Tag Archives: Mitochondrial DNA.

MtDNA variation in North, East, and Central African populations gives clues to a possible back-migration from the Middle East.

MtDNA variation in North, East, and Central African populations gives clues to a possible back-migration from the Middle East.

A.D. Holden et al.

The general timeline for human occupation of Africa has been studied extensively. However, questions involving Upper Palaeolithic migrations still persist. One remaining question is the presence of the mitochondrial M1 haplogroup in North and East Africa. Some (Quintana-Murci et al. 2004, 1999) argue that the presence of M1 in modern Africans is a remnant of the original M haplogroup that left Africa 60 kya via the Horn of Africa. Others (Forster, 2004) propose that it is instead the result of a back-migration from the Arabian Peninsula from 20 kya. This research aims to test these two competing hypotheses.

We analysed mtDNA variation in ~250 persons from Libya, Somalia, and Congo/Zambia, as representatives of the three regions of interest. Our initial results indicate a sharp cline in M1 frequencies that generally does not extend into sub-Saharan Africa. While our North and especially East African samples contained frequencies of M1 over 20%, our sub-Saharan samples consisted almost entirely of the L1 or L2 haplogroups only. In addition, there existed a significant amount of homogeneity within the M1 haplogroup.

This sharp cline indicates a history of little admixture between these regions. This could imply a more recent ancestry for M1 in Africa, as older lineages are more diverse and widespread by nature, and may be an indication of a back-migration into Africa from the Middle East. Further research on this topic includes more extensive population samples from the Middle East, as well as possible correlations of M1 to the Afro-Asiatic language family.

I’m still looking for the full text on this one.  Another mt DNA study placing M1 as Asian.

The maternal aborigine colonization of La Palma (Canary Islands)

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.

Again the indigenous Canarians show up as mainly Eurasian/North African for ancestry. Not really a surprise that L lineages show up a little. Although a lot of them seem to be in North Africa from the slave trade, a couple are older and one shows an entry into Iberia about 20,000 years ago.

Mitochondrial DNA haplogroup H structure in North Africa

Mitochondrial DNA haplogroup H structure in North Africa

Background
The Strait of Gibraltar separating the Iberian Peninsula from North Africa is thought to be a stronger barrier to gene flow for male than for female lineages. However, the recent subdivision of the haplogroup H at mitochondrial DNA (mtDNA) level has revealed greater genetic differentiation among geographic regions than previously detected. The dissection of the mtDNA haplogroup H in North Africa, and its comparison with the Iberian Peninsula and Near-East profiles would help clarify the relative affinities among these regions.

Results
Like the Iberian Peninsula, the dominant mtDNA haplogroup H subgroups in North Africa are H1 (42%) and H3 (13%). The similarity between these regions is stronger in the North-West edge affecting mainly Moroccan Arabs, West Saharans and Mauritanians, and decreases eastwards probably due to gene flow from Near East as attested for the higher frequencies of H4, H5, H7, H8 and H11 subgroups. Moroccan Berbers show stronger affinities with Tunisian and Tunisian Berbers than with Moroccan Arabs. Coalescence ages for H1 (11 ± 2 ky) and H3 (11 ± 4 ky) in North Africa point to the possibility of a late Palaeolithic settlement for these lineages similar to those found for other mtDNA haplogroups. Total and partial mtDNA genomic sequencing unveiled stronger mtDNA differentiation among regions than previously found using HVSI mtDNA based analysis.

Conclusion
The subdivision of the mtDNA haplogroup H in North Africa has confirmed that the genetic differentiation found among Western and Eastern populations is mainly due to geographicalrather than cultural barriers. It also shows that the historicalArabian role on the region had more a cultural than a demic effect. Whole mtDNAsequencing of identical H haplotypes based on HVSI and RFLP information has unveiled additional mtDNA differences between North African and Iberian Peninsula lineages, pointing to an older mtDNA genetic flow between regions than previously thought. Based on this new information, it seems that the Strait of Gibraltar barrier affected both male and female gene flow in a similar fashion.

