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Monday, March 1, 2010

Reviewing the mtDNA L lineages (notes): L2 and L5


Third and penultimate release of these notes, following
PhyloTree and Behar 2008 (fig. S1), now with L2 and L5, the oldest branches of L1''6.

L0 was dealt with here and L1 was dealt with here. L3'4'6 is dealt with here.

>>>>>L1''6
_____>>>>L2''6
_________>>>>L5
_____________>>>>>>>>>>>>>>>>>>>>>>>>>L5a
______________________________________>>>L5a1
_________________________________________>>L5a1a [Ethiopia, Kuwait]
_________________________________________>>L5a1b [Ethiopia, Chad]
_________________________________________>>>L5a1c [Pygmy]
______________________________________>>>>>>>>L5a2 [SA]
_____________>>>>>>>>>>>>>>>L5c
____________________________>>>>L5c1 [Ethiopia]
____________________________>>>>L5c2 [Egypt]
_________>>>>>>>L2'3'4'6
________________>>>>>L2
_____________________>L2a-d
______________________>>>>>>>L2a
_____________________________>>L2a1 [L2a1*: G. Bissau, NA, , Ethiopia]
_______________________________>>>>L2a1a [SA, Chad, Kenya, Nigeria, NA, Yemen, Makran]
_______________________________>L2a1b [SA, Khoisan, Kenya]
_______________________________>L2a1f [SA, Oman]
_______________________________>>L2a1c [West Africa, Ethiopia, Chad, Palestine]
_________________________________>>L2a1c2 [Burkina]
_________________________________>L2a1c3 [G. Bissau, Negev]
_______________________________>>>>>>>L2a1d [Ethiopia, Egypt]
_______________________________>>>L2a1e [?]
_______________________________>>>L2a1h [Kenya, Palestine]
_______________________________>L2a1i [West Africa]
_______________________________>>L2a1j [Morocco, Jordan]
_____________________________>>>>L2a2
_________________________________>>>L2a2a [Chad, Sudan, Pygmy]
_________________________________>>L2a2b [Pygmy, Khoisan]
_______________________>>>>>>L2b'c
_____________________________>>>>>>>>>>>>>L2b
__________________________________________>>>L2b1 [Khoisan, SA, Egypt, Arabia]
__________________________________________>>>L2b2 [SA]
__________________________________________>L2b3 [Ethiopia, G. Bissau]
_____________________________>>>>>>L2c [L2c*: West Africa, SA, Morocco]
___________________________________>L2c2 [SA, Lebanon]
_______________________>>>>>>>>>>>>>L2d [Ethiopia, Algeria, Yemen]
______________________>>>>>>>>>>>>>>>>L2e [G. Bissau]
________________>>L3'4'6 [to be dealt with later]

Notes: SA means Southern Africa (non-Khoisan), NA means North Africa, Arabia means Asian Arabs (from Arabia Peninsula or Palestine), "?" means found only in the USA.

Considerations:

L5 is easy to describe: it's essentially an Ethiopian lineage with some offshoots.

L2 instead is a total mess, with representatives scattered all around. Let's go by parts: L2 has two basal sublineages: gigantic L2a-b and tiny L2e. The latter has only been found among Mandinka of Guinea-Bissau. This may be an important clue because some other L2 lineages are also in Guinea Bissau and often among the Mandinka.

But let's still check the parts by the moment:

L2a is pretty large and scattered, even north of the Sahara and east of the Red Sea (and not always one can claim the slave trade routes as explanation of such distribution). In many cases one can think of a West African urheimat but not at all in others. One of the two basal lineages, L2a2, seems easier to read: Pygmy-related, with branches in Sudan, Chad and among the Khoisan. L2a1 instead is still a mess. I'd guess that "around Sudan or Chad or Kenya" could be a reasonable hunch for its origin.

L2b is not much clearer: South Africa, Red Sea area and again Guinea-Bissau show up. The Horn/Nile area again looks as a reasonable suspect for its origin. It's sister L2c could be more like West African originated.

L2d instead looks like from the Red Sea area again.

So I'm guessing that, with due caution, L2 might have spread from that "knot" around the Upper Nile OR West Africa - open to discussion, really.

16 comments:

terryt said...

I've been going back over my printouts of these diagrams lately.

