Louse TMRCA provides estimate for human clothing

Research on age estimates for the evolutionary divergence of head and body lice suggest that clothing was already in use when humans left Africa.

Melissa A. Topus, Origin of clothing lice indicates early clothing use by anatomically modern humans in Africa. Molecular Biology and Evolution, 2010. Open access.

The following graphic synthesizes the paper very well:

However it must be said that there are other alternative dates jumping around in the paper. For example the 95% CI estimate for head/clothes louse divergence is 29-691 Ka ago, the mean is 229 Ka and the mode just 83 Ka. So 170 Ka is just a reasonable good hunch, considering always their methods.

Also a much older date is suggested by a single author for hair loss: 3 million years ago. This however would have forced Homo erectus in Asia to make their own clothing, of which we have no evidence so far. Interestingly, the 1.2 Ka figure would allow our Neanderthal cousins to be hairy, a rather convenient biological equipment in Ice Age Europe, provided that the long chronology for Neanderthal-Sapiens divergence is correct (Gómez defends 1.3 million years, a date with strong, and growing, archaeological support).

New paper on human autosomal phylogenetics

A reader points me to a new quite interesting paper on human phylogeny from the viewpoint of autosomal DNA mainly.

Jinchuang Xing et al. Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping. Genomics 2010. Pay per view.

A copy can be found at ZohoViewer and the supplementary material is also freely available.

Abstract

High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~ 250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (F_ST) substantially decreases from ~ 16% with the HapMap II samples to ~ 11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations.

Fig. 3 click to expand

The abstract already addresses which are the most important conclusions of the paper: (1) lower genetic distances with better sampling strategies, (2) claim of large distinct founder population at the origins of the Out of Africa migration and (3) claim of greater affinity of Native Americans with Central Asians than with East Asians senso stricto. Additionally they also emphasize (4) the finding that the West Eurasian component in South Asians is of West Asian origin rather than European.

In the graphs I have noticed a couple of other details worth of mention: (5) that Pygmies appear more distinct than Khoisan from the bulk of the species (which is somewhat contradictory with the haploid phylogeny) and (6) that the closest African populations to Eurasians are "Nilotic" groups of the Kenya-Uganda-Ituri area (neither the Horn of Africa nor the Nile Basin were sampled).

I will address some of these matters now.


The migrant Out of Africa population

The authors take some time to address the issue of the migrant population in pages 20-21:

The OoA hypothesis, proposing a single OoA bottleneck followed by an expansion into Eurasia approximately 50,000 years ago, has gained extensive support from the archaeological record and genetic studies. Nevertheless, many of the historical details of this diaspora remain unclear. A common interpretation is that the OoA bottleneck was the result of a migration of a small founding population into Eurasia. Given the difference in haplotype heterozygosity between African and non-African populations and the relationship between heterozygosity and effective population size, we can estimate the effective population size of such a founding population . Within Africa, the average 100-kb haplotype heterozygosity in our data is 0.91. Immediately outside of Africa in Europe, the Middle East, and Central Asia, the average haplotype heterozygosity is 0.82 (Figure 2). A reduction of heterozygosity from 0.91 to 0.82 in a one-generation bottleneck would require an effective population size of only 5.5 individuals. While a one-generation bottleneck is an oversimplification, these estimates indicate that an OoA bottleneck resulting from the migration of a small founding population would require an extremely small population size. However, given that the archaeological record indicates a rapid expansion of modern humans into Europe and Asia in just a few thousand years , it seems unlikely that Eurasia could be populated so quickly by a such a small founding population.

A more likely explanation for the OoA bottleneck is that Eurasia was populated by a larger population that had been relatively isolated from other modern human populations for tens of thousands of years prior to the expansion. The first fossil evidence for modern humans outside of Africa is in the Middle East at Skhul and Qafzeh between 80,000-100,000 years ago, which is at least 20,000 years prior to the Eurasian diaspora. If a population of modern humans remained in the Middle East until the expansion into Eurasia, there would have been sufficient time for genetic drift to reduce heterozygosity dramatically before the Eurasia expansion. This “Middle East isolation” hypothesis provides a robust explanation for the relative homogeneity of European and Asian populations relative to African populations (see Figures 3A-B) and is supported by a recent maximum likelihood estimate of 140,000 years ago for the time of Eurasian-West African population separation. Interestingly, a recent study of the Neandertal genome suggests that the non-African individuals, but not the Africans, contain similar amount of admixture (1-4%) with the Neandertals. The authors suggest that the admixture must have happened between the Neandertals with an ancestral non-African population before the Eurasian expansion. Given the fossil, archaeological, and genetic evidence, the Middle East isolation hypothesis warrants rigorous evaluation as whole-genome sequence data become available.

I must say that the real problem is to be talking of a mere depth of 50,000 years for H. sapiens colonization of Eurasia, when that must be the date of the reflux into West Eurasia. The archaeological record for Asia east of Iran is inconclusive (too poor) and the genetic data, including the one available here, strongly suggests that South and East Asia were colonized before West Eurasia.

Hence we must be talking of a quite greater time depth such as the 75-80,000 years ago or more, as has been suggested by most population genetic analysis as of late. Certainly nothing less than 60,000 years ago minimum.

The assumption the authors make is therefore wrong so it's likely that the conclusion is also wrong.

