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Thursday, May 21, 2009

Haplogroup E1b1b1 and Afroasiatic languages


Originally found
at Dienekes.

Andrew Lancaster, Y Haplogroups, Archaeological Cultures and Language Families: A Review of the Possibility of Multidisciplinary Comparisons Using the Case of Haplogroup E-M35. Journal of Genetic Genealogy, 2009. (PDF).

The paper is a very nice and interesting meditation on the state of the art of our knowledge on the important haplogroup E1b1b or its main component E1b1b1, spread through North and NE Africa, West Asia and Europe. As a related issue, the extent and possible history of Afroasiatic languages is also explored in depth.

A must read for anyone interested in West Eurasian and African human genetics.
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21 comments:

terryt said...

That's a very good link. Thanks.

Several comments in it seem applicable to much more ancient times, especially those regarding diversification or elimination of haplogroup diversity, and separate male and female origins. I believe we should apply the same ideas to interpreting ancient haplogroup diversification and spread.

Another thing the article indicates is that effective boating in the Mediterranean does not occur until Cardial times. It is only after then that we find definite evidence for haplogroup movement across this sea. So, relatively recent there.

Maju said...

It is a very good paper indeed but we do not have to necessarily agree with everything, specially as Lancaster explores many lines of thought in order to give the reader the most broader perspective possible, something that I really appreciate.

Another thing the article indicates is that effective boating in the Mediterranean does not occur until Cardial times.

Open seas navigation for sure, not necesarily Cardial but Neolithic in any case. But high seas sailing is not the same as boating and it's quite clear to me that peoples crossed several bodies of water including Bosphorus/Dardanellos, Messina and Gibraltar straits, and also broad rivers. They did not do that just by means of swimming, obviously.

There is also quite clear evidence that Magdalenians relied significatively in sea mammals and used harpoons similar to those of historical Inuits to hunt them. This practice also requires boating (not high seas sailing though).

I'd like you to stop being so tendentious, sincerely. Science is by definition opposed to dogma.

terryt said...

I've put this little essay onto Dienekes blog. I apologise in advance for just putting the same comments up in bot places but I think we will have the more interesting discussion here, if one should develop.

Ahyway, here goes:

A summary.

The authors suggest the Sahel as a centre of origin for E-M35. This makes sense. Y-hap E as a whole seems to have occupied the complete Sahel region from east to west. According to a relatively recent diagram of Y-hap E's diversity (I'll find a link if you insist), early branches are especially common in the west, both in Mali and in the Cameroons. As branches of Y-hap E moved south, to become the major haplogroup within Africa, a branch (M35), stretching from Ethiopia to Egypt, also began to expand.

From there Y-hap E expanded along the southern Mediterranean coast, north of the Sahara, into Northwest Africa, and even out of Africa into the Middle East and Southern Europe. The article's authors argue persuasively that this branch of Y-hap E carried the language that gave rise to the Hamito-Semitic, Afro-Asiatic, or whatever else you choose to call it, languages. There is no way this migration can be connected with any original 'Out of Africa'.

And it doesn't mean at all that E's ancestors had necessarily been in Africa since Australopithecus times. In fact D (E's closest relation) is found in East Asia. It's been argued that D's expansion was centred in the mountains northeast of the Bay of Bengal. How do we explain that separation? Spaceship?

E and D are obviously related, somewhere. They presumably developed at opposite ends of a cline within a widespread population. They may even have become isolated from each other by an expansion, outside Africa, of the C/F Y-hap. Anyway D/E related haplogroups have become extinct through the region between the two surviving haplogroups.

So E could well have developed from a movement into Africa, perhaps accompanied by the enigmatic Y-hap R found in that continent. It's therefore quite possible that just one Y-haplogroup emerged from Africa to spread around the rest of the world. But did he and his descendants always take their own women with them? We have to consider Y-haps and mtDNA separately.

Maju said...

I'll find a link if you insistYes please.

terryt said...

