posted
This is a thread to discuss what's known about U6 origins without resorting to ad homimen debate to bolster proponents' weak opinions or ridicule in lieu of satisfactory fact based counter opinion. I hope current ES membership is up to the task.
From the start I will say the terms Eurasian and Caucas(ian/oid) are red flags to many posters' bulls. To that end examination of applicability of those terms re U6's divergence time and place is necessary. For instance are the Levant and the Arabian tectonic plate and their populations of over 20,000 years ago Eurasia and Caucasian or Afroasia and African? And how does flora, fauna, and climate support either designation?
Other unrelated topics I also have in mind for critical review are the Dynastic Race (but not as it was originally proposed) and A Pygmy West Africa before the mid-late Holocene? . I know many feel pygmy is pejorative but there is no other recognizable term that covers all their ethnies since all of them are not Twa. Pygmy just means "shorties" or "little people," which I don't use because of fantasy race "wee folk." I will accept an alternative term if one exists.
But back to the topic at hand. I don't claim any special knowledge here and the topic with its related subject matter is vast. However the field of population genetics does accept the fact of U6 as a Northwest African uniparental marker from ~45,000 years ago up until now.
I am going through my genetics PDFs for whatever U6 information I can find. Interestingly my first search hit was an old paper on Europe and USA Caucasians mtDNA (next post). Please critique and update.
Meanwhile here's a comparative TMRCA I put together a while back including the infamous Maca-Meyer and two more recent assessments. The suggested eras and industries are my take.
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Torroni et al. (1) defined Haplogroup U5 by the presence of sites 16192T and 16270T. Reversals of 16192T and 16192C were seen in our analysis (and also reported independently in Ref 2, L = 28 for one of our most variable sites). Using 16270T as the primary designator for this haplogroup is recommended. There were 134 individuals (7.6%) observed carrying this state. This haplogroup can be further subdivided based on the presence of 16256T and 150T. This subdivision has been described previously as U5a and U5b haplogroups, respectively, by Finnila et al. (2). Haplogroup U5a is further sub-divided by 16399G and 16291T. The U5b haplogroup is subdivided by the presence of 16189C or 16311C. Other investigators (Ref 2; Ref 3; and Ref 14) suggest additional division of the U group (U1, U2, U3, U4, U6, U7, and U8) that does not include the 16270T variation. Our analysis identified one cluster that was similar to Finnila et al.’s (2) U2 haplogroup, containing states 16051G, 16129C, 16183C, 16189C, 16362C, 152C, 217C, 340T, and 508G (n 15, 0.85%). The first two sites also are recommended by Helgason et al. (3) for the recognition of this subcluster. This subgroup would not have been considered a U haplogroup by Torroni et al. (1) as they originally recognized 16192T and 16270T as the defining variant for this cluster. Torroni et al.’s (1) earlier description matches Finnila et al.’s (2) U5a and U5b clusters but not the other U haplogroups. Also, we found that less than 1% of the individuals in the dataset (n = 17) are defined by states 16343G and 150T. This pattern is consistent with the U3 haplogroup defined by Macaulay et al. (14). Two other sub-clusters are consistent with the U4 Haplogroup of Finnila et al. (2) based on the presence of states 499A (n = 59), 16356C, and 195C (n = 34). We observed these sites as separate though related sub-clusters, and thus we have designated these as U4a and U4b. We observed six Caucasians that fit the U1 criteria of 16249C and 16189C, and five Caucasians that fit the U6 designation of 16219G and 16172C (3), although both of these frequencies fell below our cutoff for listing these sites as informative at an intermediate level. Similar to U1 and U6, we observed only six Caucasians who fit the U8 criteria of Finnila et al. (2), 16342C, and 282C; and we did not observe any U7 Caucasians.
The analyses of the Caucasian SWGDAM forensic dataset (n = 1771) demonstrate that these CR sequences are representative of European and U.S. Caucasian populations. The ten major haplogroups described in Caucasian populations were observed in this dataset at similar frequencies as have been reported in the literature (H, I, J, K, M, T, U, V, W, and X). The most common haplogroup, H, was observed for approximately 46% of the Caucasians. Haplogroups observed at intermediate levels included clusters U (15.6%), T (10.5%), J (10.0%), and K (8.9%). The haplogroups observed less frequently include W, X, V, I, and M, and these were observed in approximately 2% or less of the sample. ... Our detailed analysis of the large forensic dataset revealed the most important mtDNA CR SNPs useful for discriminating among the haplogroups of Caucasians. ... Our SNP list generated from Caucasians from Europe and the U.S. should be able to discriminate well for this target population. The reduced list identifies all of the members of the major European Caucasian haplogroups (Fig. 1, black bars). A future goal of ours is to provide additional SNP lists for the other subdivisions of SWGDAM. Other large datasets within this database that are slated for future examination include Asians, African Americans, Native Americans, and Hispanics.
Marc W. Allard et al. ... Caucasian Haplogroups ... mtDNA J Forensic Sci 2002 47:6
The Emerging Tree of West Eurasian mtDNAs: A Synthesis of Control- Region Sequences and RFLPs
Vincent Macaulay,1 Martin Richards,1 Eileen Hickey,1 Emilce Vega,1 Fulvio Cruciani,2 Valentina Guida,2 Rosaria Scozzari,2 Batsheva Bonne´-Tamir,3 Bryan Sykes,1 and Antonio Torroni2,4
Summary Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demon- strate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a no- menclature for mtDNA clusters. Hypervariable nucle- otides are identified, and the relative mutation rates of the two systems are evaluated. We point out where am- biguities remain. The identification of signature muta- tions for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sam- ple of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North Af- rican cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged »50,000 years ago.
Introduction Mapping of the variation in the modern mitochondrial landscape of Europe and the Near East is shedding light on colonization and the dispersal of peoples in this re- gion (Torroni et al. 1994a, 1996; Richards et al. 1996) and also on the etiology of a number of diseases (Hof- mann et al. 1997; Torroni et al. 1997). Because of the mode of inheritance of mtDNA (maternal transmission and lack of recombination), the mutations that have struck throughout human history trace the maternal ge- nealogy; through this genealogy and the impact that de- mography has had upon it, we can attempt to infer some- thing about prehistoric processes. Another virtue of mtDNA is that a high rate of base substitutions, com- pared with that of nuclear DNA, allows the genealogy to be captured in a fair amount of detail. However, this high rate also has its drawbacks, in that the treelike relationship of modern mtDNAs is obscured by recur- rent mutations affecting the same nucleotide positions (nps), which are often difficult to resolve. For some time, most studies of mtDNA variation have been conducted by use of one of two methods that assay largely different portions of the molecule: direct sequenc- ing of the especially fast–evolving control region (CR) and digestion of the entire molecule by means of stan- dard sets of restriction enzymes. Richards et al. (1996) produced a phylogenetic network of sequences from the first hypervariable segment (HVS I) of the CR and iden- tified six major mtDNA clusters among Europeans. By using high-resolution RFLP analysis, Torroni et al. (1994a) had previously identified four clusters (H, I, J, and K) among North Americans of European ancestry. Subsequently, Torroni et al. (1996) applied the same methodology to two Scandinavian population samples and identified five additional clusters (T, U, V, W, and X), which, together with the previous four clusters, ap- peared to encompass virtually all examined European mtDNAs. In the same article (Torroni et al. 1996), a small set of Tuscan mtDNAs previously studied for HVS I variation (Francalacci et al. 1996) was used to dem- onstrate the correlation of clusters defined with the two systems, by testing the same samples for RFLP clus- ter–diagnostic mutations. Further work in one system or the other has illuminated the phylogeny (Bertranpetit et al. 1996; Calafell et al. 1996; Wilkinson-Herbots et al. 1996; Torroni et al. 1997, 1998; Richards et al.
Concordant with a common origin of west and east Eurasians, east Asian clusters A and M are phylogenet- ically close to west Eurasian clusters I, W, and X, while west Eurasian clusters J, T, U, H, and V are close to east Asian clusters B and F. In contrast, Africans in general branch earlier in the phylogeny, except for members of L3a*. We discuss a striking exception below—namely, cluster U6 of North Africa—but another blurring ap- pears in cluster M, observed in Ethiopians (Passarino et al. 1998). It is tempting to see these patterns as signaling movement from Eurasia back to Africa.
Case Study: Origins of the Berbers
The Berbers, who speak closely related dialects of a distinct branch of the Afro-Asiatic language family, are dispersed in a patchwork throughout a huge area of Cyrenaı¨ca and the Mahgreb, as far west as the Canary Islands, and since antiquity have been widely regarded as aboriginal North Africans (Brett and Fentress 1996). Physically, they resemble other Mediterranean popula- tions, so that an investigation of their origins is of in- terest not only in its own right but also for the origins of modern west Eurasians (or Caucasians) in general. Previously, we sequenced HVS I and typed position 00073 of HVS II for 85 Berbers from the villages of the Mzab in northern Algeria, in the context of a study of mitochondrial variation in the Iberian peninsular (Coˆ rte- Real et al. 1996). We identified a novel cluster, referred to as “lineage group 6,” comprising one-third of the Berber lineages, which occurred very rarely in other pop- ulation samples and only in regions known historically to have come under North African influence, such as Iberia (!3% of Romance-speaking Iberians and absent elsewhere in Europe). This cluster therefore appeared to represent the most likely signature of the indigenous North Africans. Most of the sequences in this cluster included the HVS I motif 16172–16189–16219–16278 (with 00073G), but they clustered in a phylogenetic net- work of the Algerian sequences (fig. 6 in Coˆ rte-Real et al. 1996) with sequence type 16172–16189–16234– 16311 (also with 00073G), suggesting that the ancestral sequence was 16172–16189. An alternative ancestral se- quence, suggested by the branching pattern of the Por- tuguese network (fig. 5 in Coˆ rte-Real et al. 1996), which also contained three members of group 6, was 16172– 16219, and additional data from the Canary Islands (Pinto et al. 1996) subsequently also suggested that 16172–16219 indeed may be the ancestral sequence type. However, further confusion in the interpretion of the Berber network (which, in fact, should be more highly folded than as shown in fig. 6 in Coˆ rte-Real et al. 1996) is engendered by the conflict of position 16278 with positions 16172 and 16189, so that the African cluster L2 (referred to as “group 3B” in fig. 6 of Coˆ rte- Real et al. 1996) cannot be clearly distinguished from group 6. Therefore (at least in the absence of a suitable weighting scheme), because of the high substitution rate of the CR, it is unclear whether the supposedly indige- nous North African cluster evolved from the ancestors of modern west Eurasian or sub-Saharan African line- ages. We now have clarified this question by means of RFLP typing. To determine the cluster status of these Berber se- quences, RFLP typing was performed on at least one member of each sequence type in the data set (43 of 85 samples). The samples were typed for a restricted set of RFLPs that were diagnostic of all west Eurasian and African clusters and of some east Eurasian clusters, on the basis of the information intable 1. The following hierarchical scheme was employed: The results are reported in table 3 and are illustrated by the schematic phylogenetic network in figure 5. The “Berber cluster” is a subclade of cluster U, and we there- fore refer to it as “cluster U6.” Furthermore, a number of sequences clearly were incorrectly classified as parts of group 3A and group 3B in figure 6 and the appendix in the report by Coˆ rte-Real et al. (1996). Haplotypes 77 and 88 (table 3) were assigned to group 3A (defined by HVS I motif 16129–16223–16311 and, hence, equiva- lent to cluster I) but are, in fact, in cluster M, having undergone distinct mutations at positions 16129 and 16311. Similarly, haplotypes 25, 32, 44, 94, 100, and 102 (table 3) were assigned to group 3B (on the basis of the HVS I motif 16223–16278, which defines cluster X in Europe) but really belong to African clusters L2 and L3b. RFLP typing therefore has allowed us not only to resolve the phylogeny of the Berber cluster, but also to correct clusters that were conflated into paraphyletic clades because of a lack of phylogenetic resolution in the hypervariable CR. Cluster U6 is a sister cluster to several major and minor clusters in Europe and the Near East, including the most ancient cluster in the region, U5, which is specific to Europe and dates to »50,000 years ago (Richards et al. 1998). Cluster U also is represented in these data by clusters U3 and potential cluster U*. An advantage of the resolution of the U6 cluster is that an age estimate now can be made by use of the r statistic (Forster et al. 1996), although this is extremely provisional because the genealogy of U6 is far from star- like. For all sequences with motif 16172–16219 from the studies by Di Rienzo and Wilson (1991), Coˆ rte-Real et al. (1996), Pinto et al. (1996), and Watson et al. (1997), we estimated the time to the ancestral sequence by using a mutation rate of 1 in 20,180 years (Forster et al. 1996). The value of r for these data is 2.53, which converts to an age of 51,000 years, with a central 95% credible region of 42,500–60,500 years. Since this cred- ible region was derived under the assumption of a star- like genealogy, its width surely is underestimated. Nevertheless, it is suggestive that the age estimate is similar to that of U5, the oldest European-specific cluster, and congruent with archaeological dates for the arrival of anatomically modern humans with Upper Paleolithic (Dabban) industry in Cyrenaı¨ca, which is believed to predate 40,000 years ago (Close and Wendorf 1990). This suggests a model in which U5 and U6 diverged from a common ancestor (the Cambridge reference sequence [CRS]) in the Near East (where traces remain of U6; Di Rienzo and Wilson 1991; authors’ unpublished data) »50,000 years ago and spread along the north and south coasts, respectively, of the Mediterranean, as far as Iberia to the north and Cyrenaı¨ca to the south, »45,000– 50,000 years ago. This model is in accordance with the physical-anthropological view that the aboriginal “Mekta-Afalou” North Africans were closely related to the Cro-Magnon settlers of early Upper Paleolithic Eu- rope (Brett and Fentress 1996). The appearance of the Iberomaurusian industry in the Mahgreb may have been the result of a further pulse of westward expansion at least 22,000 years ago (Close and Wendorf 1990), and population replacement with the arrival of the Epi-Pa- leolithic Capsian industry, »9,000 years ago, seems