Saturday, November 14, 2015

Go with the flow 2- African gene flow into Europe in various eras

As part of our trilogy on African movement into Europe, this post looks at some recent findings from DNA studies. Note to fake strawmen creators- it does NOT claim Greeks, Italians, Sardinians or other of today's Europeans are wholly "Africans," or that they cease being "European" -  but that in various measures, in some eras, distinctive African gene flow into Europe can be detected well before the modern slave trade/colonial era. Some DNA studies are brought to bear on the question below. Now that the fake strawmen are out of the way- let's get down to business.

POINT A --  Greek DNA: African elements detected - Haplogroup E

African Haplogroup E appears in several European populations notably Greeks and other southern Europeans, in the Balkans zone. QUOTE:

"Haplogroup E originated in Africa. This is true also of its European subhaplogroup E3b. In Africa, this sub- group has four separate peak areas; these are in Southern Africa, Morocco, Northern Libya, and the Horn of Africa. The last two bear witness to the route from northwest Africa through Anatolia to Europe. (The frequencies are relatively high also in Anatolia.) In Europe, Haplogroup E3b has peak values (about 25%) in Albania; about equally high frequencies are also typical of some other parts of the Balkans and southern Italy."
--Kalevi Wiik (2008) Where Did European Men Come From? Jrnl Gen Genealogy, 4:35-83


"Underhill et al. (2001) showed that the frequency of the YAP+ Y haplogroup commonly referred to as haplogroup E or (III) is relatively high (about 25%) in the Middle East and Mediterranean. This haplogroup E is the major haplogroup found in sub-Saharan Africa (over 75% of all Y chromosomes). Specifically, Europeans contain the E3b sub-haplogroup, which was derived from haplogroup E in sub-Saharan Africa and currently is distributed along the North and East of Africa.. It appears that the 171 AIM test subject of this chapter may recognize the haplogroup E character as West African."
--T. Frudakis. 2008. Molecular photofitting: predicting ancestry and phenotype using DNA

"In the case of Cretan E3b3-M123 (M34) chromosomes, they most likely signal East African or Middle-Eastern gene flow rather than European, due to the scarcity of this lineage in the latter area.19, 26 Similarly, the presence of E3b-M35* individuals in the Heraklion Prefecture population could probably be attributed to an East-African or North-African contribution."
FROM: Fig 2 --Martinez et al. (2007). Paleolithic Y-haplogroup heritage predominates in a Cretan highland plateau. Eu Jrl Hu Gen. 15, 485-493

POINT B --  DNA study detects African elements in southern Europeans like Sardinians- QUOTE:

"Sardinia appears to be a particularly appropriate test case to evaluate the extent to which surnames are informative in identifying the history of Y-chromosome haplogroups. As the other European populations, almost all the Sardinian Y chromosomes belong to haplogroups E-M35, I-M170, G-M201, J-12f2 and R-M269. Haplogroups E, G and J, which are believed to have an African (E) or Middle Eastern (G and J) origin and entered Europe through different migrations,30,34,35 show frequencies in the same range as other Mediterranean populations."
--Zei et al 2003. From surnames to the history of Y chromosomes: the Sardinian population as a paradigm. European Journal of Human Genetics (2003) 11, 802-807

Italian DNA - African elements detected

Uniparental Markers of Contemporary Italian Population: Reveals Details on Its Pre-Roman Heritage Brisighelli1, et al 2012.  PLoS ONE 7(12)

Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo Á, et al. (2012) Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage. PLoS ONE 7(12)


Italy has historically been a convenient destination for human populations migrating from Africa, the Middle East and European locations, in part due to the geomorphological characteristics of the Italian Peninsula [1].

Sardinia, Sicily and Tuscany were among the first Italian territories to be occupied by humans due to their strategic location and the presence in their territories of important metal resources [5].

The record of all the populations that inhabited the Italian territory during (pre)-history is incomplete; many records were of uncertain location and/or ambiguous denomination [6].

At the time of the Roman Empire, at least two non-Indo- European populations still inhabited Italy, namely, the Ligures, in the northwestern area, and the Etruscans with settlements located in areas far from the Etruria (Tuscany and High Latium), such as the Po Plain and the coast of Campania. At the same time, Sardinia experienced the flourishing of a non-Indo-European Nuragic civilization and, then, the Phoenician colonization.

Materials and Methods

A total of individuals were sampled from along the Italian Peninsulapresenting 12 different populations (Figure 1), of them (Ladin and Grecani Salentini) being linguistic isolatesd the Lucera being a historical enclave of Arabs/Berbers coming from North Africa. A brief description of these latter three populations is given .

