomes Pais_Vasco_1KG, and Dodecad Component is either West_Asian or North_European.

All the results can be found in the spreadsheet.

Again, there is evidence of West Asian+Basque admixture in all Indo-Europeans (|Z| less than -3) except the islanders from Canarias and Orkney, and the Russians; in the latter case, Basques are probably a poor stand-in for their pre-Indo-European ancestry. So, 32 of 38 comparisons are significant.

One would expect such negative f3 statistics to also apply in the North European+Basque case. After all, there are historically known migrations of Northern Europeoids into Western Europe (both Celts as well as Germanics) which did not affect Basques linguistically; moreover, Basques are southern Europeans, and many of the tested populations are northern Europeans, who are expected to turn up as mixtures of North European+Basque. However, a total of 16 of 38 comparisons are significant, involving, as expected mostly northern European populations.

It thus appears that geography and recent history is sufficient to explain the excess of North_European in some populations. Despite having a dataset with an excess of Iberian and North European populations, not many significant f3 statistics appear, and these are mostly as expected.

In conclusion, by comparing Basques vs. Indo-Europeans there appears no good evidence for the theory that Indo-European languages were brought into western Europe by a massive migration of northern Europeoids from eastern Europe. Basques do not appear distinctive in terms of the North_European component, but they do appear distinctive in terms of the West_Asian one.

This confirms previous ADMIXTURE analyses that Basques occupy an "intermediate" position along the north-south axis of variation in Europe, and an absolutely terminal one in terms of the West Asian component.

It is very interesting that ancient DNA research has provided clues about a very "uneven" landscape of prehistoric Europe, with Sardinian-like farmers in Sweden and Northern European-like hunter-gatherers in Iberia and very little in-betweens. But, these two elements eventually did mix, and, with the addition of a new group of people emanating from the highlands of West Asia, acquired their Indo-European speech, and went on to become the living nations of Europe.

Much remains to be discovered: the first ancient DNA traces of the constituent elements must be identified in space and time, and the history of their intermixture must be tracked.

ASHG 2012 abstracts are online!

There is so much good stuff there. This year I decided against posting the full abstracts, so I'll just link to a few, adding a few sentences on why they strike me as interesting. And, since there are so many interesting ones, I'll keep updating this entry.

On the Sardinian ancestry of the Tyrolean Iceman confirms that modern Sardinians are most similar to both the Tyrolean Iceman and the Swedish Neolithic TRB individual (presumably Gok4). You can find my analysis of both in the archives of the blog. But, look here:

Strikingly, an analysis including novel ancient DNA data from an early Iron Age individual from Bulgaria also shows the strongest affinity of this individual with modern-day Sardinians. Our results show that the Tyrolean Iceman was not a recent migrant from Sardinia, but rather that among contemporary Europeans, Sardinians represent the population most closely related to populations present in the Southern Alpine region around 5000 years ago. The genetic affinity of ancient DNA samples from distant parts of Europe with Sardinians also suggests that this genetic signature was much more widespread across Europe during the Bronze Age.

As you may have guessed, I can't wait to get my hands on that Iron Age Thracian. His similarity with Sardinians is striking, because by the Iron Age, I would have thought that something akin to the modern genetic landscape would have begun to crystallize in Europe.

Y Chromosome J Haplogroups trace post glacial period expansion from Turkey and Caucasus into the Middle East confirms what I have argued about, i.e., that the West Asian highlands are responsible for the spread of haplogroup J, including, it seems into the Middle East itself. The chronology presented probably assumes the evolutionary mutation rate; also, the lack of haplogroup J in Europe pre-5ka argues for a late expansion. I am fairly convinced that out of this West Asian highlander population came the two dominant groups of West Eurasian prehistory, the Indo-Europeans and the Semites, their spread associated with a "metallurgical edge" in technology and social complexity during the Late Neolithic and Bronze Age. The latter probably picked their language from a T- or E-bearing population of the southern Levant (Ghassulians?), as these two haplogroups might link the Proto-Semites with their African Afroasiatic brethren.

Analytical inference of human demographic history using multiple individual genome sequences:

We estimate that Eurasian populations split from ancient Africans at 58,000-120,800 years ago, and the divergence time of Europeans and Asians occurred at 35,750-70,500 years ago.

This sounds reasonable, and the wide confidence intervals probably reflect current uncertainties about the mutation rate. The European/Asian split time intersects the UP and postdates the ~70ka turning point (Toba + Drying up of Arabia/Sahara). The African/European split time intersects the ~106ka Nubian complex in Arabia.

A genomewide map of Neandertal ancestry in modern humans:

We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians.

This might seem superficially at odds with the recent finding of greater Neandertal ancestry in East Asians than Europeans, but remember that levels of Neandertal admixture depend on allele frequencies of introgressed variants, and East Asians are generally less polymorphic than Europeans.

Analysis of contributions of archaic genome and their functions in modern non-Africans

Totally, we identified 410,683 archaic segments in 909 non-African individuals with averaged segment length 83,460bp. In the genealogy of each archaic segment with Neanderthal, Denisovan, African and chimpanzee segments, 77~81% archaic segment coalesced first with Neanderthal, 4~8% coalesced first with Denisovan, and 14% coalesced first with neither, validating the algorithm. Interestingly, a large proportion of all the archaic segments identified shared 88.9% similarity with Neanderthal, suggesting a single major admixture with Neanderthal at 82~121kya, right after the Africa exodus of the ancestors of modern humans.

