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Monday, March 1, 2010

Reviewing the mtDNA L lineages (notes): L1


Here I continue the task initiated in
my previous post of detailing the African mtDNA lineages as per PhyloTree and Behar 2008 (fig S1) with haplogroup L1:

>>>>>L1''6
_____>>>>L1
_________>>>>>>>>>>>>>>>>>>>>L1b [L1b-other: Fula]
_____________________________>>L1b1a [L1b1a*: West Africa]
_______________________________>L1b1a1 [?]
_______________________________>>L1b1a4 [Khoisan, Fula]
_______________________________>L1b1a2 [Ethiopia, Egypt, Negev]
_______________________________>L1b1a3 [Igbo]
_______________________________>L1b1a5 [Mauritania, Cyprus]
_________>>>>>>>>>>L1c
___________________>L1c1'2'4'6
___________________>>>>L1c1
_______________________>>>L1c1a
__________________________>>L1c1a1 [L1c1a1-other: Pygmy, Khoisan, Gabon]
____________________________>L1c1a1a [L1c1a1a*: Bakola Pygmy]
_____________________________>>>>L1c1a1
_________________________________>>>>L1c1a1a [Pygmy, Gabon]
__________________________>>>>>>>>L1c1a2
__________________________________>>>L1c1a2a [Pygmy, Gabon]
__________________________________>>>L1c1a2b [Pygmy, Gabon]
_______________________>>>>>>>>>>L1c1b [Gabon]
_______________________>L1c1c'd
________________________>>>>>>>>>>>>>>>>>L1c1c [Fula]
________________________>>>>L1c1d [Igbo, Gabon, Khoisan]
____________________>>>L1c2'4
_______________________>>>>>>>>>L1c2
________________________________>>>>L1c2a [SA, Baka Pygmies, Kenya]
________________________________>L1c2b [L1c2b*: Syria]
_________________________________>L1c2b1 [Ethiopia, SA]
_______________________>>>>>>>>L1c4 [Biaka Pygmies, Gabon, CAR]
____________________>>>>>>>>>>>>>>>>L1c6 [Gabon]
___________________>>>>>>>L1c3
__________________________>>>>>>L1c3a [West Africa, SA]
__________________________>L1c3b'c
___________________________>>>L1c3b
______________________________>>>>>>>>L1c3b1 [?]
______________________________>>>>>>>>>>>>L1c3b2 [SA, Gabon, Morocco]
___________________________>>>>>>>>>L1c3c [Gabon]
______>>>>L2''6 [to be dealt with later]


Notes: Pygmies and Khoisan are always mentioned as such, geographical locations like "Gabon" hence refer to Bantus. Fulbe and Fula are treated as single group ("Fula"). "SA" means Southern Africa, "CAR" means Central African Republic (specifically refers to a Lissongo person), "?" means only typed in the USA (no African specific locations known). L1 and its basal sublineages (L1b and L1c) are in bold type, as well as sister lineage L2''6 and the common ancestor L1''6 (for clarity).

Considerations:

L1b is widespread but clearly non-Pygmy and non-Khoisan. Instead it might have a special affinity with the Fula people, that were recently shown to be a quite peculiar group also by autsomal DNA. However it is not really clear where it's urheimat might have been (I'd say West Africa baed on where most basal lineages are found today).

L1c instead can be considered to be an essentially Pygmy lineage, with some penetration among Bantus (in Gabon particularly), this is particularly true of L1c1a but less clearly so of the other lineages probably. Still an ancestral homeland in or near Gabon is likely for the whole lineage. Notice that L1 spread could be older than that of L0, depending who you read (and in any case not too distant in time).

Hence, with the branching and scatter of L0 and L1 we are probably "witnessing" the first expansion of humankind, with one branch heading south (L0d), another heading west into the jungle (L1c), another heading towards the Ethiopian highlands (L0a'b'f'k or at least L0a'b'f) and yet another heading maybe towards West Africa (L1b). The remaining macro-lineage (L2''6), which is the major one by raw numbers today, probably represents a second expansion.

Other lineages are dealt at:
· L0
· L2 and L5
· L3'4'6


16 comments:

Kepler said...

The whole L1 affair is messy, isn't it? I understand there were already two different classifications
Here

I happen to have L1c3, although I am not small :-)

I am going to look for the article later on. In one place there they mentioend several instances of L1c3 in Guinea and cameroon. Interestingly, one of my matches comes from the last country. Reading about my region's history, there were at least 2 or 4 "cargoes" with slaves from Guinea in the XVI century.

Now, I think the groups in America do tend to be different, among other things, because they probably represented some kind of selection one way or the other

Maju said...