"L5 is easy to describe: it's essentially an Ethiopian lineage with some offshoots".

Yes. L5 parted company with L2'3'4'6 at about the same time as L0 split into two, 9 mutations. So at that time we can gain a good appreciation of how far the ancestors of the surviving mt-DNAs had spread. We have 6 haplogroups with L5 isolated at the northeast margin of the spread (somewhere in Ethiopia), L0d at the southern margin, possibly actually in South Africa (with L0a'b'f'k not quite as far south) and L1c in the west, possibly as far west as Gabon (with L1b not quite as far west). L2'3'4'6 in the middle somewhere.

The next haplogroup to launch out on its own was L2. L2a reached everywhere at 31 mutations, but that was long after L3's expansion. As you say, by that time L2e had become stranded in Guinea Bissau, where it developed a stem of 16 mutations. So L2 was able to move beyond Gabon at the 23 mutation level, if not before than. The big expansion through the Sahel looks to have happened at the 31 mutation level though. Humans had not been able to adapt to open savanah life until then.

Maju said...

These diagrams are getting obsolete. The known number of mutations may have varied a bit since I drew them.

"Humans had not been able to adapt to open savanah life until then".

Nonsense. Don't you think that other humans like Neanderthals, H. erectus, H. ergaster... were already exploiting savanna-like habitats all around the world. Are you suggesting that our kin are dumber or more ape-like than other Homo sp.?

"L2e had become stranded in Guinea Bissau"...

That the haplogroup has been sampled in Guinea-Bissau does not mean that it only exists there. The whole continent is poorly sampled and there are huge gaps.

Anyhow doesn't this new theory of yours contradict your 'jungle is no-no' hypothesis of the recent past? I think that you should ignore ecosystems and stick to the facts. Ecosystems are often not well known for the past (at least I do not know them in many cases and I doubt you do) and they are anyhow just a context and never a fence.

You can't fence the seas. Similarly you could not fence the land in hunter-gatherer times either.

terryt said...

"Don't you think that other humans like Neanderthals, H. erectus, H. ergaster... were already exploiting savanna-like habitats all around the world".

It is very doubtful that 'other humans' were exploiting savanna-like habitats. They appear to have been exploiting habitats with varied vegetation: open forest mixed with grassland. Presumably that is why populations were of limited size.

"That the haplogroup has been sampled in Guinea-Bissau does not mean that it only exists there. The whole continent is poorly sampled and there are huge gaps".

True. But the point is that Guinea Bissau is at the farthest western point of Africa, but is not part of the open grassland region. It is lightly forested.

'Anyhow doesn't this new theory of yours contradict your 'jungle is no-no' hypothesis of the recent past?"

Not at all. The jungle was a no-no until small localised groups were able to adapt to it. Humans have never been 'generally adpated' to heavily forested habitats.

"I think that you should ignore ecosystems and stick to the facts".

If you insist on ignoring ecosystems your understanding of the past will be severely limited. Ecosystems are a fact, and all species, even humans, tend to be adapted preferentially to specific ecosystems.

"Ecosystems are often not well known for the past"

They are rapidly becoming well known for much of the past through much of the earth. Pollen analysis is very revealing as it lasts virtually forever. I know rather a lot about the subject as a friend was deeply involved in researching New Zealand's past ecosystems.

Maju said...

Look, you are ignoring key environmental clues like the fact that Lake Chad was larger in the past and a true inland sea, plus marshes, in some periods, possibly including most of modern Chad state and part of its Western and Southern neighbors.

You are disdaining in general your lack of knowledge of the paleoenvironment or the actual patterns of distribution of the haplogroups in West Africa.

It's not that I "insist on ignoring ecosystems" but that we can't say much in most cases. And you are not providing materials that support your fantasy reconstruction of past environments in any case.

That's why I think you need a blog: you could work in parts and, eventually, join that past work easily, as it'd be all stored and available for discussion. Here you just thrown ideas around, without maps, graphs, methodical support, academic reference, etc.

No use for me and no use for you.

terryt said...

"These diagrams are getting obsolete. The known number of mutations may have varied a bit since I drew them".

