November 8, 2012

Refinement in the knowledge of old African Y-DNA haplogroups

New important paper refining the understanding of old branches of mostly African patrilineages (which are important to understand the ancestry of all Humankind). 

Rossaria Scozzari et al., Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree. PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0049170]

Abstract

One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.

Figure 1. Revised topology of the deepest portion of the human MSY tree.

Besides B2, A3 has also been greatly improved in its understanding suggesting recent expansions. 

Haplogroup B2 is typical from Pygmies but also found through all the Sahel from Ethiopia to Mali, among other Central African populations and even among Southern African aborigines, the Khoisan peoples. 

Haplogroup A3 is important in Sudan and the Horn of Africa, as well as among the Khoisan peoples of Southern Africa. It's also occasionally found among Bantu speakers of Southern Africa, Egyptians, West Asian peoples and has also been reported in Sardinia.


New C subclade

Besides Africa a new haplogroup C7 was reported in an Italian individual. See supp. materials.

9 comments:

  1. "a new haplogroup C7 was reported in an Italian individual".

    Now that is extremely interesting.

    "Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity".

    That too is interesting, as it is very difficult to place mt-DNA L's origin anywhere other than somewhere in East Africa. That means that the modern mt-DNA and Y-DNA originated in separate places. I find that easy to explain but others may see a problem.

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    1. C7 is not really that interesting for as long as it is a private haplogroup (like C6) found only in isolated cases, it is not distinct in fact from other C*, which, according to Wikipedia is found "at low frequencies in Asia and Oceania". They should not talk of haplogroup in fact nor give it a name until several unrelated individuals have been found to bear the same lineage IMO.

      "I find that easy to explain but others may see a problem".

      It is a problem indeed, specially as autosomal DNA diversity points towards a Southern African origin for Humankind, making it a true "trinitarian mystery", so to say. I trust the most mtDNA because it paints a very coherent, easy to trace, picture but surely the other elements also add some nuances.

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  2. "They should not talk of haplogroup in fact nor give it a name until several unrelated individuals have been found to bear the same lineage IMO".

    I agree. In passing, C6 seems to have vanished without trace. Do you know anything more about it? Last I heard was that Ebizur claimed it was from New Guinea.

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  3. This, along with Cruciani's earlier find of the most basal YDNA lineages in West/Central Africa, in addition to more recent 'rumors' regarding an earlier dating for basal YDNA lineages found in West Africa, is not enough to really settle the issue where in Africa the modern human lineage arose.

    Autosomal genetics points us South Western (Namibia) Africa, mtDNA points us to Eastern Africa and more recently, YDNA potentially points us to West Africa, while almost all material evidence is concentrated in the Rift Valley, with the most continuous record of both ancient and modern humans being best preserved exclusively in Ethiopia.

    So again, while it is fully possible the root of the YDNA arose in West Africa, I simply don't buy it, at least not yet anyway, rather, since we know that the very vast majority of YDNA lineages in West Africa is of the E1b1 (E-PN2) extraction, and since we know with a fairly high degree of confidence that E1b1 is of East African origin, I would rather speculate that these highly infrequent basal clades of A(XBT) may have been transported from East Africa to West Africa at some point in the recent past, rather than them being actual signals of a spatial origin of the Human YDNA lineage.

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    1. This paper follows Cruciani 2011 but doesn't seem to increase our information on A1b and A1a except for a few "redundant" SNPs (in red). Their findings are concentrated in A3b and, less dramatically, also B2a1a2 and C.

      Otherwise I agree that the very long branches in West Africa cannot be taken alone as evidence of anything. Still, unless they are also located elsewhere, they are what they look and they might even belong to very old divergent Homo sp. populations like Djebel Irhoud or whatever, whose mtDNA has not been preserved.

      The autosomal tendency may have been caused by incomplete sampling. Also "diversity" values may depend on the equations applied. For example Jinchuang Xing et al. 2010 get the Hema (aka Hima), from Eastern DR Congo, as their most heterozygous population but not by much. Other studies have even claimed greater diversity among tribal Indians (undersampling Africa though), etc.

      Also we do see the same kind of freaky behaviors in Y-DNA elsewhere. If we'd judge blindly only on basal diversity and geography, CT (CF'DE) would have to be considered original from India or so. However we do look at the matter from a more comprehensive and solid viewpoint provided by mtDNA, autosomal diversity and other lineages, forcing most of us to discard the weird zig-zags of Y-DNA lineages as not too important overall.

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  4. "Autosomal genetics points us South Western (Namibia) Africa, mtDNA points us to Eastern Africa and more recently, YDNA potentially points us to West Africa"

    That diversity in origin is by no means impossible, and in fact quite likely. It is surely very unlikely that modern humans evolved from a single, small population that had been genetically isolated from all others since H. erectus times.

