Tuesday, April 16, 2013

Update on Investigation into the "Mysterious" EpiPaleolithic Maghrebi Remains!

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Introduction

This entry is supposed to serve as an update and add-on to a blog entry that was first published here back in May 5th, 2010, under the heading, An Investigation into the "Mysterious" Mesolithic Maghrebi populations. The arguments made there—in the main, are still quite sound, but over the years, some DNA-assignment shuffling within the reconstructed human mtDNA phylogenetic network had taken place. This sort of thing happens quite a bit in the field of molecular genetics, usually in the form of either changing the phylogenetic location of a newly identified clade or a preexisting one, and/or renaming entire clades with new naming schemes, since researchers tend to see information about larger phenomena in the form of fragments. As such, sometimes previous information (source material), especially on newly identified clades, becomes obscure or rarer. To address a situation such as this, in the few occasions where they may have occurred, this entry has revisited elements of the aforementioned entry, modify as necessary, or simply add to information previously posted. 

 

Discussion

Another driver, though a minor one, for revisiting this subject, is the tremendous popularity of population genetics of coastal northern Africa in the so-called "west". People in the so-called "west" tend to have a bizarre fascination with coastal northern Africa, in contrast to enthusiasm greeted upon other areas of the continent, and in doing so, the people of the sub-region have been taken to "mystical" proportions, that is almost as ridiculous as speaking of extraterrestrial aliens transplanted into a new land where they would subsequently be cordoned off from preexisting inhabitants. With that said, as of this 2013 writing...

L1b and L2a subclades have tested positive for transition 16126C. L3 was earlier implicated (see older content of the main entry) in this mutation; examples for this, reportedly occur in the L3d, L3e (L3e2), and L3f clades [4].

Transition 16355T appears in subclade L5a, L2c, L2b, L2e [1], L1c3a1b, L3k1 [2], L4b2 [5] and L2d [3]. It’s worth noting the presence of this polymorphism in the so-called L-type aforementioned clades, but also, that while it appears in the R sub-haplogroup of the L3N clade, the location of both transition 16126C and 16355T in 2 mutually independent sub-haplogroups of the R clade, which are in turn mutually independent of hg N sub-haplo-groups N1a1a and N11 [2], where 16355T again appears, whereas either polymorphism is rendered absent in other sub-haplogroups of hg R and hg N super-clades, suggests that these polymorphisms have independently emerged multiple times in distinct mtDNA organelles.

These sites are thus highly polymorphic compared to some other sites, and chance occurrence in mutually independent mtDNA clades is also quite high; in other words, these polymorphisms in on themselves, cannot reliably be used in absence of additional differentiating data to draw solid conclusions about haplogroup assignment with high confidence. Also helpful, is the possible necessity of not only solid reproduction of results in more than a single individual [e.g. polymorphisms 16126C and 16355T were pinned on a single individual], but as noted in the earlier passages, solid reproductions of results involving several different runs of DNA sequencing involving the very same individuals.

More examples of convergent mutations across different mitochondrial clades, recalling other earlier posted material: Take the aforementioned mutations at np 16298 rendering the mtDNA clade assignment into divergent super-clades; to this end, L3 was given as an exampleadd hg M7b or M8, as other exemplary alternatives.

Likewise, the transition at np 16179 (16179T) has been reportedly identified in L3 (xL3M, L3N). While it remains valid that the noted mutations at np 16179 and 16298 respectively occur in hg L3h1, it is important to note, and hence clarify, that they don’t occur in a single haplotype, but two different sub-clades (L3h1b1 and L3h1a1 respectively [2]); better phylogenetic resolution of this clade over the course of nearly the last three years, i.e. since the main entry passages were posted, has now made it possible to pinpoint such specifics. On the other hand, no material yet available to the present author has shed light on occurrence of the 16179T mutation in hg V, the clade of Kefi et al.’s choice.

In the older passages of the main entry, it was mentioned that L1 could well be a relatively “distant possibility”, or alternative to that which Kefi & co. preferred to associate with the alleged incidence of the 16179T; it appears that since then, further shuffling of the human mtDNA phylogenetic network has now rendered the initial sourcing, which had led to the drawing of that assessment, obscure. However, in lieu, new publication puts forward L0dx [6], which is reportedly defined by 16179T and is reckoned to be a possible subclade of hg L0d1, as a possible candidate for DNA-assignment consideration.  Clades L4b (L4b1), L3d, and L3e (L3e1) happen to be yet other such candidates.