Originally in the supplementary material for this article:

http://www.familytreedna.com/pdf/Karafet-et-all-GR508.pdf

Found the relevant diagram I printed off way back:

http://genome.cshlp.org/content/suppl/2008/04/02/gr.7172008.DC1/SOM_2.pdf

Move down to page 21 for E haplogroup diagram. In my printed copy I have pencilled in the regions many haplogroups are found. That information came from various sources but basically E1a is found in West Africa, especially Mali, E1b1a is found pretty much throughout Africa except northeast. E1b1b is found in the northeast and Mediterranean and E2 is widespread, east and west.

Maju said...

That's not what Karafet published but your interpretation of the data. It could well be correct (some support could be drawn from the fact that DE* is only found in West Africa and Tibet) but it could also be wrong - or just uncertain.

Following my proportional representation of the Y-DNA tree we have:

1. Split between E1 and E2, quickly followed by split between E1a and E1b (guesstimated at c. 50 kya).

E1a is found mostly in West Africa, yes, but this is not the case of E2, which is found both in the East and West (with possibly stronger presence in Eastern/Southern Africa if anywhere).

So, IMO, the E1'2 plus E1a'b supernode could well represent the expansion Westward of this macrolineage in Africa, with E1a being a founder effect.

2. Split between E1b1a'b and just a moment later within E1b1b (but not E1b1a, which remains "private" for long). This supernode I estmate c. 35-40 kya and is almost simultaneous to the first expansion of E2.

This surely happened in NW Africa, be it Sudan, Egypt or Ethiopia, as the main component of this expansion is E1b1b (and not still "private", coalescent, E1b1a).

3. Expansion of E1b1a, simultaneous to that of E1a (c. 25 kya in my model). This could well be the main expansion into West Africa in fact.

At least that's how I would interpretate it.

My reasoning is that the moment of genetic split means little if the stem (private lineage, coalescence) downstream is long. What matters is when the node of, say, E1a, actually happened. And this is rather late, after E1b1b expnasion had already happened and coincident (what a nice coincidence!) with the expansion of E1b1a, which has about the same range.

Or in other words: while (surely rare lineages then) pre-E1a and pre-E1b1a existed for long in an unknown location (surely along other minor E1* and E1b1* lineages), E1a and E1b1a only became what they are when they started branching out (expanding), with all likehood as result of the arrival to West Africa.

Not sure (because I have not researched the issue enough) but my old prehistory manual mentions that a wet period began c. 22kya (though is an old datation that may need refinement and may be actually pushed back somewhat probably) and that this is coincident with the spread of "Musteroid" industries through Mali and Senegal (but not yet south of them, in the jungle strip, seemingly).

Enjoy.

Maju said...

Correction:

So, IMO, the E1'2 plus E1a'b supernode could well represent the expansion Westward of this macrolineage in Africa, with E1a being a founder effect.

Was thinking as I wrote and this is obviously incorrect following what I found later. It surely just represents a local expansive moment in East/NE Africa - as the E2 and E1a nodes do not split (expand) until much later.

terryt said...

"E1a is found mostly in West Africa, yes, but this is not the case of E2, which is found both in the East and West".

You don't seem to have actually read what I wrote: "E2 is widespread, east and west". What's the difference between the two statements?

"My reasoning is that the moment of genetic split means little if the stem (private lineage, coalescence) downstream is long".

But it's not unimportant. After all a private lineage must exist somewhere, even if only just in very limited numbers in a very limited region.

"the E1'2 plus E1a'b supernode could well represent the expansion Westward of this macrolineage in Africa, with E1a being a founder effect".

You later retract this idea but it would suggest you're open to the idea that E is an immigrant into Africa.

"the E2 and E1a nodes do not split (expand) until much later".

The split between E2 and E1 is actually the first within the E haplogroup (leaving aside E*). The split therefore must have happened long before their individual expansions. Of course they may have been living in the same community until a single expansion but I suspect that's unlikely for a number of reasons. E2 is found east and west but the earliest branch of E1 (E1a) is confined to West Africa. It may even be that E1b1b represents a movement back east from West Africa. Unlikely though, I believe. I suspect that E1b1b's line of ancestors remained in East Africa from the moment that E first entered the continent. So E1a and E2 may have moved west together, leaving some E2 in the east. E1b1a followed on later, and also moved south, leaving E1b1b behind.

