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

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

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

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

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

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

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

  1. “The real mystery is the lack of L3 and M in India”.

    Isn’t M particularly common in India? M is really a subgroup of L3 so the absense of L3 in India is easily explained. It is actually there. It’s just that it’s called M.

  2. Of course the precursor may not ever have got to India at all. It’s got to have moved through some region between Africa and India. Iranian Plateau?

  3. The real mystery is the lack of L3 and M in India

    All Eurasian mtDNA is L3. L3 is India is like 100%. And in Europe, China, Australia…

    The precursor to the M2 and M1 is missing in India.

    The precursor of these two clades is M and, underived, is missing everywhere.

  4. The early human backflow to Africa claim is completely un-substantiated, even according to your own study.

    “In Africa, haplogroup M1 has supra-equatorial distribution. As previously reported its highest frequencies and diversities are found in Ethiopia in particular and in East Africa in general. Two appreciable gradients exist. Frequencies significantly diminished from East to West and also going South to sub-Saharan areas. M1 is not uncommon in the Mediterranean basin showing a peak in the Iberian Peninsula. However, it is rare in continental Europe. Although in low frequencies, its presence in the Middle East has been well established from the South of the Arabian Peninsula to Anatolia and from the Levant to Iran.”

    Elsewhere…

    “As an outgroup of the M1 genomic phylogenetic tree we used a published Indian M30 complete sequence. When this M30 lineage is compared to the rare M sequence previously detected in two Palestinians, it is evident that it belongs to the Indian super-clade M4’30, as it shares the basal mutation 12007. More specifically it belongs to the M30 branch because it also has transition 15431. M30 has a broad geographic, ethnic and linguistic range in India.”

    …and…

    “Due to the scarcity of M lineages in the Near East and its richness in India, this region was proposed as the most probable origin of the M1 ancestor. However, recent studies based on Indian mtDNA sequences have not found any positive evidence that M1 originated in India.”

    …from earlier…

    “in two recent studies in which 24 and 56 Indian M complete sequences were analyzed no ancestral M1 lineages have been found.”

    http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1945034

    You continue

    • I don’t remember publishing it.

      You conveniently ignore that U and R1 also date back a sdamn long time, both found as far West as Cameroon now. M1 follows U and the M78 around like a lost puppy, so Gonzalez is entitled to observe they were probably part of the same e migration.

      Since you like quotes..

      The coalescence age of the African haplogroup M1 is younger than those for other M Asiatic clades. In contradiction to the hypothesis of an eastern Africa origin for modern human expansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa and in the Near East, instead of in East Africa. 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

      Sequencing of 81 entire human mitochondrial DNAs (mtDNAs) belonging to haplogroups M1 and U6 reveals that these predominantly North African clades arose in southwestern Asia and moved together to Africa about 40,000 to 45,000 years ago…..Thus, the early Upper Palaeolithic population(s) carrying M1 and U6 did not return to Africa along the southern coastal route of the “out of Africa” exit, but from the Mediterranean area; and the North African Dabban and European Aurignacian industries derived from a common Levantine source

      Not exactly supportive of an East Africa origin for M1. There sod all evidence that M itself was ever present, M1 is the only M variant found in Africa, but you get masses of M in India. M1 probably has an origin in the near east. So there are two studies now that show M1 to be Asian, not one.

  5. However, recent studies based on Indian mtDNA sequences have not found any positive evidence that M1 originated in India.

    Nor any M subclade other than hose that are stilly typically South Asian.

    But the distribution of M overall in the Indo-Pacific “T”, does not support at all a West Eurasian or African origin for this macro-clade. Also the oldest M subclades are all from that area (South, SE and East Asia, as well as Sahul). M1 is in fact the youngest of all M subclades.

    The predecessors of M1 (pre-M1, now only found derived into M1) surely migrated to West Asia (Arabia?) in very small numbers and took a time to find an opportunity for expansion.

