Saturday, April 30, 2011

Summarizing clade M1

Clade M1 has been mentioned on this site quite a few times, usually in complicated molecular genetics jargon that some may be hard-pressed to understand. At times, the jargon proves to be complicated to the point that some individuals don't even realize it, when their ideological views about this clade are being refuted beyond little to no doubt. So to address this, the goal herein is to simplify basic facts about this clade to the extent possible.

Like many other African-specific clades that have managed to spillover to other continents in any considerable way, clade M1 has been made into a subject of controversy. Much of this comes from the yearning, mainly within Eurocentric circles, to de-Africanize any clade that is implicated in any significant demic-cultural diffusion, be it for example, the now popular theory of the Neolithic agricultural revolution of the so-called "Near East" or be it the emergence of the so-called "Afro-Asiatic" language phylum in the "Near East". Clade M1 has been implicated in both of these examples. Not surprisingly, like the infliction brought to bear on clade M1, over the years efforts have been made to turn Y-DNA clade, hg E-M35—another clade implicated in the aforementioned examples of demic and cultural events, into either a "PAN Afro-Asian" clade, which would in effect downplay the fact that it is African in origin and largely specific to Africa, and/or cleanse it from being identified as an index of "sub-Saharan" ancestry. E-M78, subclade of E-M35, for instance, had gone from being initially identified with "sub-Saharan" origin to being relocated to a relatively higher latitude of origin, even though the location of origin remained in the African continent. Such relocation efforts though, were apparently not sufficient enough in some ideological circles, and so, efforts were made to make a case for the removal of the entire macrohaplogroup E from Africa. Much of the controversy that are made of clades like M1 and E-M35 are born out of a desire to cater to personal ideological concerns, because when it comes down to examining facts, the controversy fairly quickly dissipates, such that there really is no controversy! To demonstrate this around the subject of the present blog entry, i.e. clade M1, consider the following outlining:
  • Clade M1 is distributed east to west or vice versa, and sub-Saharan to the coastal Northern Africa or vice versa. It is a misnomer that the southern limit of the clade is Ethiopia or the African Horn. The clade is found as far south of the continent as Tanzania, where it co-exists alongside other non-M1 haplogroup M clades!
  • Although it has been said that clade M1 appears to have its highest concentration in eastern Africa—some suggest that the highest frequency is in Ethiopia, in the grand scheme of things, the frequency factor carries little weight. Why? Clades of the Maghreb for instance, have been determined to belong to different M1 branches and/or sub-branches from those of eastern Africa. In other words, Maghrebi examples are not a subset or derivative of the eastern African M1 gene pool. Conversely, despite its relatively lower distribution, it can be argued that the Maghrebi M1 network is relatively more diverse than that of eastern Africa, and could hence, well serve as a super set to the eastern African branch.
  •  As of the writing of this blog entry, the Maghrebi M1 clades are not sub-clades of the Ethiopian M1a or M1b. Maghrebi clades in large measure fall into fairly distinct branches, if not sub-branches, from the Ethiopian counterparts. Specifically, the Maghrebi M1 network consists of at least two divergent branches of M1, whereas the eastern African examples mainly fall under one major branch, that then branches off further into two sub-branches. On the other hand, the "Near Eastern" M1 clades are generally derivatives of the Maghrebi branch and/or eastern African branches; the "Near East" is one of the few locations wherein clades of the Maghrebi branch and the eastern African branches co-exist. This distribution pattern is most logically accounted for, through a two-pronged migration theory, wherein the first demic diffusion of M1 occurred from the Maghreb or western Sahara and into the "Near East" sometime during the Upper Paleolithic, whereas a later demic diffusion occurred from eastern Africa or eastern Sahara and into the "Near East" at around the Neolithic era and/or during the spread of proto-"Afro-Asiatic". To illustrate the divergence between western African or Maghrebi M1 clades, two schematics are provided below; the upper rendition comes from an earlier study, referenced by Kivisild et al. (2004), and the lower rendition comes from Gonzalez et al. (2007)—click on the images for higher resolution:
Cited by Kivisild et al. (2004) courtesy of Maca-Meyer et al. (2001)

