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)

European Ancestry of Ashkenazi Jews

March 8, 2014

According to a new genetic study, Ashkenazi Jews are mostly European on their maternal side, and that admixture comes from Western and Central Europe when diaspora males from the Levant arrived first in Rome and found wives among local Italian women who converted to Judaism. They then migrated further west and north and acquired other European admixture in the same way, before finally heading east. Intermixing slowed after that because they have very little Slavic or Turkic (Khazar) admixture. Their paternal side remains mostly Near Eastern. This all fits well with findings from anthropology some 75 years ago.

Overall, it seems that at least 80% of Ashkenazi maternal ancestry is due to the assimilation of mtDNAs indigenous to Europe, most likely through conversion. The phylogenetic nesting patterns suggest that the most frequent of the Ashkenazi mtDNA lineages were assimilated in Western Europe, ~2 ka or slightly earlier. Some in particular, including N1b2, M1a1b, K1a9 and perhaps even the major K1a1b1, point to a north Mediterranean source. It seems likely that the major founders were the result of the earliest and presumably most profound wave of founder effects, from the Mediterranean northwards into central Europe, and that most of the minor founders were assimilated in west/central Europe within the last 1,500 years. The sharing of rarer lineages with Eastern European populations may indicate further assimilation in some cases, but can often be explained by exchange via intermarriage in the reverse direction.

The Ashkenazim therefore resemble Jewish communities in Eastern Africa and India, and possibly also others across the Near East, Caucasus and Central Asia, which also carry a substantial fraction of maternal lineages from their 'host' communities. Despite widely differing interpretations of autosomal data, these results in fact fit well with genome-wide studies, which imply a significant European component, with particularly close relationships to Italians. As might be expected from the autosomal picture, Y-chromosome studies generally show the opposite trend to mtDNA (with a predominantly Near Eastern source) with the exception of the large fraction of European ancestry seen in Ashkenazi Levites.

Evidence for haplotype sharing with non-Ashkenazi Jews for each of the three main haplogroup K founders may imply a partial common ancestry in Mediterranean Europe for Ashkenazi and Spanish-exile Sephardic Jews, but may also, at least in part, be due to subsequent gene flow, especially into Bulgaria and Turkey, both of which witnessed substantial immigration from Ashkenazi communities in the fourteenth and fifteenth centuries. Gene flow could have been substantial in some cases—ongoing intermarriage is likely when these communities began living in closer proximity after the Spanish exile. A partial common ancestry for all European Jews—both Ashkenazi and Sephardic—is again strongly supported by the autosomal results.

Jewish communities were already spread across the Graeco-Roman and Persian world >2,000 years ago. It is thought that a substantial Jewish community was present in Rome from at least the mid-second century BCE, maintaining links to Jerusalem and numbering 30,000-50,000 by the first half of the first century CE. By the end of the first millennium CE, Ashkenazi communities were historically visible along the Rhine valley in Germany. After the wave of expulsions in Western Europe during the fifteenth century, they began to disperse once more, into Eastern Europe.

These analyses suggest that the first major wave of assimilation probably took place in Mediterranean Europe, most likely in the Italian peninsula ~2 ka, with substantial further assimilation of minor founders in west/central Europe. There is less evidence for assimilation in Eastern Europe, and almost none for a source in the North Caucasus/Chuvashia, as would be predicted by the Khazar hypothesis—rather, the results show strong genetic continuities between west and east European Ashkenazi communities, albeit with gradual clines of frequency of founders between east and west.

Costa et al. "A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages". Nature Communications, 2013.

The Jews have been left to the end because they do not as a whole fit into any single racial classification heretofore outlined. Historically the Jews of the Biblical period in Palestine were a Semitic-speaking people composed of various Mediterranean strains which had blended together at the time of the formation of the Jewish nation. These Mediterranean strains must have included a small Mediterranean type comparable to the present Yemeni Arabs; a taller, longer-faced strain with a tendency to nasal convexity, as is found among Irano-Afghan peoples today; and a straight-nosed, presumably Atlanto-Mediterranean element contributed by the Philistines.

The Jews began their expansion from Palestine as early as the time of the Babylonian Captivity; at this time they settled Mesopotamia in large numbers, and from there began an expansion into central Asia of which colonies still remain. In the Hellenistic period they migrated into Asia Minor and the Black Sea region, as well as into Egypt; these emigrants became Hellenistic Jews. Under the Romans they settled in Italy, France, and Spain, with especial concentrations in Spain and in the cities of the Rhineland. The Jews expelled from Spain in 1492 and during previous expulsions became the Sephardim, whose descendants are to be found in various countries bordering on the Mediterranean, especially Morocco, the Salonika region of what is now Greece, and Turkey. The Rhineland Jews, persecuted at the time of the First Crusade, moved eastward into Poland, the Ukraine and other central European countries, and met there and absorbed a group of Hellenistic Jews moving westward, among whom were some who had lived among the Turkish Khazars in the Crimea and elsewhere. The two groups blended and the Germanic speech of the more numerous western element prevailed. The modern Yiddish-speaking Ashkenazim are the descendants of this amalgamated body. Racially they preserve to a large measure their Mediterranean character, altered partly by Alpine admixture which has in many cases produced Dinaricization. This Alpine, as well as some Nordic, admixture was probably obtained largely in France and Germany before their departure eastward. The most persistent Palestinian Mediterranean traits which the Jews preserve is a narrowness of the face. The Jewish facial expression, by which many Jews may be distinguished, is a cultural and not a genetic character.

Carleton Coon. The Races of Europe. New York: MacMillan, 1939.

Semitic West Eurasian Ancestry in Africa

February 6, 2014

This new study confirms everything that Afrocentrists deny about Caucasoid admixture in East (and South) Africa.