Pay dirt! I’ve been looking for some kind of study into H in North Africa ever since I saw the Taforalt A-DNA study and noticed the H in it. I was curious how the H appeared in North African  Ibero- Maurasian bones before the Capsian era (which seems to be near Eastern in origin) if H doesn’t show the same time depth as X1, U and M1 in North Africa. This allows for the Taforalt remains to have some relatively recent input from the near east, which explains the lesser time depth for H but it’s presence in the 12,000 year old Moroccan bones. Thank you Biomed.

Selected quotes for my own reference:

A principal component analysis (PCA) points to subhaplogroups H1 and H3 as being primarily responsible for the Iberian-Moroccan-Saharan connection, whereas H4, H5, H7, H8 and H11 testify the Near East influence

Thus, our HVSI based coalescence ages for H1 (14.2 ± 3.0 ky) and H3 (10.3 ± 2.6 ky), in the Iberian Peninsula, are very close to those published by Pereira et al. [40] in the same area for H1 (14.0 ± 3.0 ky) and for all of Europe for H3 (11.0 ± 3.0 ky)

From our data, it can be also deduced that the presence of the H1 and H3 subgroups in North Africa could have similar expansion times as in Europe and, therefore, a late Palaeolithic settlement in the region.

As a consequence, it has been proposed that the North African gene pool has had Palaeolithic and Neolithic influences from the East, but that the impact of the historicalinvasions, such as the Arabic role, had more a cultural than a demic effect. The lack of exclusive haplotypic matches between North Africa and the Arabian Peninsula found here is in accordance with that hypothesis.

The H here seems to have the same time depth as the Y chromosome J-m267 in North Africa, so I’m going to assume they made the trip from the near East together. this seems to match the expansion of the ‘escargotiere’ people who ate massive amounts of edible snails, who seem to have an origin somewhere between Southern Turkey and the Levant.

Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup

Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup

Chad Basin, lying within the bidirectional corridor of African Sahel, is one of the most populated places in Sub-Saharan Africa today. The origin of its settlement appears connected with Holocene climatic ameliorations (aquatic resources) that started ~10,000 years before present (YBP). Although both Nilo-Saharan and Niger-Congo language families are encountered here, the most diversified group is the Chadic branch belonging to the Afro-Asiatic language phylum. In this article, we investigate the proposed ancient migration of Chadic pastoralists from Eastern Africa based on linguistic data and test for genetic traces of this migration in extant Chadic speaking populations.

Results
We performed whole mitochondrial genome sequencing of 16 L3f haplotypes, focused on clade L3f3 that occurs almost exclusively in Chadic speaking people living in the Chad Basin. These data supported the reconstruction of a L3f phylogenetic tree and calculation of times to the most recent common ancestor for all internal clades. A date ~8,000 YBP was estimated for the L3f3 sub-haplogroup, which is in good agreement with the supposed migration of Chadic speaking pastoralists and their linguistic differentiation from other Afro-Asiatic groups of East Africa. As a whole, the Afro-Asiatic language family presents low population structure, as 92.4% of mtDNA variation is found within populations and only 3.4% of variation can be attributed to diversity among language branches. The Chadic speaking populations form a relatively homogenous cluster, exhibiting lower diversification than the other Afro-Asiatic branches (Berber, Semitic and Cushitic).

Conclusions
The results of our study support an East African origin of mitochondrial L3f3 clade that is present almost exclusively within Chadic speaking people living in Chad Basin. Whole genome sequence-based dates show that the ancestral haplogroup L3f must have emerged soon after the Out-of-Africa migration (around 57,100 ± 9,400 YBP), but the “Chadic” L3f3 clade has much less internal variation, suggesting an expansion during the Holocene period about 8,000 ± 2,500 YBP. This time period in the Chad Basin is known to have been particularly favourable for the expansion of pastoralists coming from northeastern Africa, as suggested by archaeological, linguistic and climatic data.

