Monday, October 19, 2015

Did Khoisan formerly live in North Africa

The Khoisan were probably the original North Africans. The Khoisan  introduced mtDNA haplogroups and y-Chromosomes hg A1 and R1-M343 to the Berbers. .
The Khoisan are the ancestors of the Black Berbers whoes descendants probably live in Morocco and the Atlas Mountains.
The Black Berbers of the Atlas Mountains and other parts of Northwest Africa are of Sub-Saharan origin and took African mtDNA into Western Europe over 40kya. The Gibraltar Straits appears to be the most reliable route for the spread of many mtDNA haplogroups from Africa, into Europe over the past 30ky (Winters,2012), including L3(M,N) .
The Khoisan carry L1c,L1i, L2b, L3d ( Rito, et al ,2013) . The motif L3b, is widespread in western Africans. It is mainly found among populations that speak languages of the Niger-Congo family like the Mandekan.

Like most African haplogroups the control region of hg L1i include 16189,16223 and 16311, just like L3a and L3b. The mutation that connects the Khoisan to the spread of L3(M,N) is AF24. The AF24 mutation is found in LOd and among the Khoisan and Senegalese .The existence of AF24 in Senegal and Southern Africa suggest that L1c, L2b, L3d and L3e is not the result of intermarriage with Bantu immigrants , as suggested by Rito et al(2013) .

LOd is the oldest mtDNA haplogroup . This haplogroup is primarily carried by the Khoisan people (Winters,2014) . It is also found among Niger-Congo speakers in West Africa where we also find LOa in West Africa in addition to L3b.

The Cro Magnon DNA found in the ancient skeletons dates back to the Aurignacian period (Winters,2011). The Cro magnon skeletons belong to the N haplogroup.

The Cro Magnon skeletons carried N1a,N1b,N1c and N* (Winters, 2010,2011). It is characterized by motifs 00073G,10873C, 10238T and A4CC between nucleotide positions 10397 and 10400. Most of the skeletons carried hg N*.

It is obvious that L3 (M,N) had expanded into Europe prior to the Neolithic.

Frigi et al (2010), in Ancient Local Evolution of African mtDNA Haplogroups in Tunisian Berber Populations noted that: “Our results also point to a less ancient western African gene flow to Tunisia involving haplogroups L2a and L3b. Thus the sub-Saharan contribution to northern Africa starting from the east would have taken place before the Neolithic. The western African contribution to North Africa should have occurred before the Sahara’s formation (15,000 BP)”.

This would explain why Pericot and Dominguez (2005) found evidence of hg L3 at ancient Iberian sites. Luis Pericot was sure that the populations associated with the Gravettian (32kya) and Soultrean (23kya) cultures were phylogenetically Sub-Saharan African (Dominguez,2005). Dominguez (2005) found that the lineages recovered from ancient skeletons associated with these cultures belonged to the African lineages L1b,L2 and L3. Almost 50% of the lineages from the Abauntz Chalcolithic deposits and Tres Montes, in Navarre are the Sub-Saharan lineages L1b,L2 and L3.
Berber and Khoisan Y-Chromosome
The archaeological data support a migration of probable Khoisan migration from Southern Africa to North Africa. You have to remember that many populations have settled Morocco, so their might not always be a one-to-one correspondence between contemporary Khoisan haplogroups and haplogroups found among contemporary Berbers in Morocco and the Atlas mountains. But given the geography, we would expect to see elements of Khoisan relic population genes among Atlas Mountain Berbers.


Originally posted by Troll Patrol # Ish Gebor:

Figure S1. Map Showing Location of the Population Samples Considered in This Study

Populations are represented by circles and numbered as in Table S5. Sectors within circles are proportional to the frequency of haplogroup A1a (green), A1b (red) and A2-T (black). Green asterisks indicate countries were haplogroup A1a has previously been observed.


Table S1. Haplogroup Affiliation of the Seven Chromosomes that Were Re-sequenced

Table S5: Populations considered for the mutations defining major clades A1b, A1a and A2-T.

The Berbers and Khoisan also carry similar R1 haplogroups. The Khoisan in South Arica carry R1-M343 (Schlebusch,,2010). Berbers at Zenata and Oran also carry R1-M343 (Bekada, et al, 2010).

