December 30, 2010

Before I forget again: I found the reference for L2 among the Sakai (Semang) - M51a1 probably in fact

This is something that has shown up in some discussions and I had totally forgotten where I had found this reference of one Negrito from the Malay Peninsula with an L2 lineage. It is from Tanaka 2004 (table 2).

It might be a misclassification but in any case there it is. If correct, it could be a remnant from the less lucky lineages which also took part in the Eurasian colonization, along M and N but were drifted out.

Just for the record.


Update: misclassification almost certain: checking the sequence, which is a mere HVS-I one, always confsing, I realize that it lacks a key mutation defining L2  at 16390 and the other HVS-I site at the root of L2 is identical to the one of L3 (site 16311 towards CRS in both cases). Then checking within L3, I soon found that M51a1, a South Asian haplogroup, I believe, is at least as likely to correspond to the sequence described:

"Also striking is the presence in Sakai of an unequivocal representative (16223–16274–16278–16294–16309) of the sub-Saharan African L2a haplogroup (Torroni et al. 2001)"...

I did not check further because I realize now it is surely a case of misidentification because of excessive reliance on HVS-I, which is not enough in most cases to describe a haplogroup with safety. 

4 comments:

  1. L2a actually.
    Strange that mtDNA L2a is also one found deep in Europe (but is it exactly the same - or close?) :

    http://www.ncbi.nlm.nih.gov/pubmed/18398433

    Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs

    Boris A Malyarchuk et. al

    To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for Europeanspecific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.

    European Journal of Human Genetics advance 9 April 2008;

    -----
    One mtDNA L2 among 74 Norwegian samples.

    http://hpgl.stanford.edu/publications/EJHG_2002_v10_521-529.pdf

    Different genetic components in the Norwegian population revealed by the analysis of mtDNA and Y chromosome polymorphisms

    "One mtDNA molecule displayed an L2 haplotype, that is typically African, but is also sporadically found in Southern Europe * and is likely to be a result of more recent gene flow"

    * IIRC it was also found in Greece for instance.

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  2. I had not noticed it's L2a but you are right:

    "Also striking is the presence in Sakai of an unequivocal representative (16223–16274–16278–16294–16309) of the sub-Saharan African L2a haplogroup (Torroni et al. 2001)"...

    Anyhow, hold on: it lacks 16390, a defining L2 mutation (and the other one is identical to the defining L3 mutation 16311!), however all the rest looks like L2a1 (plus would-be "private" mutations 16390! and 16247. ["!" means towards CRS, following PhyloTree convention].

    It could also be an L3(xR). Actually I just found an M subclade that is at least as likely to be as L2a1: M51a1, defined under L3 by HVS-I transitions at 16278 (M51) and 16294 (there would still be two downstream "private" mutations at 16274 and 16309). It is a much more parsimonious explanation, as M51 is found in India, a less striking connection.

    As for Europe it could well have arrived in several periods, from the LGM onwards. L2 is not rare in North Africa and West Asia, you know. For instance Behar locates L2a1c and L2a1h in Palestine, L2a1d in Egypt, L2a1j in Morocco and Jordan, L2a1a1 in Yemen and Makran (Balochistan). And most of those areas were part of the Roman Empire for several centuries (for instance).

    ReplyDelete
  3. I join you in noting that even if it was a single L2 there are lots of ways that a single African woman could have made it to Malaysia via the Indian Ocean trade (e.g. a returning contingent from the founding group of Madagascar ca. 1000 CE or any time during the Colonial era from the 15th to early 20th century), in historic times, and then ended up marrying into the Sakai out of a feeling of greater cultural and appearance affinity with this group than with the majority population of Malaysia.

    ReplyDelete
  4. I think that if the woman would have arrived via the Indian Ocean trade routes, her lineage would be found among Malays, not Negritos. The appearance connection makes no sense because the socio-cultural disconnection is almost total. Besides, you can be L2 and be white or ambiguous. It's not like there are no L lineages among "Arabs" of all kinds (or even Portuguese).

    Also drift in such a small population as the Sakai/Semang must be even today pretty high, so any erratic should be absorbed, drifted out very easily.

    Anyhow it's almost for sure a case of misidentification.

    ReplyDelete

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