Thank you for posting this Igbo. I do feel obliged to point out an impossibility in the text..

According to linguistic analyses of Afro-Asiatic branches, the common ancestors of extant Chadic and Cushitic peoples inhabited East or Northeast Africa ~7,000-8,000 years before present

Because for various reasons to do with goats and sheep there’s no way Cushitic is older than 5,500 BP. The evidence does speak to Chadic being a younger arrival in the area. Is the R1b associated with it from the North?

Another interesting observation (I’ve being trying to get hold of come Chadic Mt DNA) is the amount of L3 in the area. I suspect these are the surviving remnants of the North African L3 branches that got wiped out by the Eurasian back migrations across the Maghreb about 30-35k ago. I shall have another read of this later when my kids aren’t bugging me so much. Sigh.

Using ancient DNA to examine genetic continuity at the Mesolithic-Neolithic transition in Portugal

Using ancient DNA to examine genetic continuity at the Mesolithic-Neolithic transition in Portugal

Two main mechanisms for the introduction of agriculture at the transition from the Mesolithic to the Neolithic in Portugal have been proposed: indigenous adoption and colonisation. Distinguishing between these mechanisms can be regarded as a question of genetic continuity or discontinuity at the transition. A genetic comparison of late Mesolithic and early Neolithic populations at the transition using ancient DNA is described here. Mitochondrial DNA (mtDNA) was extracted from human remains collected in several Mesolithic sites of the Sado estuary and from Neolithic cave sites. Phylogenetic analysis, based on the mitochondrial hypervariable region 1 (HVSI), and comparison with DNA from modern European populations was performed. The absence of mtDNA haplogroup J in the ancient Portuguese Neolithic sample suggests that this population was not derived directly from Near Eastern farmers. The Mesolithic and Neolithic groups show genetic discontinuity implying colonisation at the Neolithic transition in Portugal.

A study of Mesolithic and Neolithic Mt DNA from sites inPortugal.

mesoneoportugal1

J shows iself to be absent from the Mesolithic and Neolithic samples, and there was some loss of diversity in less common Hg’s. There’s a fair difference between the Mesolithic and Neolithic samples, suggestin population discontinuity-probably a large amount of immgration at the start of the neolithic, although the lack of J suggests this wasn’t from the near East

mesodna

old-dna-port

It also mentions isotope studies on the bones show a very abrupt change from the Meolithic Maritime diet to the land based Neolithic diet, the same as in Britain.

Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages

mtdna1

Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages

About a fifth of the human gene pool belongs largely either to Indo-European or Dravidic speaking people inhabiting the Indian peninsula. The ‘Caucasoid share’ in their gene pool is thought to be related predominantly to the Indo-European speakers. A commonly held hypothesis, albeit not the only one, suggests a massive Indo-Aryan invasion to India some 4,000 years ago [1]. Recent limited analysis of maternally inherited mitochondrial DNA (mtDNA) of Indian populations has been interpreted as supporting this concept [2,3]. Here, this interpretation is questioned. We found an extensive deep late Pleistocene genetic link between contemporary Europeans and Indians, provided by the mtDNA haplogroup U, which encompasses roughly a fifth of mtDNA lineages of both populations. Our estimate for this split is close to the suggested time for the peopling of Asia and the first expansion of anatomically modern humans in Eurasia [4–8] and likely pre-dates their spread to Europe. Only a small fraction of the ‘Caucasoid-specific’ mtDNA lineages found in Indian populations can be ascribed to a relatively recent admixture.

Not that I support an Indo European invasion at that date, anyway.