The hominids and tool kits common to South Africa also appear in Morocco. It is no secret that the earliest Y-chromosome haplogroups have been found in Morocco and among the Khoisan. These haplogroups belong to hg A (M91); among the Moroccans we find A1b and A1a.The Khoisan mtDNA was named originally L1a,L1d and L1k, these clades are called LoD and LoK today.

Morocco has yielded impotant new data on African prehistory. Here we find a complex and rich set of early hominids from Jebel Irhoud, Dar es-Soltan and Contrebandiers Cave.

A pan-African Middle Stone Age (MSA) culture existed that united South Africa and Morocco.The Moroccan tools are Levallois technology and Mousterian industries were used in South Africa,North Africa and western Eurasia. Dibble et al (2013) has shown that Pan-African industries included cognate scrapers, Levallois tools, Nassarius beads and engraved ostrich shells. The Moroccans and South Africans shared Levallois tools and the use of ochre, bone tools and ostrich shells. Bouaouggar et al (2007) has shown how the shell beads from Grotte des Pigeons (Taforalt,Morocco) and South Africa's Blombos Caves. The archaeological evidence is clear the Khoisan in Morocco and South Africa shared behavioral , cognitive and technological styles. The major behavioral indicators shared by the Moroccan and South African Khoisan was mining,beads, blades, ochre and bone tools between 200-40kya. It is important to note that Moroccan tools are Levallois technologies and Mousterian industries used in North Africa and Western Eurasia. We also should note that Neanderthals also used Mousterian tools.

The Boule and Vallois research makes it clear that the Bushman expanded across Africa on into Europe via Spain as the Grimaldi people. This makes it clear that the Bushman/Khoisan people were not isolated in South Africa. The Khoisan people carry the haplogroup N. The Hadza are Bushman they carry haplogroup N.


The Aurignacian civilization was founded by the Cro-Magnon people who originated in Africa. They took this culture to Western Europe across the Straits of Gibraltar. The Cro-Magnon people were probably Bushman/Khoi.

There have been numerous "Negroid skeletons" found in Europe. Marcellin Boule and Henri Vallois, in Fossil Man, provide an entire chapter on the Africans/Negroes of Europe Anta Diop also discussed the Negroes of Europe inCivilization or Barbarism, pp.25-68. Also W.E. B. DuBois, discussed these Negroes in the The World and Africa, pp.86-89. DuBois noted that "There was once a an "uninterrupted belt' of Negro culture from Central Europe to South Africa" (p.88).

Boule and Vallois, note that "To sum up, in the most ancient skeletons from the Grotte des Enfants we have a human type which is readily comparable to modern types and especially to the Negritic or Negroid type" (p.289). They continue, "Two Neolithic individuals from Chamblandes in Switzerland are Negroid not only as regards their skulls but also in the proportions of their limbs. Several Ligurian and Lombard tombs of the Metal Ages have also yielded evidences of a Negroid element.

Since the publication of Verneau's memoir, discoveries of other Negroid skeletons in Neolithic levels in Illyria and the Balkans have been announced. The prehistoric statues, dating from the Copper Age, from Sultan Selo in Bulgaria are also thought to protray Negroids.

In 1928 Rene Bailly found in one of the caverns of Moniat, near Dinant in Belgium, a human skeleton of whose age it is difficult to be certain, but seems definitely prehistoric. It is remarkable for its Negroid characters, which give it a reseblance to the skeletons from both Grimaldi and Asselar (p.291).

Boule and Vallois, note that "We know now that the ethnography of South African tribes presents many striking similarities with the ethnography of our populations of the Reindeer Age. Not to speak of their stone implements which, as we shall see later , exhibit great similarities, Peringuey has told us that in certain burials on the South African coast 'associated with the Aurignacian or Solutrean type industry...."(p.318-319). They add, that in relation to Bushman art " This almost uninterrupted series leads us to regard the African continent as a centre of important migrations which at certain times may have played a great part in the stocking of Southern Europe. Finally, we must not forget that the Grimaldi Negroid skeletons sho many points of resemblance with the Bushman skeletons". They bear no less a resemblance to that of the fossil Man discovered at Asslar in mid-Sahara, whose characters led us to class him with the Hottentot-Bushman group.

The Boule and Vallois research makes it clear that the Bushman expanded across Africa on into Europe via Spain as the Grimaldi people. This makes it clear that the Bushman/Khoisan people were not isolated in South Africa. The Khoisan people carry the haplogroup N. The Hadza are Bushman they carry haplogroup N.