    M1 follows U and the M78 around like a lost puppy

    Not really. U is much more widespread than M1 and is probably a clade that experienced an quite older expansion and diversification. The phylogeny of U is also quite complex, with some branches derived from the U node and others from a downstream one that could well be called “U2,3,4,8,9”, which in turn splits into U2 and “U3,4,8,9”. U1, U5 and U6 are the only branches directly derived from the U node and therefore probably the oldest ones in West Eurasia and some of their modern locations.

    I don’t know how to fit E-M78 with M1, sorry. Sure, they overlap a lot (in NE Africa mainly) but they do not seem particularly related.

    Sequencing of 81 entire human mitochondrial DNAs (mtDNAs) belonging to haplogroups M1 and U6 reveals that these predominantly North African clades arose in southwestern Asia and moved together to Africa about 40,000 to 45,000 years ago…

    U6 is most diverse (by large) in Iberia (ref. Maca-Meyer), where IMO it is an early UP founder effect (much like U8). Its presence in North Africa can be explained by Oranian being possibly derived from southern Iberian Gravetto-Solutrean. U6a (but only this subclade) is most diverse in Upper Egypt instead, signalling the Capsian counter-tide (along with other clades, specially Y-DNA E-M78). U6 is not the only mtDNA subclade that shows in North Africa as a subset of Iberian diversity, H and V do exactly the same.

    I am no genetcist and integral equations overwhelm me but my own home-style count strongly suggests that U and its subclades are quite older than M1.

    M1 probably has an origin in the near east.

    Fully agree with this.

    • Typo alert…should have read ‘and then M78′ Luis. I was talking about the U in North Africa Luis. I know you think U entered Africa from Iberia.

      Luis, the maps for M1 and M1a form an almost perfect match in North/East Africa.

  6. A Response To Ana M. Gonzalez et al.

    *First, a quick synopsis of the samplings, with regards to where the n=261 M1 bearing samples come from, aside from the 588 participants mentioned in one of the tables [table 2] in the study:

    From my assessment of the table, it comes from the following numbers:

    A total of 50 Europeans detected for M1.
    A total of 154 for Africans.
    A total of 28 Asians, barring 8 unknown Arabian haplotypes.
    And a total of 29 Jews, who were lumped together from the various continents.
    The sum of the above totals, amount to 261 “known” M1 lineages.

    *With regards to the authors claim about M1 or its ancestor, having “had an Asiatic origin”, the following comes to mind:

    The authors of the study at hand, themselves admit that they haven’t come across M1 ancestor in either south Asia or southwest Asia. They also take note of its highest diversity in Ethiopia and east Africa. Yet through the shaky premise of their M1c expansion time frame estimations, they build a conclusion around it, by tying it to a dispersal(s) “parallel” to that of U6 – another African marker whose immediate common recent ancestor, namely proto-U6, appears to be elusive thus far.

    Well, they wouldn’t be the only ones who have failed to come across any proto-M1 ancestor in southwest and south Asia [Indian Subcontinent mainly]:

    Based on the high frequency and diversity of haplogroup M in India and elsewhere in Asia, some authors have suggested (versus [3]) that M may have arisen in Southwest Asia [16,17,31]. Finding M1 or a lineage ancestral to M1 in India, could help to explain the presence of M1 in Africa as a result of a back migration from India. Yet, to date this has not been achieved [15], this study). Therefore, one cannot rule out the still most parsimonious scenario that haplogroup M arose in East Africa [3]. Furthermore, the lack of L3 lineages other than M and N (indeed, L3M and L3N) in India is more consistent with the African launch of haplogroup M. On the other hand, one also observes that: i) M1 is the only variant of haplogroup M found in Africa; ii) M1 has a fairly restricted phylogeography in Africa, barely penetrating into sub-Saharan populations, being found predominantly in association with the Afro-Asiatic linguistic phylum – a finding that appears to be inconsistent with the distribution of sub-clades of haplogroups L3 and L2 that have similar time depths. — Mait Metspalu et al.