It will be interesting to see what these authors get a different date than Sankararaman et al.  The mutation rate can't be at fault because these dates are mostly dependent on the recombination rate. My initial guess is that the lower rate of S. et al. may be due to limiting the analysis to alleles with MAF less than 0.1. As I said before, it is unclear whether admixture LD-based signals of admixture with Neandertals can account for the totality of the D-statistics of Non-Africans vs. Africans.

Sequencing of an extended pedigree in Western chimpanzees is interesting for a variety of reasons, but for me the primary one is the inevitable use of this pedigree to fix the chimpanzee autosomal mutation rate, which has so far been assumed to be similar to the human one. On a similar topic, Estimating human mutation rate using autozygosity in a founder population comes up with 1.21x10-8/bp/generation for humans, which is practically the same as that inferred for Iceland, and belongs to the class of slow mutation rates that have been inferred lately and which may reshape our understanding of events ranging from human-chimp speciation to the date of Out-of-Africa.

The genetic structure of Western Balkan populations based on autosomal and haploid markers

Comparison of the variation within autosomal and haploid data sets of studied Western Balkan populations revealed their genetic closeness regardless of a genetic system inspected, in particular among the Slavic speakers. Hence, culturally diverse Western Balkan populations are genetically very similar to each other. Only the Kosovars show slight differences both in the variance of autosomal and uniparentally inherited markers from the other populations of the region, possibly also due to their historically strict patrilineality. In a more general perspective, our results reveal clear genetic continuity between the Near Eastern and European populations, lending further credence to extensive, likely multiple and possibly bidirectional ancient gene flows between the Near East and Europe, cutting through the Balkans.

 Asian Expansion of Modern Human out of Africa is not very eloquent, and I think may be missing a zero in one of its numbers, but the point being made (that the major Y-haplogroup E found in Africans is descended from Asian back-migrants) is something which I also think very likely, for reasons explained here.

Paleolithic human migrations in East Eurasia by sequencing Y chromosomes:

Paleolithic human migrations in East Eurasia remains largely unknown due to the lack of sufficient markers derived from the mutations that occurred during that time frame. To tackle this problem, using the sequence capturing, barcoding technology and next-generation sequencing, we identified more than 4,000 new SNPs encompassing most single copy non-recombining region of human Y chromosome. New clades for haplogroups O, C, N, D, and Q could be geographically located. Especially, a few star-like expansions were unveiled, showing strong population growth. The phylogeny of Haplogroup N was radically rearranged, and all the N individuals could now be categorized into either a northern clade N1 or southern clade N2, revealing a Paleolithic migratory routes of the ancestors of Uralic speaking populations. Haplogroup C, especially the East Eurasia-dominant clade C3, could also be separated into at least two ancient clades, suggesting Paleolithic migrations in East Asia. Three major clades under O, M117+, M134xM117, and 002611+, each could be now further classified into several subclades. With these new findings, we proposed the modified the routes and dates for human populations’ migration, especially those in Paleolithic time. A few Y-chromosomal expansions could now be linked to certain prehistoric cultures or ancestors of language families.

Inferring and sequencing the founding bottleneck of Ashkenazim

Applying this methodology to data from self-identified AJ samples, we show 85-90% of them belong to a genetic isolate related to other Mid-Eastern populations. This group has experienced an extreme bottleneck 30-35 generations ago, with subsequent expansion greatly exceeding the growth rate across all humans. Data are consistent with bottleneck size of merely 400 founders.

Progress in the Y-chromosome phylogeny

There is much of interest in the abstracts of the DNA in Forensics 2012 conference which will start very shortly, including news on the Tyrolean Iceman (he belonged to G-L91; and G2a "featured unexpectedly high densities within or near the Ötztal Alps."), speculations about a trans-Pacific spread of a lineage found in South Americans, and many other topics besides.

But, for me, the most interesting abstracts relate new developments in the Y-chromosome phylogeny world. The titles of the 3 abstracts are:

Y-chromosomal insights from large-scale resequencing

A calibrated human Y-chromosomal phylogeny based on resequencing

Insight into human Y chromosome variation from low-coverage whole-genome resequencing

and, they all seem to be from authors working at The Wellcome Trust Sanger Institute.

Researchers used 1000Genomes low coverage data (2x) and high coverage Complete Genomics data to untangle the Y chromosome phylogeny. As expected, the 1000Genomes data weer of poorer quality, and had a large number (~14-17%) of false negatives, i.e., SNPs that were actually present in the samples were not discovered. 

I list the main findings from the three abstracts:

The TMRCA of the entire tree was ~115 KYA (thousand years ago), and of the lineagesoutside Africa ~60 KYA, both as expected. Additional insights included a rapid expansion of hg F~40 KYA, and of R1b in Europe ~5-10 KYA. The archaeological counterpart of the former isunclear, but the latter is likely to represent a Neolithic expansion of this lineage

The GENETREE TMRCA for the complete set of chromosomes examined was 105-125KYA; times for the out-of-Africa movement were 62-79 KYA, a Paleolithic expansion 37-48KYA, and the expansion of R1b in Europe 7-10 KYA; rho times were broadly similar.