That doesn't mean that the considerations they make, specially those regarding a very small colonizer population do not make sense. This small group of adventurous colonists could perfectly have colonized Asia with much more time, leaving very few remains precisely because they were few and even when they grew up in numbers they were still not many. The relatively poor situation of Asian archaeology does not help to unravel the case in either direction but we must remember that the Jawalpurram remains have clear African MSA affinities (and hence are likely to be product of our species) and these date from before the Toba event, which could well have also helped in the reduction of Eurasian heterozygosity even more, some 74,000 years ago. And there are other archaeological clues that, while not clearly conclusive, may suggest an expansion into Asia since as early as c. 110,000 years ago.

Sure, it would be also a good idea to ponder carefully about the role of the Middle Paleolithic colonists of Palestine in the whole process if that is possible. I have nothing against that but I still don't like their reasoning in this point.


The branching out of Eurasians and the two South Asian components

The neighbor joining trees (see fig. 3 above and also fig. S1 at the supplemental materials, very similar) are one of the most interesting results of this paper and the authors are clearly proud of them.

I am going to ignore this "detail" hereafter but I must however mention that the tree produced in fig. S2, after the inclusion of a North African and two Palestinian populations is however very different. This is strange but I don't know how to handle this discrepancy. It might be a point of support for their hypothesis of a long separate coalescence in the Levant? Can't say.

The two other trees however really produce a result that is an almost perfect fit with haploid phylogenies, with Eurasians branching in two in Tropical Asia (South and East Asian branches) first of all.

Then the South/West Eurasian branch shows a division between South Indians and the rest, what I interpret as a split happening still in South Asia prior to the colonization of West Eurasia. Then Pakistanis and West Eurasians branch apart and then the same happens with Europeans diverging from the West Asian/Caucasus population.

Some of the branches' positions however may be caused by ulterior admixture so let's be careful with that.

The authors also emphasize the finding (consistent with what we have seen in other papers) that the second South Asian component, related to West Eurasians, is essentially of West Asian/Caucasus affinity and not European.

I agree with this and I think that it is an important point to make. It seems to imply that an important genetic flow has existed from West Asia into South Asia, specially the Northwest part of it. Of course the flow may have happened at different historical and prehistorical periods but it is important to realize that the Neolithic Age was surely when such migrations might have caused a greater impact.

In contrast some of "European" (darker orange) component is also visible, maybe originating in the Indoeuropean flows and maybe replaceable by a more specific Central Asian component (sadly Central Asia and Siberia is only sparsely sampled in this paper) if the findings of Hui Li are to be reproduced in the context of proper sampling strategies in this delicate area. Whatever the case the European input in South Asia is very minor, even if maybe slightly larger than among West Asians/Caucasians. We can safely infer, I understand, that it reflects the real Indoeuropean genetic input via Central Asia.

Most importantly a clearly distinct South Asian component (purple) has been detected and is strong enough to make up 50% of the Pakistani gene pool and almost the totality of some South Indian populations. Also notice the distinctive Irula component (blue), which may reflect the particular long isolation of these tribals, in the past tentatively classified as "Negritos".

Notice also the minor but significant presence of the Indian component in SE Asia, specially in Thailand. I have on occasion noticed that some Thais seem to have a distinctive phenotype and maybe this is the explanation.


East Asians and Native Americans

In this aspect I want to say that I am not totally persuaded by the authors' claim of greater Central Asian affinity of Native Americans. The main reason is that the "Central Asians" they mention such as Nepalese or Kyrgyzes are possibly admixed populations that owe their position in the NJ tree to that fact.

Even the Buryats appear to show some of that admixture. In this case (and maybe in the others too) it is probably a case of Central Asian specific components indeed but components that still may reflect a very ancient admixture event in the early Upper Paleolithic process of colonization of Central Asia and the Far North.

This is a limitation of this paper: they do some chest beating about a very throughout sampling (somewhat justified indeed) but in the case of Central Asia/Siberia they are lacking and the matter seems to be left unclear.

In any case, Native Americans or rather their ancestral founder population does look like having coalesced in a complex Central Asian and Siberian sparsely populated ancient landscape prior to their arrival to Beringia and subsequent colonization of America. Haploid genetics is very strongly supportive of such scenario.

It is difficult to ascertain however whether their high divergent location in the NJ tree, in the context of the East Asian branch, owes to them having diverged very early or rather (as I suspect) to their early admixture event, maybe partly shared with Central Asians and Siberians. We would need a much improved sampling strategy in those areas to be able to get some clear ideas.

Otherwise East Asians appear to show a first division between NE Asians and SE Asians, with the divide running across China. Not much more can be said, as the sample has not sufficient coverage, specially in SE Asia and Oceania.


African curiosities

One of the details of the trees that called my attention is that, in contrast to what happens in simplified haploid genetics, Pygmies are more distant from the rest of Humankind than Khoisan. This has an explanation, I believe, as the lineages more tightly associated with the Khoisan such as mtDNA L0 and Y-DNA A have representatives in NW Africa and even Arabia, indicating a protracted divergence (or repeated re-convergence) between the southern proto-Khoisanid branch and the main proto-Afro-Eurasian one. Instead when proto-Pygmies diverged they probably did for good, in spite of recent admixture with Bantus and some ancient lineages also shared with West Africans at minority levels.

Another such detail is that the populations most closely related to Eurasians are East Africans (Hema, Luhya, Alur). Overall the African branching process is coherent with the scenario I described here at Leherensuge some months ago.

Humans in Philippines before 66,000 years ago

Julien Riel-Salvatore at A Very Remote Period Indeed echoes the latest major discovery on ancient human (sensu lato) presence in Asia.