un- likely (Brett and Fentress 1996). A greater number of founder lineages arriving in the first wave of settlement from the Near East would reduce the estimate for the time of settlement, but, at present, there is insufficient evidence for multiple founders, especially given the his- torical record of interaction (and, therefore, possible gene flow) between North Africa and the Near East. However, because of concordance between the genetic and archaeological dates, the early date proposed here is attractive. Cluster U6 comprises approximately one-third (24/ 85) of the Mozabite Berber sample. Two individuals formerly characterized as U6, on the basis of the 16172–16189 motif (Coˆ rte-Real et al. 1996), now can be regarded as a separate part of cluster U, since they lack the 16219 transition; two more individuals, un- classified in the RFLP analysis but clearly non-U, fall into an African subcluster of L3a*, on the basis of the CR-sequence motif 16223–16320 (Coˆ rte-Real et al. 1996), in which not only positions 16172 and 16189 but also position 16278 undergo recurrent mutation with respect to the U6 motif, rendering 16219 the only reasonably stable marker for U6. This highlights the dif- ficulties that may arise when the rapidly evolving HVS I sequences are used to trace the ancestry of deeply di- verged lineages, in the absence of additional character information. In contrast with the Mozabites, U6 comprises 3 (17%) of 18 Moroccan Berbers and 8 (15%) of 54 Canary Islanders (Pinto et al. 1996). Given the low frequency of U6 in Iberia, this observation indicates that a large proportion of modern Canary Islander mtDNAs mayhave been derived from the Guanches, the autochtho- nous Berber-related population of the islands, which dis- appeared following the Spanish conquest. The remaining Mozabite sequences are typical of ei- ther Europe and the Near East (Richards et al. 1998) or sub-Saharan Africa (Watson et al. 1997). The largestcluster of the remaining sequences from the Mzab is cluster H, which is the most frequent cluster in Europe and also is common in the Near East (Torroni et al. 1998), but, unlike those of Europe and the Near East, this cluster is manifestly not starlike in the Mzab, with just three predominant sequence types, suggesting recentfounder events and/or the action of drift. While two of these sequence types (the CRS and 16311) occur in both Europe and the Near East, one (16213) has been found only in Europe, possibly suggesting a European origin for the H sequences in this population. The cluster de- rived from the 16213 sequence is only »10,000 years old in Europe, suggesting that the H sequences may have arrived in North Africa within that time, during the Ne- olithic period or more recently. A European origin for many of the Berber sequences is also indicated by the presence of cluster V (Torroni et al. 1998). Another com- mon haplotype, 16148–16343, belongs to an additional subcluster of U (U3, see above) and may have been in- troduced from either Europe or the Near East. Likewise, the 16172–16189–16234–16311 sequence belongs to U, but it may be unrelated to U6 (since 16172 is a hyper- variable position) and does not have obvious relatives elsewhere. The cluster T sequence may have been intro- duced from either Europe or the Near East, but the de- rived J sequence (16069–16126–16147) perhaps is more likely to have arrived from the Near East, since the 16147 variant so far has been seen previously only in Turkey (Calafell et al. 1996). Among the 85 Mozabite subjects, there also are five L2 and four L3b sequences—identified on the basis of their HVS I motifs—indicating gene flow from sub-Sa- haran Africa, and two L3a* sequences, also of sub-Saharan origin (Coˆ rte-Real et al. 1996), indicating a total sub-Saharan component in the Mzab of 14%. This over- all picture of high European and little sub-Saharan Af- rican input also is reflected in Moroccan and Canary Islander samples (Pinto et al. 1996; J. C. Rando, F. Pinto, A. M. Gonza´ lez, M. Herna´ ndez, J. M. Larruga, V. M. Cabrera, and H.-J. Bandelt, personal communication). In summary, one-third of Mozabite Berber mtDNAs have a Near Eastern ancestry, probably having arrived in North Africa »50,000 years ago, and one-eighth have an origin in sub-Saharan Africa. Europe appears to be the source of many of the remaining sequences, with the rest having arisen either in Europe or in the Near East. Since, in Europe, cluster J appears to have accompanied the Neolithic from the Near East (Richards et al. 1996, 1997, 1998), the J sequences in the Berbers possibly may represent a North African route for the spread of the Neolithic from the Near East. With these exceptions, it is entirely feasible that all the European and Near East- ern sequences present in the northern Berbers arrived from Europe within the last 10,000 years. Iberia and the Mediterranean islands, in particular Bronze Age Sicily and Malta, clearly are implicated in this process (Brett and Fentress 1996). However, since the Nile Valley may have played an important role, particularly in the spread of the Berber language (Brett and Fentress 1996), data from this region will also be necessary before a clear picture can emerge.
posted
Points I have noted before, and shall do so here again:
The immediate ancestral clade to the U6 clade has not been identified...at least, when I last checked.
U6 is not a sub-clade of any well-defined preexisting "Eurasian" clade! So, calling it "Eurasian" has to be more of an emotional affair than science.
The more basal U6 clades are primarily found in western Africa, although a few may have made it to the so-called "Near East" but not in Europe (save for the Iberian peninsula--right next to the westernmost Maghreb; also note: "U6b is more frequent in the North whilst U6a is prevalent in the South"), which is essentially neighboring the former, while the more downstream variants are mainly found in eastern Africa, Europe and the so-called "Near East".
There are indications that the initial dispersal of U6 may have coincided with that of M1, prior (likely sometime just before the LGM) to another major one likely involving ancestors of "Afro-Asiatic" speakers.
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^ LOL Emotional affair indeed. We all know the lyinass is an agent of Mathilda and therefore has nothing but emotion invested in 'Eurasianizing' (white-washing) North Africa. She can't do with via the archaeological evidence, skeletal evidence, and not even paternal genetic lineages, so her only 'bastion of hope' is maternal genetic lineages, but even that is shaky at best. By the way, I am starting to agree with you about the African provenance of basal U6 as they seem to correlate with archaeological evidence i.e. no Eurasian but all African.
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posted
This is one of the very best I have seen. I wish some one will do a similar study for hg-H between populations Africa, Europe and South West Asia.
This thorough and well designed study. As the author states. M1 and U6 is clearly African. When Henn spoke about confirming through genetic sequences, this is what she was talking about.
Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa (2012)by Erwan Pennarun1*, Toomas Kivisild1,2)
Quote from the study
U6 and M1 both share the feature of being African-specific subclades of haplogroups otherwise spread only in non- African populations. Indeed, whilst most U clades are found in North Africa and in Eurasia, as far as the Ganges Basin, U6 is virtually restricted to North (West) Africa. For macro-haplogroup M, this African connection is even more puzzling, as haplogroups belonging to
M are mostly found only in South, Central and East Asia, the Americas and Oceania, where no M1 has yet been reported.
The Aterian, a regional variant of the Middle Palaeolithic (or Middle Stone Age), was previously thought to have existed ~40,000–20,000 years ago (KYA), and argued to mark the earliest modern humans in North Africa. These dates have been drastically reassessed and the upper bound is now closer to ~115 KYA [17] or even as old as ~145 KYA
Dating of the U6 and M1 variation in African and Middle Eastern populations has been at the centre of the debate on the timing of the back-migration to Africa and, in particular, whether these haplogroups co-dispersed with certain archaeological cultures or languages.
Basin: both are particularly prevalent in the southern Mediterranean and M1 reaches as far away as East Africa (Figures 1a and b). Yet, some of their peak frequencies only partially overlap in Northwest Africa. In contrast to high frequencies of M1 sub-clades, haplogroup U6 is rare in East/Northeast Africa and the Middle East, and is virtually absent in the Caucasus (Table 1).
It is noteworthy to point out that all the Caucasian samples fall into just one sub-clade, M1a1b2, with no variation present at the intermediate level of resolution (Additional file 3), signature of a likely founder effect.
A Southwest Asian origin has been proposed for U6 and M1 [27-29]. Yet, this claim remains speculative unless some novel “earlier” Southwest Asian-specific clades, distinct from the known haplogroups, are found in which the described so far M1 and U6 lineages are nested.
Assuming that M1 and U6 were introduced to Africa by a dispersal event from Asia, it would be difficult to accept their involvement in the first demographic spread of anatomically modern humans around 40–45 KYA, as suggested by Olivieri et al. (2006), [29] who associated these two clades with the spread of Dabban industry in Africa. *****AS SUGGESTD BY BRENNA HENN.!!!!!!*****
However, comparison of early Upper Palaeolithic artefacts from Haua Fteah and Ksar Akil does not support the notion that the early Dabban of Cyrenaica is an evidence of a population migration from the Levant into North Africa [43
A mimicry between U6 and M1 has been suggested [28,29]. Both are likely derived from a non-African ancestral clade at a similar time depth and both are largely confined to North and East Africa and the Middle East in their present-day geographic distribution. It seems, however, that the mimicry breaks down when analysing in further detail the coalescent times and frequency patterns of their sub-clades. Even at the general level, U6 is hardly found outside Northwest Africa, whilst M1 is ubiquitous throughout North Africa, East Africa and the Middle East, reaching also northern Caucasus. The coalescent age for U6a is almost 10 000 years older than that for either M1a or M1b, and most of its sub-clades coalesce before or around the LGM.
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
@Trollers & clowners Please no report spam. Make posts directly about the subject matter without a lot of extraneous peripherals:
U6 . age . provenance . associated phenotype(s)
Eurasia vs Afroasia at U6 divergence time . flora . fauna . climate
@ Everybody else Please expand and be specific about your points. Try to include some reports, data, etc., that informs your views. Hi-liting the essentials of posted report abstracts or snippets of main text is very helpful as is including the date which is a must for comparing professional views over time. Even old reports can be valueable especially when they have guesses that may not have been followed up or were followed up and disputed.
Most relevant is a multidiscipline approach with posts on the archaeology, cultural anthropology, etc. though language is mostly too late for U6 origins being tens of thousands of years before our language families.
Thanks and I hope some of the info recently posted in other threads finds its way here for sane pro, con, and neutral comment.
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Published online 2003 October 16. doi: 10.1186/1471-2156-4-15 PMCID: PMC270091 Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography
Nicole Maca-Meyer,1 Ana M González,1 José Pestano,2 C
Abstract Background
World-wide phylogeographic distribution of human complete mitochondrial DNA sequences suggested a West Asian origin for the autochthonous North African lineage U6. We report here a more detailed analysis of this lineage, unraveling successive expansions that affected not only Africa but neighboring regions such as the Near East, the Iberian Peninsula and the Canary Islands.
Results
Divergence times, geographic origin and expansions of the U6 mitochondrial DNA clade, have been deduced from the analysis of 14 complete U6 sequences, and 56 different haplotypes, characterized by hypervariable segment sequences and RFLPs.
Conclusions
The most probable origin of the proto-U6 lineage was the Near East. Around 30,000 years ago it spread to North Africa where it represents a signature of regional continuity. Subgroup U6a reflects the first African expansion from the Maghrib returning to the east in Paleolithic times. Derivative clade U6a1 signals a posterior movement from East Africa back to the Maghrib and the Near East. This migration coincides with the probable Afroasiatic linguistic expansion. U6b and U6c clades, restricted to West Africa, had more localized expansions. U6b probably reached the Iberian Peninsula during the Capsian diffusion in North Africa. Two autochthonous derivatives of these clades (U6b1 and U6c1) indicate the arrival of North African settlers to the Canarian Archipelago in prehistoric times, most probably due to the Saharan desiccation. The absence of these Canarian lineages nowadays in Africa suggests important demographic movements in the western area of this Continent.
Go to: Background Attested presence of Caucasian people in Northern Africa goes up to Paleolithic times. From the archaeological record it has been proposed that, as early as 45,000 years ago (ya), anatomically modern humans, most probably expanded the Aterian stone industry from the Maghrib into most of the Sahara [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control1]. More evolved skeletal remains indicate that 20,000 years later the Iberomaurusian makers, replaced the Aterian culture in the coastal Maghrib. Several hypothesis have been forwarded concerning the Iberomaurusian origin. They can be resumed in those which propose an arrival, from the East, either from the Near East or Eastern Africa, and those which point to west Mediterranean Europe, either from the Iberian Peninsula, across the Gibraltar Strait, or from Italy, via Sicily, as their most probable homeland [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control2]. Between 10,000 and 6,000 ya the Neolithic Capsian industry flourished farther inland. The historic penetration in the area of classical Mediterranean cultures, ending with the Islamic domination, supposed a strong cultural influx. However, it seems that the demic impact was not strong enough to modify the prehistoric genetic pool.
Linguistic research suggests that the Afroasiatic phylum of languages could have originated and extended with these Caucasians, either from the Near East or Eastern Africa and that posterior developments of the Capsian Neolithic in the Maghrib might be related to the origin and dispersal of proto-Berber speaking people into the area [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control3]. Nowadays, the Berber speakers, scattered throughout Northwest Africa from the Atlantic to the Lybic desert and from the Mediterranean shores to the south of the Sahel, are considered the genuine descendants of those prehistoric colonizers. Some important issues are pending of resolution to clarify the past and present of the North African Caucasians: To which extent the Neolithic waves substituted the Paleolithic recipients? Which is the most probable origin of these prehistoric occupants? Did they come from Europe, East Africa, Southwest Asia or are they a result of an "in situ" evolution? Is there a correspondence between the Afroasiatic diversification and the spread of Caucasians?