Cro-Magnon people carried haplogroup N:


Specific mtDNA sites outside HVRI were also analyzed (by amplification, cloning, and sequencing of the surrounding region) to classify more precisely the ancient sequences within the phylogenetic network of present-time mtDNAs (35, 36). Paglicci-25 has the following motifs: +7,025 AluI, 00073A, 11719G, and 12308A. Therefore, this sequence belongs to either haplogroups HV or pre-HV, two haplogroups rare in general but with a comparatively high frequencies among today's Near-Easterners (35). Paglicci-12 shows the motifs 00073G, 10873C, 10238T, and AACC between nucleotide positions 10397 and 10400, which allows the classification of this sequence into the macrohaplogroupN,containing haplogroups W, X, I, N1a, N1b, N1c, and N*. Following the definition given in ref. 36, the presence of a single mutation in 16,223 within HRVI suggests a classification of Paglicci-12 into the haplogroup N*, which is observed today in several samples from the Near East and, at lower frequencies, in the Caucasus (35). It is difficult to say whether the apparent evolutionary relationship between Paglicci-25 and Paglicci-12 and those populations is more than a coincidence. Indeed, the haplogroups to which the Cro-Magnon type sequences appear to belong are rare among modern samples, and therefore their frequencies are poorly estimated. However, genetic affinities between the first anatomically modern Europeans and current populations of the Near East make sense in the light of the likely routes of Upper Paleolithic human expansions in Europe, as documented in the archaeological record (37).

This suggest that haplogroup N was taken to Western Eurasia by the San people=Cro-Magnon.

In summary, the Black Berbers took African mtDNA into Western Europe over 40kya . in addition, Berbers and Khoisan continue to carry y-Chromosome haplogroups A1 and R1-M343. The Tuareg probably helped spread hg H in Europe after they invaded Europe along with other sahelians/Moors during the Islamic period.

  • References:

    Bekada A, Arauna LR, Deba T, Calafell F, Benhamamouch S, Comas D (2015) Genetic Heterogeneity in Algerian Human Populations. PLoS ONE 10(9): e0138453. doi:10.1371/journal.pone.0138453

    Cruciani, F., Trombetta, B., Massaia, A., Destro-Bisol, G., Sellitto, D., & Scozzari, R. (2011). A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa. American Journal of Human Genetics, 88(6), 814–818.

    Domínguez E.F. (2005). Polimorfismos de DNA mitocondrial en poblaciones antiguas de la cuenca
    mediterránea. Universitat de Barcelona. Departament de Biologia Animal, 2005 (PhD thesis).

    Frigi et al. (2010). Ancient Local Evolution of African mtDNA Haplogroups in Tunisian Berber Populations, Human Biology (August 2010 (82:4).

    Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, et al. (2013) The First Modern Human Dispersals across Africa. PLoS ONE 8(11): e80031. doi:10.1371/journal.pone.0080031

    Schlebusch, C.M. (2010). Genetic variation in Khoisan-speaking populations from southern Africa. University of the Witwatersrand, Johannesburg (2010 PhD thesis).

    Winters,C. (2010). Origin and spread of the Haplogroup N. Bioresearch Bull (2010) 3:116-122.

    Winters C.(2011). The Gibraltar Out of Africa Exit for Anatomically Modern Humans. WebmedCentral BIOLOGY 2011;2(10):WMC002319 doi: 10.9754/journal.wmc.2011.002319

    Winters, C. (2014). The Hadza Are Related to the South African Khoisan.

    Winters,C.(2012). There has been a Continuous Indigenous Sub-Saharan Presence in North Africa for 30ky. Comment: .

Sunday, October 11, 2015

The R1 haplogroup probably originated in Africa.


The phylogeography of R1 in Africa makes it clear that this y-chromosome is spread globally across Africa and includes the genetic structure of diverse African populations including Berber, Chadic, Cushitic, Khoisan,Pygmy, Niger-Congo, Nilo-Saharan and Semitic speaking African populations (Berniell-Lee et al, 2009; Cruciani et al, 2010; Wood et al, 2009). The fact that Dravidians carry the R haplogroup illustrate the recent introduction of R y-chromosome to Eurasia.

