Indo-Europeans Were Likely from the Near East

May 20, 2018

A new book and a new study on ancient DNA both say that the homeland of Indo-European languages was most likely south of the Caucasus Mountains in the Near East, and not in the Russian Steppe from where many later spread out. This would explain why the earliest IE languages were in Anatolia, and why IE-speakers in SW Europe have higher "Caucasus/Iran" ancestry and lower "Russian/Siberian" ancestry.

While the genetic findings point to a central role for the Yamnaya in spreading Indo-European languages, tipping the scales definitively in favor of some variant of the steppe hypothesis, those findings do not yet resolve the question of the homeland of the original Indo-European languages, the place where these languages were spoken before the Yamnaya so dramatically expanded. Anatolian languages known from four-thousand-year-old tablets recovered from the Hittite Empire and neighboring ancient cultures did not share the full wagon and wheel vocabulary present in all Indo-European languages spoken today. Ancient DNA available from this time in Anatolia shows no evidence of steppe ancestry similar to that in the Yamnaya (although the evidence here is circumstantial as no ancient DNA from the Hittites themselves has yet been published). This suggests to me that the most likely location of the population that first spoke an Indo-European language was south of the Caucasus Mountains, perhaps in present-day Iran or Armenia, because ancient DNA from people who lived there matches what we would expect for a source population both for the Yamnaya and for ancient Anatolians. If this scenario is right, the population sent one branch up into the steppe—mixing with steppe hunter-gatherers in a one-to-one ratio to become the Yamnaya as described earlier—and another to Anatolia to found the ancestors of people there who spoke languages such as Hittite.

David Reich. Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. New York: Pantheon Books, 2018.

The insight that the Caucasus mountains served not only as a corridor for the spread of CHG/Neolithic Iranian ancestry but also for later gene-flow from the south also has a bearing on the postulated homelands of Proto-Indo-European (PIE) languages and documented gene-flows that could have carried a consecutive spread of both across West Eurasia. Perceiving the Caucasus as an occasional bridge rather than a strict border during the Eneolithic and Bronze Age opens up the possibility of a homeland of PIE south of the Caucasus, which itself provides a parsimonious explanation for an early branching off of Anatolian languages. Geographically this would also work for Armenian and Greek, for which genetic data also supports an eastern influence from Anatolia or the southern Caucasus. A potential offshoot of the Indo-Iranian branch to the east is possible, but the latest ancient DNA results from South Asia also lend weight to an LMBA spread via the steppe belt. The spread of some or all of the proto-Indo-European branches would have been possible via the North Caucasus and Pontic region and from there, along with pastoralist expansions, to the heart of Europe. This scenario finds support from the well attested and now widely documented 'steppe ancestry' in European populations, the postulate of increasingly patrilinear societies in the wake of these expansions (exemplified by R1a/R1b), as attested in the latest study on the Bell Beaker phenomenon.

Wang et al. "The genetic prehistory of the Greater Caucasus". bioRxiv, 2018.

Eurasian Origin and Back-Migration of L3 and DE

January 7, 2018

This was already suggested a few years back by Farrell et al. (2013) and Shi Yan et al. (2013), and now a new study is saying the same thing again.

Background: After three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya.

Results: The coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.

Conclusions: These results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements.

Cabrera et al. "Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago". bioRxiv, 2017.

Genetic Continuity in Greece

August 8, 2017


Greek women through the ages: Minoan, Cycladic, Mycenaean, Classical, Modern  (SOURCE)


A recent study suggested based on modern samples that Greeks hadn't changed much since ancient times. Now that's been proven with ancient DNA from Bronze Age Minoan and Mycenaean Greeks. Their ancestry is mostly Anatolian Neolithic farmer with some Caucasus/Iran and less Russian/Siberian admixture (the last two related to the spread of Indo-European languages), they had dark hair and dark eyes, and there was no difference between the elites and common people. They're genetically closest to modern Southeastern Europeans, and not to Northern Europeans or Africans as different people have claimed.

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean, and most of the remainder from ancient populations related to those of the Caucasus and Iran. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter–gatherers of eastern Europe and Siberia, introduced via a proximal source related to the inhabitants of either the Eurasian steppe or Armenia. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

[...]

The elite Mycenaean individual from the ‘royal’ tomb at Peristeria in the western Peloponnese did not differ genetically from the other three Mycenaean individuals buried in common graves.

[...]

Other proposed migrations, such as settlement by Egyptian or Phoenician colonists, are not discernible in our data, as there is no measurable Levantine or African influence in the Minoans and Mycenaeans, thus rejecting the hypothesis that the cultures of the Aegean were seeded by migrants from the old civilizations of these regions.