    So, while they acknowledge the highest “frequencies and diversities” of M1 particularly in Ethiopia, and generally in East Africa., the authors base their claims about ’origins’ on their expansion estimations of M1c derivatives, presumably predominant in northwest Africa rather than east Africa, and its relative sporadic distribution in ‘Europe’ and ‘Southwest’ Asia. They attempt to buttress this, by invoking an initial parallel expansion of M1 and U6 “ancestor” lineages into north Africa via the Nile Valley [from “southwest Asia”], then an expansion from northwest Africa this time around, of U6 and M1 derivatives northward into Europe and then eastward into “southwest” Asia via the Nile Valley corridor in the Sinai peninsula, presumably with a few derivatives making their way into sub-Saharan east Africa, where they then underwent some expansion, to give rise to yet another, but later, dispersal from there into “southwest Asia” and hence, accounting for the ‘majority’ of M1 lineages in “southwest Asia” being east African derivatives than the north African [M1c] counterparts.

    *Furthermore,

    The authors gather that their observations correlate with that of other researchers, namely Olivieri et al. To this extent, they put forth that Olivieri et al.’s M1b corresponds to their M1c, the former’s M1a2 corresponds to their M1b, and the former’s M1a1 corresponds to their M1a. They go onto to add that the coalescence ages arrived by the two research group [that of Olivieri et al. and that of the present authors] also correlate. The present authors note that their coalescence time for M1c (25.7 +/- 6.6 ky) overlaps with Olivieri et al.’s coalescence time for M1b (23.4 +/- 5.6). Similarly, they note that their coalescence age for M1a (22.6 +/- 8.1ky) falls within that of Olivieri et al.’s age for M1a1 at 20.6 +/- 3.4ky. However, this makes way for great discrepancy between the said authors and Olivieri et al., whereby their coalescence age for M1b at 13.7 +/- 4.8ky falls quite short of the latter’s age for M1a2 at 24 +/- 5.7ky. Not only are the subgroup nomenclatures distinct, but this latter discrepancy makes an unsubtle difference, so as to no longer render M1c to be older than M1b, but rather, either place M1c at an age a bit younger or on par with the latter, which should be otherwise according to the present study. Though, by their own admission, the present authors favor Olivieri et al.’s methods over their own:

    As our calculations are based only on three lineages and that of Olivieri et al on six, we think that their coalescence time estimation should be more accurate than ours. In fact, when time estimation is based on the eight different lineages (AFR-K143 is common to both sets) a coalescence age of 20.6 +/- ky is obtained.

    *But if there is any indication about the tenuous nature of the above thesis, without going into other known details about M1, it would be this alternative viewpoint they came up with:

    The alternative idea entertained by the authors, is one where M1 could actually be an autochthonous northwest African lineage, which spread northward into Europe and eastward to “Southwest Asia” and east Africa. Again, to be followed by a yet later dispersal from east Africa, likely sub-Saharan east Africa, particularly the Ethiopian populations.

    *The limitations inherent in solely relying on hypervariable segment motifs:

    The status quo hasn’t changed, not withstanding the hype about the supposed older expansion timeframes from M1c derivatives, predominant in Northwest Africa, according to their study. The authors rely heavily on the hypervariable region of the mtDNA, which even they themselves don’t seem to put much faith on, as demonstrated by their noting of the need to proceed cautiously, given that random parallel mutations are known to occur across distinct macro-haplogroups and sub-clades. They also note how hypervariable nature of the control region, can lead to misleading calculations from erratic mutations, as demonstrated by the M1a2 they put forth, leading them to omit them in their lineage coalescence analysis.

    *Another thing that hasn’t been relayed through this study, is this:

    The coding regions transitions are likely to change relatively slower than those of hypervariable segments, and hence, likely to remain intact within a clade. To assist in determining which clade to place a monophyletic unit, key coding region transitions have to be identified. In the case of M1, we were told:

    We found 489C (Table 3) in all Indian and eastern-African haplogroup M mtDNAs analysed, but not in the non-M haplogroup controls, including 20 Africans representing all African main lineages (6 L1, 4 L2, 10 L3) and 11 Asians.