Abu-Amero et al (20009) reveal the fact that Dravidians carry the R haplogroups illustrate the recent introduction of Ry-chromosomes to Eurasia. The frequency of haplotype M173 in Eurasia is as follows: Anatolia 0.19%, Iran 2.67%, Iraq 0.49% Oman 1.0%, Pakistan 0.57% and Oman 1.0% . This contrast sharply with the widespread distribution of R1 in Africa that ranges between 7- 95% in various parts of Africa, especially Cameroon (Coia et al, 2005). Coia et al (2005) has revealed that no maternal Eurasian lineages have been found among Sub-Saharan Africans with a R1- M173 profile.
Haplogroup V88 has the greatest frequency in Africa. It is predominately carried by Chadic speakers, ranges between 2-60% among Central African Niger-Congo speakers (Cruciani et al, 2010). Researchers have found that the TMRCA of V88 was 9200-5600 kya (Cruciani et al, 2010). 

The phylogenetically deep haplogroup R1b is mainly found in West Africa and the Sahel, where the frequency ranges between 5-85% among various Niger Congo speakers (Cruciani et al, 2010). The paternal record of M173 on the African continent illustrates a greater distribution of this y-chromosome among varied African populations than, in Asia. 

The greatest diversity of R1b in Africa is highly suggestive of an Africa origin for this male lineage. Archaeological (Lal, 1963), genetic (Winters, 2008;2010a), placenames (Balakrishnan, 2005) and linguistic data group (Aravanan,1979,1980; Upadhyaya, 1976,1979; Winters 1985a,1985b, 1989) linking Africans and Dravidian support the recent demic diffusion of SubSaharan Africans and gene flow from Africa to Eurasia. An early colonization of Eurasia 4kya by Sub-Saharan Africans and Dravidian carriers of R1-M173 is the best scenario to explain the high frequency and widespread geographical distribution of this y-chromosome on the African continent (Winters, 2010c). Given the greatest diversity of R1- M173, this is the most parsimonious model explaining the frequency of R-M173 in Africa.


In conclusion, the R haplogroup probably originated in Africa. In my paper POSSIBLE AFRICAN ORIGIN OF Y-CHROMOSOME R1-M173 , I argue that the P clade originated in Africa because 1) the age of R-V88 and 2) the widespread nature of R1 in Africa. Researchers have found that the TMRCA of V88 was 9200-5600 kya (Cruciani et al, 2010). Eurasians carry the M269 (R1b1b2) mutation. The subclades of R1b1b2 include Rh1b1b2g (U106) (TMRCA 8.3kya) and R1b1b2h (U152) (TMRCA 7.4kya). The most recent common ancestor for R1b1b2 is probably 8kya (Balaresque et al, 2010). 

In Africa we find R-M269 and V88. Clearly, R-V88 is older than R-M269 there is no evidence of archaeological evidence of a back migration or haplogroup R into Africa, but there is evidence of the migration of the Kushites and Proto-Sahara into Eurasia from Middle Africa. The diversity of R1 haplogroups in Africa supports the proposition that the R macrohaplogroups originated in Africa, not Eurasia.

Sub-Saharan Africans introduced Haplogroup R1 to Native Americans

Haplogroup R-M173 and R-M269 was probably spread among Native Americans, by Pre- Columbian Africans, and African slaves. Controversy surrounds the origin of R1 among Native Americans. Most researchers believe it was introduced by Europeans, because M2many Europeans carry R-M269 . 

We have been lied too about Black History. When I was growing up my mother made it clear that we were part Choctaw. So in 1967, I took a survey at my High School: DuSable, in Chicago and found that over 40% of my classmates had Indian heritage.


At the time many people laughed at us because they only saw Lakota ad Apache on T.V. Today because of the WWW, there are numerous pictures of Black Native Americans on the Web. Below French artist Alexandre de Batz's renderings of Native American life in colonial Louisiana, such as "Desseins de Sauvages de Plusieurs Nations" ("Drawings of Several Native Americans of Various Nations") from 1735


Below a Blackfoot warrior by Karl Bodmer, between 1840 and 1843.

The majority of Native Americans  in North America carry haplogroup R M173.


R1-M269 probably originated in Africa. In my paper POSSIBLE AFRICAN ORIGIN OF Y-CHROMOSOME R1-M173 ; I argue that the P clade originated in Africa because 1) the age of R-V88 and 2) the widespread nature of R1 in Africa. Researchers have found that the TMRCA of V88 was 9200-5600 kya (Cruciani et al, 2010). Eurasians carry the M269 (R1b1b2) mutation. The subclades of R1b1b2 include Rh1b1b2g (U106) (TMRCA 8.3kya) and R1b1b2h (U152) (TMRCA 7.4kya). The most recent common ancestor for R1b1b2 in Europe is probably 8kya (Balaresque et al, 2010). Y-Chromosome R1b1b2 has high frequencies in England, France, Italy and Germany (Balaresque et al, 2010). Clearly, R-V88 is older than R-M269 . 