A metatarsal bone that has been found at Callao Cave in Northern Luzon island and has a minimal age of 66,700 years ago (± 1 Ka), calculated with an uranium-based methodology.

The foot bone compares well, albeit with some minor differences, with those of modern Negritos, believed to be descendants of the first colonization by Homo sapiens in the Middle Paleolithic. However the bone also compares well with other Homo species, such as Homo habilis and, more interestingly, Homo floresiensis, which is known to have lived in the not too distant island of Flores up to 12,000 years ago maybe.

The question on which species it actually belongs to may be solved in the near future as excavations progress in the Filipino cave but one thing is clear: it adds even further evidence in favor of a very early adoption of boating technology by hominins, with potential to cross sea bodies of small size.

Other such evidence is in the presence of Homo floresiensis in the remote island of Flores, never connected to the mainland and requiring in fact the crossing of several straits, the recent discovery of quartz handaxes in Crete dating apparently to as early as 130,000 years ago and the genetic reconstructions that seem to support a coastal route along southern Arabia into South Asia and beyond for the migration of Homo sapiens out of Africa.


Armand Salvador Mijares et al., New evidence for a 67,000-year-old human presence at Callao Cave, Luzon, Philippines. Journal of Human Evolution 2010. Pay per view.

Abstract

Documentation of early human migrations through Island Southeast Asia and Wallacea en route to Australia has always been problematic due to a lack of well-dated human skeletal remains. The best known modern humans are from Niah Cave in Borneo (40–42 ka), and from Tabon Cave on the island of Palawan, southwest Philippines (47 ± 11 ka). The discovery of Homo floresiensis on the island of Flores in eastern Indonesia has also highlighted the possibilities of identifying new hominin species on islands in the region. Here, we report the discovery of a human third metatarsal from Callao Cave in northern Luzon. Direct dating of the specimen using U-series ablation has provided a minimum age estimate of 66.7 ± 1 ka, making it the oldest known human fossil in the Philippines. Its morphological features, as well as size and shape characteristics, indicate that the Callao metatarsal definitely belongs to the genus Homo. Morphometric analysis of the Callao metatarsal indicates that it has a gracile structure, close to that observed in other small-bodied Homo sapiens. Interestingly, the Callao metatarsal also falls within the morphological and size ranges of Homo habilis and H. floresiensis. Identifying whether the metatarsal represents the earliest record of H. sapiens so far recorded anywhere east of Wallace’s Line requires further archaeological research, but its presence on the isolated island of Luzon over 65,000 years ago further demonstrates the abilities of humans to make open ocean crossings in the Late Pleistocene.

Exploring the Neanderthal admixture episode (1)

I mentioned the other day that a small amount of Neanderthal genes have been detected among non-African modern humans in a homogeneous way that strongly suggests it happened only within the process of migration into Eurasia and beyond.

The percentage of Neanderthal "blood" in non-Africans is estimated in 1-4% (average: 2.5%) what means the equivalent to one great-great-great-grandparent (3.13%) or great-great-great-great-grandparent (1.56%). In other words: the equivalent to one of 32-64 ancestors.

The homogeneity of the apportion across people of Eurasian ancestry (includes Oceanian and American natives) tells us that this was the situation in the Migrant Population at the arrival to South Asia, where it expanded very dynamically.

We must understand that, due to various environmental reasons (adaptation to warm climate, arid barriers and Neanderthal pressure) the Migrant Population must have been rather small between Africa and South Asia. At least that's what the genetic signature strongly suggests. However it was not too small or not too homogeneous because several lineages (2-3 at least per gender) arrived to the South Asian secondary cradle (a really small homogeneous population would surely have got its lineages more strictly fixated, i.e. one per gender).

There are many different detailed scenarios that could explain this limited gene flow but the following one is which seems to me as the simplest one on light of the available genetic and archaeological data:



Feel free to discuss, of course, it's very tentative and pretty much open to variants and alternatives.

Why did I get the main migrant population go via South Arabia? Because there are many clues that suggest so but it's again a personal choice: my best hunch.

Why did I place the main admixture event in Palestine? Because there's some archaeological evidence telling of at least contact between both species there c. 130,000 years ago (old stratigraphic date). But could have happened in many other areas of the Middle East, in Iran for instance (in which case, we could consider a single migrating population via South Arabia and consider the Palestinian episode genetically unproductive).

Just trying to figure out...

Neanderthal gene flow found in humans

Finally an aperitif from the so much expected Neanderthal genome. We will still have to wait for the other specimens from several parts of Europe but the three individuals of Vindija (Croatia) have already been sequenced and provide some interesting information.

Richard E. Green et al., A Draft Sequence of the Neanderthal Genome. Science Magazine 2010. Open access.

Abstract

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

Related materials (all open access) can be found at Special Feature: The Neanderthal Genome, also at Science Magazine.

The authors estimate that this gene flow is quantified in 1-4% of the Eurasian genome and this is the same for West Eurasians, East Asians or Papuans but not for the Yoruba nor the San. This means that, most likely, there was gene flow between the two species soon after the Out of Africa migration.

More later maybe. This is just a quick heads up.

Was Toba really so bad?

There's an interesting article at New Scientist about what is possibly the most crucial issue of human prehistory: the Toba supervolcano explosion, which happened some 74,000 years ago.

There are two parallel debates: how catastrophic was Toba and were humans (H. sapiens) already in southern Asia then. They converge at the point on how could they survive the consequences of the supervolcano.