Back-to-Africa Gene Flow in Eastern Africa


A major open question concerns the initial source of the west Eurasian ancestry in eastern Africa. The estimated mean time of gene flow in eastern Africa is around 3,000 y ago, and the amount of gene flow must have been quite extensive, because the west Eurasian ancestry proportions reach 40-50% in some Ethiopian populations (Table 1 and ref. 10). Archaeological records from this region are sparse, so Pagani et al. (10) speculate that this admixture is related to the Biblical account of the Kingdom of Sheba. However, archaeological evidence is not completely absent. During this time period, architecture in the Ethiopian culture of D'mt has an "unmistakable South Arabian appearance in many details" (19), although there is some debate as to whether these patterns can be attributed to large movements of people versus elite-driven cultural practices (19, 20). Additionally, linguistic evidence suggests that this time period was when Ethiosemitic languages were introduced to Africa, presumably from southern Arabia (21). It is perhaps not a coincidence that the highest levels of west Eurasian ancestry in eastern Africa are found in the Amhara and Tygray, who speak Ethiosemitic languages and live in what was previously the territory of D'mt and the later kingdom of Aksum.

West Eurasian Ancestry in Southern Africa


A second question is, which population or populations introduced west Eurasian ancestry into southern Africa? The best genetic proxy for this ancestry that we have found is the west Eurasian ancestry in eastern Africa (Fig. 1C), and although we do not identify modern east African populations as the best source population, this is likely due to the lack of genetic drift specific to eastern Africa (SI Appendix, section 1.2.3). The most parsimonious explanation for this observation is that west Eurasian ancestry entered southern Africa indirectly via eastern Africa (the alternative scenario of direct contact with an unsampled west Eurasian population cannot formally be excluded; however, there is no archaeological, historical, or linguistic evidence of such contact). The relevant eastern African population may no longer exist. However, such a migration has been suggested based on shared Y chromosome haplotypes (12, 22) and shared alleles/haplotypes associated with lactase persistence (2, 23) between the two regions. Furthermore, based on a synthesis of archaeological, genetic, climatological, and linguistic data Güldemann (13) hypothesized that the ancestor of the Khoe-Kwadi languages in southern Africa was brought to the region by immigrating pastoralists from eastern Africa. Our observation of elevated west Eurasian ancestry in Khoe-Kwadi groups in general (Table 1) is consistent with this hypothesis.

[...]

Conclusions


Based on these analyses, we can propose a model for the spread of west Eurasian ancestry in southern and eastern Africa as follows. First, a large-scale movement of people from west Eurasia into Ethiopia around 3,000 y ago (perhaps from southern Arabia and associated with the D'mt kingdom and the arrival of Ethiosemitic languages) resulted in the dispersal of west Eurasian ancestry throughout eastern Africa. This was then followed by a migration of an admixed population (perhaps pastoralists related to speakers of Khoe-Kwadi languages) from eastern Africa to southern Africa, with admixture occurring ~1,500 y ago. Advances in genotyping DNA from archaeological samples may allow aspects of this model to be directly tested.


Pickrell et al. "Ancient west Eurasian ancestry in southern and eastern Africa". PNAS, 2014.

Global Admixture Analysis at K=6

December 31, 2013

This new study has one of the biggest global admixture analyses ever done (185 populations at 293,832 SNPs), but it's a little hard to view so I made a more user friendly version of one of the runs. I chose K=6 because it shows clearly the divisions and admixture between the six main racial groups: Capoid (red), Negroid (orange), Caucasoid (blue), Americoid (green), Mongoloid (yellow) and Australoid (purple). Click the image below to enlarge it and scroll down for examples of the racial types.


K=2 separates African from non-African populations.

K=3 reveals a West Eurasian ancestry component [Blue].

K=4 breaks the African component into an African hunter-gatherer ancestry maximized in Bushmen such as the Ju_hoan_North [Red] and an African farmer component maximized in the Yoruba [Orange].

K=5 breaks the ENA [eastern non-African] component down into one maximized in the Karitiana from the Americas [Green] and one maximized in the Ami from Taiwan [Yellow].

K=6 reveals a south Eurasian component maximized in Papuans [Purple], which is also represented in South Asians.


Ju'hoan (Namibia)
"Capoid"
Yoruba (Nigeria)
"Negroid"
Sardinian (Italy)
"Caucasoid"


Karitiana (Brazil)
"Americoid"
Ami (Taiwan)
"Mongoloid"
Papuan (PNG)
"Australoid"

Calling Out JayMan

November 28, 2013

JayMan is an HBd blogger obsessed with IQ, heredity and achievement, and probably Richard Lynn's #1 fan. He claims to be Jamaican, which makes him either the most insanely self-hating black person on earth, or a white Nordicist pretending to be black so he can get away with insulting blacks and everyone else who isn't Northwestern European. Either way, he's an idiot.

Recently he "called me out" on his blog re: my stance on environmental factors in global IQ disparities. I had debated him there about a year and a half ago and easily won, and I guess he's been traumatized by it ever since. He links to that post in his new one, and I wondered why he would want to remind people of his defeat, but when I checked it again I noticed that he'd deleted my final reply to try and make himself look like the winner (you can read the unedited discussion here; the deleted comment is "Mar 27 2012 9:57 AM"). Then when I attempted to reply to his latest "challenge" the other day, he refused to approve that comment too. Just thought you'd want to know what a pathetic, dishonest, chickenshit loser he is...if you couldn't already tell.

Anyway, my response to his nonsense was this study showing that poverty leads to a significant drop in IQ points, and this new one which concludes similarly that the wealth of nations determines "national IQs" (not the other way around).