Late human evolution maps

Kambiz Kamrani at Anthropology.net mentions this site of a colleague and also his own dedicated page on human fossils. Both are very interesting and, using their data, I made some maps in order to better understand the chronology of recent human evolution in the range between 1.3 million years ago (oldest estimate for Neanderthal-Sapiens divergence, cf. Aida Gómez) and 60,000 years ago, when the expansion of these two species towards Asia was surely already in action.

As Asian fossils, excepted West Asia, are not relevant for my purpose (they are all Homo erectus senso lato with no transition happening there at all) I have used a base map that only includes the Western parts of the Old World.

Note: I used median ages but, when these overlapped too much with two of my arbitrary time frames, I placed them in the two relevant maps (check for safety but they are likely to be the same specimen.


1. 1.3 million years to 800,000 years ago:


While most of the findings are Homo erectus (purple dots), the likely first known individuals in the H. sapiens and H. neanderthalensis lines appear already, at the end of the period, at Atapuerca (H. antecessor) and Saldanha Bay (H. rhodesiensis).


2. 800-600,000 years ago:


We can appreciate in this period an expansion of H. rhodesiensis to the Horn of Africa and transition to H. heidelbergensis at Atapuerca (c. 600,000 years ago according to fossilized.org).


3. 600-400,000 years ago:

The expansion of Homo heidelbergensis becomes apparent in this period. Restricted to Europe however. Notice how in spite of these changes there are still many specimens categorized as H. erectus around the Mediterranean.


4. 400-200,000 years ago:


While it looks a dull map on first sight, most significant here is the existence of a fossil that may be transition between H. rhodesiensis and H. sapiens. This one is Lake Eyasi, in Tanzania (red-orange hue, not easy to appreciate possibly), dated to c. 240,000 years ago.


5. 200-60,000 years ago:



Whoa! Everything goes a lot faster now: Neanderthals and Sapiens everywhere! Well, each in their specialized area: Sapiens in and around the tropics, Neanderthals in the fresh regions of the North. Even the map caption becomes small as the earliest Neanderthal and Sapiens fossils (controversial chronology) show up in Central and East Asia respectively. I reflected this with a mere two color-coded arrows.

The oldest uncontroversial fossil of H. sapiens is Omo II (c. 195 Ka ago), followed by Herto (Idaltu) and Jebel Irhoud, in Morocco (both c. 160 Ka ago).

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).

Bonobo mtDNA... and some human implications.

Researchers from the University of Bonn have published a new paper on Bonobo mitochondrial genetics:

Gabor Zsurka et al., Distinct patterns of mitochondrial genome diversity in bonobos (Pan paniscus) and humans. BMC Evolutionary Biology. Open access.

Background

We have analyzed the complete mitochondrial genomes of 22 Pan paniscus (bonobo, pygmy chimpanzee) individuals to assess the detailed mitochondrial DNA (mtDNA) phylogeny of this close relative of Homo sapiens.

Results

We identified three major clades among bonobos that separated approximately 540,000 years ago, as suggested by Bayesian analysis. Incidentally, we discovered that the current reference sequence for bonobo likely is a hybrid of the mitochondrial genomes of two distant individuals. When comparing spectra of polymorphic mtDNA sites in bonobos and humans, we observed two major differences: (i) Of all 31 bonobo mtDNA homoplasies, i.e. nucleotide changes that occurred independently on separate branches of the phylogenetic tree, 13 were not homoplasic in humans. This indicates that at least a part of the unstable sites of the mitochondrial genome is species-specific and difficult to be explained on the basis of a mutational hotspot concept. (ii) A comparison of the ratios of non-synonymous to synonymous changes (dN/dS) among polymorphic positions in bonobos and in 4902 Homo sapiens mitochondrial genomes revealed a remarkable difference in the strength of purifying selection in the mitochondrial genes of the F0F1-ATPase complex. While in bonobos this complex showed a similar low value as complexes I and IV, human haplogroups displayed 2.2 to 7.6 times increased dN/dS ratios when compared to bonobos.

Conclusions

Some variants of mitochondrially encoded subunits of the ATPase complex in humans very likely decrease the efficiency of energy conversion leading to production of extra heat. Thus, we hypothesize that the species-specific release of evolutionary Background We have analyzed the complete mitochondrial genomes of 22 Pan paniscus (bonobo, pygmy chimpanzee) individuals to assess the detailed mitochondrial DNA (mtDNA) phylogeny of this close relative of Homo sapiens.