    These findings, and the lack of positive evidence (given the RFLP status) that the 10400 C->T transition defining M has happened more than once, suggest that it has a single common origin, but do not resolve its geographic origin. Analysis of position 10873 (the MnlI RFLP) revealed that all the M molecules (eastern African, Asian and those sporadically found in our population surveys) were 10873C (Table 3). As for the non-M mtDNAs, the ancient L1 and the L2 African-specific lineages5, as well as most L3 African mtDNAs, also carry 10873C.

    Conversely, all non-M mtDNAs of non-African origin analysed so far carry 10873T. These data indicate that the **transition 10400 C–>T, which defines haplogroup M**, arose on an African background characterized by the ancestral state 10873C, which is also present in four primate (common and pygmy chimps, gorilla and orangutan) mtDNA sequences. — Semino et al.

    …which is significant, as other M lineages are devoid of M1 coding region motifs, not to mention the M1 HVS-I package. The above does demonstrate, how M lineages likely arose on an African ‘background’ by single-event substitutions in the designated African ancestral counterparts. The ancestral transition of 10873C is substituted by 10873T in non-African non-M haplogroups, while the 10400C transition was substituted in M lineages by 10400T.

    Furthermore,…

    The 489C transition, as noted above and can be seen from the diagram, is peculiar to the M macrohaplogroup, again suggestive of unique event mutations characterizing the family:

    The phylogenetic location of the mutations at nt 489 and 10,873 (arrow) was predicted by our analysis. The seemingly shared mutation at nt 16,129 (by G, Z and M1) is very likely an accidental parallelism. The ancestral states 10400C, 10810C and 10873C are fixed in L1 (as analysed so far) and are present in the ape sequences.

    The 16129 sharing across the M1 haplogroups, seems to be one of those instances of random parallel mutation, recalling Chang Sun et al.’s observations of random parallel mutations of certain transitions across the M macrohaplogroup.

    We also know that “southwest Asian” and “European” M1 lineages are derivatives of African counterparts, and the same is true for southwest Asian non-M1 affiliated M lineages from south Asia:

    Compared to India, haplogroup M frequency in Iran is marginally low (5.3%) and there are no distinguished Iranian-specific sub-clades of haplogroup M. All Iranian haplogroup M lineages can be seen as derived from other regional variants of the haplogroup: eleven show affiliation to haplogroup M lineages found in India, twelve in East and Central Asia (D, G, and M8 ) and one in northeast Africa (M1)…

    Indian-specific (R5 and Indian-specific M and U2 variants) and East Asian-specific (A, B and East Asian-specific M subgroups) mtDNAs, both, make up less than 4% of the Iranian mtDNA pool. We used Turkey (88.8 ± 4.0%) as the third parental population for evaluating the relative proportions of admixture from India (2.2 ± 1.7%) and China (9.1 ± 4.1%) into Iran. Therefore we can conclude that historic gene flow from India to Iran has been very limited.

    With that said, Semino et al.’s older study still remains strong, the way I see it:

    haplogroup M originated in eastern Africa approximately 60,000 years ago and was carried toward Asia. This agrees with the proposed date of an out-of-Africa expansion approximately 65,000 years ago10. After its arrival in Asia, the haplogroup M founder group went through a demographic and geographic expansion. The remaining M haplogroup in eastern Africa did not spread, but remained localized up to approximately 10,000-20,000 years ago, after which it started to expand. — Semino et al.

    Elsewhere, I’ve also talked about some ‘basal’ M-like lineages in Africa; for instance, at least one of such was identified in the Senegalese sample.

    Am. J. Hum. Genet., 66:1362-1383, 2000

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

    “The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. This haplotype branches off African subhaplogroup L3a (figs.2 and3), suggesting that haplogroup M mtDNAs might have been derived from this African mtDNA lineage…”

    The relevant representation in this recap diagram:

    ^The 10397 transition is shown in the L3-M linkage, while 10394, which should show up as positive [as exemplified in the above extract] in the M macrohaplogroup, shows up negative in the linkage between L3 and non-M affiliated lineages.