The mtDNA haplogroup make-up of Italy as observed in our samples fits well with expectations in a typical European population. Thus, most of the Italian mtDNAs (,89%) could be attributed to European/African groups H (,40%), I (Ethiopian)(,3%), J (near East)(,9%), T(European) (,11%), U (European/African)(,20%; U minus U6), V(European) (,3%), X (African)(,2%) and W(Asian) (,1%); Figure 1. There are however important differences in haplogroup frequencies when examining them by main geographical

Mitochondrial DNA haplotypes of other African origin are mainly represented by haplogroups M1 (0.3%), U6 (0.8%) and L (1.2%); from here onwards, L will be used to refer to all mtDNA lineages, excluding the non-African branches N and M [60,61].

A total of 282 Y-chromosomes were analyzed for a set of Y-SNPs and were classified into 22 different haplogroups (Figure 3). Two haplogroups were not found, even though markers defining these clades were tested: N3 and R1a1. Five haplogroups represented 76.71% of the total chromosomes: R1b3, J2(near East), I(xI1b2), E3b1 and G. The frequencies averaged across populations were 26%, 21.2%, 10.2%, 9.9% and 9.2%, respectively. The remaining haplogroups sum to 23.2% in the total sample, and never above 4% in single population samples. 21.2%, 9.9% and 9.2%.(so `42% is either near East or African)

Autosomal ancestry in Italy

A panel of 52 AIMs was genotyped in 435 Italian individuals in order to estimate the proportion of ancestry from a three-way differentiation: sub-Saharan Africa, Europe and Asia. Structure analyses allowed us to infer membership proportions in population samples, and these proportions can be graphically displayed, as in Figure 2. This analysis indicated that Italians have a basal proportion of sub-Saharan ancestry that is higher (9.2%, on average) than other central or northern European populations (1.5%, on average). The amount of African ancestry in Italians is however more comparable to (but slightly higher than) the average in other Mediterranean countries (7.1%). Figure 2 shows in a triangle plot the relationships of Italians compared to other European, African and Asian populations

The North African historical legacy in South Italy
There are two mtDNA haplogroups, namely U6 and M1 that can be considered to be of North African origin and could therefore be used to signal the documented historical input of this African region into Lucera. In our full set of samples, we observed five U6 haplotypes belonging to sub-haplogroups U6a, U6a2, and U6a4. Only one of these haplotypes was observed in Lucera. However, the other three U6 haplotypes were observed in the vicinity of the population of South Apulia, and another at the tip of the Peninsula (Calabria). Regarding M1 haplotypes, we observed only two carriers in our samples sharing the same HVS-I haplotype; both were found in Trapani (West Sicily). Therefore, while South Italy shows evidence of having female introgression from North Africa, this African influence seems not to be particularly centered in the Lucera.

The sub-clade E3b1 (originating in eastern Africa) has a wide distribution in sub-Saharan Africa, Middle East and Europe. This haplogroup reaches a frequency of 8% in the North and Center and slightly higher in the South of Italy, 11% (Figure 1). It has also been argued that the European distribution of E3b1 is compatible with the Neolithic demic diffusion of agriculture [15]; thus, two sub-clades, E3b1a- M78 and E3b1c- M123 present a higher occurrence in Anatolia, the Balkans and the Italian peninsula. Another sub-clade, E3b1b-M81 is associated ith the Berber populations and is commonly found in regions that have had historical gene flow FROM Northern Africa, such as the Iberian peninsula [74,75]–[76–78], including the Canary Islands [75], and Sicily [70,79]; the absence of microsatellite variation suggests a very recent arrival from North Africa [80]. If we assume that all E3b1 represents the only Y-chromosome continental African contribution to Italy and L and U6 lineages the continental African mtDNA component, the African component in Italy is higher for the Y-chromosome (8–11%) than for mtDNA (1–2%).

The origin of sub-Saharan African mtDNAs in Europe (including Italian samples) has been recently investigated by Cerezo et al. [81]; the results indicate that a significant proportion of these lineages could have arrived in Italy more than 10,000 years ago; therefore, their presence in Europe does not necessarily date to the time of the Roman Empire, the Atlantic slave trade or to modern migration. In addition, the Northern African influence in the Italian Peninsula is evidenced by the presence of Northern African Y chromosome haplogroups (E1-M78) in three geographically close samples across the southern Apennine mountains: East Campania

