Tag Archives: Mitochondrial DNA.

The trans-Saharan slave trade – clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages

The trans-Saharan slave trade – clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages

Background: A proportion of ¼ to ½ of North African female pool is made of typical sub- Saharan lineages, in higher frequencies as geographic proximity to sub-Saharan Africa increases. The Sahara was a strong geographical barrier against gene flow, at least since 5,000  years ago, when desertification affected a larger region, but the Arab trans-Saharan slave trade could have facilitate enormously this migration of lineages. Till now, the genetic consequences of these forced trans-Saharan movements of people have not been ascertained.

Results: The distribution of the main L haplogroups in North Africa clearly reflects the known trans-Saharan slave routes: West is dominated by L1b, L2b, L2c, L2d, L3b and L3d; the Center by L3e and some L3f and L3w; the East by L0a, L3h, L3i, L3x and, in common with the Center, L3f and L3w; while, L2a is almost everywhere. Ages for the haplogroups observed in both sides of the Saharan desert testify the recent origin (holocenic) of these haplogroups in sub-Saharan Africa, claiming a recent introduction in North Africa, further strengthened by the no detection of local expansions.

Conclusions: The interpolation analyses and complete sequencing of present mtDNA sub-Saharan lineages observed in North Africa support the genetic impact of recent trans-Saharan migrations, namely the slave trade initiated by the Arab conquest of North Africa in the seventh century. Sub-Saharan people did not leave traces in the North African maternal gene pool from the time of its settlement, some 40,000 years ago.

I haven’t read the whole paper through yet, but just from reading the bit I put in bold.. I’m sure that a paper on ancient Guanche mtDNA showed an L haplotype or two present which meant they had to be present a few thousand years ago during the colonisation of the Canary islands.

 The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription

And a very ancient age for L6 crossing over into Spain (about 20 kya) from another paper. So I’m going to state emphatically this can’t be correct. Not to mention that the ceramic using Saharan Negroid ’roundhead’ population reached as far as the Acacus mountains (about 10,500 bp) and would have had some contact/gene flow with the coastal Capsians (who were  a near Eastern /Mechtoid mixed people from the cranial studies I’ve seen and the expansion dates of Y chr J1 and H mtDNA). Although  the majority of the L haplotypes in North Africa are due to the slave trade, they can’t ALL be.

I read through this this morning. The most interesting bits of the whole pdf for me were…

Clearly, the main component of the West Eurasian lineages was made of possible Iberian
expanded lineages following the post-glacial climate improvement: H1 (12.35%), V (9.88%)
and U5b (1.23%).

I’d debate the 14k age for this given in the paper… but they had to have arrived before the Taforalt people died as the H, HV /V turns up in those 12k old samples..

A few L3 sequences observed in North Africa have older co-ancestry with other sub-Saharan
regions, but as this occurs in the rarer haplogroups (almost restricted to East Africa), most
probably the scenario will change as these become better characterized. This is the case for
one L3x2 sequence observed in Algeria, which shares an older most recent common ancestor
with two Ethiopian, one Israeli and one Kuwait, at 33,165 ± 4,499 years ago, but one
Ethiopian and the Israeli and Kuwait sequences share a younger ancestor at 19,012 ± 4,200.
Also, one Egyptian L3f2b sequence shares an ancestor with a Chadic one at around 24,809 ±
5,935 years ago
. For L3h1a2 haplogroup, one Egyptian and one Lebanese sequences share a
coalescence age of 26,281 ± 6,139 years old. And for L3h1b, with an age of 36,827 ± 3,772
, one of the North African sequences (one Tunisian and one Moroccan) has a most recent
common ancestor of 14,766 ± 4,448 years old with a sequence from Guinea Bissau.

I’ve been looking for mtDNA that could have accompanied the M78 out of Africa (arriving in the near east and NW Africa about 22k ago). While M1 obviously fits that date, it’s nice to see that some of the L3 dates aren’t incompatible with the m78;  being found in Natufian areas of Israel and Lebanon. The Israel/Kuwait/Ethiopian L3 may be a back-migrating L haplotype, not incompatible with the return of M1 and U, or another haplotype caught up in the Lower Nubian expansion and fanned out into the same areas as the m78/M1.

So far, the two only complete published samples belonging to haplogroup L3k have a North
African origin, one from Libya and one from Tunisia. This haplogroup has a coalescent age of
around 29,251 ± 6,524 years old

Who/where did that come from?

But the most useful thing in the whole paper are the maps, which give a quick over view of L distribution in Africa. I’ve reworked this one in colour, as the original is a bit hard to make out in places.