Recently, molecular genetic research on North African populations has contributed new data to test the major issues proposed on archaeological, anthropological and linguistic grounds. The studies based on uniparental genetic markers have been particularly informative. Both, mitochondrial DNA (mtDNA) sequences [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control4,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control5], and Y-chromosome binary markers [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control6,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control7] detected specific North African haplotypes that confirm an ancient human colonization for this area and a sharp discontinuity between Northwest Africa and the Iberian Peninsula. From a mtDNA point of view, the most informative of these genetic markers is the North African clade U6. On the basis of complete mtDNA sequences, it has been proposed that U6 lineages, mainly found in North Africa, are the signatures of a return to Africa around 39,000–52,000 ya [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control8]. This stresses the importance of its detailed study in order to trace one of the earliest Caucasian arrivals to Africa. Although in moderate frequencies, the geographic range of this clade extends from the Near East to the Canary Islands, along the Atlantic shores of Northwest Africa and from the Sahel belt, including Ethiopia, to the southern Mediterranean rim. Out of this area, U6 has only been spotted in the Iberian Peninsula [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control9-The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control12], Sicily [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control13], in the north European Ashkenazic Jews [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control14], and in Ibero-America. The presence in the latter is, most probably, the result of the Spanish and Portuguese colonization [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control15,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control16].
In order to construct an unambiguous phylogeny for this clade and infer precise ages for the whole group and for its derivatives, we have fully sequenced eleven mitochondrial lineages representing the main branches of U6. Subsequently, we analyzed the geographic distribution range and relative diversity of these subclades, to deduce their most probable expansion origins based on sequence information of the first hypervariable segment (HVSI) of the mitochondrial control region and on new RFLPs, discovered to be diagnostic for them.
Go to: Results A new sublineage for U6
Haplogroup U splits from R by mutations 11467, 12308 and 12372. Three branches sprout from this root: U5 (3197, 9477, 13617 and 16270), U6 (3348 and 16172) and the rest of the U clade defined by mutation 1811 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control8,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control17,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control18]. For this reason, a representative of U5 was chosen as an outgroup.
The phylogenetic tree based on complete mtDNA U6 sequences, confirms that this clade is defined by mutations 3348 and 16172 (Fig. (Fig.1).1). The former can be detected by RFLP analysis using MboI [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control15]. The existence of three subgroups is also evident. U6a was defined by the presence of HVSI mutations 16172, 16219 and 16278 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control4] and now by 7805 and 14179 in the coding region, that can be tested by RFLPs -7802 MaeI and +14179 AccI, respectively. Subgroup U6b was characterized by HVSI mutations 16172, 16219 and 16311 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control4], to which mutation 9438 (detectable by RFLP -9438 HaeIII) can now be added. The new clade U6c is defined by HVSI mutations 16169, 16172 and 16189 and at least by mutations 4965 and 5081, that can be tested by RFLPs +4963 Aci I and -5079 Tsp509 I, respectively. In addition, a subgroup, U6a1, has been detected within U6a characterized by the addition of HVSI mutation 16189 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control4]. In the same way, HVSI mutation 16163 classifies subgroup U6b1, autochthonous of the Canary Islands [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control19]. Within the coding region, this subgroup can be further defined by RFLP + 2349 MboI.
From Fig. Fig.1,1, an important question rises about the constant mutation rate in the coding region. The mean number of substitutions accumulated in U6b lineages (Table (Table1)1) is significantly smaller than those in U6a (P = 0.013) and is near significance in U6c (P = 0.058). These differences are mainly due to the number of mutations accumulated in the coding region. Following others [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control20], we used the likelihood-ratio test [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control21] to asses whether the mutations accumulated on the different branches were compatible or not with a uniform rate. The difference between the values obtained for the uniform clock model (L0 = -23060.25) and for the variable rate model (L1 = -23032.22), was statistically significant at the 5% level. So, the simpler clock-like tree was rejected. On the other hand, the substitution ratio between coding vs. HVSI region is double in U6a than in U6b or U6c (Table (Table1).1). Furthermore, taking into account the ratio of synonymous vs. non-synonymous substitutions in the coding region, again the U6a value doubles that of U6b or U6c, reaching a significant level (P = 0.0237, in a two-tailed Fisher exact test). Both selection and stochastic processes have to be invoked to satisfactorily explain these data. A bias in lineage sampling is the most probable cause of the different substitution ratios between D-loop and coding regions: the U6b and U6c lineages were chosen for their different geographic origin and, comparatively, large divergence in HVSI, whilst for U6a we chose central representatives of the different subclusters excepting that of the Canary Islands. In relation to the differences in synonymous vs. non-synonymous ratios, they could be attributed to the action of purifying selection, having a stronger effect on the older U6a lineages. From this, we deduced that both U6b and U6c spread more recently. Finally, the apparent differences in substitution rates between U6b and U6a or U6c could better be the result of genetic drift, so that the founder lineage that originated the U6b subgroup was less evolved than those that originated U6a and U6c. However, we have to point out that in a similar case, in which significant differences were found in the number of mutations accumulated on two clades of haplogroup L2, selection was suggested as the most probable cause
Geographic distribution of U6 lineages
Fig. Fig.22 shows the reduced median network obtained from the 56 U6 haplotypes found for the HVSI region between positions 16086–16370. The basal motif for haplogroup U6 has varied as new data have been added. Algerian sequences [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control9] suggested that the ancestral sequence harbored mutations 16172 16189. Additional data [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control4] considered 16172 16219 as the most probable ancestral motif. However, the complete sequence of the individual with this motif relocates it in U6a, presenting a back mutation in HVSI position 16278. Our data points to 16172 as the only substitution present in the basal motif. Unfortunately, the high recurrence of this mutation makes it insufficient to diagnose this haplogroup. The highest frequencies for haplogroup U6 as a whole are found in Northwest Africa (Table (Table2),2), with a maximum of 29% in the Algerian Berbers [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control9]. Subgroup U6a and its derivative U6a1 present the widest geographic distribution, from the Canary Islands in the West, to Syria and Ethiopia in the East, and from the Iberian Peninsula in the North, to Kenya in the South. In contrast, U6b shows a more limited and patched distribution, restricted to western populations. In the Iberian Peninsula, U6b is more frequent in the North whilst U6a is prevalent in the South. In Africa, it has been sporadically found in Morocco and Algeria in the North, and Senegal and Nigeria in the South, pointing to a wider distribution in the past, or to gene flow from a geographic focus which has still not been sampled. Curiously, two Arab Bedouins [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control22] with the same haplotype (16111 16172 16219 16311 16362), are the only Eastern representatives classified as U6b. It would be very interesting to test the 9438 HaeIII restriction enzyme to confirm this classification. Furthermore, subgroup U6b1 characterized by mutation 16163, is restricted to the Canarian Archipelago and the Iberian Peninsula. The geographic distribution of the new subgroup U6c, characterized by the basic motif 16169 16172 16189, is even more localized. It has only been found in the Canary Islands and Morocco. It could also be present in Algeria, if the two individuals with haplotype 16172 16189 16234 16311 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control9], classified as U* by RFLP analysis [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control5], belong to this subgroup. Like for U6b, an autochthonous U6c subcluster (characterized by mutation 16129) was also detected in the Canarian Archipelago.
Relationships between areas
Linearized FST values distinguished three significantly differentiated geographical areas: Continental Africa, the Iberian Peninsula and the Canary Islands (Table (Table3).3). Nucleotide diversities within areas (Table (Table3)3) ranged from 3.253 in the Iberian Peninsula to 2.059 in East Africa. At first sight, it is striking that diversities are larger in the Canary Islands and Iberia than in Africa. We think that demographic processes are responsible of this situation. In Africa, the geographic and social isolation of the different Berber groups [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control23], could have promoted a loss of diversity by genetic drift. On the contrary, the presence in the Canary Islands and Iberia of representatives of all, or nearly all, U6 subclades, some of them not detected nowadays in the Continent, strongly point to the existence of several migratory waves from Africa, possibly at different times, which have increased their variability. This explanation is reinforced when the number of segregating sites (S) are taken into account. This value is larger in West Africa (5.10 ± 1.5) than in the Canaries (2.60 ± 1.0) and the Iberian Peninsula (3.90 ± 1.4), but East Africa presents a lower value (3.2 ± 1.4). The fact that U6b and U6c have a restricted western distribution undoubtedly contributes to this Continental difference. However, the younger U6a1 branch contradicts this general trend. For this subclade, East and West Africa are statistically differentiated (P = 0.016), and the former presents a higher nucleotide diversity (1.55 ± 1.11) than the latter (0.98 ± 0.75). Geographic distributions and diversity values of U6 are congruent with a western origin and radiation for all subclades excepting U6a1 that, most probably, had an eastern origin.
Radiation ages
Radiation ages for U6 and its subclades have been estimated on the basis of complete coding and HVSI sequences (Table (Table4).4). In general, ages obtained from HVSI are larger than those deduced from the coding region. Both approaches present inconveniences for the time estimates. It has been demonstrated that the coding region has evolved at a roughly constant rate [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control24]. However, as relatively few clades are fully sequenced, stochastic and/or intentional sampling may bias the representation of the chosen lineages. On the other hand, HVSI estimations are based on a large number of individuals minimizing sampling errors. However, we deal with a short sequence that has not evolved at a constant rate across all human lineages [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control24]. Furthermore, from the phylogeny of complete U6 sequences (Fig. (Fig.1),1), it has been deduced, once more, that empirical time estimations are not independent of the demographic history of the population sampled. Therefore, we have taken coalescence ages only as rough time frames into which lineage expansions could have occurred. Adopting a conservative position we have used ages based on the coding region whenever possible.
Discussion {b]African U6 origin and expansions
Discarding the Canary Islands, because the most ancient human settlement seems to be no earlier than 2,500 ya [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control25], and the Iberian Peninsula, because there are no consistent traces of U6 lineages in Europe, Northwest Africa is left as the most probable place from where the African U6 subclades radiated. Another point is to decide whether the proto-U6 ancestor was also of African origin. Although it cannot be completely excluded, this hypothesis seems highly improbable even invoking strong bottlenecks in African populations. It is clear that the whole haplogroup U is an offshoot of macrohaplogroup N. [/b]This lineage, together with macrohaplogroup M, were the only ones that, belonging to the star radiation of L3 in Africa, left this continent to colonize Eurasia. Five mutations separate N from the root of the African L3 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control8], and there are only late evolved N lineages in Africa, whereas representatives of the full N radiation are present in Eurasia. Thus, this continent would be the logical homeland of the proto-U6 that came back to Africa and spread in its northwest area around 30,000 ya (Table (Table4).4). Its most probable route had to be through East Africa. So, the loss of variability in this area is puzzling, although posterior demic expansions affecting East Africa might be the cause. This date roughly corresponds to the Paleolithic occupation of the Maghrib by the Iberomaurusian culture and to the age of the evolved Homo sapiens sapiens skeletons found in this area. Only one of the three U6 subclades, U6a, experienced a great geographic radiation spreading west to the Atlantic shores and east, crossing Africa, to the Near East. A posterior offshoot of this clade, U6a1, has a similar distribution. The upper bound for these expansions are around 28,000 and 17,000 ya, respectively (Table (Table4).4). Genetic diversities are congruent with a west to east expansion for U6a and a more probable east to west expansion for U6a1. Furthermore, the absence of U6b and U6c lineages in the East suggests that the population from which the U6a colonizers originated also lacked these lineages or presented them in very low frequencies. The fact that 5 of the 8 U6a haplotypes detected in the Near East are unique of this area (Fig. (Fig.2),2), points to prehistoric demic movements as the most probable cause of the U6a Africa to Asia migration, although historic events cannot be completely ruled out. In frame with the estimated age of U6a are archaeological data supporting early migrations from Africa into the Near East [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control26]. The expansion of Caucasians in Africa has been correlated with the spread and diversification of Afroasiatic languages. There are different hypothesis to explain the Afroasiatic origin. For some, it would be the result of a Neolithic demic diffusion from the Near East to Africa [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control27,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control28]. For others, the Afroasiatic originated in Africa and had a posterior demic spread to West Asia [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control29,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control30]. A third possibility is that Afroasiatic languages spread mostly through cultural contacts either from Africa or from Asia [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control31]. Only demic diffusions could be correlated with U6 expansions detected here. Since an upper bound of 15,000 ya has been estimated for the proto-Afroasiatic origin, it seems that the coalescence age for U6a predates by far the origin of the Afroasiatic phylum. However, the recent spread of U6a1 is more in frame with the emergence of a proto-Afroasiatic language. This U6a1 expansion would favor an East African origin for the Afroasiatic and a posterior expansion to West Africa and West Asia. However, a Near Eastern origin, most probably predating the Neolithic expansion, cannot be ruled out.
Iberian U6 origin and expansions
In Europe, U6 lineages have been consistently sampled only in the Iberian Peninsula. It has been mentioned that U6 nucleotide diversity is higher in Iberia than in Africa [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control12]. This has been confirmed here (Table (Table3).3). However, S is greater in West Africa. Considering the isolation of the different Berber groups we think that, in this case, the latter is a better diversity measure. The absence of U6 representatives in the rest of Europe, is also an argument against the hypothesis that these lineages could have migrated to North Africa from Europe. Naturally, this does not exclude that other mitochondrial lineages could have followed this route. Most probably, the presence of these African lineages in Iberia is the result of northward expansions from Africa. The time of this expansion has been predominantly attributed to either the Arab/Berber occupation that lasted seven centuries [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control10] or to prehistoric immigrations of North Africans to Iberia [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control12]. Both processes could have contributed to model the U6 landscape in Iberia. First, haplotype matches show that 10 of the 19 U6 lineages detected in Iberia are not present in Africa (Fig. (Fig.2),2), which points against only one recent immigration. Second, the geographic distribution of the U6 lineages in Iberia is puzzling. Whereas the U6b lineages, nowadays very scarce in Africa, are mainly detected in the Northwest, the U6 lineages found in highest frequencies in Africa are predominant in the south, where the Islamic rule lasted longer. At the light of these results we propose that U6b in Iberia is the signal of a prehistoric North African immigration that could have also brought some U6a lineages. Its actual northern range could be the result of a forced retreat due to the arrival of new southern incomers to Iberia. However, the U6a distribution is better explained as the result of more recent gene flow from North Africa. The age of U6b (approx. 10,000 ya) might be considered as an upper bound for the prehistoric wave. Curiously, around this time the Iberomaurusians began to be displaced by the incoming Capsian culture in the Maghrib. On archaeological grounds, it has been proposed that Iberomaurusians slowly retreated towards the Atlantic coast from where they sailed to the Canary Islands and southwards to the Malinese Sahara [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control2]. Coincidentally, these are the same places where the U6b lineages have been spotted (Fig. (Fig.22).