"a wet period began c. 22kya".

Sounds about right. Especially as you link it to Mali and Senegal. Incidently, I visited both those countries many years ago. As you say, E seems to have moved but slowly into the heavily forested, or jungle, regions. Sound familiar?

Maju said...

What's the difference between the two statements? .

No difference: I was just reviewing the sequence on my own parameters, step by step.

But it's not unimportant. After all a private lineage must exist somewhere, even if only just in very limited numbers in a very limited region.

It is not unimportant it is just impossible to locate with any certainty. Clade A (arbitrary name) may for instance be restricted to a small number of related people in, say, mountain Sweden for milennia and then suddenly expand by founder effect in Wyoming maybe (and even go extinct in Sweden son after that - why not?). The value of randomness at the stem stage is huge: it's almost pure Chaos: the lineage may survive or not with every single generation and, if it survives, it may migrate or not with every singular carrier. It is not a people or an important faction of it but just the opposite: a father-to-son (or mother-to-daughter) inheritance, whose location may vary totally on individual life-events and not on population level ones. You just cannot track that.

Only when it does expand you can deduce: it must have happened somewhere around here (Wyoming in the previous example).

You later retract this idea but it would suggest you're open to the idea that E is an immigrant into Africa.

No. My phrase "Westward in Africa" meant from East to West Africa.

... the earliest branch of E1 (E1a) is confined to West Africa.

E1a is not "earliest" with respect to E1b. If you judge at the stem stage, pre-E1a and pre-E1b are identically old (logically). If, instead, you judge from the branching node where each clade is properly defined, E1b and even E1b1b are apparently quite older than E1a - at least judging from our current knowledge on defining SNPs.

As you say, E seems to have moved but slowly into the heavily forested, or jungle, regions. Sound familiar? .

There must have been an older colonization of West Africa judging from MtDNA. I'm now considering that the (probably simultaneous) expansion of L2 and L3 (in West and East Africa respectively, IMO) must have happened c. 100 kya. This means that L2 expanded surely with Y-DNA B first of all and that the E1a and E1b1a expansion was possibly a largely male-dominated migration.

This also means surely that the forest area was populated from old (as the Pygmy or, if you wish, Papuan or Negrito cases also suggest in different contexts). Not sure of what archaeological culture would correlate with that though (Acheulean?) but I cannot easily second your idea that humans would not live in the fertile jungles for some unknown reason (and instead love the freezing steppes).

terryt said...

"Clade A (arbitrary name) may for instance be restricted to a small number of related people in, say, mountain Sweden for milennia and then suddenly expand by founder effect in Wyoming maybe (and even go extinct in Sweden son after that - why not?)".

Totally agreed. Haplogroups certainly go extinct. So in many cases we have no idea where a particular haplogroup originated, even if a few lines without the downstream mutations survive.

"My phrase 'Westward in Africa' meant from East to West Africa".

So from where before then? As shown by your example above we have no way of knowing. Perhaps from Wyoming. Even though DE has been found in West Africa there's no way of knowing if it arrived there from East Africa with some larger migration, as an individual or in greater numbers. Or even if it originated in West Africa. And there's certainly no way of knowing if DE arrived in Africa from beyond that continent. You wrote earlier, 'Split between E1 and E2, quickly followed by split between E1a and E1b (guesstimated at c. 50 kya)'. This is much more recent than any date you've claimed for the major exit from Africa (I largely agree with your early date, by the way). So DE is unlikely to descend from some Australopithecus male whose descendants had never left Africa.

"the lineage may survive or not with every single generation".

If it doesn't survive there's no way it can leave descendants.

"If, instead, you judge from the branching node where each clade is properly defined, E1b and even E1b1b are apparently quite older than E1a".