[...]

Phenotype prediction from genetic data has enabled the reconstruction of the appearance of ancient Europeans who left no visual record of their pigmentation. By contrast, the appearance of the Bronze Age people of the Aegean has been preserved in colourful frescos and pottery, depicting people with mostly dark hair and eyes. We used the HIrisPlex tool (Supplementary Information section 4) to infer that the appearance of our ancient samples matched the visual representations (Extended Data Table 2), suggesting that art of this period reproduced phenotypes naturalistically.

We estimated the fixation index, FST, of Bronze Age populations with present-day West Eurasians, finding that Mycenaeans were least differentiated from populations from Greece, Cyprus, Albania, and Italy (Fig. 2), part of a general pattern in which Bronze Age populations broadly resembled present-day inhabitants from the same region (Extended Data Fig. 7).

The modern Greek samples used in the study for comparison are not the best. Thessaloniki is in the north of the country, the Coriell database doesn't provide specific origins, and there are only two Cretans. I believe that if Mycenaeans were compared to their descendants in the Peloponnese, continuity would be nearly perfect instead of just very strong.


Lazaridis et al. "Genetic origins of the Minoans and Mycenaeans". Nature, 2017.

Reconstruction of an Ancient Egyptian

July 21, 2017


A 3,500-year-old noble Egyptian called Nebiri has been brought back to life through modern forensics.

Scientists have reconstructed the face of the ancient mummy, and discovered he had a prominent nose, wide jaw, straight eyebrows and moderately thick lips.

[...]

Nebiri is thought to have been a member of the Egyptian elite who served as the Chief of the Stables, looking after royal horses, during the reign of Thutmoses III, a pharaoh from the 18th Dynasty of ancient Egypt.

His remains were discovered in the Valley of the Queens in Luxor in 1904, but as the tomb has been plundered, just his head and jars containing his organs remained.

Researchers from the University of Turin have now used a range of facial reconstruction techniques to produce an impressive facial approximation.

To reconstruct his face, the researchers used a mixture of computer modelling and anthropological research.

The team then used a computer programme to start to build up a picture of the Egyptian's face.

[...]

Speaking to Live Science, Raffaella Bianucci, who led the study, said: 'He was between 45 [and] 60 years old when he died.


Shivali Best. "The face of Nebiri revealed: Scientists reconstruct the head of the ancient Egyptian 'Chief of Stables', 3,500 years after he died of heart failure". MailOnline – Science & Tech, 11:01 BST, 20 June 2017.

Genetics of Peloponnesean Greeks

April 27, 2017

This new study refutes Nordicist and Afrocentrist claims of population replacement in Ancient Greece, showing that modern Peloponnesean Greeks are most closely related to other Southern Europeans, and far from both Slavic and non-European groups. They're also distinct from Greek-speaking populations in Asia Minor, only partly overlapping with those on the Aegean coast nearest to Greece.

Peloponnese has been one of the cradles of the Classical European civilization and an important contributor to the ancient European history. It has also been the subject of a controversy about the ancestry of its population. In a theory hotly debated by scholars for over 170 years, the German historian Jacob Philipp Fallmerayer proposed that the medieval Peloponneseans were totally extinguished by Slavic and Avar invaders and replaced by Slavic settlers during the 6th century CE. Here we use 2.5 million single-nucleotide polymorphisms to investigate the genetic structure of Peloponnesean populations in a sample of 241 individuals originating from all districts of the peninsula and to examine predictions of the theory of replacement of the medieval Peloponneseans by Slavs. We find considerable heterogeneity of Peloponnesean populations exemplified by genetically distinct subpopulations and by gene flow gradients within Peloponnese. By principal component analysis (PCA) and ADMIXTURE analysis the Peloponneseans are clearly distinguishable from the populations of the Slavic homeland and are very similar to Sicilians and Italians. Using a novel method of quantitative analysis of ADMIXTURE output we find that the Slavic ancestry of Peloponnesean subpopulations ranges from 0.2 to 14.4%. Subpopulations considered by Fallmerayer to be Slavic tribes or to have Near Eastern origin, have no significant ancestry of either. This study rejects the theory of extinction of medieval Peloponneseans and illustrates how genetics can clarify important aspects of the history of a human population.