Canary Islands U6 origin and expansions
At a genetic level, the Berber origin of the Guanches, the aboriginal population of the Canary Islands, and their survival after the Spanish occupation, has been inferred from the high frequency of U6 lineages in its modern population (Table (Table2),2), similar to that of North Africa [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control19,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control32]. This fact has been recently confirmed in a mtDNA sequence study on aboriginal remains [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control33]. It was found that in the Guanche maternal gene pool, U6b1 and U6a were present at frequencies of 8.22% and 1.37%, respectively. U6c was probably also present in the aboriginal pool as a haplotype (16129 16169 16172 16189), now known to belong to subhaplogroup U6c, was proposed as a probable Canarian founder type [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control19]. As in Northwest Iberia, U6b was the dominant U6 subclade carried by the North African settlers of the islands. All three subclades are present in the modern Canarian population at frequencies of 1.3%, 13.0% and 3.3% for U6a, U6b and U6c, respectively, which is indicative of a broad aboriginal component in the present maternal pool. Perhaps, the comparatively higher frequency of U6a lineages might be attributed to an additional Berber input as result of the slave trade after the Spanish conquest [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control34,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control35]. What remains enigmatic of the indubitable North African prehistoric colonization of the Archipelago is that it was carried out by people whose U6 lineages mainly belonged to the U6b subclade that has only been spotted in very low frequencies in the modern African populations of Morocco, Algeria, Senegal and Nigeria (Table (Table2).2). Moreover, the U6b and U6c insular haplotypes belong to the autochthonous U6b1 and U6c1 branches differing by substitutions 16163 and 16129, respectively, from all their African counterparts. As the most probable arrival of the first prehistoric Canarian settlers was around 2,500 ya, it is highly improbable that these mutations occurred on the islands. Therefore, we expected to find these Canarian lineages in some place of Africa. However, after extensive sampling they have still not been detected. It is possible that they are present somewhere in low frequencies but, in any case, this phylogeographic distribution suggests that Northwest Africa suffered important demic displacements in the past.
Besides U6, other genetic markers such as 110(-) haplotype of the CD4/Alu system [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control36], and the M81 Y-chromosome binary marker [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control6,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control7], point to an ancient and autochthonous human presence in Northwest Africa. An eastward decline in M81 frequencies has been detected, regrettably the lack of extensive intra-M81 microsatellite diversity studies in Africa precludes phylogeographic comparisons as those done with mtDNA. There are other coincidences between mtDNA data and other systems. For instance, using classical genetic markers, it was found that the Iberian Peninsula showed smaller genetic distances with East Africa than with West Africa [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control37]. The same pattern was observed for Y-chromosome studies [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control7], both in line with our results (Table (Table3).3). More studies with other genetic markers are necessary to corroborate, complement or even contradict the proposed U6 landscape.
In summary, the phylogeography, nucleotide diversity, and coalescence ages of U6 lineages show that this clade came back to Africa in Paleolithic times. Its most probable origin was the Near East and not Europe, and since then, its presence in North Africa has been permanent. The focus of the first African expansion, detected by the spread of U6a, was Northwest Africa reaching the Near East also in the Paleolithic. The posterior U6a1 radiation most probably occurred in Northeast Africa again extending to the Near East. This movement is correlated in time with the attributed origin and expansion of Afroasiatic languages. This U6a1 wave also arrived to the Maghrib, the Northwest African margin, where the more localized U6b and U6c lineages were spreading. This movement is in time frame with the Capsian culture. Based on archaeological and anthropological grounds, it has been speculated that these incomers slowly pushed away the aboriginal residents [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control2]. It could be in that time when U6b reached the south of the Iberian Peninsula from where it was displaced to the north where it persists today. The U6b and U6c diaspora also reached the Atlantic fringe from where they sailed to the Canary Islands. Two autochthonous U6 lineages (U6b1 and U6c1), present today in the islands, attest the survival of those aboriginal North Africans until nowadays. The fact that these Canarian lineages have not been detected in Africa and that, in contrast to the ubiquitous U6a and U6a1, the U6b and U6c lineages are scarcely spotted in present African populations, may be clues of past important demographic movements in this western area
Methods Complete mtDNA lineages
We have fully sequenced eleven mitochondrial lineages belonging to different subclades of the North African subhaplogroup U6. DNA extraction, amplification and manual sequencing methods have already been described [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control8].
HVSI and RFLPs
A sample of 332 Andalusians, 1 Algerian Berber, 89 Moroccan Berbers, 23 individuals from Cape Verde, 96 from Madeira, 34 Mauritanians, 24 Moroccans and 12 Saharans were sequenced for the HVSI region from 16000 to 16390, and RFLP characterized as detailed [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control11,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control12]. In order to distinguish putative U6 members, all these subjects and the U individuals from a sample of 1059 previously published [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control4,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control11,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control12,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control19,The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control38], were amplified with primers L3073/H3670 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control8], and tested for the presence of the 3348 MboI site [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control15], that characterizes all U6 members.
Phylogenetic analyses
Phylogenetic relationships among complete mtDNA sequences were established using the reduced median network algorithm [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control39]. In addition to our eleven sequences, four lineages were added: U6 and U5b [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control8] (Accession numbers: AF382008 and AF381980, respectively) and for the coding region, H84 and H229 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control18].
U6 phylogeographic analyses
In addition to our 611 samples, 41 populations where U6 haplotypes have been detected were included in our phylogeographic analysis (Table (Table2).2). Relationships among the different U6 haplotypes were inferred using the reduced median network algorithm [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control39]. To resolve reticulations, the highly recurrent mutations 16129, 16189, 16311 and 16362 were less weighted.
Differences in accumulated mutations among U6 branches
The non-parametric test, resampling probability estimates for the difference between the means of two independent samples (http://faculty.vassar.edu/lowry/VassarStats.html), was used to calculate the significance level of accumulated mutations between the different U6 subclades. The likelihood-ratio test, as implemented in TREE-PUZZLE [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control21], was used to check between a uniform clock or variable site model in the U6 tree.
U6 diversity and differentiation within and between areas
Arlequin package [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control40] was used to evaluate the U6 diversity within areas using nucleotide diversity (π) and segregating sites (S). Affinities between areas were obtained by means of linearized FST [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control41].
Time estimates
For HVSI, the age of clusters or expansions was calculated as the mean divergence ρ from inferred ancestral sequence types [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control42] and converted into time by assuming that one transition within np 16090–16365 corresponds to 20,180 years [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control43]. The standard deviation of the ρ estimator was calculated as previously described [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control44].
For the complete sequences only substitutions in the coding region (15,447 nucleotides), excluding indels, were taken into account. The mean number of substitutions per site to the most recent common ancestor of each clade (ρ) was estimated, and converted into time using two substitution rates: 1.7 × 10-8 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control24] and 1.26 × 10-8 [The following popper user interface control may not be accessible. Tab to the next button to revert the control to an accessible version.Destroy user interface control45].
posted
For those who missed the point. What Kivisild is stating is the laws of Physics cannot be broken. It is still impossible to be two places at the same time. Huh?
He is stating that Henn’s title assertion and Oliveria’s and Cruciani’s theory of “back-migration” is nonsense. Indigenous Africans were firmly established in North West Africa(35kya - age of U6) when at the same time they were suppose to be “back-migrating” across the Arabia into North Africa. Added to that AMH has just set foot off the continent into Arabia. Also keep in mind AMH was also “IN” NW Africa (Aterian) 140,000ya!!! Long before humans entered Arabia.
Also as the study states U6a and U6b are clearly siblings attested to their location on the North West tip of Africa. In other words where you find one you find the other. This is characteristically found with siblings where their center of mutation and dispersion is NW Africa.
BTW: The same pattern is seen with E1b1a and E1b1b. Whch led many to speculate that the dreaded E1b1a/E1bib is actually East African or maybe Central North African lineages.
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And as far as phenotype goes…we don’t really know. Let me make a guess.
Two eyes, two ears Large teeth Brown/Black Skin Curly/straight hair Aquiline nose Prognathic Black skin Long face Full lips Hairless or reduced body hair Gracile like most Africans
The Roman Egyptians, Garamantes and Sub-Saharan Africans (Neolithic period) have a similar phenotype. We don’t know what the first two look like but we have an idea of the Roman Egyptians. Or do we?
Are they saying Fayum type peoples were inhabited sub-saharan Africa during the Neolithic times.
I am thinking of this…
Are Caucasoid from Sub-Saharan Africa?
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From Academia.edu – On the Garamantes of the Fezzan Libya Page 401 to 406
Quote:
The North African populations used for the assessment of the Garamantian biological affinities were all approximately contemporary to the Garamantes. The only exception is the Sub-Saharan samples, which are Neolithic, thus, predating the Garamantian civilization, although no further specification of their date is available. A list of the populations used
From Figure 7.22, it can be seen that the Garamantes cluster most closely to the SubSaharan Africans and secondarily to the Roman Egyptians from Alexandria and the Nubians from Soleb. Populations from Algeria and Tunisia are somewhat more distant but still rather close to the Garamantes. The most distant groups appear to be the Sudanese Jebel Moya and Kerma, as well as those from Gizeh.
Finally, as far as the biological affinities of the Garamantes are concerned, they appear to cluster most closely to the Sub-Saharan Africans and the Roman Egyptians and secondarily to populations from Algeria and Tunisia. Althougb Nubians from Soleb seemed to be close to the Garamaotes on the cladogram, their statistical di fference as well as the di stance between the Garamantes and the other Sudanese groups was significant. Because of the relatively small size of the sample, more detailed
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
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quote:Originally posted by xyyman: [QB] For those who missed the point. What Kivisild is stating is the laws of Physics cannot be broken. It is still impossible to be two places at the same time. Huh?
He is stating that Henn’s title assertion and Oliveria’s and Cruciani’s theory of “back-migration” is nonsense. Indigenous Africans were firmly established in North West Africa(35kya - age of U6) when at the same time they were suppose to be “back-migrating” across the Arabia into North Africa.
back migration is said by Henn to have occured 12kya
major climactic change, the drying of the Sahara occured inside that time to the present
there are no fossil records of a population living in North Africa after the last green period NA hunter gatherer Capsian Culture which began 12,000 years ago and ended 8.000 years ago and the Sea People/Phoenicians who migrated from Eurasia to the Maghreb 3500-4000 years ago.
There's 4000 years of no fossil record in between these periods. The is no evidence of continuity between prehistoric Maghrebian populations and modern Maghrebian populations
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Mitochondrial Haplogroup H1 in North Africa: An Early Holocene Arrival from Iberia Claudio Ottoni equal contributor, Giuseppina Primativo equal contributor
Abstract
The Tuareg of the Fezzan region (Libya) are characterized by an extremely high frequency (61%) of haplogroup H1, a mitochondrial DNA (mtDNA) haplogroup that is common in all Western European populations. To define how and when H1 spread from Europe to North Africa up to the Central Sahara, in Fezzan, we investigated the complete mitochondrial genomes of eleven Libyan Tuareg belonging to H1. Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000–9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x, which appear to be specific for North African populations, but whose frequencies can be extremely different even in relatively close Tuareg villages. Overall, these findings support the scenario of an arrival of haplogroup H1 in North Africa from Iberia at the beginning of the Holocene, as a consequence of the improvement in climate conditions after the Younger Dryas cold snap, followed by in situ formation of local H1 sub-haplogroups. This process of autochthonous differentiation continues in the Libyan Tuareg who, probably due to isolation and recent founder events, are characterized by village-specific maternal mtDNA lineages.
Introduction
In the last few years the story of human migrations has been extensively reconstructed thanks to the contribution of archaeology and genetics, particularly the latter through the study of the two uniparentally transmitted genetic systems: mitochondrial DNA (mtDNA) and Y chromosome. The study of maternal genealogies appears to indicate that the peopling of the Eurasian continent by modern humans likely began around 60–70 thousand years ago (kya) through the ‘southern coastal route’ from the Horn of Africa via Arabia and South Asia, up to Australasia [1], [2], [3], [4], [5]. However, alternative exit scenarios, including a more northern route into the Levant and multiple waves of migration (see Kayser 2010 [6] and Majumder 2010 [7] for a review), have recently regained some momentum after the postulated detection of some Neanderthal nuclear DNA variation in the genomes of modern Eurasians [8]. The ‘southern coastal route’ scenario instead implies that, blocked by deserts, humans could not move from the Arabian Gulf area into the Levant earlier than 50 kya, when climate conditions improved [9]. Entrance into the Levant paved the way to the dispersal of modern humans both north-westward into Europe and south-westward into Northern Africa [10], [11]. During the Last Glacial Maximum (LGM), approximately between 26.5 and 19 kya [12] ice sheets largely covered large portions of North America and Europe. In warmer regions of the world, the climate was cooler and drier and deserts spread over large regions, particularly in Northern Africa, Middle East and Central Asia [13], [14]. Accordingly, during the LGM, humans concentrated in refugial areas of southwestern Europe, in the Balkans and Levant, and on the east European plains [9], [15], [16]. The subsequent Bølling warming, around 15 kya, triggered re-expansion processes which led to the resettlement of Central and Northern Europe. Genetic signatures of these expansions are evident in mtDNA genealogies, for instance haplogroups H1, H3 and V contributed to the gradual re-peopling of Europe from the Franco-Cantabrian refuge in the postglacial [17], [18]. Similarly, though to a lesser extent, H5*(xH5a), H20 and H21 may be associated to a postglacial population expansion phase in the Caucasus area [19]. Although restricted to the Mediterranean coast, an expansion took place also from the Italian peninsula northward, as attested to by the haplogroup U5b3 [20].