One of the interesting patterns I noticed was the (quite possibly superficial) relation to the expansion of non-L haplotypes and L3h in E/SE Africa. Also the hotspot for L3h in Northern Sudan, makes me wonder if it may not have been a travelling companion to the non-African mt DNA’s at some time. Unlike Maju, I’d say this looks like it has an origin on the Nile rather in Ethiopia, as it seems to have a relation to the expansion pattern of the M1/M1a/m78  from Lower Nubia/Egypt.

I’m going to have a dig to see what I can find on L3h now…

Mitochondrial DNA and Y-Chromosome Variation in the Caucasus

Mitochondrial DNA and Y-Chromosome Variation in the Caucasus

We have analyzed mtDNA HVI sequences and Y chromosome haplogroups based on 11 binary markers in 371 individuals, from 11 populations in the Caucasus and the neighbouring countries of Turkey and Iran. Y chromosome haplogroup diversity in the Caucasus was almost as high as in Central Asia and the Near East, and significantly higher than in Europe. More than 27% of the variance in Y-haplogroups can be attributed to differences between populations, whereas mtDNA showed much lower heterogeneity between populations (less then 5%), suggesting a strong influence of patrilocal social structure. Several groups from the highland region of the Caucasus exhibited low diversity and high differentiation for either or both genetic systems, reflecting enhanced genetic drift in these small, isolated populations. Overall, the Caucasus groups showed greater similarity with West Asian than with European groups for both genetic systems, although this similarity was much more pronounced for the Y chromosome than for mtDNA, suggesting that male-mediated migrations from West Asia have influenced the genetic structure of Caucasus populations.

An older paper, but one I hadn’t taken a look at.

Unfortunately there isn’t as much detail on the mt DNA.

From one long ago read text, I can remember that one North Caucasus late neolithic site had a tendency to have Mediterranean male crania with the more robust local females. This could support that  population movements into the area from the Iran/Turkey area (birthplace of the Neolithic) may have been male lead, which might give a clue as to how each the Caucasus population has such a heterogenous Y chromosome profile.

mtDNA diversity in Sudan (East Africa)

mtDNA diversity in Sudan (East Africa)

A major effort must be put in East and sub-Saharan African mtDNA diversity characterisation for the construction of an informative database. We contribute 102 new HVRI + HVRII Sudanese sequences. As expected this sample is highly diverse, mainly constituted of unique haplotypes (2.07% random match probability for HVRI alone), 72.5% of which belong to sub-Saharan haplogroups.

Somehow this slipped past me last year- I think because it came out in the school holidays. It’s a bit short on detail unfortunately. A bit like this blog entry.

mt DNA from La Palma Guanche remains

The maternal aborigine colonization of La Palma (Canary Islands)
Teeth from 38 aboriginal remains of La Palma (Canary Islands) were analyzed for external and endogenous mitochondrial DNA control region sequences and for diagnostic coding positions. Informative sequences were obtained from 30 individuals (78.9%). The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription. The bulk of the aboriginal haplotypes had exact matches in North Africa (70%). However, the indigenous Canarian sub-type U6b1, also detected in La Palma, has not yet been found in North Africa, the cradle of the U6 expansion. The most abundant H1 clade in La Palma, defined by transition 16260, is also very rare in North Africa. This means that the exact region from which the ancestors of the Canarian aborigines came has not yet been sampled or that they have been replaced by later human migrations. The high gene diversity found in La Palma (95.22.3), which is one of the farthest islands from the African continent, is of the same level than the previously found in the central island of Tenerife (92.42.8). This is against the supposition that the islands were colonized from the continent by island hopping and posterior isolation. On the other hand, the great similarity found between the aboriginal populations of La Palma and Tenerife is against the idea of an island-by-island independent maritime colonization without secondary contacts. Our data better fit to an island model with frequent migrations between islands.

More ancient DNA from native North Africa, showing a mainly Eurasian origin for the mt DNA.  The standard result for all ancient North African ADNA.

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.

Spotted on Dienekes, I’ll dig up the full text to add to my Egyptian DNA page later. I’d debate that the J1 was all historic though, bearing in mind the Capsian J1 input into the area, but it is pretty far North. It’s a pretty small sample size (35) for the Y chr info.

Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated “relict” populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia 65,000 years ago was rapid, most likely taking only a few thousand years.

An older paper, but I like to keep everything I find for reference As a minor point, the calculted age for M here is 64k, but last time I saw it in print it was more like 74k ago. The last age for L3 I saw was more in the 100k area.

Egyptian Y DNA and mt DNA reference

All the info I could find, collected in one place from assorted studies, mainly for my own ease of reference. I’ve kept putting this off, but finally here I am.