    **^To put the above compilation into perspective, and keep it simple, the point is this:

    Semino et al.’s demonstration of certain characteristic basic coding transitions of the M super-haplogroup [not including the key coding region motifs unique to the M1 family], springing directly from African ancestral motifs, don’t require that M1 has to have a proto “non-African” M1, whereas an Asian origin of M1 would necessitate an Asian proto-M1 lineage that would explain the relatively young expansion ages of M1 and lack of descendancy from pre-existing Asian M lineages. This hasn’t been achieved either by the present study or ones prior to it.

    Getting to the gist:

    Basal M mtDNA ~ between c. 60 – 80 ky ago

    And then, M1 ~ between ~ c. 10 – 30 ky ago

    The studies I posted, suggest that the basal motifs characteristic of the M macrohaplogroup arose in Africa, anywhere between 60 – 80 ky ago [since they would have likely been in the continent by the time of the 60 ky ago or so OOA migrations] . Sometime between 60 ky and 50 ky ago [some sources place it between 75 – 60 ky ago], these L3 offshoots were carried outside of Africa, amongst early successful a.m.h migrations, which resulted in the populations now living in the Indian-subcontinent, Melanesia and Australia who have these lineages. Not all the basal African L3M lineages, as Semino et al. convincingly put it, left the continent, as indicated by the basal L3a-M motif detected in Senegal, M1 diversity in Africa, particularly East Africa, both M1 and other M lineages detected in Ugandan samples, and lack of descendancy of M1 from older-coalescent Asian macrohaplogroup. Rather, it appears that the basal L3M lineages which remained in Africa, underwent a relatively limited demographic intra-African expansion until relatively recently, i.e. between 10 – 30 ky ago, compared to the Asian L3M derivatives, which underwent major expansions, naturally within the quantitatively smaller founder immigrant groups, i.e. the founder effect.

    M1 is likely the culmination of relatively more recent demographic expansions of basal L3M lineages in the African continent, with M1 derivative being a successful candidate, in what could have possibly involved other derivatives which might not have expanded to the same level intra-continentally, and subsequently, extra-continentally as well.

    M1 has strongly been correlated with the upper Paleolithic expansion of proto-Afrasan groups across the Sahara to coastal north Africa, and further eastward via the Sinai peninsula.

    http://exploring-africa.blogspot.com/2008/01/response-to-ana-m-gonzalez-et-al-2007.html

    • Read, it laughed at it, and observed how Exploring Africa carefully clipped the quote to leave out that the L3a was possibly present in Senegal from a back migration. It also doesn’t deal with the latest publication that also points the finger out of Africa for the Origin of M1, and ignores that Gonzalez observed older ancestral M1 in the Near East.


      the most ancestral M1 lineages have been found in Northwest Africa and in the Near East

      BTW, date for M1 is way older than 10k, which EA put as a lower date range; expansion dates for the M1 offshoots in Africa are in the 22k and older region. Also, M1 and M1a show the exact same distribution as M78, and they all appear to spread out from southern Egypt, not North Africa. Look at the maps, I put a link on the previous comment.

  7. Do you mean M1 and U6a? I will assume you do.

    It would not surprise me if they expanded together in many areas. Admittedly I have not read much on M1 specifically but I understand that, like U6a, it seems centered in Upper Egypt/Lower Sudan, right?

    For the U6 question I just see that U6a and U6b appear similarly old based on SNP count (U6c should be more recent in its limited expansion) but only the first exists in North Africa and more importantly in NE Africa, where the haplogroup should have coalesced according to the Asian origin theory. Instead in Iberia you find all three major clades (only place) and the fourth is a small lineage limited to… Egypt? No. Ethiopia? No. Arabia? No. Morocco maybe? Nope. The answer is: Sardinia.