Pan genus mtDNA phylogeny (fig. 1)
PanTrog = Pan troglodytes (chimpanzee), PP = Pan paniscus (bonobo)

It is very apparent that bonobos have three major mtDNA haplogroups, named A, B and C.

Unlike humans (or at a lesser extent common chimpanzees), bonobos live in a well defined area of the SW Congo basin, limited by rivers, and have therefore never experienced a expansion since they became separated from their chimpanzee cousins. This makes them a good reference to better understand how demographic expansion affected our genetics, specifically our mtDNA.


Chronology

The authors say that the most recent common ancestor (MRCA) of all bonobos (by mtDNA) lived some 540,000 years ago (430-670 Ka. with 95% confidence interval).

If the graph above has a scale (and I understand it does) and assuming this estimate is correct, then the divergence of both Pan species happened c. 2.1 million years ago (1.7-2.6 Ma at 95% CI) - using simple linear maths.

Notice that Caswell 2008 already suggested a possible divergence age of 1.5-2.0 Ma in order to make it coincident with the formation of the Congo basin as we know it, a geological phenomenon that was surely itself the cause of the chimp-bonobo divergence. In my own words back then:

That the chimpanzee-bonobo split should be move backwards in time to at least 1.29 million years ago. And, that if the human-chimp divergence age is actually older (8 million years instead of 7), then this event would be coincident with the formation of the Congo river (1.5-2 Myrs BP), that many people belive is at the origin of bonobo speciation.

So I think we can confirm that the Pan paniscus speciation event happened most likely some 2 million years ago, when some undifferentiated Pan became isolated from the rest in the SW Congo basin on purely geological reasons.

It is also said that:

The maximal nucleotide difference between bonobo groups is, however, 1.5 times higher than in humans, and thus somewhat closer to the distance between modern humans and the extinct Neandertal.

While this affirmation is unspecific on the details, it seems to weight against the shortest claimed divergence ages for the two big-headed human species.


Bonobo reference sequence is a mix

The authors find that the bonobo reference sequence (GeneBank) seems to be not a genuine one but a mix of two rather unrelated ones. Hence they propose deprecating the extant reference and use the closest one of theirs, PP23, as new reference.


Purifying selection

The authors find strong support for purifying selection in both bonobos and humans. However some of this funtional constraint seems to have been lifted for some groups when humans spread around the world, specially to colder locations. Therefore they suspect it related to the metabolic determinants of high tropical temperatures. However some of this constraint may have been already lifted still in Africa as the branch leading to humans evolved hairlessness and sweat.

For ATPase, the nonsynonymous/synonymous (dN/ds) ratio is lowest among the Khoisan (haplogroups L0 and L1 essentially) and highest in haplogroup A. However other Siberian/Native American haplogroups (C and D) do not show anything so extreme, so rather than thinking in terms of positive selection, the authors argue that it is loss of evolutionary constraint what we see here:

Therefore, we conclude, in agreement with others [16], that the observed increase of dN/dS values for the mitochondrial ATPase genes in humans cannot be interpreted in favor of positive selection at colder climate conditions, but rather is the result of the release of strong evolutionary constraints during population expansion and migration of modern humans.

Another interesting finding is surely that one of the three bonobo haplogroups displays a mutation at locus 8344A>G, which is strongly implicated in MERRF syndrome (a mildly incapacitating degenerative disease) in humans. However they suspect that a nearby bonobo-specific mutation, present in all bonobo mtDNA, may be acting to prevent this effect in bonobos.

More evidence for arrows 60,000 years ago

New findings at Sibudu cave (KwaZulu-Natal, South Africa), add evidence in favor of a very ancient use of bow and arrow by Homo sapiens. These findings are small stone points which keep traces of blood and bone from the impacts and also of the resin used to glue them to the shafts.

Forensic analysis of this evidence seems to discard that they were used as hand-held spear points but must have been shot with much greater energy. However I cannot find any reasoning that excludes their possible shooting with atlats.