Egyptian  Y chromosomes

From Luis et al 2004.


 Which places the African Y chromosomes (this is a lower Egyptian sample group) at about 42%. I was most interested by the expansion time for the Eurasian hg’s. Luis et al estimated an expansion time of 13.7–17.5 ky for the K2 lineages in Egypt, although it also states the K2 could have accompanied R1*-M173 back into Africa in the paleolithic along with the U and M1.

Like the R1*-M173 males, the M70 individuals could represent the relics of an early back migration to Africa from Asia, since these chromosomes are not associated with the G-M201, J-12f2, and R1-M173 derivatives, lineages that represent more-recent Eurasian genetic contributions.

It also describes J-12f2 as a marker of the Neolithic expansion. Although looking through the Sudanese Y chromosome study it Hassan puts it down as a recent Arab marker, although no expansion dates are mentioned in his paper, so I’m not sure on what basis that conclusion was drawn. The J is complicated to unravel. After a read of Cruciani 2004 it would seem about 90% of the  J-12f2 is Arabic in origin, but the M172 (J2) is rather older and probably Neolithic, although this doesn’t seem to agree with the age estimates for J-12f2 in this paper. It would seem that J has made several entrances to North Africa.

From Lucotte 2003, which needs this Keita paper to understand it. Haplotypes V, XI and IV are all Pn2 derived (E). VII and VIII are considered Arabic, so I’m assuming J1 is VIII and VII is J2.


The other study that deals with numbered and not named groups is by Franz et al. This puts Hg 1 (E) at 44% in Egypt (Cairo) and J  (Hg 9) at 35%, but unfortunately the rest of the information is a bit vague.

From Arredi 2004 which had a small study of upper and lower Egyptians as part of a North Africa overview.

Lower Egypt (0f 44 samples)

  • 1 A3b2*
  • 4 E3b3a
  • 12 E3b1
  • 2 E3b
  • 5 E3b2
  • 1 J2f1
  • 3 J2
  • 3 F
  • 4 J
  • 1 O
  • 1 K2
  • 4 R1
  • 1 R1a*
  • 2 P

Upper Egypt (of 29 samples)

  • 2 E3b3a
  • 5 E3b1
  • 2 E3b2
  • 1 I
  • 1 J2
  • 5 F
  • 6 J
  • 3 K2
  • 4 R1

Which places AfricanY DNA at 59%, and J at 18% in Lower Egypt, which is close to the Lucotte study. Upper Egypt has a much more diverse profile (oddly) with J at 20% and African Y chromsomes at a much lower 31% with the ‘old in Africa’ R1 and K making up 24% of this (pretty small) sample. Having seen this study I’ve been obliged to dig into the origin of F, and it does look like an ‘ancient in Africa’ Y chromosome (Karafet 2008) as it turns up in the Bantu in South Africa.

From Wood et al 2005,which is in here provisionally until I can check the paper personally as I’ve borrowed it from Maju’s comments.

3/92 = 3.3% A3b2-M13
2/92 = 2.2% B2a1a-M152
1/92 = 1.1% E-SRY4064(xE1a-M33, E2-M75, E1b1-P2)
1/92 = 1.1% E1a-M33
2/92 = 2.2% E1b1a-P1(xE1b1a7-M191)
1/92 = 1.1% E1b1a7-M191
8/92 = 8.7% E1b1b1-M35(xE1b1b1a-M78, E1b1b1b-M81)
28/92 = 30.4% E1b1b1a-M78
4/92 = 4.3% E1b1b1b-M81

2/92 = 2.2% F-P14(xG-M201, H1-M52, I-P19, J-12f2, K-M9)
2/92 = 2.2% G-M201
1/92 = 1.1% I-P19
21/92 = 22.8% J-12f2
1/92 = 1.1% K-M9(xL-M20, M1-M4, N1-LLY22g, O-M175, P-P27, T-M70)
7/92 = 7.6% T-M70
1/92 = 1.1% R-M207(xR1-M173)
2/92 = 2.2% R1-M173(xR1a1-SRY10831b, R1b1-P25)
4/92 = 4.3% R1b1-P25(xR1b1b2-M269)
1/92 = 1.1% R1b1b2-M269

T formerlyK2, I believe. Finally I find a source for the R1b in the Sudan and Cameroon.

Finally a study of J (Giacomo 2004) found the Egyptian sample to be 23.4% J and with more clarity this was..

  • 6 J1
  • 1 J2*
  • 2 J2
  • 1 J2f
  • 1 J2fl

I can’t help noticing there’s a fair amount of variance between these studies. But still the overall picture you get from Lower Egypt is about half native African, with most of the other Eurasian Hg’s dating back into prehistory.