    The problem some see for an Iberian origin is that U6 is rare in the rest of Europe (except some presence in Italy and maybe France) but Southern Iberia was a reciever of population in all the UP (except for maybe a minor expansion limited to Asturias and, sure, the likely projection in North Africa with the Oranian). So if they had a founder effect with Aurignacian or Gravettian colonization, that could perfectly have never expanded into the rest of Europe… but would have expanded into North Africa with Oranian culture (as surely happened with H and V and, IMO, even maybe K, part of U8 another U subclade whose highest diversity is among Basques).

    Again this may be a problem of misinformation by geneticists, for many of which there is no clear difference between the Franco-Cantabrian region (apparently at the origin of a good deal of the European genetic pool, quite strongly supported by archaeology) and southern Iberia (that in fact did not provide the origins of any expansion into the European continent). A founder effect in southern Iberia therefore would still be basically found in Iberia and nowhere else… wouldn’t it be for the Oranian culture.

    Another possibility would be that U6a and the other U6 subclades would have split in West Asia before moving into Africa and Europe respectively but that doesn’t seem to make any sense.

    But the theory that claims that U6 coalesced in Egypt and mysteriously got disowned of all subclades but U6a in its region of origin, while all them are found in SW Europe (and except U6c, shared with Morocco, nowhere else) doesn’t make any sense to me either. Moreso as I can’t see clear the archaeological premises for an Egyptian origin of Oranian, while I do see the precursors of Oranian in the Gravetto-Solutrean of SE Iberia: all-covering Solutrean retouch, back-tipped arrow points with “wings”, etc. Not to mention the Upper Egyptian UP art argued to resemble European cave art (rare but existent as well in southern Iberia) way too much.

    This doesn’t mean that subclade U6a, wich seems to have coalesced in Upper Egypt (this subclade is most diverse there) would not have partly expanded with M1 in Africa and elsewhere from that area.

  8. mathilda anyone with half a brain can recognize the inconsistencies and problems with Gonzalez et al.’s control region-derived coalescence age estimations; not only is its accuracy hampered by insufficiency of Intra-M1 phylogenetic representation, but also due to the homoplasic events that are often associated with the hypervariable region. As noted, the authors’ forced omission of their M1a2 markers from their estimations for instance, is bound to contribute to the throwing off their age estimations. The “Near Eastern” section of the Great Rift Valley have 1) no upstream markers of neither M1, L3, nor even that of the Asian M macrohaplogroup; rather, this region has only downstream derivatives of these markers. 2) The ancestor of M1 has not been located in either south Asia [which is essentially home to the Asian M family] or the “Near East”. 3) However, the lineages necessary to give rise to M1 are all present in Africa, as exemplified by the 10873C [emphasis added] marker [Semino et al.] at the RFLP position 10873, which transcends M macrohaplogroup, having been identified amongst L1, L2 and L3 clades; on the other hand, all non-African non-M clades, which are all essentially ultimately derivatives of the African L3 superclade, have 10873T [with emphasis]. This suggests that African M1 and the Asian M macrahaplogroup derive from an earlier bifurcation event that took place in Africa, which transcended L3. Furthermore, “middle-of-the-road” evolutionary clade of L3a, descendant of L3 but older than other M-designated L3 lineages and found in a Senegalese sample, adds to this theme of Africa having all the necessary markers to give rise to M1. Further more, that the authors propose two origin theories, is further testament to the fragile nature of their theory.

    Now, I’ve dumben down the M1 piece further down by several notches; alas, these things are too complicated for feeble-minds.

    • The problems with what you just posted…

      1. I’m not using Gonzalez for the dates-I’m using Olivieri’s recent study that also points out of Africa for M1 (you know, the one you pretended doesn’t exist and that uses twice as many lineages as Gonzalez to date it). You’ve overlooked that Gonzalez and Olivieri both get similar dates, over 20k as an average for the dispersal of M1 in North Africa, and when combined their results support each other.