Evidence of trans-Mediterranean contacts between Northern Africa and Western Europe has been assessed at the level of different genetic markers (e.g. [21], [22], [23], [24]). With regards to the mtDNA, the high incidence of H1 and H3 in Northwest Africa, together with some other West European lineages (i.e. V and U5b), reveals a possible link with the postglacial expansion from the Iberian Peninsula, which not only directed north-eastward into the European continent [17], [18], [25], but also southward, beyond the Strait of Gibraltar, into North Africa [26], [27]. So, besides the ‘autochthonous’ South-Saharan component, the maternal pool of Northern Africa appears to be characterized by at least two other major components: (i) a Levantine contribution (i.e. haplogroups U6 and M1, [11]), associated with the return to Africa around 45 kya, and (ii) a more recent West European input associated with the postglacial expansion.
Within the West-European component in North Africa, H1 is the most represented haplogroup with frequencies ranging from 21% in some Tunisian Berber groups to 1% in Egypt [28]. Recently, an extremely high incidence of H1 (61%) has been reported in a Tuareg population from the Central Sahara, in Libya [29]. Tuareg are a semi-nomadic pastoralist people of Northwest Africa, who speak a Berber language. MtDNA analyses performed on the Libyan Tuareg have highlighted their genetic relatedness with some Berber groups and other North African populations, mainly resulting from the sharing of a common West-Eurasian component. A high degree of homogeneity in the Libyan H1 lineages was observed, suggesting that the high frequency of H1 in the Tuareg may be the result of genetic drift and recent founder events.
To better define the nature and extent of H1 variation in the Tuareg from Libya we have now determined the complete sequence of eleven of their mtDNAs belonging to H1. The comparison of these H1 sequences with those already available from Europe and North Africa provides new clues on how and when H1 spread in Northern Africa up to the Central Sahara.
Results
The most parsimonious tree encompassing eleven complete H1 mtDNAs from the Tuareg together with four previously published sequences from Tunisia [35], one Berber from Egypt [17] and two Jewish Moroccans [36] is illustrated in Figure 1. All Tuareg sequences clustered into three clades that had not been previously reported and thus were termed H1v, H1w and H1x. Five sequences grouped into the sub-clade H1v1 defined by the transition at np 4313. One Tunisian sequence (# 8) did not cluster into H1v1 but was closely related, since it harbored the mutation at 10314 that defines the clade H1v (Figure 1). The sub-clade H1v1 splits into two branches defined by the transitions at np 9148 (clade H1v1a) and 14560 (clade H1v1b). Three Tuareg mtDNAs formed the novel clade H1w that is defined by the transition at np 8966, while the last three Tuareg mtDNAs, apart from the HVS-I transitions at 16037 and 16256, were found to harbor mutations at nps 7765 and 10410 in the coding region (clade H1x). The Tuareg complete mtDNAs have been deposited in GenBank, under the accession numbers reported in Table S1.
Divergence values (rho statistics and ML estimates) and the age in years of the most recent common ancestor of the main clusters are reported in Table 1, according to the evolutionary rate estimates described in Soares et al. [32] and Loogväli et al. [33]. The two evolutionary rates provide a coalescence time of about 8–9 kya for the whole H1 haplogroup in North Africa. As expected, the North African-specific clades are characterized by younger ages ranging from about 3.8 to 6.7 kya for H1v, and from 2.1 to 7.9 kya for H1v1. The youngest clades were found to be H1w and H1x, with an age of about 0.8–1.1 kya. The survey of diagnostic markers 4313, 8966, 9148 and 14560 in 50 individuals characterized by the CRS-263 haplotype showed that all of these clustered within the two novel sub-clades H1v1 and H1w identified by initial sequencing of the eight entire mtDNAs characterized by the CRS-263 control-region motif. Overall the 64 Libyan Tuareg mtDNAs belonging to H1 (Table S2) were mostly distributed between the clades H1v1 (38%) and H1w (53%), with a minor component (9%) belonging instead to clade H1x. Within H1v1, half of the Libyan Tuareg (i.e. 12 individuals, equal to 50%) were characterized by the transition at np 9148 (sub-clade H1v1a) and half by the transition at np 14560 (sub-clade H1v1b). It is worth noting the extensive village-specificity of the sub-clades. Indeed H1v1b and H1w harbored frequencies of 22% and 63% in Al Awaynat, but were not found at all in Tahala, and 80% of the mtDNAs from the village of Tahala were members of H1v1a in contrast to the only four out of 54 (7%) from the village of Al Awaynat. Similar to H1v1a, haplogroup H1x was also shared between the two groups with two instances in Tahala and four in Al Awaynat.
An up-to-date map of the H1 spatial distribution in Africa and West Eurasia is illustrated in Figure 2. Frequency data and other details of the populations from the literature included in this survey are reported in Table S3 and in the supplementary References S1. There is an evident frequency peak in the Central Sahara associated with the Libyan Tuareg, who show the highest frequency value (61%) among all the populations considered in the analysis. Since the high frequency of H1 in the Libyan Tuareg is most likely the result of random genetic drift and founder events, we also investigated the H1 distribution removing the Libyan Tuareg sample and thus leaving only previously reported data (Figure 3). As expected, frequency peaks in the European continent were observed in the Iberian Peninsula, whereas in Northern Africa the rather high frequency values in Morocco and Tunisia became apparent. More southward, among the Tuareg from the Sahel region [37], a frequency peak is also observed. To further evaluate the extent of H1 variation in the Tuareg from Libya relative to that of Moroccans, Tunisians and Sahelian Tuareg samples, HVS-I data from the four groups were employed to calculate the diversity indices reported in Table 2. The sharp homogeneity of H1 in the Libyan Tuareg, who show extremely low values of haplotype diversity (0.165), is straightforward. Moroccans, Tunisians and the Tuareg from Sahel were found to be much more diverse than the Libyan Tuareg, with haplotype diversities of 0.577, 0.633 and 0.595, respectively. Similarly, the values of nucleotide diversity and average number of nucleotide differences observed in Morocco (0.309 and 1.056), Tunisia (0.316 and 1.081) and among the Tuareg from Sahel (0.234 and 0.800) are all much higher than those of the Libyan Tuareg (0.098 and 0.335).
Discussion
The H1 phylogeny based on complete North African sequences reveals a degree of branch diversification that is almost undetectable when using only control region data. Moreover, when compared to the H1 phylogeny built using complete sequences from Europe [17], [19], [38], [39], it appears that the novel branches H1v, H1w and H1x identified during the course of this study are all African-specific. This finding suggests that these H1 sub-clades most likely arose in North Africa after the arrival of the H1 European founder sequence, corresponding to the H1 node in Figure 1. The issue of the North African specificity of H1v, H1w and H1x needs to be corroborated by additional survey of H1 variation in Western Europe, especially in Iberia, but for the moment none of the European complete mtDNA sequences belonging to H1 were found to belong to these clades. This scenario is further supported by the overall age of haplogroup H1 in North Africa. Using the evolution rates recently proposed by Soares et al. [32] and Loogväli et al. [33], haplogroup H1 shows a coalescence time of approximately 8–9 ky (Table 1), in agreement with the hypothesis of an early arrival and radiation of H1 in the African continent in the first half of the Holocene, as a consequence of the postglacial expansion from the Iberian Peninsula. An arrival from Iberia explains the extent of H1 variation observed in North African populations (Table 2). Indeed, Moroccans and Tunisians, the populations geographically closest to Europe, harbor the highest diversity values for all considered indices. Thus, the coastal areas of northwestern Africa, after the arrival of the Iberian founder H1 mtDNAs, probably acted as centers for the subsequent diffusion of H1 in the internal regions of North Africa. The rather high frequency of H1 in the Tuareg from Sahel (23.3%), in association with intermediate diversity values, is in agreement with the proposal that drift played a major role in shaping the genetic structure of inland populations after they were entrapped in the Sahel belt by the desertification of the Sahara [37]. As for the Libyan Tuareg, the extremely low values of the diversity indices confirm that the outstanding high frequency of H1 in this population is the result of even more recent founder events.
The H1 phylogeny shows a link between the Tuareg of Libya and one Tunisian at the level of clade H1v (Figure 1). Therefore, the H1v coalescence time of about 4–7 ky (Table 1) might correspond to an ancestral split within a nomadic population of Northwest Africa, which led also to the formation of a derived Central Saharan population. The H1v1 sub-clade most likely arose in this population of Central Sahara, which, in turn, contributed extensively to the mtDNA pool of the modern villages of Tahala and Al Awaynat. However, the distribution of the H1v1 lineages in the two Tuareg villages, with H1v1b found only in Al Awaynat and 80% of H1v1a in Tahala and only 7% in Al Awaynat, indicates a rather sharp distinction and a village-specificity of the modern mtDNA gene pool. This is probably the result of peculiar long lasting cultural practices in the Tuareg, who define the affiliation to tribes by matrilineal descent [40], and points to a high degree of isolation between the two villages, at least at the maternal level, regardless of their geographic proximity.
The migratory dynamics which took place over the last 2 ky in the hyperarid Central Sahara, and which possibly led small Tuareg groups with different maternal ancestries to mix and separate from one another [29], [41], [42], could explain the presence of the other two clades, H1w and H1x (respectively 53% and 9% of the total H1 mtDNAs analyzed), in the Libyan Tuareg sample. It should be noted that historically this phase coincides with the decline of the Garamantes, whom the Tuareg consider as their ancestors according to oral traditions [43], [44], [45]. These people inhabited the Fezzan between 2.7 and 1.8 kya and established state-entities based on sedentary settlements and the trans-Saharan caravan trade system. It is plausible that the dismantling of the Garamantian society led small groups to separate as distinct tribes, or alternatively to blend into larger groups.
The French colonization, in the early 20th century, might have also determined the admixture of different Tuareg groups. Indeed, when the Tuareg were confined to restricted areas, there was a decline in their socio-political system and a forced mixture of previously separated tribal groups [46]. Nevertheless, the hypothesis that the three H1 clusters detected here in the Tuareg were all present in the same founder group cannot be totally ruled out, particularly since we are dealing with a small and isolated human group in which genetic drift might have significantly affected the make-up of the mitochondrial pool.
Overall, the results of this study support the hypothesis that most of the West Eurasian maternal contribution detectable in Northwest African populations is likely linked to prehistoric (i.e. the post-glacial expansion from the Iberian Peninsula) rather than more recent historic events [26], [27], [37]. Furthermore, the data presented confirm that the analysis of complete mtDNA sequences represents a valuable tool to reveal not only the spatial patterns beneath large-scale colonization events, but also those of smaller-scale dispersals which may have contributed to the origin of modern populations. In this regard, additional efforts in the full mtDNA analyses of nomad Northern African populations might resolve the debate concerning their origin and their mutual relationship.
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Mitochondrial DNA haplogroup H structure in North Africa Hajer Ennafaa1
Some of these haplogroups, including the X1 [12], U6 [11,13] and M1 [13,14], although of West Asian origin, have Paleolithic coalescence ages in North Africa.
On the other hand, for those mtDNA haplogroups pre-eminent in North Africa, that have been analyzed at deep genomic and phylogeographic levels, such as U6 and M1, a Palaeolithic settlement and Middle East roots have been proposed
Maca-Meyer N, González AM, Pestano J, Flores C, Larruga JM, Cabrera VM: Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genetics 2003,
Conclusions The most probable origin of the proto-U6 lineage was the Near East. Around 30,000 years ago it spread to North Africa where it represents a signature of regional continuity. Subgroup U6a reflects the first African expansion from the Maghrib returning to the east in Paleolithic times. Derivative clade U6a1 signals a posterior movement from East Africa back to the Maghrib and the Near East. This migration coincides with the probable Afroasiatic linguistic expansion. U6b and U6c clades, restricted to West Africa, had more localized expansions. U6b probably reached the Iberian Peninsula during the Capsian diffusion in North Africa. Two autochthonous derivatives of these clades (U6b1 and U6c1) indicate the arrival of North African settlers to the Canarian Archipelago in prehistoric times, most probably due to the Saharan desiccation. The absence of these Canarian lineages nowadays in Africa suggests important demographic movements in the western area of this Continent.
Olivieri A, Achilli A, Pala M, Battaglia V, Fornarino S, Al-Zahery N, Scozzari R, Cruciani F, Behar DM, Dugoujon JM, Coudray C, Santachiara-Benerecetti AS, Semino O, Bandelt HJ, Torroni A: The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 2006, 314:1767-1770. PubMed Abstract | Publisher Full Text
González AM, Larruga JM, Abu-Amero KK, Shi Y, Pestano J, Cabrera VM: Mitochondrial lineage M1 traces an early human backflow to Africa. BMC Genomics 2007, 8:223.
The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasian ancestor has been demonstrated.
Conclusion This study provides evidence that M1, or its ancestor, had an Asiatic origin. The earliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this early spread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin. Both western and eastern M1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelism between subclade ages and geographic distribution of M1 and its North African U6 counterpart strongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in the European Continent and nearby islands possibly had a Jewish instead of the commonly proposed Arab/Berber maternal ascendance.