Mutation 16124T/C, as noted in the main entry, could allow for assignment into hg L3, with 16124T reported in L3b1a [2], and 16124C reported in L3e2 (L3e2a [4]), L3d and L3b, for example. The earlier notes of the main entry also briefly noted possible assignment into L3, with regards to the alleged transition to T polymorphism at np 16239; possible L3 candidates for this are reportedly L3d again, and L3e (L3e2 and L3e2b [4]), while the mutation is found across other L-type clades, namely hg L0 (L0f2, L0d1), L1b ( L1b2), L2a (L2a1c2 [2]), L2e and L4b (L4b1).

The aforementioned L3h1b1 clade had been implicated in the polymorphism at np 16179; however, the same clade had also been implicated in the earlier entry as a possible candidate for clade assignment for the polymorphisms at np 16172 (16172C) and np 16126 (16126C). With regards to the latter situation, it appears that DNA network reshuffling hasonce againnow rendered the primary source for this observation either obscure or outdated, in contrast to what the situation was back in 2010. The subclade which may have had the necessary nucleotide attributes that fit these two latter polymorphisms under L3h1b may have been reassigned to some other position within the mtDNA network. As such, it’s only fitting to look towards what currently available information suggests:

Citing from earlier posting, it was noted...

The positions "16172C" and the aforementioned "16126C" could place a specimen (Taf XXIV) in a rare L3h1b1 marker, and likewise, Taf V19E in either some L3h1b1 derivative, L1a subclade, or even M1 subclade, which all have variants bearing the 16172C mutation, assuming that Kefi et al.'s reports for either specimens doesn't involve exogenous mutations, and that homoplasic mutational events took place across hgs L3h1b1, L1a, U6, M1 and possibly, per Kefi et al.'s reckoning, JT in the HVR1 control region. - An Investigation into the "Mysterious" Mesolithic Maghrebi populations, 2010.

The earlier noting of 16172C location within Hgs M1, U6, and L1a still have merit, although it’s worth noting that L1a has been re-assign in the network or treated as L0a in some publications. L1, L3e1, L3, and L4b2a2 (L4b2a2b) have all tested positive for 16172C polymorphism.

With regards to the 16174T mutation, also mentioned in the notes from 2010 (main entry), L0f1 clade has tested positive for 16174T [2], as did L3 [4], which is worth pointing out, as it appears that Kefi et al. treated that mutation [not to dismiss the record that it has been located in U6-identified DNA] as another primary identifying polymorphism for U6 consideration in DNA assignment, although it is otherwise rarely treated as such in many other publications. So, it appears that all three polymorphisms, namely 16126C, 16172C, and 16174T have appeared in L3 clades [4]; in other words, the DNA assigned to U6 by Kefi et al., could just as well be outright placed in L3.

To build on the last few observations, L3e2b clades (including L3e2b1a1, L3e2b3 sub-clades [4]) have tested positive for both 16126C and 16172C [4]. There is rarely, if any, publication that treats 16126C as a primary identifying polymorphism for U6, yet Kefi et al. has treated this mutation just as that.

References are as follows:

1 - Kerchner.com

2 - PhyloTree.org

3 - Howell et al. 2004, African Haplogroup L mtDNA Sequences Show Violations of Clock-like Evolution.

4 - Family Tree DNA

5 - SNPedia

6- Schlebusch et al. 2013, MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa

— Kefi et al. (2005), Mitochondrial Diversity of the Population of Taforalt (12,000 years b.p. - Morocco): A Genetic Study Approach to the Peopling of North Africa.

Recommended reading:  An Investigation into the "Mysterious" Mesolithic Maghrebi populations

3 comments:

Tony D said...

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Tony D said...

Hello. I recently took a DNA test through 23andme and my maternal haplogroup came back as L3H1b. They listed the origins as north Africa. In your extensive research what ancient ethnic group or tribe is this haplogroup most common. Thank you for your time.

Mystery Solver said...

Tony,

L3h1b by itself is somewhat generic. Perhaps additional nucleotide information narrows it down to the regions with the maximum likelihood. As far as the distribution of the clade goes, L3h looks to be something of a pan-African clade, while the subclade L3h1b appears to have a somewhat sporadic distribution spanning eastern Africa, the Maghreb, and western Africa. Distribution seems to be relatively rare in southern Africa. It doesn't appear to be closely linked with the so-called Bantu dispersals, as it is also noticeably low to rare in associated samples.