      2. Moaning there is no ancestral M in India is dumb as a support for an African origin, as it doesn’t occur in Africa either. But you do get masses of different types of M in India, some very ancient, I’ve seen a date of over 87k estimated in one Asian branch. You only get one relatively young M in Africa, and it shows a close affinity to the movements of U in North Africa, which is Asian. Two points against an African origin of M1 (younger age and less diversity).

      However, the lineages necessary to give rise to M1 are all present in Africa

      3. Nope. You need to read more up to date papers, you are using data ten years old (and now heinously outdated) to base your arguments on, which is probably why your age for L3 at 50k was so massively innacurrate – M is over 65 at least, you do the maths.

      The 10400 C > T transition defines M, not 10873 C. (Semino, the study you quote) and so far all the evidence is that it had a single origin, and nothing points to it being in Africa. Sure, it descends from an African mt DNA with 10873 C, but the actually M defining mutation is absent in these African L clades (by defintion really). All that shows is that Eurasian mt DNA is descended from African mt DNA, (duh) and that the split from L3 to N was outside Africa and possibly L3 had been in Asia for a while when it happened; 10873 with a C to T transition is typical of Eurasian non-M (N), and it isn’t seen in L. L3a is ancestral to M and N, (source Kittles), the one you observe in Senegal, but it lacks 10400 C>T. If anything the lack of N in Africa (a first generation offspring of M like M) is indicative the it was L3 that left Africa and not M.

      So all that you did is show that L types with 10873 C (L3) are ancestral to M and N, and that 10873 T occurred in Eurasia-again duh. BTW; Semino says there’s no evidence the 10400 C > T transition has arisen more than once, so it’s not looking like a spontaneous mutation in East Africa from some stray L mother- all you’ve done is list the mutations that L and M have in common, not point out the long ignored mother of M1.

      Your entire case is built on Semino’s old and way less complex study of M1 which is now pretty antiquated. His dates for M don’t match anything published after 2005 and are corrected by later larger studies with beter resolution involving M1 and M, yet you chose to cling to it like it’s gospel. It’s still got an OOA date of 65k on it, for heavens sake.

      The only reason you take issue with the M1 being Asian in origin is that it demonstrates a significant input from Asia into Africa at a very ancient date, and it ‘contaminates’ East Africans if it’s not African in origin. This is not an intellectual quibble with the origin of M or M1.

  9. Totally with Mathilda here: M is a single haplogroup defined by a number of SNPs (that do not happen twice) shared by all M subclades. It has a single origin and, by deduction from the derived diversity, it is generally accepted that this origin coalesced in South Asia or not far away from it (in Asia in any case).

    You can maybe argue that, after the separation from M, M1 back-migrated to Africa and coalesced there before expansion (instead of West Asia) but that’s how far you can go.

    If M would have coalesced in Africa, we should see most of the derived diversity in Africa and maybe nearby areas like West Asia. We do not: all M subclades but M1 are distributed in South and East Asia, plus Sahul and Native America, all very far from Africa.

    Besides, Africa has an incredible mtDNA diversity. I see no reason why an ancestral clade coalescing there would not leave any traces. And I see no reason not to expect a bifurcation at the root M, if this haplogroup would have diverged in Africa – i.e. M1 would not hang directly from the M node like all the other M subclades but from a pre-M one, lacking some of the mutations leading to M, which must have developed only in the journey/coalescence in Asia. In other words: it would be L3-something and not M.

    That is… unless you believe in magical intercontinental teleportation was part of MP tehcnologies. ^^

  10. The power of shamans knows no bounds.😉

  11. Lius: “M1 would not hang directly from the M node like all the other M subclades *but from a pre-M one, lacking some of the mutations leading to M*, which must have developed only in the journey/coalescence in Asia. *In other words: it would be L3-something and not M.*”

    I think that is what Richard is trying to show when He speaks of the Senegalese sample is that sample shows something that seems to be a precursor to M – Both characteristics of M “DdeI site at np 10394 and an AluI site of np 10397” are seen in the Sample from Senegal. (Below)