It confirmed Hg E (Bantu), O (China) and R1b (Europe) expansions associated with the Neolithic transitions in different parts of the world, and revealed that the expansion in Europe was the most extreme. One novel finding was a striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement, suggesting a previously unknown event of importance to male demography at this time.

I would say that these results are consistent with my "two deserts" theory and the climatic history of Africa and the Near East. Of course, I don't think there was a 60ky Out-of-Africa event, for a number of different reasons that I've written about to death. With respect to Y chromosome phylogeny, it is important to highlight one more time where I'm coming from:

The major African Y-haplogroup E belongs to the DE subclade of the CT clade:

I have color-coded the Eurasian lineages as "green", and the African ones as "red". Now, those who think that the age of CT corresponds to Out-of-Africa believe that this event was accompanied by a massive bottleneck which is responsible for the reduced genetic diversity of Eurasians compared to Africans.

But, the question is obvious: if there was such a massive bottleneck in Eurasian ancestors, then how come it is the Eurasians (the bottlenecked population) that ended up with most of the CT descendants?

There really is no archaeology to support a 62-79ky Out-of-Africa, the only archaeology (and anthropology) in support of Out-of-Africa relates to the pre-100ky period, with things like the Nubian complex, the Mt. Carmel hominins, Jebel Faya, and others links between Africa and the Near East.

There are no genetics to support it either: track every paper that has argued for ~60ky Out-of-Africa, and you will invariably find a 2.5x10-8/bp/generation or similar mutation rate and/or a recent human-chimp calibration hiding somewhere in the details. While the mutation wars rage, it is not certain how they will be resolved, but I would put money on the true mutation rate ending up much lower than the one dominating the literature, and, consequently, Out-of-Africa being much earlier.

Getting back to the topic, the "striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement" corresponds to the UP Revolution in west Eurasia. So, to recapitulate my thinking in bullet form:

1. Pre-100ky Out-of-North Africa (Mt. Carmel, Nubian, Jebel Faya?)
2. c. 70ky climate crisis in North Africa-Arabia. Reduction of Y-chromosome diversity: CT founder.
3. 70-50ky. Modern human biocultural evolution accelerates as they (i) face climate crisis, (ii) face new environments as they move out of North Africa-Arabia, (iii) face archaic humans in Eurasia and Africa.   Haplogroup DE is group of "southern"  Out-of-Arabians heading east (D) or west (E); Haplogroup CF is group of "northern" Out-of-Arabians, some of which head east (C) or stay around (F).
4. 50-40ky. Culmination of the process leads to UP/LSA Revolution: 

• In East: some F descendants come to dominate over the early D and C settlers
• In West Eurasia: other F descendants break through the Neandertal bottlecap and invade Europe with UP technologies
• In Africa: E descendants (descended from DE back-migrants) kick-start the Lower Stone Age.

.

Paleolithic Europeans may have been substantially Neandertal-admixed

In Oetzi the Neandertal Champion, I suggested a way to determine whether the higher Neandertal admixture in Oetzi suggested by Sams and Hawks is due to his Near Eastern Neolithic or European Paleolithic ancestry.

The basic idea is simple: first build a map of Oetzi's ancestry with a tool that distinguishes between the Near East and Europe. I did this with my West Eurasian cline (weac2) calculator. The output of this procedure is to calculate admixture proportions for Oetzi across the genome. In some windows along his chromosomes, he will appear to be 100% Atlantic_Baltic (European-centered component), in others 100% Near_East, and in some intermediate, or possessing some other component. At each window we have an Atlantic_Baltic and a Near_East admixture score.

Secondly, we need to calculate a score of Oetzi-Neandertal (Vindija) similarity in the same window. I used the Neandertal data from the Harvard HGDP, and my own copy of the Oetzi genome which I've created by intersecting a SNP file provided by Andreas Keller with the Stanford HGDP set of SNPs. In the end I combined Oetzi and Vindija in a common set of 37,320 SNPs, removing all SNPs with missing alleles. One could get more SNPs by not taking these various intersections and working with full genomes, but this set of SNPs suffices for my purposes.

In any case, I used 0/1/2 coding and took the absolute value of the Oetzi minus the Vindija value, normalizing by dividing with the number of SNPs in each window. That was my Score variable, and the lower the value the more Oetzi matches Vindija.

The idea is simple: does Oetzi tend to appear "Near_East" or "Atlantic_Baltic" in places along his genome where he is close to Neandertals?

I limited myself to windows where there were at least 10 SNPs common between Oetzi and Vindija, as well as windows where the sum of Atlantic_Baltic and Near_East was at least 95%, so there was good evidence that these two components were responsible for the whole diploid pair of segments. A total of 1,128 windows remained. The results are as follows:

Cor("Near_East", Score) = +0.082
Cor("Atlantic_Baltic", Score) = -0.079

These are small, but significant, and we should remember that relative levels of Near_East and Atlantic_Baltic vary for reasons unrelated to Neandertal ancestry in most of the genome. Here is a plot of the Score variable for the 1,128 windows, ordered from high-to-low:

There is a group of windows with particularly low Score, so perhaps these represent the strongest evidence for Neandertal ancestry in Oetzi. Any such ancestry may mostly consist of small segments, so my not-so-dense sieve formed by the small number of studied SNPs is probably missing a lot of Neandertal segments that may turn up with full genome comparisons.