But E1b is defined by the P177 mutation whereas E1a doesn't have that. When the mutation occurred is impossible to determine but it must have marked a separation of the two lines. A line of E haplogroup men without the mutation must have survived to become E1a. E1a's ancestors accumulated the mutations M33 and M132 but must have survived somewhere. E1b's expansion may well be more ancient than E1a's but that doesn't mean the haplogroup as a whole is older. Basal E1a must be older than subsequent branches within E1b.

"There must have been an older colonization of West Africa judging from MtDNA".

And Y-chromosome, but not Y-hap E. Y-hap B is probably long-established in the West African forest.

"but I cannot easily second your idea that humans would not live in the fertile jungles for some unknown reason (and instead love the freezing steppes)".

Neither place is prime human real estate. Jungles may well be fertile but a real jungle is extremely difficult of access, and human exploitation. Even New Zealand forest not eaten out by introduced mammals is very difficult to move through. Most such heavily forested regions were virtually uninhabited before Europeans arrived here with their timber milling and other effective forest clearing technologies. And in SE Asia many fairly sizable mammals are still occasionally discovered. So even today jungles are not densely inhabited, if at all.

And I have never claimed humans migrated through 'freezing steppes'. I'm sure you realise the climate has not always been as it is today. Although mostly much colder over the last 100,000 years just a few mild years would have been sufficient for rapid expansion through well-watered regions of what are today 'freezing steppes'. And even in such regions today there are well-watered, relatively warm, sheltered valleys where humans survive quite well.

Maju said...

So from where before then? As shown by your example above we have no way of knowing.

East/NE Africa has high diversity, not just in haplogroup E but overall and is a safe bet for the origin of humankind as a whole, as well as for the E1b1b expansion, which is as much as saying the E and E1 expanson IMO. Archaeology would tend to support this, I think.

And there's certainly no way of knowing if DE arrived in Africa from beyond that continent.

At the current stage of knowledge certainly not. But Africa is undersampled, so I bet for Africa.

You wrote earlier, 'Split between E1 and E2, quickly followed by split between E1a and E1b (guesstimated at c. 50 kya)'. This is much more recent than any date you've claimed for the major exit from Africa...

IMO (and mainstream opinion too), E and pre-E never left Africa (until the E1b1b expansion). Logically they coalesced in East Africa until the time of their expansion arrived. This time nevertheless is not too distant in time from that of the great Asian lineages and might well be somehow linked (climatic conditions? technology?).

So DE is unlikely to descend from some Australopithecus male whose descendants had never left Africa.

Why Australopithecus? We are talking modern humans here and between AMH and Australopitehcus there is a whole 2 million years of Homo spp.

If it doesn't survive there's no way it can leave descendants.

Obviously. That's what I mean by not surviving in fact: no descendants by a haploid line (there can be other descendants though: daughters of a man, sons of a woman).

E1b's expansion may well be more ancient than E1a's but that doesn't mean the haplogroup as a whole is older.

It does mean that: there's no haplogroup until it is large enough to be so. What you call "E1a" is not yet E1a but a private E1* lineage that would eventually lead to it (lucky guys!).

So even today jungles are not densely inhabited, if at all.

"If at all"? Tell me of a single jungle that is not inhabited please. The habitat may have some cons but is still perfectly inhabitable and in fact the main habitat of many "first peoples" everywhere.

And I have never claimed humans migrated through 'freezing steppes'.

Oh you did so indeed, just because you thought that it would be easier to go to Australia via Altai than via Bangla Desh. And you come over that idea once and again every time you can.

And even in such regions today there are well-watered, relatively warm, sheltered valleys where humans survive quite well.

Man, if you can't go naked all year long it's not natural human habitat. Your modern Eurocentric concept of "warm" means in fact very cold.

terryt said...

"Why Australopithecus?"

Those modern human Y-chromosomes must have come from somewhere. I was having a dig at those who seem to believe that modern humans have evolved from a series of species who had survived in Ethiopia since Australopithicus days, never moving far from home.

If you continue to claim that Y-hap E cannot possibly be an immigrant into Africa we're wasting our time here. You're a casualty of your own comment elsewhere on your own blog: "most of us have suffered religious 'education' and surely still struggle with that trauma".