The debate seems to be quite hot and multifaceted: for some the catastrophe was really bad while for others only half that bad, for some humans were already in South Asia as evidenced by the toolkits so similar to African ones while others guided by the dubious molecular clock approaches prefer to consider a post-Toba out of Africa migration and yet others would push the dates of the migration back to c. 125,000 years ago, right at the Abbassia Pluvial, when there's abundant evidence also of H. sapiens in North Africa and Palestine.

A lot of information and synthesis of the various viewpoints can be found in the abstracts of the Oxford conference titled "The Toba Super-Eruption: A critical moment in human evolution?", which are freely downloadable as PDF.

Another tentative mtDNA chronology

[Updated Aug 6 2010: there was a key error in the steps between L3'4'6 and L4 and L3. In other words: I totally forgot about the L4'3 node and the three CR mutations defining it, pushing L(xL4'3) ahead in time some est. 9000 years. Corrected the main est. chronology now but left the text untouched otherwise]

Take what follows with the proverbial pinch of salt please. It's nothing but a working note.

Method:

The first West Eurasian lineages that show up in the downstream CR mutation count are R0 and M1, at 30 CR mutations counting from "Eve" (7 downstream of L3).

The first European-specific lineages are H and V at 33 CR mutations (10 from L3).

These facts may serve to generate a tentative chronology using the simplest molecular clock methodology: 1 CR mutation = 1 time unit.

A further control may be the place of K1 at 48 CRM (21 from L3), the most recent important clade showing signs of expansion in Europe/WEA, which should not be more recent than Neolithic.

The safest date for the colonization of Europe, which surely included an starlike expansion like the one we see at H, is that of Aurignacian expansion c. 40 Ka ago. A reasonable (but speculative) date for the arrival of H. sapiens to West Asia is c. 50 Ka ago.

This makes CRM=10/3=3.33 Ka.

To make calculations simpler I will round down this rate to CRM=3 Ka and take age(H,V)=40 Ka. as main reference.

Control: K1: 40-(3x11)=7 Ka ago. Fits perfectly: 7 Ka ago is roughly when Neolithic arrived to Central Europe, where K has been detected aboundantly in aDNA from the period and may be coincident with the expansion of K1.


Results:

• 148 Ka - Root ('Eve')
• ...
• 133 Ka - L1''6
• ...
• 121 Ka - L0, L1, L2"6 --- Beginning of Abbassia Pluvial
• ...
• 115 Ka - L0a'b'f'k
• ...
• 109 Ka - L5
• ...
• 100 Ka - L2'3'4'6, L0a'b'f
• ...
• 91 Ka - L0a'b, L0d, L1c --- End of Abbassia Pluvial
• 88 Ka - L0f
• 85 Ka - L3'4'6, L0d1'2
  
• ...
  
• 79 Ka - L2, L0a
• 76 Ka - L2a'd, L3'4
  
• 73 Ka - L4
• 70 Ka - L3 --- Out of Africa migration?
• 67 Ka - L4b, L3a, L3b'f, L3c'd'j, L3e'i'k'x
• 64 Ka - L3i, L3h
• 61 Ka - M, L1b, L3e ---- Beginning of Eurasian Expansion
• 58 Ka - L2b'c, L3f, M1'51, M3a, M3c, M4"64, M5, M9, M12'G, M13'46'61, M25, M29'Q, M32'56, M33, M34'57, M35, M40'62, M44, M49 ---- Arrival to East Asia and Melanesia
• 55 Ka - L1b1a, L2a, N, M30, M37, M7, M9a'b'c'd, M14, M17, M56, M36, M42, M52'58, M60, D --- Arrival to Australia
• 52 Ka - R, L0d3, L3d, M3b, M4a, M4b1, M4b2, M45, M13, M21, M27, M39, M71, N1'5, N9, S --- Final pan-Eurasian wave
• 49 Ka - R0, L4a, L3k, L3x, M2, M38, M43, M6, M8, G, M31, M54, O (N12), R2'JT, R6, R11'B7, B4'5, R30, R31, P ---- Colonization of West Asia
• 46 Ka - D4, L3e1, M1, M4c, M5a, E, Q, M32a'b, M53, N1, HV, R9, R12'21,
• 43 Ka - M63, M11, M29, M41, M73, D1, N2, N9a, N22, HV0a, JT, R5, R9b, U
• 40 Ka - H and V, L0k, L2a1, L3b, M1a, M64, M8a, Z, M12, Y, A, X, R0a, F, U6, U2'3'4'7'8'9 ---- Colonization of Europe, North Africa and NE Asia
• 37 Ka - M10, N5, N9b, X2, H1, H2, H3, H6a, H6b, H7, H9, H10, H13, H14, H15, H16, H17, R8, U6b, U4'9, U8
• 34 Ka - C, D4a1, A2, R0a2, H2a, H8, H11, H12, H18, H19, J, U3, U5, U6a --- Beginning of coldest conditions
• 31 Ka - L6, L3c, L3j, H4, J1, U5a, U6d ---- Gravettian
• 28 Ka - L2d, M7a1a, M23, R2, J1c, J2, R7, R11, U1, U5b
• 25 Ka - L2e, N1a, I, U6c, U2b, U5b3, U9
• 22 Ka - W, J2b, U4 --- Solutrean
• 19 Ka - K, D4h3a
• 16 Ka - M51, T, K2 --- Magdalenian, end of coldest period
• 13 Ka - T1
• 10 Ka - T2, K2a --- End of Ice Age, earliest Neolithic, Epipaleolithic
• 7 Ka - K1 --- European Neolithic
• 4 Ka - K1a1, T2b
  

Note: bold type is arbitrary for perceived "most important haplogroups", however font size reflects the presence of star-like nodes: large size for 5-12 branches, largest size for >15 branches. Clades are listed in logical phylogenetic order with a few exceptions when a single node seems to define a whole phase, in which case they have been listed first. All suggested dates are in thousand years (Ka) ago.

