YAP, signature of an African–Middle Eastern migration into northern India

YAP, signature of an African–Middle Eastern migration into northern India

Suraksha Agrawal1,*, Faisal Khan1, Atul Pandey1, Manorama Tripathi1 and Rene J. Herrera2

YAP, an Alu insertion polymorphism found on human Y-chromosome is present in two lineages worldwide, corresponding to M145/M203/SRY4064 (haplogroup E) and M145/M203/M174 (haplogroup D) polymorphisms respectively. First lineage belonging to haplogroup D is specific to Japan and other Southeast Asian populations, while haplogroup E is confined to Sub-Saharan African, Middle Eastern and Southern European populations. In the present study, 1021 Y-chromosomes belonging to nine different populations of North India were analysed for YAP insertion and four other single nucleotide polymorphisms (SNPs) to delineate the two lineages. Out of nine populations only one, i.e. Shiya Muslims revealed presence of YAP element at a frequency of 11%. Further analysis based on four additional  SNPs revealed that all the YAP+ve samples could be  categorized under African/Middle East-specific haplogroup E lineage. Interestingly, Sunni Muslims who historically have the same origin, i.e. from the Middle east showed a complete lack of YAP+ve lineage similar to other castes. We hypothesize that unlike Sunnis, Shiya Muslims due to their lesser number and less admixture with other caste groups of India, still carry the ancestral YAP+ve lineage, which in all probabilities is one of the founder haplogroups. All Middle Eastern populations show the presence of this lineage in almost similar frequency. Our study shows the presence of YAP+ve lineage in North Indian populations, reflecting an African/Middle Eastern migration into North India

This week’s reading is into Y chromosome DE, so I’ m chasing down papers that can help me figure out the earliest out of Africa Y chromosome movements. It’s not looking like DE is East African in origin, although I think North Africa is possible given the distribtion of DE, E and D. I’m starting to suspect if the OOA populaiton movement was one swift sudden expansion. Did it stall for a while In NE Africa? I’m no longer buying the Gate of Tears as an OOA exit. Looking at other later population movements the Horn doesn’t seem to play any part in the movements from Eurasia and Africa until about 10k ago.

10 responses to “YAP, signature of an African–Middle Eastern migration into northern India

  1. Well, I see no mystery in some E being among some minoritary South Asian Muslims (a recent founder effect probably). But anyhow…

    This week’s reading is into Y chromosome DE, so I’ m chasing down papers that can help me figure out the earliest out of Africa Y chromosome movements. It’s not looking like DE is East African in origin, although I think North Africa is possible given the distribtion of DE, E and D. I’m starting to suspect if the OOA populaiton movement was one swift sudden expansion. Did it stall for a while In NE Africa? I’m no longer buying the Gate of Tears as an OOA exit. Looking at other later population movements the Horn doesn’t seem to play any part in the movements from Eurasia and Africa until about 10k ago.

    I am more and more persuaded that the main route of exit from Africa was the Nile, rather than Bar el-Mandeb and that the timeline is much older than most models consider.

    Was there a stall? Surely yes. In my SNP-based chronological estimates, you can see that there is a very long coalescence period between CF and F, the best studied (and most common) Eurasian macrohaplogroup. Instead between the F and NOP nodes (including IJK and K in between) the transition is very quick (I estimate some 8000 years only), what strongly suggests a “late” expansion within Eurasia after a recession and bottleneck. This F-K explosion could well have happened after Toba catastrophe but this is just a conjecture.

    I have not made timeline estimates for Eurasian mtDNA yet but the overall pattern seems similar: a rather long coalescence after the OOA and then two succesive but somewhat distinct “explosions” before a more continuous, yet regionalized, expansion of the Upper Paleolithic.

    But regarding DE the situation still looks like having two different centers: one (D) in Eastern Asia and another (E) in Africa. DE* has been found mostly in West Africa (Nigeria, Guinea) but it seems two samples have been found in Tibet too. So it’s possible, even probable, that DE branched out in an yet undifferentiated form before becoming D in Asia and E in Africa.