Maju said...

If you continue to claim that Y-hap E cannot possibly be an immigrant into Africa we're wasting our time here.

For me Y-DNA E looks African and Y-DNA D a derived Asian version. Is it the opposite possible? Yes but only in very theoretical terms.

MtDNA in Africa south of the Sahara is 99% native without possible discussion, and I tend to associate Y-DNA E with the African L3 subclades, at least some of them. Overall DE looks African too.

I don't know why do you want people to go to anywhere else and then back without leaving any trace. That's forcing logic (though, of course, it's technically possible - but only that).

You're a casualty of your own comment elsewhere on your own blog: "most of us have suffered religious 'education' and surely still struggle with that trauma".

In my "religious education" Adam and Eve were never real people: they were mythological figures like Herakles or whatever. Jesuits (nor most Catholics) do not believe in a literal interpretation of the Bible: they are teleological evolutionists and take the OT with loads of salt.

They are still castrating neo-Judaists with a problem with sexuality, natural freedom and free thought - specially if this free thought is critical of Yaveh, the Pope and their empty weekly rituals. But that's not what you mean here, right?

I do think that there are regions that played most important roles in the short and fast human expansion of the last 100,000 years or so. These are South, East and NE Africa and South and SE Asia. That is what the genetic data suggests and has nothing to do with any myth.

What I refuse to accept is that there were total demic replacements in most places. Once we reached a place we remained there till today, at least in most cases. The main exception could be West Asia-North Africa, where there is no clear sign of continuity. But the exception is not the rule.

Ebizur said...

According to the "global human mtDNA haplogroup tree" at http://www.phylotree.org/, mtDNA haplogroups M and N are sister taxa of haplogroups L3a, L3b'c'd'j, L3e'i'k'x, L3f, and L3h. If this is correct, then haplogroups M and N might as well be called "L3m" and "L3n." Hypothetically, if one supposes that L3m (i.e. haplogroup M) and L3b'c'd'j share a more recent common ancestor than either shares with L3n (i.e. haplogroup N), then it is plausible that Y-DNA haplogroup D might have spread with mtDNA haplogroup (L3)m, and Y-DNA haplogroup E might have spread with mtDNA haplogroup L3b'c'd'j. Similar scenarios could be formulated with any combination consisting of one of either mtDNA M or N plus one monophyletic subset of L3(xM, N). In any case, Maju should not be able to avoid finding that an almost total extirpation of a certain stratum of Y-DNA has occurred in one or another region of the world.

Maju said...

Well, I have no reason to think that any two L3 sublineages are more related than any others. For me, at the current state of knowledge L3 is a starlike haplogroup with 7 daughters, 2 Asian and 5 African.

Also, considering the distribution, I'd say that D, probably the oldest Y-DNA lineage in East Asia, should be coupled if anything with the expansion of N and possibly also some M subclades. I'd made Y-DNA F more directly related to mtDNA M back then, if anything.

This is because mtN and Y-D share an apparent Eastern early geography, whle mtM and Y-F seem more concentrated in South Asia instead.

In any case, Maju should not be able to avoid finding that an almost total extirpation of a certain stratum of Y-DNA has occurred in one or another region of the world.

In West Asia/North Africa if anywhere. I cannot think any other place, after the corresponding founder effects at colonization. As I said before, the exception is not the rule.

terryt said...

"Tell me of a single jungle that is not inhabited please".

Large tracts of New Guinea/Irian Jaya are uninhabited as are large tracts in SE Asia. It's in such regions that biologists find previously unknown largish species.

"I don't know why do you want people to go to anywhere else and then back without leaving any trace".

We see many examples of that. So what's the problem? No region connects D and E for a start.

"In any case, Maju should not be able to avoid finding that an almost total extirpation of a certain stratum of Y-DNA has occurred in one or another region of the world".

Agreed.

"What I refuse to accept is that there were total demic replacements in most places".

Probably not 'most' but certainly in'several'. I'd guess that severe and prolonged drought was the main cause of such lack of continuity in 'West Asia-North Africa'.