L1c3 is (mostly) Bantu, even if it probably spread from the same ancestry and area as the L1c of Pygmies. L1c3 is in fact the only L1c subclade that is not found among Pygmies:

·L1c3a: Mozambique, S. Africa, Mauritania, G. Bissau, USA (2) and Dominica.
·L1c3b: Gabon, Mozambique, Morocco, USA (2), Dominica.
·L1c3c: Gabon.

If you suspect Moroccan/Canarian ancestry, as you have suggested before, check the downstream details of your lineage. It's not impossible even if not the most likely option.

"Reading about my region's history, there were at least 2 or 4 "cargoes" with slaves from Guinea in the XVI century".

Guinea back then was the whole West Africa.

"Now, I think the groups in America do tend to be different, among other things, because they probably represented some kind of selection one way or the other".

I don't think so (at least in most cases). Africa is huge and clearly undersampled and poorly researched.

"The whole L1 affair is messy, isn't it? I understand there were already two different classifications
Here"

L1c4 has been placed under L1c2'4. Not sure what happened to L1c5 (probably got renamed). Thanks for the link anyhow.

Kepler said...

I know I have Canarian ancestors, as so many in Venezuelans, but so far from the side of grandfathers of both grandmothers.
Very few records were kept or could be kept (insects are really bad there) and anyway, guys were incredibly promiscuous back then.

I think the reference is to The Gambia: pirate John Hawkins landed in Borburata and sold the slaves there:
http://www.timesonline.co.uk/tol/news/world/article677647.ece
That place is just some hours donkey-drive (back then) from where I was born, in Valencia.

Of course, there were other ships and we will probably never know.

Still, the African population in Venezuela is lower than in cuba, Hispaniola or the English/French colonies or the Dutch Antilles, so there is some chance I got it from there (although the canary origin is another option).

I don't think there are many people with immediate links to Morocco in Latin America (apart from the links we have from the Andalus times).

I am just thinking now: it could be interesting to get some machine learning based on genetic databases and some normalized records on slaves in the Americas.

I do think there was some selection: slave traders were catching people who were in some weak position (although Africans sold people from their own communities, many got the slaves from other groups) but healthy. Also: they were less likely to transport pygmeys to the Americas. Pygmeys simply cannot transport the same amount of cargo.

I know nurture influences height a lot and very fast and yet my impression is that blacks in the Americas tend to be considerably higher than the blacks I see in Europe.

Maju said...

"Still, the African population in Venezuela is lower than in cuba, Hispaniola or the English/French colonies or the Dutch Antilles, so there is some chance I got it from there (although the canary origin is another option)".

But I have also read about the 19th century "whitening" of large areas of Latin America by means of large European immigration. This process surely affected Venezuela more than most other countries.

From Wikipedia: "By the middle of the 16th century not many more than 2,000 Europeans lived in present-day Venezuela". And already mentions African slaves at the mines of Yaracuy (near Valencia). It comes to say that until the 18th century, Venezuela was essentially a marginal area, as the center was further east. In that century further many slave cargoes were brought in order to establish a cocoa plantation economy (the big business of Basque traders back then) and also to work at the haciendas.

It seems that at the time of independence the vast majority were mestizo/mulatto people, not whites. The population was then of some 800,000 to one million people and may have even declined after independence at first.

Kepler said...

Venezuela did not have so many slaves already in 1799. Alexander von Humboldt wrote quite some about that. He was in Venezuela for some 16 months. I think back then the population was mostly mestiza/mulata/everything else, then came the European component and then the Indian and African. A lot of "whites" then were killed or went away during the Independence time (see Boves http://es.wikipedia.org/wiki/Jos%C3%A9_Tom%C3%A1s_Boves )
Venezuela did not get as many Europeans in the XIX century as others. We started to get them after WW2.
But as we have said before: a white landowner was bound to have a lot of "queridas".

Here you have a good "Historia de Venezuela":
http://www.youtube.com/watch?v=tn4PkRdsJC0

Maju said...

I can't watch videos of any sort since some weeks ago. Seemingly they have tweaked some javascript and neither firefox nor epiphany can deal with them anymore.

Interestin that story of Boves.

"Venezuela did not get as many Europeans in the XIX century as others. We started to get them after WW2".

Well, I did not mean as the South Cone in any case but probably more than the Andes or Mexico. Anyhow it would not be "after WWII" but since 1937, when the Spanish Civil War caused many to exile, often in Latin America (most Basques then went to Venezuela, in fact).

m2709 said...