The main adjustments to the L tree as posted by you are the addition of L2d and L2a5. Each has a very long stem from their respective root: 12 mutations and 20 respectively. Interestingly they both branch off close to the roots of haplogroup L2a and L2b'c'd so their exact origin would be very informative. Members of L2 spread virtually everywhere through Africa, but where from is the question. L2d popped up in a study concerned mainly with the Khoisan, so may be South African. L2d popped up in a hospital in Galicia, but the individual is almost certaily a recent immigrant. But from where?

"Look, you are ignoring key environmental clues like the fact that Lake Chad was larger in the past and a true inland sea, plus marshes, in some periods, possibly including most of modern Chad state and part of its Western and Southern neighbors".

But surviving haplogroups there are not so ancient, so presumably early inhabitants died out or moved during periods of aridity. L0a3 has a stem of 13 mutations and has been found only in Chad (one individual?). Its stem suggests it became isolated at the time of the OoA. Something similar is seen in haplogroup L0a1b, found in both the Sudan and Chad. Again its origin is no earlier than the OoA. Both these haplogroups belong to the not-quite-so-far-north-as-L0d version of l0.

L1c1c has been found only amoung the Fula, a group widespread and disconnected through the savannah, perhaps originating around Lake Chad. But again L1c1c became isolated at the 23 mutation level and remained isolated for 17 mutations. L1c belongs to the not-quite-so-far-west-as-L1b version of L1.

No other L haplogroups look to have reached Chad until after the L3 expansion.

Maju said...

"But surviving haplogroups there are not so ancient"...

Is L1 more recent than the Mousterian Pluvial? It must be older than the Abbassian Pluvial, so Lake Chad was at times huge when humankind expanded in Africa.

You were a moment ago discussing L5, L0, L0d, L0a'b'f'k, L1c, L1b, L2, L2a, L2e and L3... why do you hide now behind the skirts of their remote descendants?

"L1c1c has been found only amoung the Fula, a group widespread and disconnected through the savannah, perhaps originating around Lake Chad. But again L1c1c became isolated at the 23 mutation level and remained isolated for 17 mutations".

Do you mean that the private precursor of L1c1c branched out at 23 mutations (M=23) but that we have no idea what was she and her descendants doing until M=23+17?

Your jumping to conclusions based on your absurd, untenable and never properly formulated "stem hypothesis" makes you confused.

In any case M=23 is approx. the OoA and the L3 node, so it'd be the Abbassia Pluvial more or less.

"The main adjustments to the L tree as posted by you are the addition of L2d and L2a5".

Are you sure? I'm glad to hear that.

terryt said...

"L1c belongs to the not-quite-so-far-west-as-L1b version of L1".

I got that wrong. L1c is the far western version of L1.

"Is L1 more recent than the Mousterian Pluvial? It must be older than the Abbassian Pluvial, so Lake Chad was at times huge when humankind expanded in Africa".

L1 first coalesced at the 5 mutation level, whenever that was. But your own diagrams show that no L haplogroup so far found in Chad is any older than the 23 mutation level. The time when humanking expanded FROM Africa, not before. Of course that doesn't mean humans had never reached lake Chad until that period. It's just that they must have become extinct there, although older haplogroups may yet be found round Lake Chad.

"You were a moment ago discussing L5, L0, L0d, L0a'b'f'k, L1c, L1b, L2, L2a, L2e and L3... why do you hide now behind the skirts of their remote descendants?"

In what way am I hiding 'behind the skirts of their remote descendants'? Those haplogroups presumably left descendants in the regions they had reached. So the present haplogroups can provided us with considerable information as to their remote origins.

"Do you mean that the private precursor of L1c1c branched out at 23 mutations"

Yes.

"but that we have no idea what was she and her descendants doing until M=23+17?"

We have a very good idea what her ancestors were doing, and where they were doing it. It is just that you're too obstinate to see it.

"Are you sure? I'm glad to hear that".

They are the only ones I found. Mind you I started with your list of the updates although I did look quickly through the others.

Maju said...

"But your own diagrams show that no L haplogroup so far found in Chad is any older than the 23 mutation level".

I think, using geometric inference, that L1 and L2 as a whole coalesced near Lake Chad (south and east of it respectively). If you can only see the finished present-day haplogroups, I'm quite sure that there is not even one that is so old, not even in Ethiopia.

