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 G├╝ldemann (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.