    Also I find in my timeline estimates that DE appears to have branched much later than C,F. This brings me to conjecture that some DE migrated OOA after the main C,F migration and that was able to make founder effects only in some parts of East Asia (what surely means it was very minoritary within the early Eurasian genetic pool and that has been “drifted out” elsewhere – unless an East/SE Asian urheimat for Eurasians is proposed, something so far unheard of).

    E instead begins branching out much later, primarily within Africa, at roughly the same time that the major subclades of F (like IJ, H, NO or P) do – and maybe also around the time C branches out.

    I wonder if Early Eurasians coalesced in the Levant in low numbers being eventually displaced by the Neanderthal expansion of c. 60,000 BP. Or if this coalescence happened in all the subrtopical Asian belt, having a bottleneck largely because of Toba and Neandrthal expansion (roughly contemporary), after which they expanded massively.

    There’s nothing comparable to DE in mtDNA but there is something comparable to CF (i.e. C, D, E and F): L3. Oddly enough, while CF shows higher diversity in Asia, L3 does in Africa instead. It suggests that there was a more strict bottleneck effect in Asia on women than men, while in Africa instead it suggests male-dominated expansions. I don’t understand well why this happened that way.

  2. Lots of assumptions in that study.

    Haplogroup E in Europe is found well spread around Europe due to the movement of farmers out of SE Europe towards Central Europe and the NW Europe. It is found more often than haplogroup J in most of Europe. Haplogroup J1 is almost exclusively found in Southern Europe, and there only at low frequences; haplogroup J1 is as Middle Eastern an indicator of origin as can be whether pre Neolithic, Neolithic or due to recent migrations due to the Islamic conquest of Southern Europe. I am assuming the study of Daghestani haplogroup J1 indicates a pre agricultural origin in NE Caucasus of the haplogroup.

    How do the researchers know that the Muslim population in India is of Middle Eastern origin? Surely any Middle Eastern, Muslim, traders would be outnumbered local Indians. Anyhow haplogroup E is not diagnostic of the Middle East. It could be directly African from NE and E Africa specifically the Horn of Africa travelling up the Indian Ocean from Africa.

    Haplogroup E is of African origin, despite some subclades of E being of Middle Eastern or SE European in origin. The differences between the SE European and North African E1b1 are minor (to me), and only of consequence to Europeans trying to prove a non North African origin to their Haplogroup E. The mystery is how haplogroup E ended up the commonest haplogroup in Africa among mostly Bantu language speakers when the haplogroup appears to originate in the interface between Caucasoids and non Caucasoid Africans.

    The researchers should have tested M267 which is a surer method of estimating Middle Eastern admixture (as it is very common in the Middle East) but that haplogroup, J1, is rare in India.

  3. me too, I think that E are from north africa not east africa !
    ED cluster ,D and E1b1b1 are caucasian !!!!!!!!
    who are the bantu in reality ? ARE THEY mixed race?

  4. …can someone tell me more about the neander
    expansion of 60k bpe?

  5. I use Africa as a geographical term. Haplogroup E is older than any ethnic groups or races.

    My point is that haplogroup E is not diagnostic of the Middle East. Haplogroup J is diagnostic. In India haplogroup J1 is practically non existent unlike in Pakistan where ties to the Muslim world have been present since the Islamic push after the death of Muhammad. The missing J1 says to me that very little Middle Eastern admixture is present in India.

  6. …can someone tell me more about the neander
    expansion of 60k bpe?