The BBC article that is the source of this information claims that this finding pushes the use of bow and arrow back some 20,000 years, however bone points found at the same site two years ago, and also dated to c. 60 Ka, already suggested this.

Mitochondrial Eve lived some 200,000 years ago

Just for the record.

Contrasting several simpler and more complex models of mtDNA molecular clock evaluation seem to show coincidence at least in this aspect our shared oldest grandma (by purely matrilineal ancestry) lived some 200,000 years ago.

Krzysztof A. Cyrana and Marek Kimmel, Alternatives to the Wright–Fisher model: The robustness of mitochondrial Eve dating. Theoretical Population Biology, 2010. Pay per view.

According to the news article at Science Daily:

Each model has its own assumptions, and each assumption has mathematical implications. To further complicate matters, some of the assumptions are not valid for human populations. For example, some models assume that population size never changes. That is not true for humans, whose population has grown exponentially for at least several thousand generations. Other models assume perfect mixing of genes, meaning that any two humans anywhere in the world have an equal chance of producing offspring.

Cyran said human genetic models have become more complex over the past couple of decades as theorists have tried to correct for invalid assumptions. But some of the corrections -- like adding branching processes that attempt to capture the dynamics of population growth in early human migrations -- are extremely complex. Which raises the question of whether less complex models might do equally well in capturing what's occurring.

"We wanted to see how sensitive the estimates were to the assumptions of the models," Kimmel said. "We found that all of the models that accounted for random population size -- such as different branching processes -- gave similar estimates. This is reassuring, because it shows that refining the assumptions of the model, beyond a certain point, may not be that important in the big picture."

Lucy's knives

New evidence in form of unmistakable stone-tools' marks on bone, push back the earliest known systematic use of tools to an species that was surely not still "human" (in the sense of belonging to the genus Homo) but to Australopithecus afarensis or another similar (but unknown) species. This happened some 3.4 million years ago in the central-northern Ethiopian highlands.



Australopithecus afarensis, the species to which the famous fossil Lucy belonged to, is the only hominin species known to have lived in that space-time. However until now it was commonplace to think that they were vegetarians and did not use tools.

It seems now that such ideas were wrong and that Lucy's species, with a brain barely larger than that of a chimpanzee, was already using not just random rocks but sharp ones able to cut meat. Forensic analysis leaves no room to doubt the marks are product of cutting tools and not animal fangs or paws.

This has potentially interesting implications for the evolutionary history of human brain and intelligence, as well as our highly precise hand, both tightly associated to tool use.

More detailed news stories at Science Daily and BBC.

Ref. Shannon P. McPherron et al., Evidence for stone-tool-assisted consumption of animal tissues before 3.39 million years ago at Dikika, Ethiopia. Nature, 2010. Pay per view.

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.

Life in the cold, life under the heat

Gathering here a couple of at least curious news I read recently at Science Daily. They have nothing to do with each other except one thing: they both deal with life at extreme temperatures.


Being human is cool... literally so.

Benjamin Passey and colleagues report that temperatures were hellishly high most of the time in one of the most likely cradles of human evolution: the basin of Lake Turkana, including the last three million years.

This may support the thermal hypothesis of human evolution, that would explain why we don't have any fur and sweat so much (intended for cooling) and also maybe why we walk on only two legs, reducing the direct impact of both the Sun and the overheated soil.

The article does not mention it but I recall reading some time ago that even brain size increase has been attributed tentatively to such heat challenge, as larger brains would prevent fainting under the heat allowing our ancestors to exploit the territory at noon, when predators are enjoying their siestas. That would also explain why we keep "natural hats" of hair on our heads, of all bodily places (and I'd dare hunch it might also explain thinly curled hair, still overwhelmingly dominant among tropical peoples, as a means to secure free circulation of air near it).

Source article.


Where water is a rock... methane fills the rivers. Life in Titan?

This in fact was already known. What is new is that astronomer Chris McKay suspects that the chemistry of Titan could well be indicative of the existence of some form of life on it.

Saturn's satellite Titan, as you probably know, has many similitudes with Earth's environment, just that with a much lower temperature range that does not allow water to melt ever. At such freezing temperatures, methane, an organic compound, takes the role of water switching between liquid and gaseous states in the hazy orange atmosphere of this planetoid, the largest moon of the Solar System.