"I'd say that D ... should be coupled if anything with the expansion of N and possibly also some M subclades. I'd made Y-DNA F more directly related to mtDNA M".

I'd agree with that. But what about Y-hap C? No girlfriends?

"I cannot think any other place".

Central Asia perhaps?

Maju said...

Large tracts of New Guinea/Irian Jaya are uninhabited as are large tracts in SE Asia. It's in such regions that biologists find previously unknown largish species.

I asked for whole jungles, not arbitrarily "large tracts". Anyhow, some areas of the Amazon jungle are uninhabited now but that was not the case in the past. And anyhow such areas can only support so much density.

We see many examples of that. So what's the problem? No region connects D and E for a start.

What strongly favors a *rapid* coastal migration model, at least for that clade. Small bands moving relatively fast through the southern regions of Asia, small enough to suffer strong drift but large enough as a whole population to have sufficient initial diversity for such "odd" founder effects.

Probably not 'most' but certainly in'several'.

One AFAIK.

I'd guess that severe and prolonged drought was the main cause of such lack of continuity in 'West Asia-North Africa'.

That's claimed in fact but specialy for North Africa. West Asia, IMO, can only be explained because of Neanderthal takeover. Otherwise there are enough good refuge areas in that region for people to have survived (in fact Neanderthals did but probably there was not room for two species anymore).

I'd agree with that. But what about Y-hap C? No girlfriends? .

C in my reconstruction appears to have expanded later than D and F, so I take it as a private lineage before expansion. If I'm wrong on that, then like D.

Central Asia perhaps?.

No. No evidence of AMH populaton before UP, too cold and arid and full of likely hostile Neanderthals.

Ebizur said...

"No region connects D and E for a start."

This is not completely true. The distributions of Y-DNA haplogroups D and E do overlap in Central Asia, most notably among the speakers of Southeastern Common Turkic (AKA Uyguric or Karluk, i.e. Uyghurs, Uzbeks, etc.), but also in northwestern Han Chinese. Haplogroup DE* has been observed in nearby Tibet. So, it seems that the western parts of the PRC contain the world's greatest diversity of DE-YAP subclades, but it is difficult to draw any conclusion about the history of haplogroup DE on this basis without detailed investigation of the subclades of haplogroup E found in this region and among the Iranic peoples.

Maju said...

Yah. What everybody, including myself, expects is just some West Asian E lineages, correlated with thers like J - what would make a lot of sense, considering the prehistory and history of the region. I'd be surprised if it'd be otherwise, sincerely - but, well, surprises are always exciting and hence welcome.

But so far Central Asia has always appeared to be a mix of East and West Eurasian ancestries, not anything else.

terryt said...

"What strongly favors a *rapid* coastal migration model, at least for that clade".

D is hardly 'coastal'. The only regions it's found that could remotely be called so are the Andamans and Japan, and it could easily have walked to Japan. Even the regions of SE Aia where it is found were virtually all connected to the mainland at times of low sea level, so no open water travel is required apart, perhaps, from the Andamans.

"The distributions of Y-DNA haplogroups D and E do overlap in Central Asia".

But I'd guess that E is almost certainly a relatively recent arrival in Central Asia, especially if it's true that it originated in Africa (which I actually doubt). I didn't realise that 'Haplogroup DE* has been observed in nearby Tibet'. Thanks for that.

Maju said...

I have already mentioned Hong Shi'08 that shows prety clearly that it has "Daic" origins - read mainland SE Asia.

Tibetan and Japanese D, even if old and more important in numbers are quite clearly derived. Now, D2 and D3 have not yet been detected in SE Asia (and have local Tibetan and Japanese roots) but considering that D1 and D* appear centered in that area, I (and the authors) feel quite sure that the origin of D was in SE Asia and that it is the oldest Y-DNA clade east of the Ganges Delta.

D obviously "refuged" in Tibet and Japan (as well as Andaman) when secondary waves (F and C in Y-DNA terms) advanced over it but, as expected, enough D* (and D1) remained in the core area of SE Asia.