But I challenge you to apply geometrical principles, dot by dot, and see what you come with. You should learn something from the exercise, like less irking-questioning from an unripe viewpoint.

terryt said...

"I think, using geometric inference, that L1 and L2 as a whole coalesced near Lake Chad (south and east of it respectively)".

Possibly so. Gabon is 'south' of Lake Chad, so I basically agree. But I would place L1 as fairly well south of the lake because it seems to have been unable to move west beyond the Niger Delta or even the mountains of Cameroon.

"If you can only see the finished present-day haplogroups, I'm quite sure that there is not even one that is so old, not even in Ethiopia".

Ethiopia may not be the centre of human development that you imagine it to be. L5 is the earliest surviving Ethiopian haplogroup, possibly as early as the 9 mutation level, but perhaps not actually in Ethiopia at that stage. Both L5a and L5c are present in Ethiopia with L5c also in Chad and L5c also in Egypt. L5 may not actually have entered Ethiopia until long after L5 had formed. Before L5 coalesced we have L0d in the 'Khoisan', certainly as early as the 9 mutation level. In fact I've come to suspect that pre-L0''6 represents the Blombos Cave population. So L2''6 is actually the product of a northward movement from there. L1b looks to be 'West African' as early as the 5 mutation level, and certainly by the 9 mutation level, but no further west than Gabon.

"But I challenge you to apply geometrical principles, dot by dot, and see what you come with".

I've just done it.

terryt said...

"with L5c also in Chad and L5c also in Egypt".

Sorry. L5a also in Chad and L5c also in Egypt.

ANTONIO FLORENTINO said...

Dear Friend Maju! Reviewing the G DNA lineages (notes): L2 and L5 realize I was missing something on the mtDNA haplogroup L2a1c1, I would like you to inform me about this haplogroup, thank you!

Maju said...

Can't say. PhyloTree reports that lineage to Behar 2008, which is the source for these notes but maybe there has been a change in the nomenclature since then. Rather than you making me work, I would rather make you work, revising this study's specific markers in order to see how they fit with the current nomenclature because maybe there are some differences with Behar's notation in 2008.

Check http://www.phylotree.org/tree/subtree_L.htm and see how the September 2012 (latest) version of the nomenclature compares with Behar's one in 2008 (compare the mutations between both references). You can also check for other L2a1c sublineages described after 2012 by searching for the references (at the right margin).

You must understand that this is time-expensive work and that also requires the right kind of motivation. You may be personally interested in those lineages but for me they are just small pieces of the wider picture.

Anyhow if you have specific doubts that I can help you with I'll be glad to help you. And if, in the future after due research you feel like you have found something interesting worth sharing with the World, I'll be glad to help you in order to write an publish an entry, for which I would be glad to lend you my blog (assuming I agree with its interest, but in principle yes because I do have an interest in African genetics and wish there would be more of that).

Feel free to email me at lialdamiz[AT]gmail[DOT]com. Just don't load me with work, please.

ANTONIO FLORENTINO said...

you had every reason Maju friend! the nomenclature was changed in the tree http://www.phylotree.org/tree/subtree_L.htm, mtDNA Haplogroup L2a1c1 became L2a1c1a

ANTONIO FLORENTINO said...

Maju friend! I sent an email ok?

ANTONIO FLORENTINO said...

http://www.phylotree.org/tree/subtree_L.htm
L2a1c1 C198T G930A T3308C T8604C FJ460560 Behar 2008b

L2a1c1a C6311T JQ412577 JQ705046 Behar 2012b

these were the changes in the nomenclature of mtDNA to mtDNA L2a1c1 L2a1c1a

Maju said...

I revisited the supplemental material of Behar 2008 and L2a1c1 does exist but is only sequenced (as of that paper) in America (three USA samples, and that's the reason it's not listed above, even if it does exist).

The overall look of L2a1c is that the lineage is West African for what interests you (i.e. not from Congo nor Angola nor Gabon nor Mozambique, etc.) The two modern countries that repeat once and again in the overall L2a1c list are Burkina Faso and Guinea Bissau, so that's most likely the area of your matrilineal ancestors (with due caution, of course). Guinea Bissau or nearby countries (Guinea, Senegal, etc.) most probably. Finding a specific "tribe" is probably beyond our possibilities, at least at the present state of knowledge.