Figure 2: Genetic similarity of Peloponneseans, Sicilians and Italians. PCA analysis of several European populations. (a) Notice the north to south distribution of the populations and that the Peloponneseans are placed to the far right of the graph and overlap with the Sicilians. (b) PCA analysis of Southern European populations illustrating the close relationship between Peloponneseans, Sicilians and Italians (TSI is an Italian population). (c) Network analysis illustrating the high connectivity between the Peloponnesean populations as well as between the Peloponneseans, the Sicilians and the Italians. Notice the distance between Peloponneseans and the Slavic, and Near Eastern populations. Peloponneseans are connected with the Near Eastern populations through Crete and Dodecanese.



Figure 3: Testing the theory of replacement of medieval Peloponneseans by Slavs and Asia Minor settlers. (a) PCA analysis shows the broad separation of Peloponneseans from four populations of the Slavic homeland (Ukrainians, Polish, Russians and Belarusians). (b) PCA comparisons of the Peloponneseans with three Greek-speaking Asia Minor populations shows only partial overlap with the population of the Asia Minor Aegean coast.



Supplementary Figure 2: Comparisons of Peloponneseans with non-European populations. PCA analysis of Peloponneseans and A. Near East. B. Caucasus. C. North Africa. D. East Africa. E. Arabia. F. West Siberia populations.


Stamatoyannopoulos et al. "Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks". Eur J Hum Genet, 2017.

Scythians Had East Asian Ancestry

March 24, 2017

Nordicists have often claimed that Iron Age Scythians were blonde, blue-eyed "Aryans" most similar to modern Northern Europeans, but ancient DNA analysis shows they were a mix of Yamnaya people from the Russian Steppe (who were mostly brunet) and East Asian Mongoloids.

During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.

[...]

Since the PCA of west Eurasia in Fig. 4 does not allow one to examine the ancient samples in relation to contemporary East Asian populations, we also carried out PCA of all 2,345 modern individuals in the Human Origins dataset, onto which we also projected the ancient individuals (Fig. 5). It is evident from this PCA that ancestry of the Iron Age samples falls on a continuum between present-day west Eurasians and eastern non-Africans, which is in concordance with the mitochondrial haplogroup analyses. The eastern Scythians display nearly equal proportions of mtDNA lineages common in east and west Eurasia, whereas in the western Scythian groups, the frequency of lineages now common in east Eurasia is generally lower, even reaching zero in four samples of the initial Scythian phase of the eight to sixth century BCE (group #1 in Fig. 2), and reaches 18–26% during later periods (sixth to second century BCE; #2 and #3) (Supplementary Table 7).

The Scythian samples are in black:


Figure 5 | Principal component analysis. PCA of ancient individuals (according colours see legend) projected on modern individuals of the Human Origins dataset (grey). Iron Age Scythians are shown in black; CHG, Caucasus hunter-gatherer; LNBA, late Neolithic/Bronze Age; MN, middle Neolithic; EHG, eastern European hunter-gatherer; LBK_EN, early Neolithic Linearbandkeramik; HG, hunter-gatherer; EBA, early Bronze Age; IA, Iron Age; LBA, late Bronze Age; WHG, western hunter-gatherer.


Unterlander et al. "Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe". Nature Communications, 2017.

First Ancient Egyptian Genomes

March 14, 2017

This is a talk that will be given at the 82nd annual meeting of the Society for American Archaeology in Vancouver, BC, Canada from March 29–April 2, 2017. New genome-wide data show that Ancient Egyptians had less Sub-Saharan African ancestry than Modern Egyptians and were closely related to Middle Easterners, which will surely upset Afrocentrists. More ancient genomes from earlier periods should follow soon.

[203] Ancient Egyptian Mummy Genomes Suggest an Increase of Sub-Saharan African Ancestry in Post-Roman Periods


Krause, Johannes (Max Planck Institute—SHH), Verena Schuenemann (Institute for Archaeological Sciences, University of Tübingen), Alexander Peltzer (Department for Archaeogenetics, Max Planck Inst), Wolfgang Haak (Department for Archaeogenetics, Max Planck Inst) and Stephan Schiffels (Department for Archaeogenetics, Max Planck Inst)

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia, and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we mtDNA and nuclear DNA from mummified humans recovered from Middle Egypt that span around 1,300 years of ancient Egyptian history from the Third Intermediate to the Roman Period. Our analyses reveal that ancient Egyptians shared more Near Eastern ancestry than present-day Egyptians, who received additional Sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Hopefully a deeper transect, into the Old Kingdom, Early Dynastic, and Predynastic, is to follow. My prediction (I would be happy to be wrong) is that this DNA came from tooth or bone — I think mummified soft tissue has mostly been a source of disappointment. Differential relatedness of modern Copts and non-Copts to the ancient samples would be something to look out for.