    Not much can be said. Neanderthals evolved in Europe from H. antecessor (and this one from local H. erectus most likely, which had been in the subcontinent since c. 900,000 BP). They were constrained to Europe for most of their history but c. 60,000 BP you begin to find their remains in West Asia and even Central Asia, what is evidence that they expanded over areas previously occupied by H. sapiens (at least there is aboundant evidence of AMH in Palestine dated stratigraphically to c. 130,000 BP and later, though this very old datation is controversial and c. 100,000 is surely a safer estimate).

    me too, I think that E are from north africa not east africa !
    ED cluster ,D and E1b1b1 are caucasian !!!!!!!!
    who are the bantu in reality ?

    I think NE Africa (the area around the Nile) is a much safer guess for the origin of E1b1b and possibly for that of all E. This area (roughly) may also be at the origin of haplogroup A, what may mean that the origins of Humankind as a whole are in that region around modern Sudan.

    When people say “East Africa” in these contexts they think of Sudan-Ethiopia-Kenya more or less and when they say “NE Africa” they think of Sudan-Egypt and sometimes Ethiopia too. So they are talking about the same thing more or less, even if they cannot be too precise.

  7. The missing J1 says to me that very little Middle Eastern admixture is present in India.
    Does lack of J1 matter if those Shias had Iran or Azerbaijan ancestry (Many ruling classes of Shias in India I suppose were Azeri Turks)?

    Though E among Shias can be African geneflow too. I would suspect it might be Siddis. I have read that many Siddis assimilated with native Muslims in North India.

  8. …neander expansion, 60k bc. tks, luis.
    on christopher seddon’s site, he says neander
    expanded and contracted/interacted with
    emerging afr cromag according to climate,
    i.e., when cold neander moved into area,
    when calid, ooaf moved in. looking for the source of judea, i came across, ayuthia/
    ayodhya/yuthia, hindu city of rama(now
    oudh) given by hobson-jobson(great anglo-
    indian dictionary, highly recommend for
    its imaginative treatment of sourcing) as
    root of judea, which immediately set off
    the nauatl beacon in my brain as being,
    ayotl(N)=turtle(heart of the water), ayotli(N)=
    squash, ayocotli(N)/haricot(Fr)=green beans
    (the -cotli means cut: they have to be snapped).
    and, yes, the turtle neander were there out of their caves, living on a 40% diet of ayotl(turtle), and messing with seeds/semilla(sp)/cemitta(N)=
    center look(at the cause), and, except for the usual hunter-gathering, is the earliest sign of
    agriculture, mixed with orchard culture, as
    in mt. ca(r)mel/camel(cf. post on, many
    names for camel)/camileua, camiliui(N)=
    to ripen, turn yellow(fruit), the hebrew has
    carmel=fruitful. and all this at 60k bc.
    since that flash, the early root for judea,
    5k bc nauatl has refined it to, yuhti(N)=
    from the beginning, siring words such as,
    just/justice/yu(r)t/even, yeti(neander).
    justice is a matter of going back to first causes,
    but shouldn’t be an excuse for playing tag with them. another word in the running is, yotl(N)=
    only(the swiss, yodel)/yod(hebrew)=10th
    letter(digits of hand/10)/iota(gk)/yo(sp)=
    1st person sing./I(english)=1st person sing./
    jot(E/noun/verb). in the 50k yrs of levantine
    neander/cromag interface, the longest period
    on the planet with, 10k yrs for iberia/iber/
    (r)iver/iueli(N)=powerful(hibernate/hibernian/
    inverness/neander bear worship/invierno(sp)/
    hiver(Fr), and 6k yrs for the intimacy known
    as the chatelperronian doghouse(pun), ah,
    in the 50k yrs of climatic expansion and
    retraction between neander and cromag,
    hebrew was laden with nauatl and neander
    cross, earlier and more fully charged than
    even altai/altia(N) japanese, or the 8k bc
    suomi swampy finns. let me google the finn
    haplo group for anothe piece of the bear/
    deer puzzle. quitoa/qu(r)i(s)to a tleco
    t/l/res/co rise(n)=who speaks has risen=
    quitoa tleco(N).

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