This figure from the Gonzalez et al article found that 10 out of 19 subjects in the study carried R1b1-P25 or M269. This is highly significant because it indicates that 53% of the R1 carriers in this study were M269, this finding is further proof of the widespread nature of this so-called Eurasian genes in Africa among populations that have not mated with Europeans.

Gonzalez et al proposes a West to East spread for P-25, with a possible entry of this clade into Europe via Gibraltar. There is a variety of R haplogroups in Africa.


Finding Africans carrying R-M269, in addition to V88, is nothing new. As early as 2009 R-M269 was found in Africa.

 Berniell-Lee et al (2009) found in their study that 5.2% carried Rb1*. The frequency of among the Bantu ranged from 2-20. The frequency of R1b1 among the Pygmy populations is 5% (Berniell-Lee et al, 2009). The frequency of R1b1 among the Guinea-Bissau populations was 12% (Carvalho et al,2010). Gonzalez et al found a high percent of R-M269 in Guinea.
Most Eurasians carry the M269 (R1b1b2) mutation. The subclades of R1b1b2 include Rh1b1b2g (U106) (TMRCA 8.3kya) and R1b1b2h (U152) (TMRCA 7.4kya)


The most recent common ancestor for R1b1b2 in Europe is probably 8kya (Balaresque et al, 2010). Y-Chromosome R1b1b2 has high frequencies in England, France, Italy and Germany (Balaresque et al, 2010) .Clearly, R-V88 dating to 9kya, is older than R-M269 .
In summary the frequency of R-M269 in Africa and age of V88, suggest that R-M269 originated in Africa. The presence of Black Native American communities on the Eastern Seaboard, a region where R1 is found suggest that it was these Black Indians who introduced R1 to America, not Europeans.

Tuesday, October 6, 2015

Is the R y-chromosome a Hunter-Gatherer Genome


Henn et al presents conclusive evidence that African hunter-gatherer (HG) populations share a number of ancestral lineages including B264*; although they are geographically distinct populations situated among agropastorial groups (1). An interesting finding of Henn et al was the discovery of the Eurasian clade R1b1b1a1a among the Khomani San of South Africa (1).

Henn et al was surprised by this revelation of R-M269 among this Khoisan population. As a result, he interviewed the carries of R1b1b2a1a, and learned that no members of their families had relations with Europeans. The presence of R lineages among HG populations is not new. Wood et al reported Khoisan carriers of R-M269 (2). Bernielle-Lee et al, in their study of the Baka and Bakola pygmies foud the the R1b1* haplogroup (3). These researchers made it clear that the Baka samples clustered closely to Khoisan samples (3).

The most common R haplogroup in Africa is V88. Given the interaction between HG groups and agropastoral groups they live in close proximity too, we would assume that African HG would carry the V88 lineage. Yet, as pointed out above the HG populations carry R-M269 instead of V88 (1-3). The implications of R-M269 among HG populations, and Henn et al’s of shared African HG genome suggest that R-M269 may represent a HG genome. 

The low frequency of this Eurasian clade among HG populations may not support this conclusion, the distribution of R-M269 among HG populations needs further research into the origins of the R y-chromosome among African populations. 


1. Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Comas D, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL, Feldman MW. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5154-62. Epub 2011 Mar 7. 

2. Wood,E.T., Stover,D.A., Ehret,C., Destro-Bisol,G., Spedini,G., McLeod, H., Louie,L., Bamshad,M., Strassmann,B.I., Soodyall,H., Hammer,M.F. 2005. Contrasting patterns of Y-chromosome and mtDNA variation in Africa:evidence for sex-biased demographic processes. European Journal of Human Genetics, 13:867-876.

3. Berniell-Lee G, Calafell F, Bosch E, Heyer E, Sica L, Mouguiama-Daouda P, van der Veen L, Hombert JM, Quintana-Murci L, Comas D. Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages. Mol Biol Evol. 2009 Jul;26(7):1581-9. Epub 2009 Apr 15.