    “The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. ”

    Factiods about Senegal.
    -Highest frequency of E3a in Africa.
    -E3* sampled around 3%
    -M35* sampled around 5%

  12. I think that is what Richard is trying to show when He speaks of the Senegalese sample is that sample shows something that seems to be a precursor to M – Both characteristics of M “DdeI site at np 10394 and an AluI site of np 10397″ are seen in the Sample from Senegal. (Below)

    But that doesn’t say anything of M1 as such, that hangs not from pre-M (L3a or whatever) but from M and has at least 11 SNPs in between. It may point for an origin of pre-M in Africa but of all M, not just M1. We already knew that M and N derive from African clades but that says nothing about M1 or N1.

    “The Asian mtDNA phylogeny is subdivided into two macrohaplogroups, one of which is M. M is delineated by a DdeI site at np 10394 and an AluI site of np 10397. The only African mtDNA found to have both of these sites is the Senegalese haplotype AF24. ”

    Factiods about Senegal.
    -Highest frequency of E3a in Africa.
    -E3* sampled around 3%
    -M35* sampled around 5%

    It’s interesting. M35 nevertheless is considered a South Asian haplogroup, though it has some erratics in Central Europe (Slovakia) too. Maybe it participated in an early migration westward that managed to leave some erratics (more like a founder effect would seem) as far as Senegal.

    And maybe that happened within the expansion of E3 (in general E is believed to be of East African origin, not sure about E3 right now, especially as nomenclature has danced in this clade a lot as of late).

  13. Ok, well what doest that mean?
    Poorly studied Mali : 40% of the Sub-saharan lineages belong to L3a. L3a is sampled all over Africa. Your Statement I dont understand.

  14. M35 is not Asian. M35 is generally seen in Horn Africans and Sudanese Nilo Saharans.
    E3* is also African and only sampled here in Africa. E3* is also called P2 or E1b1*
    Luis – Thanks I understand what you are trying to say. I did not understand what the original poster meant by saying
    “It is THE precursor to M and N, it’s L3a.”

  15. my L2a includes ashenazi Jews, why?

  16. M35 is not Asian. M35 is generally seen in Horn Africans and Sudanese Nilo Saharans.

    You must mean M35 as in “mutation M35 in some Y-DNA lineage” and not as in haplogroup M35 (mtDNA by default). After checking it seems it’s E1b1b1c. Ok.

    You got confused and confused me and surely everyone around. If you mean E1b1b1c write that or at least E-M35. Whetever the case you confused mtDNA M with an Y-DNA marker that uses the letter “M” in the nomenclature (meaning it was discovered by Underhill’s team – nothing else).

    Luis – Thanks I understand what you are trying to say. I did not understand what the original poster meant by saying
    “It is THE precursor to M and N, it’s L3a.”

    We’re talking mtDNA here. L3 is the African lineage from where M and N derive (not so sure about L3a, most trees make it derive directly from the L3 node).

    When he mentions that lineage M is found somewhere in Senegal, he seems to intend that M could have coalesced in Africa and not Southern Asia, as it’s normally understood. But it’s surely just some M1 or soemthing with an easy explanation. In the best and most interesting case, it might be some sort of pre-M, derived before M really made its way out of Africa. That would be a really “interesting” finding, if true.

    my L2a includes ashenazi Jews, why?

    Why not. Jews seem to have a most variegated mtDNA pool, sign of their many travels and migrations through history. It seems that they took local wifes (or concubines or whatever) wherever they arrived (not very khoser surely in regards to descent but very much in line with the real patriarchal tradition of this sect).

  17. ANTHROPOLOGIQUE

    I’m no geneticist but, from everything I have read, I suspect that the vast majority of L mtDNA in Iberia (and there is very little) derives from Asia. L (Y-DNA) is practically non existent in Iberian populations.

    New , more advanced testing is sorely needed to determine origins. The last few studies that were done had some significant methodology issues, including the use of non-representative samples (e.g., Gonzales et al. 2003).

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