I am L1c2b1 and I find it difficult to follow where this subclad group originated. I am African American with some Indian features. Have traveled to India, Tunisia, Morocco, Egypt and several countries in South America and have come across similar facial features. Interested in your comment.

Maju said...

I do not know what to say, m2709, really. The lineage is reported by Behar in Ethiopia and Southern Africa so, on first sight it looks an East African clade. Its cousin L1c2a is found also in Kenya and SA (plus Biaka Pygmies), while its sister L1c2b* is only found in Syria (an OoA flow or a later erratic?)

In general L2c2 looks to me as an East African clade.

"Have traveled to India, Tunisia, Morocco, Egypt and several countries in South America and have come across similar facial features".

That does not need to have anything to do directly with either maternal or paternal lineages, which are in the end just a drop in an river of multiple (tending to infinite) sources.

I sometimes think I can find akin features in individuals from peoples that are not related, this may well be a product of mere randomness. But hard to say more without seeing the specific faces, really. It's also possible that East Africans (or some among them) have closer genetic and hence phenotype afinity to Eurasians (very speculative) - I once met online an Ethiopian who claimed his country had all the human phenotypes (in black/brown skin + curly hair version). He showed us photos of "Ethiopian Nordic", "Ethiopian Mongoloid", etc. Even if a bit forced at times it was quite impressive too. :D

Maju said...

Btw, you may be interested in the African Ancestry Project that Razib initiated recently.

terryt said...

"Hence, with the branching and scatter of L0 and L1 we are probably 'witnessing' the first expansion of humankind, with one branch heading south (L0d), another heading west into the jungle (L1c), another heading towards the Ethiopian highlands (L0a'b'f'k or at least L0a'b'f) and yet another heading maybe towards West Africa (L1b). The remaining macro-lineage (L2''6), which is the major one by raw numbers today, probably represents a second expansion".

That's pretty much the way I see it although I would have only L5actually 'heading towards the Ethiopian highlands', and then not really into the 'highlands' at that early stage. L5 looks to have become isolated from the other haplogroups while its two branches developed their long stems. So Ethiopia does not look to have been central to the early human expansion.

Although L1''6 developed a stem of 5 mutations once it had parted company with L0 it looks to have been the haplogroup that entered the new region. Its expansion is earlier than that of L0, which underwent a longer period of drift. By the time that L0 split into two L1 had already parted company with L2''6, which itself had split into two: L1b and L1c.

L1b developed a stem of a further 20 mutations before it spread widely through much of Africa and beyond at 31 mutations. That doesn't help much in any search for its urheimat, although you could be correct with, 'L1b is widespread but clearly non-Pygmy and non-Khoisan. Instead it might have a special affinity with the Fula people'.

L1c, on the other hand, looks to have become isolated somewhere in West Africa at 9 mutations and developed a stem of 10 more mutations before diversifying. It was certainly present as far west as Gabon by the time of L3's expansion. But it could have reached Gabon some time before thenn. L1c looks to be specifically West African. L1 seems to have been blocked from further westward expansion in Gabon though. That's as far west as it gets. Some time after L3's expansion members of L1 moved deeper into the forest and either joined or became Pygmies. L1c1a is specifically Pygmy but the other L1c1 haplogroups are not. L1c1b is 'Gabon', L1c1c is 'Fula' and l1c1d is 'Igbo, Gabon and Khoisan'.

No L haplogroups can be shown to have entered either the Sahel/grassland of Chad/Birkina Faso or the tropical rainforest of the Congo Basin until at least the 23 mutation level. That indicates that humans had been tied to a relatively narrow ecological region until then.

Maju said...

Y-DNA actually suggests that they were living in the Western Sahel at that time. Also the Sahel extends into East Africa anyhow.

terryt said...

"Y-DNA actually suggests that they were living in the Western Sahel at that time".

It may 'suggest' such, but other interpretations are just as valid. A1b is present in Berbers but also in the Bakola Pygmies. They can hardly be called Sahelian. A1b's movement into the Sahel may well post-date the OoA. A1a is perhaps a more likely candidate as it is spread through much of West africa, including the Atlas. But it is very thinly spread so not too much can be claimed for it.

ANTONIO FLORENTINO said...

Hello Maju!
Which African tribe belongs mtDNA L1c1'2'4'6

Maju said...

To no one in particular: it's a large haplogroup, emphasis in "group". Long ago there was a woman who was the first one with that lineage but AFAIK there are no unmutated descendants that retain it, just derived ones.

ANTONIO FLORENTINO said...

Thank You Very Much friend Maju!

Will Dodson said...

Does anyone know anything about L1c1c'd