In any case, the median Atlantic_Baltic for all windows is 46.48%, and the median Near_East one is 52.78%. But, let's see how these numbers look when we consider the lowest quantiles of Score (=more Neandertal matching):

These numbers kinda speak for themselves. Of course, it is wrong to equate Near_East = Neolithic and Atlantic_Baltic = Paleolithic. On the other hand, the assumption that these two components possess a greater relationship with the Neolithic farmers and the Paleolithic Europeans respectively, seems justified.

So, it seems that in regions where Oetzi matches the Vindija genome, he tends to be "Atlantic_Baltic". The implication is that Paleolithic Europeans were more Vindija-like than incoming Neolithic ones from the Near East. Oetzi may have been more Neolithic farmer than Paleolithic hunter-gatherer across his whole genome, but the situation is reversed for regions suggestive of Neandertal ancestry.

The idea that Upper Paleolithic Europeans were admixed with Neandertals is not new. Its most recent prominent champion is Milford Wolpoff (figure on the left is from one of his most recent works, showing a Copper Age European male (top) sharing features with La Chapelle Neandertal (middle) at the exclusion of Herto (an archaic H. sapiens from Ethiopia), indicating a degree of continuity from Neandertals to more recent Europeans.)

Just how Neandertal-admixed were the Paleolithic Europeans? If Hawks is correct in his claim that Oetzi was ~5.5% Neandertal, and given that Oetzi appears to have been overall more than 50% incoming farmer and less than 50% local hunter-gatherer (conservatively), then it is easy to conclude that even ~10% Neandertal for Paleolithic Europeans may not be too far from the truth. We'll have to see what their actual ancient DNA looks like to confirm the hypothesis found in this post.

Finally, since it's my custom to resuscitate old physical anthropology when it matches modern observation, here's Carleton Coon's 1939 Races of Europe, from his "Statement of Aims and Proposals":

At any rate, the main conclusion of this study will be that the present races of Europe are derived from a blend of (A), food-producing peoples from Asia and Africa, of basically Mediterranean racial form, with (B), the descendants of interglacial and glacial food-gatherers, produced in turn by a blending of basic Homo sapiens, related to the remote ancestor of the Mediterraneans, with some non-sapiens species of general Neanderthaloid form. The actions and interactions of environment, selection, migration, and human culture upon the various entities within this amalgam, have produced the white race in its present complexity.

I'd say that if these results are confirmed by subsequent research, then "bullseye" is a good way to describe the above passage.

(But, I will not refrain from spoiling the fun a little bit, by pointing out that the potential high similarity of UP Europeans with the Vindija genome may be due, at least in part, to gene flow from UP Europeans-to-European Neandertals in that particular specimen. Now, it may be that such gene flow may have gradually made the European Neandertals more modern-like, and thus facilitated their eventual full absorption into the gene pool of subsequent Europeans. But, we don't know that for sure. A second Neandertal genome, preferably a pre-contact one will be the decisive factor in determining the direction of gene flow conclusively.)

3-population test and east Eurasian-like admixture in Europe or The Isle of Refuge

The 3-population test (Reich et al. 2009) allows one to detect the presence of admixture in a population X from two other populations A and B. The value

f3(X; A, B)

is negative when X does not appear to form a simple tree with A and B but appears to be a mixture of A and B.

In a previous entry, I noted that continental European populations, and especially northern Europeans appear to have East Eurasian-like admixture on the basis of the 4-population test. The results of that test are more difficult to interpret, because the quantity f4(X, Y; A, B) can take significant negative or positive values depending on the relationships of populations X, Y with A, B. When A, B are East Eurasian and African populations respectively, and X, Y are West Eurasian ones, East Eurasian-like admixture in a northern European population will affect the f4 quantity similarly as African-like admixture in a southern Caucasoid one. This is not a problem with the f3 test, although caution is needed: a negative value indicates deviation from "treeness" and admixture, but a positive one does not reject admixture.

The f3 statistics were calculated with the threepop program of TreeMix with -k 500 over a set of 598,467 SNPs.

I have used 3 Asian/American reference populations (Karitiana from South America, CHB Chinese, and Papuans) and calculated the following:

f3(West Eurasian 1; West Eurasian 2, Asian/American)

As noted above, negative values of this indicate that West Eurasian 1 can be seen as an admixed population of West Eurasian 2 + Asian/American. The set of 14 West Eurasian populations used is:

CEU, TSI, Tuscan, Orcadian, French, French_Basque, North_Italian, Bedouin, Palestinian, Druze, Mozabite, Adygei, Russian, Sardinian

I thus report 2*(14 choose 2)*3 = 546 values of f3. Hence, I did not privilege Sardinians as a reference point, but instead tried all pairs of West Eurasian populations, and 3 different American/Asian references. There results can be found in the spreadsheet.

Out of the 546 triples, 64 show an f3 score less than Z less or equal to -3, and are thus significant.

The following populations have such a score in at least one pairwise comparison, when they are set as West Eurasian 1, and thus appear to have east Eurasian-like admixture

CEU, Russian, French, Adygei, TSI, Tuscan, Orcadian, North_Italian, Palestinian  

Note that east Eurasian-like admixture cannot be rejected for the other populations, but it can be confirmed for the above. Moreover, the mean strength of the observed effect for the significant comparisons was Z=-5.5 for Papuan reference, Z=-10.2 for CHB, and Z=-10.9 for Karitiana, again suggesting a northern origin of the east Eurasian-like admixture, albeit without so major a difference between Karitiana and CHB as in the 4-population test.