Comments:

Of course there's no way I know of properly estimating the effective mutation rate at each space-time, which should be affected by issues as population size and, with low population levels specially, purely random accidents (drift). Still, I would prefer a logarithmic approach, with longer times/mutation towards the past and smaller ones towards the present.

That would probably be better because it would allow to push the L2 and L3'4'6 expansion towards a more realistic date at the beginning of the Abbassia Pluvial, when we see clear signs of expansion in North Africa and Palestine and also would push the root of the tree (the earliest genetic signal of expansion of H. sapiens) closer to the oldest known fossils c. 160 Ka.

Another issue is the known length of downstream branches, even in some well studied lineages, which appear almost "frozen" since their expansion. This seems to happen in particular to large star-like lineages like M and H (not sure why) but, in any case, the high variability in the length of the lineages towards the present is an anomaly that I would rather not have to face.

In this regard, notice the star-like expansions within the K and T haplogroups by the end of the (always tentative) chronology, wouldn't they be better some 3,000 years earlier? That way T2 and K2a could take part in the Magdalenian expansion, while K1a1 and T2b would belong to the Neolithic expansion. But maybe they fit well with Epipaleolithic and what I imagine as some phase of the Indoeuropean expansion... somehow.

A corrected 2.7 Ka/CRM ratio would fix that.

But it would also push the oldest dates forward quite a bit (for instance the root would be at just 129 Ka), so I feel I need a more refined approach: which should probably be a logarithmic or quasi-logarithmic equation that could account for estimated population sizes. However my maths skills are terribly rusty...


See also PhyloTree for a whole comprehensive mtDNA phylogeny.

The early expansion of H. sapiens in Africa (mtDNA)

As you probably know, I have been working as of late on the puzzle of the early human mtDNA, in the context of Africa, using particularly Behar 2008 as reference.

I published some stuff previously (L0, L1, L2 & L5, L3'4'6 and considerations on Arabian L(xM,N)) and went into a lengthy discussion with Terry about where exactly did the various L lineages coalesce and, of course, human prehistoric boating abilities (an impossible for him before the arrival to almost mythical archipelago of Wallacea, aka Eastern Indonesia).

So I took my time to estimate the composite centroids of each lineage, at every level, from bottom up. Some centroids are plainly valid as likely origins for the major clades, while a few others are more questionable (see below). After a subjective but common-sensical revision of these I came up with the following maps that reconstruct early human expansion:


First expansion:

There seem to be basically two moments of demographic expansion, the first one happened at about 9 (coding region) mutations downstream of the most recent common ancestor (mitochondrial Eve), where the nodes of L0, L1 and L2"6 are in the phylogenetic tree, maybe corresponding with some favorable conditions, which are hard to unravel.


This map shows the earliest expansion at the very phylogenetic origin of the species (purple arrow) and the subsequent three populations generated, defined by the mtDNA lineages L0, L1 and L2"6, all three showing some sign of expansion around the 9th CR mutation (i.e. approximately at the same time, if the molecular clock makes any sense whatsoever).

Of course, L1 and L2"6 shared phylogeny for 5 CR mutations (L1"6), what seems to mean that they had reached Central Africa by that time.

The location that may cause more controversy is that of L0 around Lake Tanganyika, because this lineage is most commonly associated with Khoisan people. However only the L0d1'2 subslineage is totally exclusive of this macro-ethnicity and other L0 lineages are scattered towards the Nile and even as far as Kuwait. The overall centroid, as well as those of L0d and L0a'b'f'k, showed up around there, so I decided that it stands that way, even if admittedly origins around Ethiopia-Sudan or Southern Africa can also be argued for (as did Doron Behar).


Second expansion:

The second major expansion is located at around the 20th CR mutation downstream from "Eve" and in my opinion may be correlated with the Abbassia Pluvial, some 120-90,000 years ago, which probably improved living conditions allowing for significative demographic growth.

It is also the prelude of the migration out of Africa into Asia.


At this moment we see L0 finally splitting up clearly between a northern and a southern group, the latter leading to the Khoisan peoples.

We also see signal of expansion of L1c (but not yet L1b), which correlates best with Pygmies (and also some other peoples of the jungle belt essentially).

And we see the split of L2'3'4'6 (the branching of L5 is earlier, just marked it for the record), first between Western (L2) and Eastern (L3'4'6) populations, centered at Central Africa and what seems to be Eritrea respectively. Then L3'4 split up, with L3 expanding rapidly in Ethiopia, Sudan and towards Lake Chad and L4 scattering along the Rift Valley down to Tanzania, where it is still the most important lineage among the Hadza and Sandawe. L3, of course, also expanded eastward towards Asia where its sublineages M and N would find enormous opportunities.

The minor lineage L6 would not expand till a later moment, so at this time it was yet some "private" L3'4'6*. I suspect that it also benefited from the Out of Africa migration, along with L4b and some L0 subclades, because it's highest basal diversity is in Yemen, suggesting it coalesced there.

A word of caution must be said about the area of origin of L2. The actual composite centroid happens to be at the Niger but this location is the product of basal sublineage L2e, which is only represented by one individual in Behar's data, who happens to live at Guinea Bissau. But the major subclade, only diverged from L2 by a single CR mutation (unlike L2e, which has a very long stem), is L2a"d and this one has a clear center at Chad and, secondarily, the CAR.