If any of these talks is going to really upset some people, it’ll be this one.

LINK

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UPDATE 06/01/17: The study that goes with this talk is out now, and the Ancient Egyptian samples cluster with ancient Neolithic Levantines, and modern Bedouin, Palestinian and Lebanese Arabs.

ABSTRACT: Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.


Figure 4 | Principal component analysis and genetic clustering of genome-wide DNA from three ancient Egyptians. (a) Principal Component Analysis-based genome-wide SNP data of three ancient Egyptians, 2,367 modern individuals and 294 previously published ancient genomes, (b) subset of the full ADMIXTURE analysis (Supplementary Fig. 4).


Schuenemann et al. "Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods". Nature Communications, 2017.

Natufians NOT Sub-Saharan African

June 20, 2016

This new ancient DNA study refutes the Afrocentrist claim that Natufians were from Sub-Saharan Africa or had Negroid admixture.

Craniometric analyses have suggested that the Natufians may have migrated from north or sub-Saharan Africa, a result that finds some support from Y chromosome analysis which shows that the Natufians and successor Levantine Neolithic populations carried haplogroup E, of likely ultimate African origin, which has not been detected in other ancient males from West Eurasia (Supplementary Information, section 6). However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1).


Lazaridis et al. "The genetic structure of the world's first farmers". bioRxiv, 2016.

Related: Natufians NOT Source of European Neolithic

Phenotypes of Hunters and Farmers

March 2, 2015

Europeans are descended from prehistoric hunter-gatherers and farmers. Here's what we know about the origins and physical appearance of these two populations from anthropology (Coon 1939, Pinhasi 2012) and genetics (Lipson 2012, Lazaridis 2014), along with representations of what they might have looked like:

Mesolithic Hunters had broad faces, dark skin, light eyes and were intermediate between Western and Eastern Eurasians. So to represent them I chose a Uralic Norwegian Lapp that I darkened and gave blue eyes.

Neolithic Farmers had narrow faces, light skin, dark eyes and were Western Eurasian, closest to modern Sardinians. So I chose an untanned, long-faced Mediterranean soccer player from Sardinia to represent them.


Of course, they didn't all look exactly the same. We know that there was diversity and overlap in some of their traits (Gamba 2014). But in general, the phenotypic variation we see in Europe today is the result of waves of settlements by these two distinct types from Siberia and the Middle East since ancient times, and the mixing that occurred between them in different proportions (Haak 2015), plus selective pressures favoring further depigmentation in some places.

AIMs Overestimate Admixture

September 8, 2014

AIMs are a subset of SNPs chosen for their informativeness about ancestry and often used by geneticists instead of genome-wide data to save time and money. However, according to Galanter et al. (2010), this can lead to errors and overestimations of admixture, especially when the panel of AIMs is very small:

Ancestry informative markers (AIMs) have been used as a cost-effective way to estimate individual ancestral proportions in admixed populations such as African Americans and Latinos. [...] We compared differences in ancestry estimated with different size AIMs panels with ancestry estimated from genomewide markers. [...] There was an inverse correlation between the number of AIMs used to estimate ancestry and mean and standard deviation of the error in ancestry estimation. Using AIMs, African ancestry was consistently overestimated, while the major ancestral component (European in Puerto Ricans and Native American in Mexicans) was systematically underestimated. Using 300 or fewer AIMs consistently produced a standard deviation of ancestry estimation error of 10% or greater. [...] There is both systematic bias resulting in overestimation of African ancestry (and underestimation of other continental ancestry) and random error. Such error is inversely proportional to the number of AIMs used.

Bauchet et al. (2007) found that even larger panels of AIMs, while somewhat more accurate, still lead to a loss of structure, and therefore an overestimation of admixture, compared with using the full SNP data set:

Using <1,200 EuroAIMs of the type available in this panel gradually leads to loss of consistent structure and a corresponding increase in misclassification of individual origins (fig. 7C).


While the number of AIMs used is clearly a big factor in the accuracy level of results, another problem is that AIMs may not even be as informative about ancestry as they claim, according to Bolnick et al. (2007):

Furthermore, some of the most "informative" AIMs involve loci that have undergone strong selection, which makes it unclear whether these markers indicate shared ancestry or parallel selective pressures (such as similar environmental exposures in different geographic regions) or both.

Hopefully, all this criticism will get more notice, and geneticists will stop trying to cut corners by using these inferior markers for quantifying individual ancestry.

Related: Overestimated Admixture in Brisighelli (2012)