But, it is worth reading the raw data. For example, note above that of the Middle Eastern and North African populations, only Palestinians show a negative f3 score in any pairwise comparison. And actually they only do so for f3(Palestinian; Sardinian, Papuan) with a Z-score of -4.1. So, it appears that Palestinians have undergone admixture of a different sort than Europeans.

Significant differences were observed for Sardinians as West Eurasian 2 in 21 cases, for French Basque in 11 cases, for North_Italian and TSI in 6 cases, for CEU, Orcadian, French, and Tuscan in 4 cases. So, it appears that other populations appear east Eurasian-liked admixed relative to Sardinians, and a couple of populations (Russian and Adygei) also appear so admixed relative to west Europeans.

Oetzi the Tyrolean Iceman

The fact that Europeans appear admixed with an east Eurasian-like element when compared with Sardinians does not mean that Sardinians may not also be admixed with this element. I used the genome of the Tyrolean Iceman (Keller et al. 2012) to test whether Sardinians appear east Eurasian-like admixed relative to the Iceman.

f3(Sardinian;Karitiana,Oetzi) = 5.36496e-06 (Z=0.00940612)

This might indicate no admixture, but f3 can detect admixture but can't prove non-admixture. The f4 is suggestive:

f4(Sardinian,Oetzi;Karitiana,San) = -0.00221783 (Z=-3.06251)

You should probably not take my word for the above. It may appear that, contrary to expectation, Oetzi was more east Eurasian-like than modern Sardinians. Indeed, in my initial analysis of him with ADMIXTURE, I found that he was 2.8% East_Asian, which would point to an East Eurasian shift of Oetzi relative to Sardinians, and which might be consistent with the f4 result. On the other hand, the negative f4 score could be related to African-like gene flow. On balance I would say that Sardinians appear quite similar to Oetzi.

Gok4 and Ajv52

Furthermore, I carried out the same analysis on Neolithic samples from Sweden (Skoglund et al. 2012). The number of SNPs here is much smaller. Results are:

Gok4 (TRB farmer): f4(Sardinian,Gok4;Karitiana,San) = -0.00167365 (Z=-1.23616)
Ajv52 (PWC hunter-gatherer): f4(Sardinian,Ajv52;Karitiana,San) = -0.004676 (Z=-3.76048)

While I would not bet the farm on these results (because of the small number of SNPs and the fact that they're based on a single individual), they do seem to suggest that these Neolithic Swedes were east Eurasian shifted relative to Sardinians. For example, for my Swedish_D sample, I get f4(Sardinian, Swedish_D; Karitiana, San) = -0.00372751 (Z=-22.8715). The Z-score is stronger (probably because of the much larger number of SNPs), but the f4 value of Ajv52 is lower (more east-Eurasian like). Modern Swedish_D appears intermediate between Gok4 and Ajv52, so this may suggest that Mesolithic Europeans may be, at least in part the source of this element.

(Comparison with Brana-1 Mesolithic Iberian indicates a negative non-significant f4 score, but with an even smaller number of SNPs).

In sum total, my experiments with ancient DNA samples from Europe suggest a little more east Eurasian-like shift relative to Sardinians (or conversely a little more African-like shift in Sardinians). Both Oetzi (who has the highest quality genome) appears to be so-shifted, but Ajv52 (a Neolithic northern hunter-gatherer) appears to be so as well. I am sure that if we get more high quality ancient DNA from Europe, some clear pattern may emerge, but I would not speculate further on the basis of these initial results.

Isle of Refuge

The above set of experiments has revealed once more that "there's something about Sardinians." There is perhaps a reason for the fact that the arrival of population elements from continental Europe seems to have bypassed them to some degree, or, at least affected them least. However it was that continental Europeans got their east Eurasian-like shift, the great tank of European genetic variation does not seem to have achieved equilibrium with the little cup of Sardinia. Something stood in the way.

Sardinia is the west-most of the large Mediterranean islands. It is more distant from mainland Europe/Asia than the other big islands (Cyprus, Crete, Sicily, and Corsica).

And, unlike islands much smaller than itself, its size has probably been instrumental in helping it afford it a certain autonomy and continuity of population. Only Sicily is largest, but one can practically swim across the Strait of Messina to reach it from the Italian peninsula.

Hence, a combination of large size, western geographical location, and distance from the mainland have contributed to the continuity of its population. But, geography may not have been sufficient if other events had not taken place. Through a combination of favorable geography and historical contingency, the Sardinians made it to the present largely unscathed, and, among their other graces, can now help scientists figure out what happened to the rest of us.

Oetzi the Neandertal champion

John Hawks reports that Oetzi, the Tyrolean Iceman appears to be much more "Neandertal" than any modern person. This is a very intriguing finding, which would have monumental implications about our understanding of our past.