Courtesy of Gonzalez et al. (2007)
  • In relation to the point immediately above, one would expect either Ethiopian or Maghrebi M1 distribution to be duplicitous of the "Middle Eastern" distribution pattern, if they were the derivatives of the "Middle Eastern" examples rather than vice versa.. This would be true, even if a scenario was envisioned wherein the Maghrebi examples came largely from an earlier dispersal than the eastern African counterparts; instead what we have, is that the "Near East" contains derivatives of clades of either region! On a side note, it's almost inconceivable to imagine a later M1 arrival with would-be migrants from  the "Near East" avoiding the Maghreb altogether, presumably in contrast to an earlier arrival, and instead choosing to go straight down south and settle eastern Africa.
  • All the prototype clades necessary to beget clade M1 are located in Africa. In contrast, no territory outside of Africa carries any such prototype clades. A good example of a prototype clade for M1, is the African AF24 haplotype. There is no evidence that the restriction site duo (np 10394 & np 10397) that this haplotype shares with the M haplogroup happened more than once, which implies that the bifurcation event that led to emergence of M haplogroup occurred in Africa before an OOA migration! Here is a simple schematic that provides an illustration of this (restriction site(s))—click on the image for hi resolution:
Courtesy of Quintana-Murci et al. (1999)
  • Haplogroup M is the ONLY non-African-specific mtDNA family that shares the ancestral 10873C site with the African L-type haplogroups, including a segment (most) of African L3 clades.For illustration, again see the above posted Quintana-Murci et al. diagram.
  • Some have seized on the "Phylotree" site's bridging of M1 with M51 and M20 clades under the M1'51 banner via the singular 14110 nucleotide position, to make a case for the "Asian origin". This condition does not make either M51 or M20  a sister clade of M1 any more than it makes any other south Asian-specific M subclade M1's sister clade. The nucleotide substitution in question has been implicated in a few other distinct M clades rather than just a single other clade, outside of either M51 or M20, and in fact, appears to be nothing more than a recurrent mutation. In other words, the substitution doesn't appear to be a UEP. It is found in for example, a singular extreme downstream sub-clade of one M sub-branch and then it appears as a basic transition in another M sub-branch. This suggests a recurrent mutation, as opposed to a unique event.
Estimation of possible location of origin of clade M1: Within the vicinity of central Sahara, before dispersing west and east. That would explain the divergent pattern between western African or Maghrebi examples and the eastern African examples. Nucleotide specifics indicate that M1 clade's earliest expansions likely took place in the direction of western Africa, before establishing itself in the African Horn and further south thereof. Examination of M1 clades outside of Africa mainland suggest that early demic movements of hg M1 may have involved at least two major dispersals: one just prior to the Ogolian aridity, and another, at or near the recession of the aridity, likely coinciding with the spread of proto-"Afro-Asiatic" language from Africa and into the Arabian plate.

Calling for caution: Some folks take websites like "ISOGG", and perhaps to lesser extent—"Phylotree", as though they were words of a supernatural being, i.e. that they are infallible. However, data from these sites are primarily compiled from preexisting published material, although in some instances, as noticeably featured on the ISOGG website, the reader is informed that the information was collected via personal correspondence with some author or another; indeed, these sort of sites can prove to be quite resourceful, but it would be a mistake to assume that every information posted on these are necessarily always accurate, and not warranting additional efforts at verification on a personal level. For its part, the ISOGG site for example, puts out this disclaimer:

ISOGG (International Society of Genetic Genealogy) is not affiliated with any registered, trademarked, and/or copyrighted names of companies, websites and organizations.
This Y-DNA Haplogroup Tree is for informational purposes only, and does not represent an endorsement by ISOGG.

*Be on the lookout for possible future updates.

Quintana-Murci et al (1999), Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa.

Kivisild et al. (2004), Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears.

Maca-Meyer et al. (2001), Major genomic mitochondrial lineages delineate early human expansions.

Gonzalez et al. (2007), Mitochondrial lineage M1 traces an early human backflow to Africa

—Personal notes 2020 & 2011.

Additional on-site reading material:

Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007

Following Trails of the Cro-Magnon - II


Too Tall Jones said...

Good write-up. I like this key sentence: "All the prototype clades necessary to beget clade M1 are located in Africa. In contrast, no territory outside of Africa carries any such prototype clades."

I do not see this line of reasoning discussed much in various academic journals or books. Questions:

1) What are your thoughts on the concept of "back migration" itself?
and specifically that of Hap M? I can hardly see people from say 'M" loaded India deciding to walk back to East Africa and settle down? The concept seems shaky on its face.