The Making of the African mtDNA Landscape

The Making of the African mtDNA Landscape

Africa presents the most complex genetic picture of any continent, with a time depth for mitochondrial DNA
(mtDNA) lineages 1100,000 years. The most recent widespread demographic shift within the continent was most probably the Bantu dispersals, which archaeological and linguistic evidence suggest originated in West Africa 3,000–4,000 years ago, spreading both east and south. Here, we have carried out a thorough phylogeographic analysis of mtDNA variation in a total of 2,847 samples from throughout the continent, including 307 new sequences from southeast African Bantu speakers. The results suggest that the southeast Bantu speakers have a composite origin on the maternal line of descent, with ~44% of lineages deriving from West Africa, ~21% from either West or Central Africa, ~30% from East Africa, and ~5% from southern African Khoisan-speaking groups. The ages of the major founder types of both West and East African origin are consistent with the likely timing of Bantu dispersals, with those from the west somewhat predating those from the east. Despite this composite picture, the southeastern African Bantu groups are indistinguishable from each other with respect to their mtDNA, suggesting that they either had a common origin at the point of entry into southeastern Africa or have undergone very extensive gene flow since.

An old paper from 2002 that I’m posting for reference while I’m hunting down info on L3a.

Paragroup L3A
We here define two previously unlabeled subclades of L3A, L3f, and L3g. The lineages remaining within L3* represent ~20% of all L3A types in Africa. Although they are distributed throughout the continent, they reach the highest frequencies in East Africa, where they account for about half of all types from this region. This frequency profile suggests an origin for L3 in East Africa (Watson et al. 1997). This is supported by the evidence that the out-of-Africa migration, which took place from a source in East Africa 60,000–80,000 years ago, gave rise only to L3 lineages outside Africa.

mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

The mtDNA variation of 74 Khoisan-speaking individuals (Kung and Khwe) from Schmidtsdrift, in the Northern Cape Province of South Africa, was examined by high-resolution RFLP analysis and control region (CR) sequencing. The resulting data were combined with published RFLP haplotype and CR sequence data from sub-Saharan African populations and then were subjected to phylogenetic analysis to deduce the evolutionary relationships among them. More than 77% of the Kung and Khwe mtDNA samples were found to belong to the major mtDNA lineage, macrohaplogroup L* (defined by a HpaI site at nucleotide position 3592), which is prevalent in sub-Saharan African populations. Additional sets of RFLPs subdivided macrohaplogroup L* into two extended haplogroups—L1 and L2—both of which appeared in the Kung and Khwe. Besides revealing the significant substructure of macrohaplogroup L* in African populations, these data showed that the Biaka Pygmies have one of the most ancient RFLP sublineages observed in African mtDNA and, thus, that they could represent one of the oldest human populations. In addition, the Kung exhibited a set of related haplotypes that were positioned closest to the root of the human mtDNA phylogeny, suggesting that they, too, represent one of the most ancient African populations. Comparison of Kung and Khwe CR sequences with those from other African populations confirmed the genetic association of the Kung with other Khoisan-speaking peoples, whereas the Khwe were more closely linked to non–Khoisan-speaking (Bantu) populations. Finally, the overall sequence divergence of 214 African RFLP haplotypes defined in both this and an earlier study was 0.364%, giving an estimated age, for all African mtDNAs, of 125,500–165,500 years before the present, a date that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa.

I’m going through a lot of DNA studies atthe moment looking for evidence of M1 and M. Apparently one  HG, L3a, seems closely related to it, as L3a is the precursor to M.

The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. This haplotype branches off African subhaplogroup L3a (figs.2 and3), suggesting that haplogroup M mtDNAs might have been derived from this African mtDNA lineage; however, it is also possible that this particular haplotype is present in Africa because of back-migration from Asia.

I was entertained to see someone was using this to claim M1 was African in origin on another site.. leaving out the inconvenient back-migration from Asia at the end of the quote. Since M itself seems absent in Africa, and M1 traces the path of U in North and East Africa pretty closely, it’s now pretty much a done deal that M1 arrived in North Africa from West Asia. The real mystery is the lack of L3 and M in India, but the Toba eruption could easily have caused a wipe out across India that erased the first immigrants there. I’d like to observe that this L3a seems to have followed the North African population movements that curved southwards down into the West coast of Africa, so I think that its from the back migration may be possible, or at least dating to the expansion from upper Egypt about 24k ago with a origin from the Nile area. I shall have a dig into L3a distribution, something I should have done a while ago.