But what is new and interesting is that scientists expected that natural chemistry in Titan would produce lots of acetylene but Cassini has failed to find any of it so far. The most likely chemistry for life without water at such gelid temperatures would be a metabolism of acetylene by hidrolization (reaction with hydrogen instead oxygen, as usually happens on Earth) and, according to McKay, the available data seems to indicate that this is actually happening on Titan.

Still, Mark Allen, says that all non-biological explanations are not still ruled out. Acetylene might be just degraded by solar radiation for example.

But the aboundance of organic compounds on Titan is so overwhelming that it is difficult to think that life has not evolved upon them at the slightest chance. This last is my opinion.

Source article.

On some details of the Neanderthal genome draft

Still chewing on the Neanderthal genome draft (Green 2010). Only today I have got some time to dwell on some of its details.


Alleles specific to all Homo sapiens (and not to Neanderthals)

It's interesting not just that some of us carry a small apportion of Neanderthal alleles but also the list of alleles that are exclusive of our species. Green et al. dwell on this matter in the section titled A catalog of features unique to the human genome.

There is a list of 78 alleles (table 2) that are fixated in the derived (non-Chimpanzee) form in the species Homo sapiens exclusively and found in their ancestral state among Neanderthals. Many are not really known their role but others seem to accumulate in certain processes such as skin (sweat...), melanin, smell, vision, sperm motility, hormonal and cellular division regulatory processes. This suggests me that there were some marked biological and appearence differences among the two species in spite of the proximity.

Therefore the inter-species barrier was possibly rather high even if still not total.

The authors emphasize specially five alleles in which more than one SNP is different, suggesting greater differences. These are specially related to skin morphology and regulatory substitutions (specificity).

Also the studied certain regions in clear rapid evolutionary change in the line leading to humans called HARs. The vast majority of these HARs had already evolved before the Neanderthal-Sapiens transition but a few (c. 1.7%) had not yet and belong specifically to Homo sapiens.

These human-specific HARs include genes related to mental functions (associated with mental disorders such as Dow syndrome, schizophrenia and autism) as well as a the RUNX2 (CBFA1) gene that would be related to changes in skull, clavicle and ribcage morphology.


Are Chinese slightly 'more Neanderthal' than other Eurasians?

Less definitely, when working with the comparative data at table 4, I find that the Han Chinese sample (n=2) appears very slightly but maybe significantly "more Neanderthal" than the other Eurasians, including the only Japanese. The Chinese individuals differ from the African sample in Neanderthal alleles by an average factor of 5.05 (4.95 and 5.15), while the non-Han Eurasian average is 4.21 (3.93-4.65), that is: almost a point more. Only one European individual (4.65) really approaches the Han Chinese figures, which differ by almost a whole point (0.92) from the rest.


This, of course, can only be a very preliminary indication but it does seem intriguing and potentially meaningful. The fact that the greatest difference is with the, otherwise very close, Japanese could even point to some greater diversity patterns in East Eurasia in regard to Neanderthal genes in us, and, considering the tiny sample sizes, even in much of the rest of Eurasia.

Some experts' opinions on the Neanderthal genome's implications

From Quo magazine (in Spanish). Translated some sentences here:

J.L. Arsuaga, co-Director of Atapuerca archaeological site: These are only some some results and we will have to wait. It is a contribution in some humans of just some 2%, what would not be really relevant.

C. Lalueza Fox, member of the research team of El Sidrón cave: This year we will see published the Thousand Genomes' Project, that aims to sequence a thousand human genomes, and will be interesting to see if the percentage of Neanderthal genes is kept, in which frequency, in which populations.

Jordi Agustí, member of the research team of Dmanisi site: It does not fundamentally invalidates what was believed so far: that they were different or almost different species.

E. Baquedano, member of the research team of Pinilla del Valle site: We will have to admit that Humans and Neanderthals belong to a single species even if they are distinct subspecies.

In the same magazine but a separate interview, anthropologist Erik Trinkaus, defends his theory on admixture in Europe some 40,000 years ago only and is disdainful of the use of aDNA and the comparison of a "pathetic" sample of just 3 Neanderthal individuals with just "five modern humans" (sic, actually it's five modern human populations comprising 12 individuals). He refers us to his 2007 anatomical paper.

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.

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.