Similarly, I ended up with a composite centroid at Yemen for L3 after considering M and N. But I can't ignore the absence of basal L3 sublineages in South Arabia, so I decided that the result without M and N is much more likely to reflect the reality.


The actual centroids:

Prior to the above maps, and after hard work, I came up with this preliminary map. The composite centroids here are the "raw" ones, without further consideration:



But, as said above, I have serious caveats about L2, L3 and L6 specially. I think that the areas depicted in the other maps reflect better the likely reality, with L2 coalescing at Chad, L3 at Sudan and L6 most probably at Yemen after the out-of-Africa episode.

As said before, I also have some caveats about the coalescence area of L0 but I can't come up with a clear alternative (it'd be either Ethiopia or Southern Africa but both weight about the same), so I left it that way.

Of course, the ultimate place of origin of Humankind (Homo sapiens), or at least of the most recent common ancestor (mtDNA Eve), remains a mystery. But guess that somewhere in the vast geography of Eastern Africa is a quite reasonable conjecture (Southern and Central Africa are also possibilities).

_______________

Erratum: there is an error with minor lineage L5 (thanks to Terry for noticing) but luckily doesn't affect much the overall picture. I made a meaningful error when calculating the centroid of L5a, what, in the maps here pushes the centroid of L5 significantly but not dramatically to the south, to South Sudan at the border with SW Ethiopia to be precise. In turn this affects the centroid of L2"6, L1"6 and "Eve", pushing them also proportionately southwards (not too much but something anyhow). The rest of the nodes are not affected, as they depend only of the downstream geography.

I think it's no big deal but I might correct the maps later on... if my perfectionist side prevails over my lazy one.

Are we overlooking the signature of the Out of Africa?

In my recent review of mtDNA L(xM,N), following mostly Behar 2008, I noticed that some of those lineages have distributions that either partly or totally do not seem to correspond with Africa South of the Sahara, but clearly penetrate since old times into West Asia, North Africa or both.

So I wonder: aren't some of them remnants of the migration Out of Africa, which never really made it to South Asia?

Let's see. The mutation count between "mitochondrial Eve" and the L3 node is of 23 (coding region only), to M is of 26 and to N of 28. This is roughly the "time frame" of the Out of Africa. By the "time" of 30 CR mutations the backflow of Eurasian mtDNA to West Asia was already beginning (mostly in form of R derivatives but also M1 and N1, and later some other N subclades too) and this became a clearly dominant flow. Also since M1 specially, scattered into East Africa, it's possible that there was a second flow from Africa in that period of colonization of West Asia that was, no doubt, coincident with the early Mousterian Puvial, when the region became less arid.

I find that the following lineages, normally tagged as "African", should have been involved in the Out of Africa episode:

L4b: at 24 mutations appears to have almost the same age as L3. It has two basal lineages: L4b1, which is only found in Yemen, and L4b2, typical of the Hadza and Sandawe, and found also among Ethiopians (with offshoots in Southern Africa and Arabia) and the Lisango of DR Congo and/or CAR.

L0f2: at 24 CR mutations looks only slightly younger than L3 and surely older than M. One of its sublineages (L0f2a) is only found at Oman, while the other is at Ethiopia (L0f2b).

L0a1b: at 26 CR mutations should have the same age as M. One of its sublineages is only found in Arabia Peninsula (L0a1b2), while the other is shared between Morocco and Southern Africa (L0a1b1).

L5c: at 28 CR mutations appears to be as old as N. One of its sublineages is found at Egypt (L5c2) and the other at Ethiopia (L5c1).

L3e2: at 29 CR mutations appears of the same age as R. L3e2a is shared by West and North Africa, while L3e2b has two lineages that are only found in Jordan (one of the L3e2b*) and Oman and Egypt (L3e2b2).

L6 shows 38 mutations, however the root of its very long stem is necessarily older than L3 (as it's the oldest branch of L3'4'6). Today it looks like Yemen harbors the highest diversity, with offshoots at Ethiopia and Egypt.

There are others but seem younger than the 30 mutations that I decided as limit and may represent other flows, maybe related to the arrival of M1 to East Africa.

It's quite striking, to say the least, that these lineages have been overlooked, they really appear to my eyes as participants of the OoA at a more modest scale, never reaching South Asia or beyond.

Also notice that Yemen and Oman appear insistently in this list. All mentioned lineages, except L5c and possibly L3e2 should represent local fixation processes when people took the coastal route via southern Arabia.


Update (Mar 14): corrected error re. L0f2 (nomenclature and mutation count).

I'd like also to add L3i to the list. It looks to me as centered at coastal Yemen and of similar age (slightly younger, 2 mutations downstream from L3, 25 from "Eve") as M.


Update (Mar 21): Browsing through the East Asian mtDNA data at Tanaka 2004, I just spotted 1/20 (5%) L2 among the Sakai (Semang Negritos) of southern Thailand (Trang province). Not sure what to think but it is odd indeed. Another unlikely survival?

Update (May 5): Map of a plausible Abbassia Pluvial (120-90,000 years ago) Out of Africa migration with the candidate mtDNA lineages to have participated in it (red: L3, purple: other):

Reviewing the mtDNA L lineages (notes): L3, L4 and L6

And here it goes the last note of the series. See previous posts for L0, L1, L2 and L5.

Again based on PhyloTree and Behar 2008. However I have also considered Tishkoff 2007 for the case of the Hadza and Sandawe within L4b2 (formerly L4g or L3g).