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Recent advances in the understanding of the maternal and paternal heritage of southand southwest Asian populations have highlighted their role in the colonization of Eurasia byanatomically modern humans. Further understanding requires a deeper insight into the topology ofthe branches of the Indian mtDNA phylogenetic tree, which should be contextualized within thephylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzedmtDNA control and coding region variation in 796 Indian (including both tribal and castepopulations from different parts of India) and 436 Iranian mtDNAs.

 The results were integratedand analyzed together with published data from South, Southeast Asia and West Eurasia.Results: Four new Indian-specific haplogroup M sub-clades were defined. These, in combinationwith two previously described haplogroups, encompass approximately one third of the haplogroupM mtDNAs in India. Their phylogeography and spread among different linguistic phyla and socialstrata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealedpatterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed theidentification of different assemblies of shared mtDNA sub-clades.

Conclusions: Since the initial peopling of South and West Asia by anatomically modern humans,when this region may well have provided the initial settlers who colonized much of the rest ofEurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared betweenIndian and Iranian populations and exhibit coalescence ages corresponding to around the earlyUpper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. Incontrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent

mt-dna-india m-maps u-map-india 

Click to enlarge all images.

The quest for finding the origin of haplogroup M and a plausible scenario for the peopling of Eurasia.

Based on the high frequency and diversity of haplogroupM in India and elsewhere in Asia, some authors have suggested (versus [3]) that M may have arisen in SouthwestAsia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 inAfrica as a result of a back migration from India. Yet, to date this has not been achieved [15], this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa [3].Furthermore, the lack of L3 lineages other than M and N(indeed, L3M and L3N) in India is more consistent withthe African launch of haplogroup M. On the other hand,one also observes that: i) M1 is the only variant of haplo-group M found in Africa; ii) M1 has a fairly restricted phy-logeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly inassociation with the Afro-Asiatic linguistic phylum – afinding that appears to be inconsistent with the distribu-tion of sub-clades of haplogroups L3 and L2 that havesimilar time depths. That, plus the presence of M1 without accompanying L lineages in the Caucasus [32] and [ourunpublished data], leaves the question about the origin of haplogroup M still open.

The paper gives the age of M2 at about 70k, with 21k either way.  Reading through it there seems to be more of a case for M appearing in the Arabian area, the same for the later M1 and U. Call me mad but I think the absence of M in general could be down to the Toba eruption, which must have had some serious impact in South Asia as it put down ash 2m thick all over India.

A study of the L1c haplogroup of the mitochondrial DNA

A study of the L1c haplogroup of the mitochondrial DNA.
page 7

In this communication, we present a study of the human mitochondrial haplogroup L1c which has been carried out on a total of 455 individuals from 27 African and American populations using both hypervariable regions 1 and 2. The results obtained lead us to draw three main conclusions. First, the time to the L1c most recent common ancestor (TMRCA) has been estimated as 90,000 ± 13,000 YBP, substantially older than the previous estimate (59,650 ± 11,800) and in agreement with archaeological dating. Second, we observed that L1c frequencies reach very high values in Western Pygmies populations (from 86% to 98%), hunter-gatherers supposed to be the most ancient inhabitants of this area. Third and finally, the median networks built using our dataset change the phylogeny of the entire haplogroup. In fact, we present a substantially modified structure for the sub-haplogroups L1c1 and L1c3 and identify a new clade, L1c4 which contains mostly sequences from Pygmies.

Taking into consideration the L1c phylogeographic features together with archaeological knowledge, we propose that the hunter-gatherers communities living in Central Africa at least 40,000 YBP could be the ancestors of both Bantu and Western Pygmy populations. These two groups could have separated later on, because of the cycles of expansion and fragmentation of the forest environment occurred till 12,000 YBP. As the next step of this research, we will sequence the complete mtDNA genome in order to test the robustness of the new phylogeny.

Nice to see an older date for this.