Furthermore, he speculates that:

Paleogenetic evidence from Neandertals, the Neolithic and other eras has the potential to transform our knowledge of human population dynamics. Previous work has established the level of contribution of Neandertals to living human populations. Here, I consider data from the Tyrolean Iceman. The genome of this Neolithic-era individual shows a substantially higher degree of Ne- andertal ancestry than living Europeans. This comparison suggests that early Upper Paleolithic Europeans may have mixed with Neandertals to a greater degree than other modern human populations. I also use this genome to evaluate the pattern of selection in post-Neolithic Europeans. In large part, the evidence of selection from living people’s genetic data is confirmed by this specimen, but in some cases selection may be disproved by the Iceman’s genotypes. Neolithic-living human comparisons provide information about migration and diffusion of genes into Europe. I compare these data to the situation within Neandertals, and the transition of Neandertals to Upper Paleolithic populations – three demographic transitions in Europe that generated strong genetic disequi- libria in successive populations.

In our twitter exchange he seems open to the possibility I suggested that Oetzi might have excess Neandertal admixture from the Near Eastern Neolithic. He says: "@dienekesp Not impossible if there were relict Neandertals in West Asia. OTOH, UP morphology is consistent with > Neandertal."

Indeed, most of the argument for Neandertal admixture has focused on Neandertal morphological traits in UP Europeans. But, West Asia has been proposed as a site for modern human-Neandertal mixing, and a number of West Asian Neandertals appear to share modern traits. 

There is a way to test whether the excess Neandertal admixture in Oetzi is due to his Mesolithic European or Neolithic Near Eastern component.

Make a map of sites where Oetzi has a signal of Neandertal admixture. Then, use a tool, such as my weac2 calculator which contrasts Europe (Atlantic_Baltic component) with the Near East (Near_East component). It is expected that a signal of Upper Paleolithic European ancestry will lurk in the Atlantic_Baltic component, while a signal of Near Eastern Neolithic ancestry will lurk in the Near_East component.

If the excess Neandertal occurs at regions of Oetzi's genome with an excess of Atlantic_Baltic then the UP European scenario is confirmed; otherwise the Neolithic Neandertal scenario is supported.

I have already made a map of Oetzi's genome. His overall admixture proportions using weac2 are:

  1.05%  Palaeoafrican       

 43.94%  Atlantic_Baltic     

  0.00%  Northeast_Asian     

 51.52%  Near_East           

  1.54%  Sub_Saharan         

  0.00%  South_Asian         

  1.95%  Southeast_Asian     

and a fine scale map of his ancestry can be found here (NCBI 36 positions). I used a window of 100 SNPs, advanced by 10 SNPs. Admixture estimates within each window are obviously noisy, but if there is a pattern where Oetzi is more "Neandertal" in Atlantic_Baltic vs. Near_East regions, it ought to jump out.

So, anyone can look at regions where Oetzi matches Vindija and see whether Near_East or Atlantic_Baltic will carry the day in the Neandertal championships!

Assessing Neolithic Europeans with 'weac2'

I have used the West Eurasian cline calculator 'weac2' to assess the Tyrolean Iceman and Neolithic Swedes. The admixture proportions can be seen below, and appear largely consistent with all previous analyses of the same individuals:

It is interesting that Gok4, the Swedish Megalithic TRB female belongs to the Atlantic_Baltic and Near_East components, while the two major Y-chromosome haplogroups associated with West European Neolithic sites so far are I2a1 and G2a (Treilles and Dolmen of La Pierre Fritte) whose distribution very well parallels these two components: Atlantic_Baltic/I2a1 in Europe, and Near_East/G2a in the Near East.

The simplest explanation, based on the available evidence, is that the Neolithic populations of Europe were descended from G2a-bearing pioneers entering Europe from the southeast, and encountering an I2a1-bearing population of pre-farmers in Europe itself. The high frequency of I2a1 in Sardinia, as well as the presence of G2a in that population serves to underscore the substantial genetic continuity between ancient Neolithic Europeans and modern Sardinians.

The absence of the South_Asian component in 'weac2' in all of these individuals is also important. This component captures ancestry (both Caucasoid and Ancestral South Indian) from further east and south, where both G2a/I2a1 are quite rare. As I have noted before, both Europe and South Asia have been affected in late/post-Neolithic times by migrations from West Asia.

It is tempting to associate this population movement with the spread of Indo-European languages, and we can only eagerly await more autosomal ancient DNA samples that will reveal the arrival of the "missing components" over the Neolithic substratum.

Iceman's sheep belonged to mtDNA haplogroup B

This establishes that the main mtDNA haplogroup (B) of extant European sheep was already present in the ~5.3ky old sheep hair shafts of the Tyrolean Iceman's clothing. The fact that the precise sheep sequence (like that of its bearer's) has not been identified in modern sheep testifies to the importance that drift and/or selection has played in the recent evolution of the species.

PLoS ONE 7(3): e33792. doi:10.1371/journal.pone.0033792

Phylogenetic Position of a Copper Age Sheep (Ovis aries) Mitochondrial DNA

Abstract Top

Background

Sheep (Ovis aries) were domesticated in the Fertile Crescent region about 9,000-8,000 years ago. Currently, few mitochondrial (mt) DNA studies are available on archaeological sheep. In particular, no data on archaeological European sheep are available.

Methodology/Principal Findings

Here we describe the first portion of mtDNA sequence of a Copper Age European sheep. DNA was extracted from hair shafts which were part of the clothes of the so-called Tyrolean Iceman or Otzi (5,350 - 5,100 years before present). Mitochondrial DNA (a total of 2,429 base pairs, encompassing a portion of the control region, tRNAPhe, a portion of the 12S rRNA gene, and the whole cytochrome B gene) was sequenced using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products. We have compared the sequence with the corresponding sequence of 334 extant lineages.