Lower Egypt is about 55% African, mainly E3b, E and then A.

The next largest group is J, which is unfortunately a bit hard to separate out from Neolithic expansion, Capsian expansion, earlier historic population movements and the Arab expansion, but it averages out at 25% from all five studies, with possibly a third of it attributable to non historic expansions (J2, a little  Capsian J1).

After this comes the ‘old in Africa’ haplotypes, which make up the bulk of the remaining Y chromosomes about 19% (again averaging the studies, the HG vary in proportion but they came up near 19% overall).

Which takes Lower Egypt into the low 80% area for paternal ancestry traceable to the dynastic era and earlier. One would assume the Arab expansion didn’t bring anywhere near as much maternal DNA with it, although some tribes did settle in Egypt.

Egyptian mitochondrial DNA

From Berbers at Siwa Oasis (north west Egypt) and from Egyptians at Gurna (upper Egypt area) Detail here.

Siwa; Of 78 samples.

  • Eurasian  45
  • Asian (M) 1
  • North African (U6 and M1) 13
  • Sub Saharan 19

24% SSA, 75% Eurasian/N African.


  • H 5 14.7
  • I 2 5.9
  • J 2 5.9
  • L1a 4 11.7
  • L1e 2 5.9
  • L2a 1 2.9
  • M1 6 17.6
  • N1b 3 8.8
  • T 2 5.9
  • U 3 8.8
  • U3 1 2.9
  • U4 2 5.9
  • L3*(a) 2 5.9
  • L3*(b) 1 2.9

29% SSA, 71% Eurasian/N African.

Surprisingly little difference between them. Lower Nubia came in at about 60% Eurasian an ancient mummy test- and while it’s correct that L3 also comes into the category marked out as Eurasian, it’s actually pretty close to the DNA study of modern Nubians. Unless the invading armies of history were all women there’s no plausible scenario to explain such a huge influx of Eurasian ancestry in such a relatively short space of time, as the Y chromosome presence of Arabs in the area just isn’t that massive in the modern lower Nubia area.

From Krings 1999. Which also shows that Egyptian maternal DNA is roughly 25% sub Saharan and 75% Eurasian. 



Ancient Egyptian DNA

To obtain the frequencies of these mtDNA types, amplification of the HVRI region and three RFLP markers was conducted. The authors succeeded in analysing RFLP markers in 34 samples and HVRI sequences in 18 of the samples. Both populations, ancient and contemporary, fit the north-south clinal distribution of “southern” and “northern” mtDNA types (Graver et al. 2001). However, significant differences were found between these populations. Based on an increased frequency of HpaI 3592 (+) haplotypes in the contemporary Dakhlehian population, the authors suggested that, since Roman times, gene flow from the Sub-Saharan region has affected gene frequencies of individuals from the oasis.

Which suggests the proportion of sub Saharan lineages is higher now than it once was at Dahkleh (SW Egypt). Bearing in mind that the Arab slave trade in African women seems to have accounted for about 10-15% of the maternal DNA in Arabia, this would seem the most likely cause in the increase of sub Saharan lineages. It would seem that post dynastic inflow maternal from sub Saharan African is passably close match to the paternal immigration from Arabs, and that these are probably the two most influential factors in immigration in post dynastic Egypt.

Not strictly speaking Egyptian but still relevant.

Copts from the Sudan, from Hassan 2008.

  • 13/33 J1
  • 5/33 B
  • 2/33 E3b
  • 5/33 E3b1
  • 2/33 J2
  • 1/33 K
  • 5/33 R1b

Nubians from the Sudan

  • 3/39 B
  • 3/39 E3b
  • 6/39 E3b1
  • 4/39 F
  • 2/49 I
  • 16/39 J1
  • 1/39 J2
  • 4/39 R1b

The high level of J1 is quite a surprise in both of these. Particlarly since Copts aren’t supposed to marry out. A y chr study of Cairo Copts could be informative as to just how much mixing there has been between the two groups there.

One thing that became apparent after reading through these DNA studies was that there was a somewhat higher level of African male ancestry in Egyptians than in a lot of the East African groups, and that the Horn Africans and Egyptians are really made up of very similar ancestries (West Asian, North East African and East African with a little Bantu here and there) but in varying ratios.

Reference list.

  1.  Luis 2004
  2.  Cruciani 2004
  3. Lucotte 2003
  4. Wood 2005
  5. Franz 2002
  6. Hassan 2008
  7. Krings 1999
  8. Arredi 2004
  9. Karafet 2008
  10. Giacomo 2004