Phylogeographic parallelism between M1 and U6 haplogroups There are striking similarities between the geographical dispersals and radiation ages observed here for M1 lineages and those previously published for the North African U6 haplogroup [40]. It was proposed that U6a first spread was in Northwest Africa around 30,000 ya. Coalescence ages for M1 also fit into this period and the oldest clade M1c has an evident northwestern Africa distribution; however it had to have a wide geographic range as some M1c lineages are today still present in Jordanians (Figs. 1 and 2). It is curious that this prehistoric Near Eastern colonization was also pointed out by the uniqueness of the U6a haplotypes detected in that area. A posterior East to West African expansion around 17,000 ya was indicated by the U6a1 relative diversity and distribution. Again, age, relative East to West diversities and geographic range accurately correspond with the M1a1 expansion detected here. More recent local spread of lineages U6b and U6c also parallel the M1b and M1c1 distributions. Furthermore, these similarities also hold outside Africa. U6 lineages in the Iberian Peninsula have been considered traces of northward expansions from Africa. Based on the uneven distribution of U6a and U6b lineages in Iberia, with the former predominating in southern and the latter in northern areas, it was proposed that U6b in Iberia represents a signal of a prehistoric North African immigration whereas the presence of U6a could be better attributed to the long lasting historic Arab/Berber occupation [40]. Again, this pattern is accurately repeated by the M1c and M1a distribution in the Iberian Peninsula, the northwest African M1 being more abundant in northern areas (56%) and the East African M1a in southern areas (85%) although, due to the small sample size, difference does not reach a significant level (p = 0.07). Additional support to the hypothesis of a prehistoric introduction are the recently detected presence of a Northwest African M1c lineage in a Basque cemetery dated to the 6th–7th centuries AD, prior to the Moorish occupation [42], and the ancestral phylogenetic position of another Basque M1d sequence (Fig. 1) that does not match any African sequence. Finally, two autochthonous U6 lineages (U6b1 and U6c1) traced the origin of the Canary Islands prehispanic aborigines to Northwest Africa [43]. Although exclusive M1 lineages have not been detected in the Canary Islands, it is worth mentioning that those sampled belong to the Northwest African area [44]. Outside Africa and the Iberian Peninsula, as with U6, M1 has been mainly detected in other Mediterranean areas with main incidences in islands such as Sicily. It is customary to attribute these incidences to the above mentioned Arab/Berber historic occupations. However, taking into account the major Jewish assignation for all the M1a haplotypes detected in Europe, the possibility of a Jewish maternal ascendance for at least some of these lineages should not be rejected.
We don't need postings of complete reports especially when the poster presents no value add -- independent analysis, critique, comment.
Maca-Meyer presents something totally untenable, U6 as Caucasian implying origin and a phenotype non-existant 35,000 years ago.
This is why Eurasia vs Afroasia at that distant time is an integral element in this discussion. Eurasian implies Caucasian but the Levant and Arabian plate are much more Afroasian than any thing else.
If U6 did arise in the Levant&Arabian plate 35k, and this applies to the parent U haplogroup too, what was the region like between 60 and 30k and was it indusive to development of the so-called Caucasian phenotype(s). Is it more likely to have housed Northeast and East African phenotypes that much later further developed toward the features associated with Maca-Meyers undefined "Caucasians?"
This is why the nomenclature is no arbitrary name game.
Does the physical anthropology of Eurasians 60 - 30k support any notion of Caucasians as we know them. Where is the line separating the Caucasians from the caucasoids since even a subset of non-white Africans and others are labeled caucasoid implying Caucasian origin or admixture where none exists.
Maca-Meyer definitely reveals her Eurocentric streak by using straight up Caucasian instead of the more ambiguous caucasoid.
In all fairness we can't ignore Kivisild where he says "A mimicry between U6 and M1 has been suggested [28,29]. Both are likely derived from a non-African ancestral clade at a similar time depth and both are largely confined to North and East Africa and the Middle East in their present- day geographic distribution."
I have been struggling trying to tie that in with "A Southwest Asian origin has been proposed for U6 and M1 [27-29]. Yet, this claim remains speculative unless some novel “earlier” Southwest Asian-specific clades, distinct from the known haplogroups, are found in which the described so far M1 and U6 lineages are nested."Posts: 8179 | From: the Tekrur straddling Senegal & Mauritania | Registered: Dec 2011
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Mitochondrial Haplogroup H1 in North Africa: An Early Holocene Arrival from Iberia Claudio Ottoni equal contributor, Giuseppina Primativo equal contributor
Abstract The Tuareg of the Fezzan region (Libya) are characterized by an extremely high frequency (61%) of haplogroup H1, a mitochondrial DNA (mtDNA) haplogroup that is common in all Western European populations. To define how and when H1 spread from Europe to North Africa up to the Central Sahara, in Fezzan, we investigated the complete mitochondrial genomes of eleven Libyan Tuareg belonging to H1. Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000–9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x, which appear to be specific for North African populations, but whose frequencies can be extremely different even in relatively close Tuareg villages. Overall, these findings support the scenario of an arrival of haplogroup H1 in North Africa from Iberia at the beginning of the Holocene, as a consequence of the improvement in climate conditions after the Younger Dryas cold snap, followed by in situ formation of local H1 sub-haplogroups. This process of autochthonous differentiation continues in the Libyan Tuareg who, probably due to isolation and recent founder events, are characterized by village-specific maternal mtDNA lineages.
Introduction
In the last few years the story of human migrations has been extensively reconstructed thanks to the contribution of archaeology and genetics, particularly the latter through the study of the two uniparentally transmitted genetic systems: mitochondrial DNA (mtDNA) and Y chromosome. The study of maternal genealogies appears to indicate that the peopling of the Eurasian continent by modern humans likely began around 60–70 thousand years ago (kya) through the ‘southern coastal route’ from the Horn of Africa via Arabia and South Asia, up to Australasia [1], [2], [3], [4], [5]. However, alternative exit scenarios, including a more northern route into the Levant and multiple waves of migration (see Kayser 2010 [6] and Majumder 2010 [7] for a review), have recently regained some momentum after the postulated detection of some Neanderthal nuclear DNA variation in the genomes of modern Eurasians [8]. The ‘southern coastal route’ scenario instead implies that, blocked by deserts, humans could not move from the Arabian Gulf area into the Levant earlier than 50 kya, when climate conditions improved [9]. Entrance into the Levant paved the way to the dispersal of modern humans both north-westward into Europe and south-westward into Northern Africa [10], [11]. During the Last Glacial Maximum (LGM), approximately between 26.5 and 19 kya [12] ice sheets largely covered large portions of North America and Europe. In warmer regions of the world, the climate was cooler and drier and deserts spread over large regions, particularly in Northern Africa, Middle East and Central Asia [13], [14]. Accordingly, during the LGM, humans concentrated in refugial areas of southwestern Europe, in the Balkans and Levant, and on the east European plains [9], [15], [16]. The subsequent Bølling warming, around 15 kya, triggered re-expansion processes which led to the resettlement of Central and Northern Europe. Genetic signatures of these expansions are evident in mtDNA genealogies, for instance haplogroups H1, H3 and V contributed to the gradual re-peopling of Europe from the Franco-Cantabrian refuge in the postglacial [17], [18]. Similarly, though to a lesser extent, H5*(xH5a), H20 and H21 may be associated to a postglacial population expansion phase in the Caucasus area [19]. Although restricted to the Mediterranean coast, an expansion took place also from the Italian peninsula northward, as attested to by the haplogroup U5b3 [20].
Evidence of trans-Mediterranean contacts between Northern Africa and Western Europe has been assessed at the level of different genetic markers (e.g. [21], [22], [23], [24]). With regards to the mtDNA, the high incidence of H1 and H3 in Northwest Africa, together with some other West European lineages (i.e. V and U5b), reveals a possible link with the postglacial expansion from the Iberian Peninsula, which not only directed north-eastward into the European continent [17], [18], [25], but also southward, beyond the Strait of Gibraltar, into North Africa [26], [27]. So, besides the ‘autochthonous’ South-Saharan component, the maternal pool of Northern Africa appears to be characterized by at least two other major components: (i) a Levantine contribution (i.e. haplogroups U6 and M1, [11]), associated with the return to Africa around 45 kya, and (ii) a more recent West European input associated with the postglacial expansion.
Within the West-European component in North Africa, H1 is the most represented haplogroup with frequencies ranging from 21% in some Tunisian Berber groups to 1% in Egypt [28]. Recently, an extremely high incidence of H1 (61%) has been reported in a Tuareg population from the Central Sahara, in Libya [29]. Tuareg are a semi-nomadic pastoralist people of Northwest Africa, who speak a Berber language. MtDNA analyses performed on the Libyan Tuareg have highlighted their genetic relatedness with some Berber groups and other North African populations, mainly resulting from the sharing of a common West-Eurasian component. A high degree of homogeneity in the Libyan H1 lineages was observed, suggesting that the high frequency of H1 in the Tuareg may be the result of genetic drift and recent founder events.
To better define the nature and extent of H1 variation in the Tuareg from Libya we have now determined the complete sequence of eleven of their mtDNAs belonging to H1. The comparison of these H1 sequences with those already available from Europe and North Africa provides new clues on how and when H1 spread in Northern Africa up to the Central Sahara.
Results
The most parsimonious tree encompassing eleven complete H1 mtDNAs from the Tuareg together with four previously published sequences from Tunisia [35], one Berber from Egypt [17] and two Jewish Moroccans [36] is illustrated in Figure 1. All Tuareg sequences clustered into three clades that had not been previously reported and thus were termed H1v, H1w and H1x. Five sequences grouped into the sub-clade H1v1 defined by the transition at np 4313. One Tunisian sequence (# 8) did not cluster into H1v1 but was closely related, since it harbored the mutation at 10314 that defines the clade H1v (Figure 1). The sub-clade H1v1 splits into two branches defined by the transitions at np 9148 (clade H1v1a) and 14560 (clade H1v1b). Three Tuareg mtDNAs formed the novel clade H1w that is defined by the transition at np 8966, while the last three Tuareg mtDNAs, apart from the HVS-I transitions at 16037 and 16256, were found to harbor mutations at nps 7765 and 10410 in the coding region (clade H1x). The Tuareg complete mtDNAs have been deposited in GenBank, under the accession numbers reported in Table S1.
Divergence values (rho statistics and ML estimates) and the age in years of the most recent common ancestor of the main clusters are reported in Table 1, according to the evolutionary rate estimates described in Soares et al. [32] and Loogväli et al. [33]. The two evolutionary rates provide a coalescence time of about 8–9 kya for the whole H1 haplogroup in North Africa. As expected, the North African-specific clades are characterized by younger ages ranging from about 3.8 to 6.7 kya for H1v, and from 2.1 to 7.9 kya for H1v1. The youngest clades were found to be H1w and H1x, with an age of about 0.8–1.1 kya. The survey of diagnostic markers 4313, 8966, 9148 and 14560 in 50 individuals characterized by the CRS-263 haplotype showed that all of these clustered within the two novel sub-clades H1v1 and H1w identified by initial sequencing of the eight entire mtDNAs characterized by the CRS-263 control-region motif. Overall the 64 Libyan Tuareg mtDNAs belonging to H1 (Table S2) were mostly distributed between the clades H1v1 (38%) and H1w (53%), with a minor component (9%) belonging instead to clade H1x. Within H1v1, half of the Libyan Tuareg (i.e. 12 individuals, equal to 50%) were characterized by the transition at np 9148 (sub-clade H1v1a) and half by the transition at np 14560 (sub-clade H1v1b). It is worth noting the extensive village-specificity of the sub-clades. Indeed H1v1b and H1w harbored frequencies of 22% and 63% in Al Awaynat, but were not found at all in Tahala, and 80% of the mtDNAs from the village of Tahala were members of H1v1a in contrast to the only four out of 54 (7%) from the village of Al Awaynat. Similar to H1v1a, haplogroup H1x was also shared between the two groups with two instances in Tahala and four in Al Awaynat.
An up-to-date map of the H1 spatial distribution in Africa and West Eurasia is illustrated in Figure 2. Frequency data and other details of the populations from the literature included in this survey are reported in Table S3 and in the supplementary References S1. There is an evident frequency peak in the Central Sahara associated with the Libyan Tuareg, who show the highest frequency value (61%) among all the populations considered in the analysis. Since the high frequency of H1 in the Libyan Tuareg is most likely the result of random genetic drift and founder events, we also investigated the H1 distribution removing the Libyan Tuareg sample and thus leaving only previously reported data (Figure 3). As expected, frequency peaks in the European continent were observed in the Iberian Peninsula, whereas in Northern Africa the rather high frequency values in Morocco and Tunisia became apparent. More southward, among the Tuareg from the Sahel region [37], a frequency peak is also observed. To further evaluate the extent of H1 variation in the Tuareg from Libya relative to that of Moroccans, Tunisians and Sahelian Tuareg samples, HVS-I data from the four groups were employed to calculate the diversity indices reported in Table 2. The sharp homogeneity of H1 in the Libyan Tuareg, who show extremely low values of haplotype diversity (0.165), is straightforward. Moroccans, Tunisians and the Tuareg from Sahel were found to be much more diverse than the Libyan Tuareg, with haplotype diversities of 0.577, 0.633 and 0.595, respectively. Similarly, the values of nucleotide diversity and average number of nucleotide differences observed in Morocco (0.309 and 1.056), Tunisia (0.316 and 1.081) and among the Tuareg from Sahel (0.234 and 0.800) are all much higher than those of the Libyan Tuareg (0.098 and 0.335).