Conclusions/Significance

A phylogenetic network based on a new cladistic notation for the mitochondrial diversity of domestic sheep shows that the Otzi's sheep falls within haplogroup B, thus demonstrating that sheep belonging to this haplogroup were already present in the Alps more than 5,000 years ago. On the other hand, the lineage of the Otzi's sheep is defined by two transitions (16147, and 16440) which, assembled together, define a motif that has not yet been identified in modern sheep populations.

Link

Another look at Oetzi with 'euro7' and 'world9' calculators

After taking the first look at the genome of the Tyrolean Iceman, I decided to run him through a couple more calculators developed by the Dodecad Project.

The first one was euro7 which has a little bit more resolution within Europe. Oetzi was:

• 37.8% Southwestern
• 37.7% Southeastern
• 22.5% Northwestern
• 1.9% African
• 0.1% Far_Asian

These results are consistent with his K12b "Atlantic_Med" major ancestral component, and he appears once again to be a very close match for the Sardinian components using the same calculator.

The second one was world9 which is a "global" calculator that includes Amerindian and Australasian components. Oetzi was:

• 47.3% Atlantic_Baltic
• 46.4% Southern
• 3.1% Caucasus_Gedrosia
• 1.7% Australasian
• 0.9% African
• 0.6% East_Asian

Again, these match quite well the world9 values for Sardinians, who are a bit more Atlantic_Baltic and a little less Southern than Oetzi, as noted before for the K7b comparison that is similar to world9, with the addition of the Amerindian and Australasian components.

Overall, this is a nice demonstration that Oetzi's genome is indeed Sardinian-like as argued by Keller et al., and also that the Dodecad Project calculators based on the idea of "zombies" are indeed working as they're supposed to. (Note that the previous K=7 and K=12 comparisons were not based on "zombies", but produced quite the same conclusion as the supervised runs in this post).

This is even more impressive as only ~44k SNPs were used in these various experiments, intersecting the set of SNPs I have for Oetzi (1,459,228 SNPs mapped to hg18, or 156,691 SNPs intersected with my main Stanford HGDP reference), with the ~160-170k SNPs used in my various calculators after linkage disequilibrium-based pruning.

So, despite an about 4-fold reduction in the number of SNPs, the results are excellent. Hopefully, in the future, I'll find some time to create new calculators that use all ~160k of Oetzi's SNPs, although intersection with all the dozen Illumina-based datasets I currently have available leaves only ~72k SNPs in all.

But I have to say that I'm already growing tired of Oetzi, with his Sardinian-like predictability: what's the next ancient genome in the works? (e-mail me if you want to tip me)

A first look at the genome of the Tyrolean Iceman

Thanks to the publication of the Tyrolean Iceman's (reconstructed on the left) genome sequence, by Keller et al. (2012), I have been able to include him in a joint analysis with 2,671 other individuals, previously assembled for the K7b and K12b calculators of the Dodecad Project.

I have essentially repeated the unsupervised ADMIXTURE analysis from scratch, with two differences:

• The dataset now includes Oetzi, and
• The number of markers has been reduced to 44,435 by intersecting the 166,770 SNPs used in K7b/K12b with the SNPs available for Oetzi

I had predicted that Oetzi would turn out "Mediterranean" in his genomic profile, and the published analysis seems to have confirmed this by discovering that his closest modern kin are Sardinians, a Mediteranean population. Sardinians are usually modal for the various "Mediterranean", and "Atlantic_Med" components inferred by the Dodecad Project.

Thankfully, the ADMIXTURE analysis in both the K=7 and the K=12 case, resulted in the same solution as in K7b and K12b, despite the inclusion of Oetzi and the fact that a smaller number of markers were used. There are slight variations in the admixture proportions compared to the K7b/K12b numbers, and an expected increase in "noise levels" in the minor components, but the overall solution appears to be the same.

The results for Oetzi and the reference populations, including Dodecad populations with 5+ members are included in the spreadsheet.


Below, I will briefly comment on them.

K=7


Oetzi turns out to be 51.9% "Southern" and 43.1% "Atlantic_Baltic" in the K=7 analysis, with noise levels of the other components. The salient point is that he seems to be lacking the "West Asian" component, unlike most Europeans, except Basques and Sardinians, who have:

Basques: 27.6% "Southern" and 69.5% "Atlantic_Baltic"
Sardinians: 46.2% "Southern" and 52% "Atlantic_Baltic"

So, Oetzi does appear to be most Sardinian-like in this analysis, and indeed to be a little more "Southern" than extant Sardinians. This is consistent with Keller et al. (2012) which finds him to cluster with Sardinians and to be a bit more "southern" (in PCA space) than Sardinians.

K=12

Oetzi turns out to be 57.7% "Atlantic_Med" and 22.3% "Caucasus" in this analysis. Once again, this makes him quite similar to Sardinians who are 64.9% "Atlantic_Med" and 21.3% "Caucasus". Two components are salient in their absence: the "Gedrosia" component which is present in non-Sardinian modern Italians, and the "North_European" component which is also present in the same.