Finally, in agreement with uniparental markers, analysis of AIMs/SNPs as carried out in the present study indicated that Italy shows a very minor sub-Saharan African component that is, however, slightly higher than non-Mediterranean Europe. This agrees with the recent findings of Cerezo et al. [82] based on the analysis of entire mtDNA genomes pointing to the arrival in ancient and historical times of sub-Saharan African people to the Mediterranean Europe, followed by admixture. THE PRESENT STUDY REPRESENTS THE LARGEST META-ANALYSIS CARRIED OUT TO DATE FOR THE ITALIAN PENINSULA.(DEC2012)

POINT C --  Ancient Europe- African DNA elements detected in Mesolithic "La Brana" sample- Quote:

"The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times... With respect to two recent well-studied adaptations to changes in diet, we found the ancient genome to carry the ancestral allele for lactose intolerance.. These results suggest the La Brana hunter-gatherer was poor at digesting milk and starch, supporting the hypotheses that these abilities were selected for during the later transition to agriculture."
--Olalde, Inigo, et al. "Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European." Nature 507.7491 (2014)


POINT D --  Internal African movement of gene variants developed in Africa. -Study shows that Haplogroup R1b1 in central Africa not due to 'back migration' from Asia but movement from the south.
"Human Y chromosomes belonging to the haplogroup R1b1-P25, although very common in Europe, are usually rare in Africa. However, recently published studies have reported high frequencies of this haplogroup in the central-western region of the African continent and proposed that this represents a 'back-to-Africa' migration during prehistoric times. To obtain a deeper insight into the history of these lineages, we characterised the paternal genetic background of a population in Equatorial Guinea, a Central-West African country located near the region in which the highest frequencies of the R1b1 haplogroup in Africa have been found to date. In our sample, the large majority (78.6%) of the sequences belong to subclades in haplogroup E, which are the most frequent in Bantu groups. However, the frequency of the R1b1 haplogroup in our sample (17.0%) was higher than that previously observed for the majority of the African continent. Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa. The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene."
--Gonzalez et al. 2013. The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88. Eur J Hum Genet. 2013 21(3):324-31


POINT E --  Southern Europeans show gene flow from several areas including Africa-

"Southern European groups (SEE, SCE, SDN, SWE, and BA) on the other hand derive ancestry from African and Near Eastern World Regions. In particular, ancestry from groups most similar to contemporary populations from in and around the Levant (lev; which we define as the World Region containing individuals from Syria, Palestine, Lebanon, Jordan, Saudi, Yemen, and Egypt) is present across Italy (SCE), Sardinia (SDN), France and Spain (SWE), and Armenia (IA; Figure 2B). Interestingly, North (nafII) and West (waf) African ancestry is also seen entering Southern Europe, suggesting a key role for the Mediterranean in supporting gene flow back into Europe [8, 26, 27]. Dates for the influx of this admixture are broad and generally fall within the first millennium CE (Figure 3B) although are more recent in BA and SWE, including French (frenc24: 728 CE [424–1011 CE]) and Spanish (spani27: 1042 CE [740–1201 CE]; spani9: 668 CE [286–876 CE]) clusters, consistent with migrations associated with the Arabic Conquest of the Iberian peninsula [8, 11, 28] and earlier movements in and around Italy [29]."
--George B.J. Busby, et al 2015. [b]The Role of Recent Admixture in Forming the Contemporary West Eurasian Genomic Landscape. Current biology: CB (Impact Factor: 9.57). 09/2015; 25(19).

POINT F --  Irony: if classic "racial" models are used, Europeans themselves are a "hybrid" or "mixed" breed, one-third African, two-thirds Asian.

".. it appears that Europeans are about two-thirds Asians and one-third African."
(--Luigi Luca Cavalli-Sforza (2000). Genes, peoples and languages. FARRAR STRAUS AND GIROUX Publishers)

"Nuclear DNA studies also contribute to the deconstruction of received racial entities. Ann Bowcock and her colleague's interpretation (Bowcock et al. 1991; Bowcock et al. 1994) of analyses of restriction-site polymorphisms and microsatellite polymorphisms (STRPs) suggests that Europeans, the defining Caucasians, are descendants of a population that arose as a consequence of admixture between already differentiated populations ancestral to (some) Africans and Asians. Therefore, Caucasians would be a secondary type or race due to its hybrid origin and not a primary race". This compromises the racial schema and also invalidates the metaphysical underpinnings of the persisting race construct, which implies deep and fundamental differences between its units. In this case if the interpretation of Bowcock and her colleagues (1991) is correct then one of the units is not fundamental because its genesis is qualitatively different from the other units and even connects them."
-- S.O.Y. Keita and Rick Kittles. (1997) The Persistence of Racial Thinking and the Myth of Racial Divergence, American Anthropologist, New Series, Vol. 99, No. 3 (Sep., 1997), pp. 534-544 

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mechta-Afalou- a part of Africoid diversity

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