Discussion
The H1 phylogeny based on complete North African sequences reveals a degree of branch diversification that is almost undetectable when using only control region data. Moreover, when compared to the H1 phylogeny built using complete sequences from Europe [17], [19], [38], [39], it appears that the novel branches H1v, H1w and H1x identified during the course of this study are all African-specific. This finding suggests that these H1 sub-clades most likely arose in North Africa after the arrival of the H1 European founder sequence, corresponding to the H1 node in Figure 1. The issue of the North African specificity of H1v, H1w and H1x needs to be corroborated by additional survey of H1 variation in Western Europe, especially in Iberia, but for the moment none of the European complete mtDNA sequences belonging to H1 were found to belong to these clades. This scenario is further supported by the overall age of haplogroup H1 in North Africa. Using the evolution rates recently proposed by Soares et al. [32] and Loogväli et al. [33], haplogroup H1 shows a coalescence time of approximately 8–9 ky (Table 1), in agreement with the hypothesis of an early arrival and radiation of H1 in the African continent in the first half of the Holocene, as a consequence of the postglacial expansion from the Iberian Peninsula. An arrival from Iberia explains the extent of H1 variation observed in North African populations (Table 2). Indeed, Moroccans and Tunisians, the populations geographically closest to Europe, harbor the highest diversity values for all considered indices. Thus, the coastal areas of northwestern Africa, after the arrival of the Iberian founder H1 mtDNAs, probably acted as centers for the subsequent diffusion of H1 in the internal regions of North Africa. The rather high frequency of H1 in the Tuareg from Sahel (23.3%), in association with intermediate diversity values, is in agreement with the proposal that drift played a major role in shaping the genetic structure of inland populations after they were entrapped in the Sahel belt by the desertification of the Sahara [37]. As for the Libyan Tuareg, the extremely low values of the diversity indices confirm that the outstanding high frequency of H1 in this population is the result of even more recent founder events.
The H1 phylogeny shows a link between the Tuareg of Libya and one Tunisian at the level of clade H1v (Figure 1). Therefore, the H1v coalescence time of about 4–7 ky (Table 1) might correspond to an ancestral split within a nomadic population of Northwest Africa, which led also to the formation of a derived Central Saharan population. The H1v1 sub-clade most likely arose in this population of Central Sahara, which, in turn, contributed extensively to the mtDNA pool of the modern villages of Tahala and Al Awaynat. However, the distribution of the H1v1 lineages in the two Tuareg villages, with H1v1b found only in Al Awaynat and 80% of H1v1a in Tahala and only 7% in Al Awaynat, indicates a rather sharp distinction and a village-specificity of the modern mtDNA gene pool. This is probably the result of peculiar long lasting cultural practices in the Tuareg, who define the affiliation to tribes by matrilineal descent [40], and points to a high degree of isolation between the two villages, at least at the maternal level, regardless of their geographic proximity.
The migratory dynamics which took place over the last 2 ky in the hyperarid Central Sahara, and which possibly led small Tuareg groups with different maternal ancestries to mix and separate from one another [29], [41], [42], could explain the presence of the other two clades, H1w and H1x (respectively 53% and 9% of the total H1 mtDNAs analyzed), in the Libyan Tuareg sample. It should be noted that historically this phase coincides with the decline of the Garamantes, whom the Tuareg consider as their ancestors according to oral traditions [43], [44], [45]. These people inhabited the Fezzan between 2.7 and 1.8 kya and established state-entities based on sedentary settlements and the trans-Saharan caravan trade system. It is plausible that the dismantling of the Garamantian society led small groups to separate as distinct tribes, or alternatively to blend into larger groups.
The French colonization, in the early 20th century, might have also determined the admixture of different Tuareg groups. Indeed, when the Tuareg were confined to restricted areas, there was a decline in their socio-political system and a forced mixture of previously separated tribal groups [46]. Nevertheless, the hypothesis that the three H1 clusters detected here in the Tuareg were all present in the same founder group cannot be totally ruled out, particularly since we are dealing with a small and isolated human group in which genetic drift might have significantly affected the make-up of the mitochondrial pool.
Overall, the results of this study support the hypothesis that most of the West Eurasian maternal contribution detectable in Northwest African populations is likely linked to prehistoric (i.e. the post-glacial expansion from the Iberian Peninsula) rather than more recent historic events [26], [27], [37]. Furthermore, the data presented confirm that the analysis of complete mtDNA sequences represents a valuable tool to reveal not only the spatial patterns beneath large-scale colonization events, but also those of smaller-scale dispersals which may have contributed to the origin of modern populations. In this regard, additional efforts in the full mtDNA analyses of nomad Northern African populations might resolve the debate concerning their origin and their mutual relationship.
Although the topic of this thread is U6, I'll just touch on the above on H1 for a moment. Why is it these high frequencies of H1 are found in the south of Libya i.e. the Fezzan instead of in the north in the coastal areas if we are to assume H1 in North Africa is of European provenance?? Also, the dates of its introduction to North Africa coincide with the Neolithic, yet why is there no skeletal evidence of Europeans in Libya during that time period, let alone central and southern Libya before the formation of the modern Sahara? Interesting how despite this alleged European heritage, the people of the Fezzan were depicted as very dark by the Egyptians and even the Romans described them as 'Aethiopes' and 'Nigritai'.
Again, it is this assumption that H was introduced from the outside of Africa, yet both H and V as well as their ancestor HV are found in Africa. What's more is that even HV's ancestor R0 is found in East Africa from the Sudan to the Horn and especially the former in very high frequencies. It is a wonder to me why non of these experts don't postulate an indigenous origin for these clades.
Speaking of which, here again circled in green are the 'Eurasian' clades found in the African continent.
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Tukuler
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Please, please don't let trollers prompt you to drift away from U6: how old? from where? associated originating phenotypes? Thank you.
= = =
Older reports are to see if their positions are currently the concensus, has been falsified, or is one among any number of viable alternatives.
I think I see what defines macrohaplogroup U in al~Zahery (2003) Table 2. While no control region sequence can, RFLP HinfI +12308 does for K and all U haplogroups found in Iraq including the only U6 sample al~Zahery found.
Fig 2 presents this visually clear phylogeny
Some text:
Haplogroup U, which has in Iraq a frequency comparable to haplogroup H, does not play an important role in the PC analysis. This is probably due to the heterogeneous distribution of its numerous sub-clades not available for most of the populations. When the different sub-clades are separately considered (Richards et al., (2002), U5 correlates with H and pre-V, concentrated in the European pool, while U1 with haplogroup pre-HV concentrated in the Near Eastern pool. As illustrated in Fig. 2, haplogroup U exhibits in Iraq all its most common sub-groups with the exception of the rare U8 (Finnila et al., 2001). Indeed, haplogroup U5, which does not appear in the network (constructed with 52 mtDNAs), was observed in one subject included in the larger Iraqi sample (N¼116) reported by Richards et al. (2000). According to these authors, the Iraqi U5 mtDNA belongs to the highly derived European subcluster U5a1a, and is due to recent gene flow from Europe. The finding of the U6, which is typical of Berbers and North Africans (Macaulay et al., 1999), may be considered the result of contact with these populations. On the contrary, the presence (2.6% of 116 sub-classified mtDNAs) of haplogroup U7, which is very rare in Europe, can be regarded as indicative of a genetic connection between Southwestern Asia (Iran, Arabia, Anatolia, the two Caucasus regions, and India) and Eastern Africa (Nile Valley) where it is also found (Tambets et al., 2000).
. . . .
MtDNA gene flow is revealed by the presence of the European haplogroups V and U5 (1.4%), the North African haplogroup U6 (0.9%), the sub-Saharan African haplogroups L1 and L2 (4.2%), and the East-Asian haplogroups M and B (2.3%).
N. Al-Zahery et al. ... mtDNA polymorphisms in Iraq ... Molecular Phylogenetics and Evolution xxx (2003) xxx–xxx doi:10.1016/S1055-7903(03)00039-3
From this report I see the common root of all U sub-clades including U6 which is Northwest Africa specific despite heavy Eurasian provenance for the other U subhaplogroups of the report.
No N was found and R was minimal but African related haplogroups (women who may've travelled alongside the U's at 19%) were minimal; M and L1 both 1.4% and L2 at 2.8%. Like N, no L3 was found.
Absence of L3 and N with negliable R may indicate U expanded earlier elsewhere before entering Iraq.
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Tukuler
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A caveat re HVS-I sequencing alone to determine mtDNA haplogroups:
It is clear that relying on the HVS-I variation alone to infer Hgs and sub-Hgs such as M1, Z, U5, U6, and HV1 is prone to inaccuracies. In addition, HVS-I haplotypes alone cannot identify Hgs or sub-Hgs that have no defining motifs and ignores the possibility of homoplasy and back mutations. For example, it is clear that some of the mtDNA genomes appearing in our database as U* might actually belong to Hg U4 but, as they did not contain the diagnostic HVS-I position 16356C and in the absence of additional coding-region genotyping, we could not label them as such. Moreover, some of the sub-Hg definitions inferred from the HVS-I, for example within Hgs J and T, will have to be revised in the future as studies using complete mtDNA sequences prove they do not represent monophyletic clades [20,37]. Therefore, whenever analysis is done within an Hg, we refer only to one of the 23 Hgs directly inferred from the 22 SNPs genotyping to avoid any HVS-I based Hg labeling misinterpretations.
Doron M. Behar et al Genographic Project ... Mitochondrial DNA Database PLoS Genet 3(6), 2007
The above report has a good section explaining homoplasy. That being said Behar (2012 supplement) shows A16129G as common to U U1 U3 U4 U5 U6 U7 and K though not as a solo motif. A16129G appears in many other mtDNA haplogroups but not, at least per this report, in various sub-clades of a single macro-hg like it does for U (N being an exception).
But note that U6 only has A16129G and no other mutations shared by almost all the other U sub-clades i.e., the CRS A16129G T16187C C16189T T16223C G16230A T16278C C16311T.
Doron M Behar et al. Supplemental Data A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root The American Journal of Human Genetics, Volume 90; 2012
This is an important report. It proposes abandoning the Eurocentric RCRS ordering of the phylogeny in favor of RSRS rooting that splits into African L0 and L1'2'3'4'5'6. L3 of course roots M and N and thus the rest of the known mtDNA phylogeny. RCRS falsely posits R/U/HV/H as the referencing "root."
We don't need postings of complete reports especially when the poster presents no value add -- independent analysis, critique, comment.
LOL What do you expect? The lyinass will brainlessly parrot any author or source she thinks supports her agenda yet offers nothing of her own thoughts likely because she doesn't understand the very material she cites!
quote:Maca-Meyer presents something totally untenable, U6 as Caucasian implying origin and a phenotype non-existant 35,000 years ago.
This is why Eurasia vs Afroasia at that distant time is an integral element in this discussion. Eurasian implies Caucasian but the Levant and Arabian plate are much more Afroasian than any thing else.
If U6 did arise in the Levant&Arabian plate 35k, and this applies to the parent U haplogroup too, what was the region like between 60 and 30k and was it inductive to development of the so-called Caucasian phenotype(s). Is it more likely to have housed Northeast and East African phenotypes that much later further developed toward the features associated with Maca-Meyers undefined "Caucasians?"
This is why the nomenclature is no arbitrary name game.
Does the physical anthropology of Eurasians 60 - 30k support any notion of Caucasians as we know them. Where is the line separating the Caucasians from the caucasoids since even a subset of non-white Africans and others are labeled caucasoid implying Caucasian origin or admixture where none exists.
Maca-Meyer definitely reveals her Eurocentric streak by using straight up Caucasian instead of the more ambiguous caucasoid.
Right you are! Of course what you point out was pointed out by the rest of us many times before.
As for physical evidence of human remains. We have Nazlet Khater man of Egypt dated 33-30 kya not long after U6 arose supposedly in 'the Levant' and entered Egypt.
Nazlet Khater man was the earliest modern human skeleton found near Luxor, in 1980. The remains was dated from between 35,000 and 30,000 years ago. The report regarding the racial affinity of this skeleton concludes: "Strong alveolar prognathism combined with fossa praenasalis in an African skull is suggestive of Negroid morphology. The radio-humeral index of Nazlet Khater is practically the same as the mean of Taforalt (76.6). According to Ferembach (1965) this value is near to the Negroid average." The burial was of a young man of 17-20 years old, whose skeleton lay in a 160cm- long narrow ditch aligned from east to west. A flint tool, which was laid carefully on the bottom of the grave, dates the burial as contemporaneous with a nearby flint quarry. The morphological features of the Nazlet Khater skeleton were analysed by Thoma (1984). The 35,000 year old skeleton was examined using multivariate statistical procedures. In the first part, principal components analysis is performed on a dataset of mandible dimensions of 220 fossils, sub-fossils and modern specimens, ranging in time from the Late Pleistocene to recent and restricted in space to the African continent and Southern Levant. ---Thoma A., Morphology and Affinities of the Nazlet Khater Man; Journal of Human Evolution, vol. 13, 1984
Nazlet Khater falls closer to the Late Palaeolithic Nubian samples . . . If an ancestral descendant relationship existed between Nazlet Khater and the Late Palaeolithic Nubian specimens, then regional continuity persisted among the Upper/Late Pleistocene populations of the Upper Nile region. The Nazlet Khater specimen is part of a relict population which is a descendant of a larger sub-Saharan stock, which extended as far north as present day upper Egypt sometime during the Last Interglacial period, or the early part of the Last Glacial period. In such a scenario, the Nazlet Khater belongs to a relict population which retained some of the morphological features [form & structure] that were present among Middle Stone Age populations, but no longer present in other contemporaneous sub-Saharan and North African populations. ---The Position of the Nazlet Khater Specimen Among Prehistoric and Modern African and Levantine Populations, Ron Pinhasi, Departent of Biological Anthropology, University of Cambridge, U.K., Patrick Semal, Belgian Institute of Natural Sciences, Belgium; Journal of Human Evolution (2000) vol. 39, 269–288.