    "since we know that the very vast majority of YDNA lineages in West Africa is of the E1b1 (E-PN2) extraction, and since we know with a fairly high degree of confidence that E1b1 is of East African origin, I would rather speculate that these highly infrequent basal clades of A(XBT) may have been transported from East Africa to West Africa"

    But E is very much a downstream haplogroup. Almost anything could have happened between A's first appearance and the development of E. And E's ancestor could just as easily have been transported from West Africa to East Africa at some point in the recent past.

    "Still, unless they are also located elsewhere, they are what they look and they might even belong to very old divergent Homo sp. populations"

    If the molecular-clockology is anywhere near relevant the basal A belongs to a period before 'modern' humans had even appeared. The modern haplogroups did not appear out of thin air. They must have had some pre-modern ancestry.

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    1. Evolution mostly happens by divergence, so relative isolation is a must have at the origin of our species. Also that's what the mitochondrial genealogy says: we don't see many different chimp-related lineages converging in one species, ours: not at all. What we see is a single lineage (so-called "Eve") diverging in various bouts of expansion: first L0 and L1, then L2, L3 and others, M, N and R, etc.

      Now this relative isolation may have some nuances to fine-tune but it's clear that the species did not arise simultaneously everywhere. That's simply absurd, impossible and contrary to evidence.

      First of all I essentially discard the autosomal diversity "evidence" because different papers say different things. It's clearly in Africa (only one paper finds higher diversity in Indian tribals, while many do in Africa) but the exact location may be impossible to identify because the autosomal genome is a very complex matter.

      So what remains are the two divergent early "A1" lineages in West Africa. But hold on that I read a rumor online, Dienekes referencing twitter about an "A00" new lineage, whatever that means. Excluding this rumor, they may be inputs from a related "Homo pre-sapiens" or even early diverged fully H. sapiens population from that region but probably the last word on the matter remains to be said.

      Wait and see.

      "But E is very much a downstream haplogroup".

      Precisely. Based on mtDNA, I can't deduce a colonization of West Africa long before the OoA. Central Africa around the Chad and such yes (L1c and L2). So that West Africa was settled with mostly E lineages makes some sense.

      However we know that some H. sapiens (Jebel Irhoud) were in NW Africa (and therefore maybe West Africa also) at least 35 Ka before any evidence of the OoA and the related East and Central African expansions (L3, L2...) So maybe the explanation is just Jebel Irhoud (or something related).

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  5. "Evolution mostly happens by divergence, so relative isolation is a must have at the origin of our species".

    'Relative isolation'. But how relative was that isolation? You may not have seen this 2006 John Hawks paper. Sorry, it's a 'google':

    http://www.google.co.nz/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CCEQFjAA&url=http%3A%2F%2Fwww.paleoanthro.org%2Fjournal%2Fcontent%2FPA20060101.pdf&ei=1vSiUN7gPM-5iAfwo4HQCg&usg=AFQjCNF2WtathnV17xMivJRXLynQe6Y58Q

    The question then becomes, 'were 'archaics' separate species, or merely subspecies.

    "Also that's what the mitochondrial genealogy says: we don't see many different chimp-related lineages converging in one species, ours: not at all".

    But whatever species we care to look at all mt-DNA lines must converge to a single line if we go back far enough. But that point of origin may not indicate the point of origin of that species. It is extremely unlikely that any species has actually evolved from just a single female, or male for that matter. There must be at least several individuals in any founding population. Besides which that 'founding population' would be almost certainly able to breed with its near neighbours. Unless you're going to suggest that a small group of pre-modern humans woke up one morning and suddenly found they were modern humans.

    "First of all I essentially discard the autosomal diversity 'evidence' because different papers say different things".

    But that is simply because they look at 'different things'. One thing we can be reasonably certain of is that human (or any other species') evolution is no simple thing. We're returning to the Garden of Eden syndrome here.

    "It's clearly in Africa (only one paper finds higher diversity in Indian tribals, while many do in Africa) but the exact location may be impossible to identify because the autosomal genome is a very complex matter".

    But it may have involved a sizable region within Africa.

    "Based on mtDNA, I can't deduce a colonization of West Africa long before the OoA".

    But 'humans' of some sort obviously lived there. And isn't it the case that admixture from an archaic West African population is now fairly well accepted? Just because the West African mt-DNA has not survived in the modern human species does not necessarily mean at all that aDNA does not survive.

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  6. I'm not sure if you've read this at John Hawks' blog, but it is surely relevant:

    "Genetic information from ancient skeletons has transformed our understanding of human origins. For more than 160 years, anthropologists defined humanity in contrast to the Neandertals. Now it is clear that the genealogical ties between living people include Neandertals and other archaic humans within our biological species. An accounting of the shared genetic ancestry in humans worldwide and the ancient Neandertal and Denisova genomes helps to show the pattern of population structure in the Middle Pleistocene populations that gave rise to modern humans. Our species included variations that no longer exist today, while our evolution within the last 100,000 years has been a process of amalgamation and rejoining of populations that were once much more different. As we redraw our genealogical boundaries to recognize this pattern of relationships and evolution, we are beginning to discover the way that the present traits of humans around the world emerged in a variable population".

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