Discussion


If we compare Oetzi with modern Europeans, he certainly appears to be most Sardinian-like. If we compare him to modern Italians (the samples N_Italian_D, North_Italian, as well as the neighboring Tuscan, TSI30, and C_Italian_D) populations, he appears to possess many of the same components (including Atlantic_Med, Caucasus, Southwest_Asian, and Northwest_African in non-trace quantities).

This of course does not indicate that Oetzi was of "mixed" ancestry, since ADMIXTURE components are but imperfect reflections of ancestral populations. It does, however, indicate that his profile consisted of many of the same elements found in Italy today, but in different proportions. Moreover, any additional or "exotic" ancestry in Oetzi cannot have existed in substantial amounts so as to render the inferred proportions (in terms of modern populations) nonsensical.

The three exceptions to this rule are the "West_Asian" component in K=7 and the "Gedrosia"/"North_European" components in K=12, which are conspicuous in their absence. And, given that all three of these have their present-day center of weight in more eastern longitudes, we can be fairly certain that present-day Italians have been affected by people from the east, by one or more routes.

This is, again, reasonable, and in agreement with the observation of Keller et al. (2012) -pictured on the left- that the Iceman occupies a "western"/"southern" position relative to modern Italians, and is consistent with the idea that modern Italians were formed by an eastward shift (in the case of more southern Italians) and a northeastward shift (in the case of more northern Italians).

We can have near-absolute certainty that a "North European" element was present in northernmost Italy by at least the first half of the first millennium BC, the time of the Hallstatt culture of Central Europe and of historical references about the arrival of Celts in Cisalpine Gaul. Oetzi is dated to the latter half of the 4th millennium BC. Hence, there is an intervening period of about 2.5k years between the two; it will be interesting to sample individuals from that time period to see when -within that time interval- the arrival of this trans-Alpine element occurred. It will also be very interesting to sample individuals from further north, east, and west, to ascertain the full spatial extent of "Oetzi-like" individuals during the early Copper Age.

Similarly, we can be certain that more "eastern" elements were present in Southern Italy by at least the time of the Greek colonization, which occurred at much the same time as the arrival of the Celts in the north. However, since all Italians are eastward shifted relative to Oetzi, even those from furthermost north, it is likely that the eastward shift of modern Italians preceded the historical colonization and that some of the myths preserved by Roman and Greek writers about eastern origins of various pre-archaic Greek and pre-Etruscan Italian peoples may hold an element of truth.

At present, we are disadvantaged by the fact that we are trying to place ancient individuals within a modern genetic landscape. Oetzi's genome suggests the fluidity of this landscape as we move into the past. Thankfully, it is all but certain that we will soon obtain full genome sequences from other prehistoric and historic individuals from different spots in space and time, so our understanding of how West Eurasians came to be is only bound to improve.

Complete genome of the Tyrolean Iceman

I'll update this post once I read the paper. I could not locate a source for the data after a quick scan of the paper, but:

After genotyping, we merged both HapMap and 1,000 Genomes genotypes with the Popres/Iceman-merged dataset, resulting in a final analysis dataset containing 125,729 SNPs. PCA was then performed on all samples, excluding the five 1,000 Genomes samples, which were subsequently projected onto the PC space inferred from the rest of the dataset.

UPDATE: The Iceman's genome can be found at the http://icemangenome.net site.

UPDATE I (Y-chromosome):


From the paper:

We addressed this issue here by analysing the G2a4-defining L91 SNP in 7,797 chromosomes from 30 regions across Europe. Fig. 3d shows the spatial frequency distribution of G2a4 throughout Europe. The highest frequencies (25 and 9%) occur in southern Corsica and northern Sardinia, respectively, (Fig. 3e) while in mainland Europe the frequencies do not reach 1%.

UPDATE II (Autosomal DNA): 

In terms of autosomal DNA, the Iceman clearly clusters with modern Sardinians, and also appears slightly more removed than them compared to continental Europeans. Interestingly, at least as far as the PC analyssi shows, Sardinians appear to be intermediate between the Iceman and SW Europeans, rather than Italians. Perhaps, this makes sense if the Paleo-Sardinian language is indeed related to languages of Iberia.

I don't see a downloadable version of the Iceman's genome at the icemangenome.net site, but I've asked the corresponding author for a PLINK/EIGENSOFT version of it. I anticipate that, as I've predicted, this will appear to be largely "Mediterranean" according to Dodecad v3, or "Atlantic_Med" according to the newer K12b calculator. It appears that there has indeed been Sardinian continuity against a backdrop of European discontinuity.

UPDATE III (Sardinians):


The Iceman's genome also places the Sardinian genetic isolate into new light. Two explanations have been proposed for the fact that Sardinians appear genetically distinctive vis a vis continental Europeans:

1. Sardinians have lost due to drift alleles that were present in continental Europe
2. Continental Europeans have gained alleles that were not present in their Sardinian-like ancestors

The Iceman's genome argues strongly in favor of the latter hypothesis: continental Europeans, or, at least North Italians c. 5,300 years ago were more Sardinian-like, and they have become less Sardinian-like up to the present, probably due to an influx of new populations, carrying new alleles. As more ancient DNA is recovered, we will slowly witness the transformation of gene pools over time.

Nature Communications 3, Article number: 698 doi:10.1038/ncomms1701

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

Andreas Keller et al.

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

Link

Thomas Tartaron lecture on Ötzi the Iceman