As for archaeology, I'm unfamiliar with Nazlet Khater's culture, though I'm certain there is no indication of Eurasian derived origins.
quote:In all fairness we can't ignore Kivisild where he says "A mimicry between U6 and M1 has been suggested [28,29]. Both are likely derived from a non-African ancestral clade at a similar time depth and both are largely confined to North and East Africa and the Middle East in their present- day geographic distribution."
I have been struggling trying to tie that in with "A Southwest Asian origin has been proposed for U6 and M1 [27-29]. Yet, this claim remains speculative unless some novel “earlier” Southwest Asian-specific clades, distinct from the known haplogroups, are found in which the described so far M1 and U6 lineages are nested."
As Explorer stated all the basal U6 haplotypes found so far are in West Africa. As for M1, I could be mistaken but I thought East Africa has the highest frequency of M1 specifically in the Horn area. Why does it sound like they are saying it has higher frequencies in Arabia?
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I posted relevant studies. You didn't want the article posted. I have abided and not posted further large excerpts
Djehuti is a troll and fvcking asshole for the following reasons. As he soon as he re-enters he forum he changes my name in every single quote and he throws in other insults and condescension. he goes out of his way to make numerous replies to my posts
That is the definition of a troll. I just read an article about how trolls bring down the mental level of a discussion. he thinks he's justified because I don't have the same points of view as other people here.
When a civilized converstaion is going the troll comes in and does things like changes people's names in quotes and other insults. You don't see the troll because at the same time they are posting information you like. The troll's goal is to polarize the conversation and that is exactly what Djehuti does. You don't care because you are more in sympathy with his point of view.
The insults begin and people become more emotional in their replies, the conversation becomes polerized at a less intellgent level lacking nuance. dana does the same thing. They start with insults. The goal is polarize and encourage low life counter-insults hoping less popular points of view will be snuffed by mob rule who picks size I can go there and destroy this thread and forum worse than anybody has ever done.
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I'm taking your advice Takruri and not biting the angry troll's bait.
Anyway, getting back to your topic, as I said the only skeletal evidence I know of that dates to the time period of the alleged entry of U6 into Northeast Africa presumably from the 'Near East' is Nazlet Khater.
^ Note the introduction of the paper affirms what has been stated time and again by later studies including the one here that Africans had greater cranial diversity then until after the Holocene than they do now.
Anyway, one thing I forgot to add was the cultural context. Apparently the Nazlet Khater sites were quarry sites where the people mined chert for their tools.
Here is further information from a source by Vermeersch:
Apparently the Nazlet Khater skeleton showed signs of physical stress especially in the vertebral area showing that he did heavy labor in the mines.
Note that 30,000 BP is also the time period when the Khormusan Culture arose in northern Sudan and spread throughout North Africa overtaking and succeeding the Aterian Culture.
I haven't been able to find that many sources on the Khormusan.
From wiki: The Khormusan industry in Egypt began between 40,000 and 30,000 BC. Khormusans developed advanced tools not only from stone but also from animal bones and hematite. They also developed small arrow heads resembling those of Native Americans, but no bows have been found. The end of the Khormusan industry came around 16,000 B.C. with the appearance of other cultures in the region, including the Gemaian.
I'm still looking for this paper: 'The Khormusan: an Upper Pleistocene industry in Sudanese Nubia' A.E. Marks (1968)
The only other thing I know about the Khormusan is that most of its tools which were slightly more advanced than the Aterian consisted of fishing tools, specifically hooks. Thus the Khormusans were known as the 'fishing people' of North Africa.
I personally tend to identify the Khormusan expansion from the Sudan with hg M1 if one could identify it with a genetic clade. Although there is the fact that U6 is also found as far south as Kenya.
There is another culture contemporary with the Khorumusan in coastal North Africa, specifically in Libya called the Dabban Culture which utilized back blades and burins similar to those of Upper Paleolithic Southwest Asia and Europe which seems to fit the scenario of a Eurasian U6, though the origins of the Dabban are still unclear and that the culture is Eurasian remains tenuous.
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Tukuler
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quote:Originally posted by the lioness,: I posted relevant studies. You didn't want the article posted. I have abided and not posted further large excerpts
You like to troll and clown around. Please, not here. You can rise above it. Thank you.
We all know U6 is Northwest Africa specific. That does not necessarily correlate to derivation from an immediate Africa located ancestral haplogroup.
This thread is to examine what's known about U6 specially focusing on her momma and nana. Were they African, Afroasian, or Eurasian and if the last whether Maca-Meyer's Caucasian designation is accurate or not. To this end related material from archaeology, anthropology, climatology, etc also play a role and are welcome additions. Also works on contemporaneous non-U Hgs and even nrY Hgs can shed light.
I don't care what scientific (but not any proprietary) reports are referenced as basis of informed opinions. Excerpts from pertinent reports are vital to this thread but not the whole report especially when you don't hi-lite relevant major points nor provide any independent analysis, critique or worthwhile commentary. Publication date of posted report snippets is necessary for chronological comparative purposes between all supplied reports.
Besides in above posts, see here for an example of snipping and hi-liting
EDIT: I see by your below post you are not interested in the topic just being a clown. And just like a acting out toddler you went and ruined the format of my thread with that outsized rude curse. Watch out I could become vindictive phuckup your threads too except that would be what you want to take away emphasis from knowledge building/sharing in order to further disgrace this site as juvenile and sophmoric and so unreliable for learners.
And to think all I asked was for you to follow a few simple guidelines like everybody else.
Nuff said, no more attention from me to you.
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quote:Originally posted by the lioness,: ^^^ fvcking asshole
I think the asshole is the one ignoring my no-flame request trying to derail this thread.
Nobody take any bait please.
Tukuler,
I think this study will be helpful in your quest.
Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages
--Mol Biol Evol (2007) 24 (3): 757-768.
quote: Evolutionary history of mtDNA haplogroup structure in African populations inferred from mtDNA d-loop and RFLP analysis. (A) Relationships among different mtDNA haplogroup lineages inferred from mtDNA d-loop sequences and mtDNA coding region SNPs from previous studies (Kivisild, Metspalu, et al. 2006). Dashed lines indicate previously unresolved relationships. (B) Relative frequencies of haplogroups L0, L1, L5, L2, L3, M, and N in different regions of Africa from mtDNA d-loop and mtDNA coding region SNPs from previous studies. (C) Relative frequencies of haplogroups L0, L1, and L5 subhaplogroups (excluding L2 and L3) in different regions of Africa from mtDNA d-loop and mtDNA coding region SNPs from previous studies. Haplogroup frequencies from previously published studies include East Africans (Ethiopia [Rosa et al. 2004], Kenya and Sudan [Watson et al. 1997; Rosa et al. 2004]), Mozambique (Pereira et al. 2001; Salas et al. 2002), Hadza (Vigilant et al. 1991), and Sukuma (Knight et al. 2003); South Africans (Botswana !Kung [Vigilant et al. 1991]); Central Africans (Mbenzele Pygmies [Destro-Bisol et al. 2004], Biaka Pygmies [Vigilant et al. 1991], and Mbuti Pygmies [Vigilant et al. 1991]); West Africans (Niger, Nigeria [Vigilant et al. 1991; Watson et al. 1997]; and Guinea [Rosa et al. 2004]). L1*, L2*, and L3* from previous studies indicate samples that were not further subdivided into subhaplogroups.
See the gene-tree, it shows the mtDNA on African Hg's.
quote:Originally posted by the lioness,: I posted relevant studies. You didn't want the article posted. I have abided and not posted further large excerpts
You like to troll and clown around. Please, not here. You can rise above it. Thank you.
We all know U6 is Northwest Africa specific. That does not necessarily correlate to derivation from an immediate Africa located ancestral haplogroup.
This thread is to examine what's known about U6 specially focusing on her momma and nana. Were they African, Afroasian, or Eurasian and if the last whether Maca-Meyer's Caucasian designation is accurate or not. To this end related material from archaeology, anthropology, climatology, etc also play a role and are welcome additions. Also works on contemporaneous non-U Hgs and even nrY Hgs can shed light.
I don't care what scientific (but not any proprietary) reports are referenced as basis of informed opinions. Excerpts from pertinent reports are vital to this thread but not the whole report especially when you don't hi-lite relevant major points nor provide any independent analysis, critique or worthwhile commentary. Publication date of posted report snippets is necessary for chronological comparative purposes between all supplied reports.
I wasn't clowing on this thread. I posted two relevant articles on U6. I was asked to not post full articles and then I stopped.
^^^^^ so this to you personalized baiting of me, changing my name etc. is not clowning. This is why you failed as a modertor at reloaded because you are not fair and you are a fvcking snob. Even after I stopped posting you are still being a bytch Posts: 42919 | From: , | Registered: Jan 2010
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
quote:Originally posted by Dj:
the only skeletal evidence I know of that dates to the time period of the alleged entry of U6 into Northeast Africa presumably from the 'Near East' is Nazlet Khater.
There's scanty if any evidence for U6 in the "Near East" during the Paleolithic when U6 coalesced more than 25,000 years ago, thus yes an allegation this thread investigates.
quote:I personally tend to identify the Khormusan expansion from the Sudan with hg M1 if one could identify it with a genetic clade. Although there is the fact that U6 is also found as far south as Kenya.
Thanks for the Nazlet Khater and Khormusan infos.
I think Kenyan U6 is actually U6a which is 10,000 years younger than U6 and not so much relevant for U6 origins since U6a shows a NW African origin and moved eastward.
quote: There is another culture contemporary with the Khorumusan in coastal North Africa, specifically in Libya called the Dabban Culture which utilized back blades and burins similar to those of Upper Paleolithic Southwest Asia and Europe which seems to fit the scenario of a Eurasian U6, though the origins of the Dabban are still unclear and that the culture is Eurasian remains tenuous.
This is why I hoped for broad membership involvement with this thread. I think not so long ago someone posted updated Dabban material that refuted those similarities with western Eurasia. See references 42 and 43 in Pennarun (2012).
Posts: 8179 | From: the Tekrur straddling Senegal & Mauritania | Registered: Dec 2011
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Tukuler
multidisciplinary Black Scholar
Member # 19944
posted
Now that Lyin' Ass Fuckuptions has ruined the thread's right margin can all please be careful to hit the enter key to end a line instead of relying on the forum to do it for you, so that no one has to keep scrolling left to right and right to left every other line just to try to read a post. Thanks.
Never asked it not to post just to be circumspect in it posts as far as bandwidth and value add is all.
Can't say it was done out of emotional immaturity or intent to derail this thread because of info unpalateable to its anti-African anti-black agenda.
Posts: 8179 | From: the Tekrur straddling Senegal & Mauritania | Registered: Dec 2011
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quote:Originally posted by Tukuler: [QB] Now that Lyin' Ass Fuckuptions
^^^^ this guy is not serious about the discussion of haplogroups.
I warned him and he's still trying to provoke by perpetuating DJehutis spoof on my name. He wants to play games
Posts: 42919 | From: , | Registered: Jan 2010
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quote:Originally posted by Tukuler: [QB] Now that Lyin' Ass Fuckuptions
^^^^ this guy is not serious about the discussion of haplogroups.
I warned him and he's still trying to provoke by perpetuating DJehutis spoof on my name. He wants to play games
It's tiresome, but do you understand this?
quote: We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades.
quote: No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic."
--Erwan Pennarun, BMC Evolutionary Biology 2012, 12:234 Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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posted
Guys let chill out like Tukuler said, this thread is interesting.
Lioness don't let the insults get you.
Anways...Like I said what is the exact age of U6? Some people estimate somewhere 50-20k years.
Posts: 1135 | From: Top secret | Registered: Jun 2012
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quote:Originally posted by Son of Ra: Guys let chill out like Tukuler said, this thread is interesting.
Lioness don't let the insults get you.
Anways...Like I said what is the exact age of U6? Some people estimate somewhere 50-20k years.
quote: For example, U6a1 and M1b, with their coalescent ages of ~20,000–22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture.
--Erwan Pennarun, BMC Evolutionary Biology 2012, 12:234 Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa
quote:Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa
The mitochondrial haplogroup M, first regarded as an ancient marker of East-Asian origin4, 5, has been found at high frequency in India6 and Ethiopia7, raising the question of its origin.(A haplogroup is a group of haplotypes that share some sequence variations.) Its variation and geographical distribution suggest that Asian haplogroup M separated from eastern-African haplogroup M more than 50,000 years ago.
Two other variants (489C and 10873C) also support a single origin of haplogroup M in Africa.
These findings, together with the virtual absence of haplogroup M in the Levant and its high frequency in the South-Arabian peninsula, render M the first genetic indicator for the hypothesized exit route from Africa through eastern Africa/western India. This was possibly the only successful early dispersal event of modern humans out of Africa.
quote:Evolutionary history of mtDNA haplogroup structure in African populations inferred from mtDNA d-loop and RFLP analysis.
(B) Relative frequencies of haplogroups L0, L1, L5, L2, L3, M, and N in different regions of Africa from mtDNA d-loop and mtDNA coding region SNPs from previous studies.
posted
Sad how this Eurocentric troll has tried to destroy a great thread like this, by alTakruri!
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Tukuler
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Tukuler
multidisciplinary Black Scholar
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quote:Originally posted by Troll Patrol: Sad how this Eurocentric troll has tried to destroy a great thread like this, by alTakruri!
Ya know how it is with the jealous.
Ya know it wasn't 'bout I asked of her
I mean **** like the obvious
- don't post a whole report when it's still available for free
- hi-lite the good points of report excerpt
- add some original analysis
- attempt a critique if warranted
- make some kind of original commentary on the report.
**** I even encouraged the bitch and she phucks my thread over in return
Why
j e a l o u s y
It's funny really. Made me mad at first. But now I'm laughing.
How come. The angry temper tantrum one is the loser of the dozens
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