2) What are some recent authors that lend material weight of data to the indigenous African scenario?

Noir said...

Mystery solver,

You are a wonderful, sentient, human being. Thank, you! Very deeply, for sharing your studies and setting the record straight.

I find the same so-called scientist/and inferioritist, in the arts, philosophy and psychology.

Psychotic, and envious psuedo- scientist and the entities supporting their madness do not understand that fundamental principles of the universe (melanin) is balance, justice, harmony, and truth.

If so they would simply reveal the findings as they present without tinkering. But, No!, they don't give the Ancient Afrykans credit for their magnificent civilizations... .

They and others simply steal Km identity. And assume Black African identity.

So-called, "white supremacy" is a balled-faced, lie. As science bears out.

However, in their psychotic, hubris and rabid, envy they are driven to lie, cheat, omit, etc... . To continue the lie.

Keep up the good, fight!.

I look forward to reading each article.

P.S. I am researching melanin and the Dogon people. Have you any information regarding those subjects?.

Peace to you!


Ann said...

European 'Cro-Magnon' : The Big Lie?

I ran across this article regarding the 'African' mtDNA in Paglicci-Man. It directly contradicts the 'Caucasian-European-ness' and suggests another mutation be found to make the mtDNA more distant from mtDNA L3.

Please read it and tell me what you think.

Link to my site:

Link to article:

“A likely case of mosaic structure is hidden in a recent high-profile publication,51 where the authors claimed to have retrieved authentic mtDNA information for two approx 24 000-year-old European ('Cro-Magnon') human specimens. The variation in the first hypervariable segment of the D-loop (HVS-I:16024–16400) was assessed in two labs with 2–4 primer pairs. It was asserted that specimen Paglicci-25 is identical to rCRS and Paglicci-12 differs from rCRS by a transition at 16223 in HVS-I. According to the authors, specific mtDNA sites outside HVS-I were also analysed ('by amplification, cloning, and sequencing of the surrounding region'), but no details were given in the paper, except reporting that Paglicci-25 has -7025 AluI and bears nucleotides A at 73, G at 11719, and A at 12308, whereas Paglicci-12 shows G at 73, C at 10873, T at 10238, and AACC at 10397–10400. These additional analyses were only carried out in one lab and not duplicated in a second lab. The authors further asserted that the mtDNA of both specimens belong to typical Near Eastern haplogroups. In particular, the mtDNA of specimen Paglicci-12, with claimed mutations at sites 73, 10873, and 16223 but none in the stretch 10397–10400 relative to rCRS, was regarded as a member of haplogroup N. They have, however, confused the roles of C and T at 10873 in the mtDNA phylogeny – in fact, C at both sites 10400 and 10873, as observed in Paglicci-12, indicates that this mtDNA haplotype should rather not belong to either of the Eurasian/Oceanian haplogroups M and N, which completely cover the non-African mtDNA pool. Therefore, we would be led to sort this mtDNA lineage into an (unknown) African subhaplogroup of the superhaplogroup L3; but this does not sit easily with the claimed nucleotide A at 10398.

So, I checked out mtDNA and L3 and found this:

L3e1a3 : 10398A.

No problem.


L3e - West-Central Africa. It is the most common L3 sub-clade in Bantu-speaking populations.[12] L3e is suggested to be associated with a Central African origin and is also the most common L3 subclade amongst African Americans, Afro-Brazilians and Caribbeans [Anderson, S. 2006, Phylogenetic and phylogeographic analysis of African mitochondrial DNA variation ;]

L3e1 - Central Africa origin and is found in Algeria, Cameroon, Angola...

But the same contentious mutation is also before L3, as shown here:

L1c1a1 10398A, 14034C, 16223C.
L3e1a3 10398A.

Details of mtDNA L1c:

Haplogroup L1. 107,600–174,300 YBP
Possible place of origin : Central Africa. Ancestor : L1-6. Descendants : L1b, L1c


Defining mutations : 3666, A7055G, 7389, 13789, 14178, 14560[2 : van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation 30 (2): E386–E394. doi:10.1002/humu.20921. PMID 18853457. Retrieved 2009-05-20 ;]

Has this error with the T>C been resolved, or is Paglicci Man really an 'African-European' after all?