As in previous posts, only coding region mutations were considered and labelled as ">". Here it goes the reference for L3, L4 and L6:

>>>>>L1''6
_____>>>>L1
_____>>>>L2''6
_________>>>>L5
_________>>>>>>>L2'3'4'6
________________>>>>>L2
________________>>L3'4'6
__________________>>>>>>>>>>>>>>>>>>>>L6 [L6a: Yemen, Egypt]
______________________________________>L6b [Ethiopia, Yemen]
__________________>>>L3'4
_____________________>L4
______________________>>>>>>>>L4a
______________________________>>>>>L4a1 [Ethiopia, Arabia]
______________________________>L4a2 [Ethiopia, Yemen]
______________________>>L4b
________________________>>>>>>>>>>>>>>>>>>>>>>>L4b1 [Yemen]
________________________>>>>>>L4b2 [unspecified clade: Hadza, Sandawe]
______________________________>>L4b2a
________________________________>>>>L4b2a1 [Ethiopia]
________________________________>>>L4b2a2 [Ethiopia, Arabia, Khoisan]
______________________________>>>>>>>>>>>>>L4b2b [CAR]
_____________________>>L3
_______________________>L3a [Ethiopia]
_______________________>L3b'f
________________________>>>>>>>>>L3b [L3b*: Chad, Kenya]
_________________________________>L3b1
__________________________________>L3b1a [West Africa, NA, SA, Chad, Ethiopia, Arabia, Makran]
__________________________________>>L3b1b [Burkina, NA]
_________________________________>L3b2 [West Africa]
________________________>>>L3f
___________________________>>L3f1
_____________________________>>>>>L3f1a [Chad, Ethiopia]
_____________________________>>>>>>L3f1b [L3f1b*: West Africa, Levant, Ethiopia, Egypt]
___________________________________>>L3f1b1 [SA, Khoisan]
___________________________________>L3f1b2 [Yemen, Jordan]
___________________________________>>>L3f1b3 [Chad]
___________________________________>L3f1b4 [SA, Kenya, Oman]
___________________________>L3f2 [L3f2*: Ethiopia]
____________________________>>>>>>L3f2b [Chad, Egypt]
___________________________>>>>>>>>>>L3f3 [Ethiopia, Chad]
_______________________>L3c'd'j
________________________>>>>>>>>>>>>L3c [Ethiopia, Yemen]
________________________>>>>>L3d
_____________________________>L3d1-5 [L3d1-5*: Kenya, Chad, Syria]
______________________________>L3d1
_______________________________>>>L3d1a [L3d1a*: Yemen]
__________________________________>L3d1a1 [West Africa, Chad, Kenya, SA, Yemen, Brahui]
_______________________________>L3d1b [West Africa, Chad, Ethiopia]
_______________________________>>>>>L3d1c [North Africa]
_______________________________>>L3d1d [SA]
______________________________>>L3d2 [Burkina]
______________________________>>>L3d3 [L3d3*: Jordan]
_________________________________>>>>L3d3a [SA]
________________________>>>>>>>>>>>>L3j [Sudan]
_______________________>L3e'i'k'x
________________________>>L3e [L3e*: Chad, Tunisia, Levant]
__________________________>>>>>L3e1
_______________________________>L3e1a1 [Arabia]
_______________________________>>>>L3e1a2 [SA, Khoisan]
_______________________________>L3e1a3 [SA, Oman]
_______________________________>L3e1b [SA, Palestine]
_______________________________>>>>>L3e1c [Chad, Syria]
_______________________________>>>L3e1d [SA]
_______________________________>L3e1e [Kenya, Cameroon]
__________________________>L3e2 [L3e2b*: Ethiopia, Zaire, G. Bissau, Jordan]
___________________________>>>L3e2a [West Africa, NA]
___________________________>L3e2b1 [Burkina]
___________________________>L3e2b2 [Oman, Egypt]
__________________________>L3e3'4'5
___________________________>L3e3'4
____________________________>>>>>>L3e3
__________________________________>>L3e3a [SA, Kenya, Arabia]
__________________________________>>>>>L3e3b [Cameroon, Burkina, Chad]
____________________________>>>>L3e4 [G. Bissau, SA, Lebanon]
___________________________>>L3e5 [Ethiopia, Burkina, NA]
________________________>L3i
_________________________>>>L3i1
____________________________>>>L3i1a [Sudan]
____________________________>>L3i1b [Ethiopia, Yemen]
_________________________>>>>>>L3ei2 [Ethiopia, Oman]
________________________>>>>>>L3k [NA]
________________________>>>>>>L3x
______________________________>L3x1 [Ethiopia, Yemen]
______________________________>L3x2
_______________________________>L3x2a [Ethiopia, Arabia]
_______________________________>>>>>>>L3x2b [Algeria]
_______________________>>L3h
_________________________>>>>>L3h1
______________________________>L3h1a
_______________________________>>>>>>>>>>L3h1a1 [Sudan]
_______________________________>L3h1a2 [L3h1a2*: Egypt, Lebanon]
________________________________>>>>>>>>>L3h1a2a [Tanzania, Ethiopia, Yemen]
______________________________>>L3h1b [L3h1b*: G. Bissau, Tunisia]
________________________________>L3h1b1a [Ethiopia, Chad]
_________________________>>>>>>>>>>>>>>>>>L3h2 [Ethiopia]
_______________________>>>M [Eurasia, Oceania, America]
_______________________>>>>>N [Eurasia, Oceania, America]

Notes: "SA" means non-Khoisan Southern Africans (often Mozambicans), "NA" means North Africa (several locations), "Arabia" means Arabian Peninsula and Levant (several locations).

Considerations:

L6 is either Ethiopian or Yemeni by origin. Probably Yemeni.

L4 looks Ethiopian by origin or at least East African.

L3 is, naturally, a more complex clade. It has 7 basal sublineages, most subdivided in many further branches. Let's see:

L3a is clearly Ethiopian again.

L3b'f has two subclades: One is L3b, whose main sublineage, L3b1 looks West African but whose upstream "asterisk" diversity appears more easterner (Chad, Kenya). L3f has three subclades: L3f2 and L3f3 look original from somewhere between Chad and Ethiopia, L3f1 is more scattered but should also have that same area of origin overall. So I guess that L3b'f as a whole originated around the Upper Nile, with only L3b1 being clearly a West African offshoot.

Of L3c'd'j three subclades, two are small and concentrated again around the Upper Nile: L3c in Ethiopia/Yemen and L3j in Sudan. The other lineage, L3d, is widely scattered but, considering all the details in Behar's data, I'd say that it also expanded from that Upper Nile area.

Of L3e'i'k'x, two of its four sublineages (L3i and L3x) appear again to be original from the Upper Nile area, L3k seems restricted to North Africa (with an age estimate by Behar of almost 40 Ka), while L3e is again the largest and most complicated sublineage. I'll make some risky bets here and suggest that L3e1 originated in East Africa, L3e2 somewhere in the Central-West African Savanna, L3e3'4 around Southern Chad or the CAR and L3e5 in Egypt. Overall the Nile looks like the most likely origin for L3e'i'k'x.

L3h looks Ethiopian by origin.

M has an obvious South Asian origin, while N may have spread from SE Asia.

Overall L3 looks like having coalesced at the Upper Nile: maybe in Ethiopia or not too far away in any case.

And that's all folks.

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.

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

Reviewing the mtDNA L lineages (notes): L0

As it seems that there is a lot of confusion (including myself) on where are the various L(xM,N) lineages found and therefore on the patterns of spread of earliest humankind, I'm taking notes from Behar 2008 (specifically the figure S1).

Here it goes L0 (only CR mutations considered, marked as ">").

>>>>>>>>>L0
_________>>L0a'b'f'k
___________>>>>>L0a'b'f
________________>>>L0a'b
___________________>>>>L0a
_______________________>L0a1
________________________>L0a1a [Nile, Burkina, scattered, Bissau, Chad]
________________________>>L0a1b [L0a1b*: Sudan, Chad]
__________________________>L0a1b1 [S. Africa, Morocco]
__________________________>L0a1b2 [Arabia]
________________________>>L0a1c [Ethiopia, Iran]
________________________>L0a1d [Ethiopia, Yemen]
_______________________>>>>>>>>>>>L0a4 [Kenya]
_______________________>>>>>>L0a2
_____________________________>>L0a2a
_______________________________>L0a2a1 [SA, Kenya]
_______________________________>>L0a2a2 [SA, Arabia, Sindh]
_____________________________>>>>>L0a2b [Pygmy]
_____________________________>>>>>>>>L0a2c [Ethiopia]
_____________________________>>L0a2d [Kenya]
_______________________>>>>>>>>>>>>>L0a3 [Chad]
____________________>>>>>>>>>>L0b [Ethiopia]
_________________>>>>L0f
_____________________>>>>>>>>>>>>>>>>>>L0f1 [SA]
_____________________>>>>L0f2
_________________________>>>>L0f2a [Ethiopia]
_________________________>>>>>>>>>>>>>>>>L0f2b [Oman]
___________>>>>>>>>>>>>>>>>>>>>>>L0k
_________________________________>>>>>>L0k1 [Khoisan]
_________________________________>>>>>>>>L0k2 [Yemen]
_________>>>>>>>>>>L0d
___________________>>L0d1'2
_____________________>>>>>L0d1
__________________________>>>>L0d1a [Khoisan, SA]
__________________________>>>>>>L0d1c [Khoisan, SA]
________________________________>>>L0d1c1 [Khoisan, SA]
__________________________>>>>L0d1b [Khoisan]
_____________________>>>>>>L0d2
___________________________>>>>>>>>L0d2a [Khoisan, SA]
___________________________>>>>>>>>>>>>L0d2b [Khoisan]
___________________________>>>>>>>>>>>>>L0d2c [Khoisan, SA]
___________________>>>>>>>>>>>>>L0d3 [Khoisan, Kuwait]

Notes: "SA" means Southern Africa (non-Khoisan), "Arabia" means Arabia peninsula when several locations mentioned. L0 and its two basal sublineages in bold type (for clarity).

Considerations:

While L0d looks very much Khoisan-specific and hence part of the earliest split of Humankid, L0a'b'f'k appears to have a more northernly center of expansion.

L0a would appear to have got an East African urheimat, however it's widely scattered, with some very old lineages only found in North Africa, Peninsular Arabia or even as far East as Iran (see fig. S1 of the paper for details), which can't be considered part of the slave trade.

L0b is Ethiopian, L0f Ethiopian and Omani (again too old the split to consider it part of the slave trade), while L0k is found among Khoisan and Yemenis (and again it looks as an old split).

Other lineages are dealt with in the following threads:
· L1
· L2 and L5
· L3'4'6

Update (Mar 8): corrected L0d3, which included two more basal mutations than actually has.