L0k lineages found in Zambia

Only the abstract is available to me as of now:

Chiara Barbieri et al., Ancient Substructure in Early mtDNA Lineages of Southern Africa. AJHG 2013. Pay per view (6 month embargo, then freely accessible) → LINK [doi:10.1016/j.ajhg.2012.12.010]

Abstract

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.

See also at my old discontinued blog Leherensuge:

• Reviewing the mtDNA L lineages (notes): L0
• The early expansion of H. sapiens in Africa (mtDNA)

Notice from these last that both L0k and L0d have minor presence in Arabia (L0k2 in Yemen, and now it seems also in Zambia, and L0d3, shared between Khoisan and Kuwaitis).

Very skeptic on claim of Neolithic flow from India to Australia

I feel quite skeptic about the claims held by this paper but in any case it is worth mentioning.

Irina Pugach et al., Genome-wide data substantiate Holocene gene flow from India to Australia. PNAS 2013. Pay per view (6-month embargo, then freely accessible) → LINK [10.1073/pnas.1211927110 ]

Abstract

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India. 

The evidence for this claim is all derived exclusively by statistical inference on autosomal DNA. Suspiciously enough, even if the authors claim admixture levels of as much as 11% and as recent as a mere 4000 years ago, no patrilineage (Y-DNA) nor matrilineage (mtDNA) [correction: see update below] has been ever detected that could be associated with this purported migration. 

Additionally c. 4000 years ago Southern India, the alleged origin of the genetic flow, was already immersed in a flourishing agricultural economy and it looks very strange that the migrants, people who were exchanging crops with Africa for example, would not carry a single element of this new economy to the island continent. Of course this inconsistency could easily be fixed by merely arguing that the molecular clock estimates used tick too quickly, which is a general problem anyhow and therefore no real surprise.

If the hypothesized migration happened earlier, in the Epipaleolithic or Late Upper Paleolithic, then it would also be easier to explain that, with smaller populations, genetic drift could have caused the extinction of whatever Indian uniparental markers that the migrants carried with them initially. It still causes my eyebrows to rise instinctively. 

Even then, if this was the case, we should be able to identify some sort of techno-cultural elements that the migrants may have carried with them, like microlithic stone technologies or whatever. As far as I know nothing of the like exists. 

The only techno-cultural burden that the migrants might have brought with them to Australia would therefore have been the dingo, but this dog has lots of relatives in Island SE Asia, where the authors could not detect any significant Indian admixture.

So the hypothesis looks weak to me. Let's see the evidence they present:

Above we can see the ADMIXTURE K=4 result, probably not the optimal one (which would probably produce an Australian-specific cluster (mostly but not fully masked as Papuan) and surely two different Indian ones, partly masked as European and Onge affinity) but the one the authors decided to show us as evidence for their hypothesis.

Not only this is surely not the optimal clustering level but also Australian Aborigines are comparatively undersampled, while Indian weight is overwhelming. This is a clear example of how NOT to design a scientifically useful sampling strategy for ADMIXTURE-like comparisons like this (because oversampled populations tend to overshadow the rest just by the weight of numbers). 

As it is, this graph proves nothing but rather suggests that some Indian affinity is part of Australian Aborigine ancestral or founder specificity, when compared with Papuans. This may have many explanations first of which is a mere artifact by reason of a poor sampling and depth design of the experiment. ADMIXTURE is a powerful neutral tool, just a like a test tube or the Geneva particle accelerator, but what we do with it may well not be neutral, either by reason of mischievous manipulation or mere error.

In this case I find the test very poorly designed and executed. If I have some time later in the weekend, I may try to perform an alternative test according to my humble possibilities - I promise nothing however.

A complementary test that the authors perform used Tree Mix. As I have discussed elsewhere, TreeMix often produces very strange results and I do not consider it a reliable tool at all, but for whatever is worth here it is what they got:

While the purported migrations generated by the Tree Mix algorithm appear to suggest a secondary genetic flow from India to Australia (orange arrow at C) the data on which such result is based (D) only gives the most tenuous level (green) of extra genetic affinity between Southern Indians (DRA) and Australian Aborigines (AUA). Meanwhile the highly questionable algorithm identifies Dravidians and North Chinese (CHB) as being genetically very close (blue), when they are not in fact.

So what do I get from this paper? TreeMix' usual senseless noise and apparent mismanagement of ADMIXTURE, a powerful tool when used properly.

Less than inconclusive, I'd say. But your take of course.

Update: G Horvat (see comments) points me to Kumar 2009 (so far unchallenged at PhyloTree)  for a shared mitochondrial lineage between Australia and India, known as M42. This haplogroup has the following structure (each → indicates a coding region mutation according to PhyloTree, Kumar originally listed a few more):

• M 
• → M42'74 
• → M42 
• →→→→ M42a (Australian Aborigines)
• → M42b (India)
• →→ M74 (South China, Vietnam, India)

This allows for a potential mtDNA backing of this purported connection, however it is a very small lineage and Kumar claimed that M42 coalesced long ago, in the context of the first colonization of Asia and Australasia by Homo sapiens:

The divergence of the Indian and Australian M42 coding-region sequences suggests an early colonization of Australia, ~60 to 50 kyBP, quite in agreement with archaeological evidences. 

Yet the relatively long stem leading to M42a does allow for a later time-frame of arrival to Australia. Neolithic anyhow looks still most unlikely to me.


Update (Jan 18): Dingo DNA:

An important element to consider here are the origins of the dingo as the Australian wild dog is known. This dog variant suffered a strong founder effect upon arrival to Australia described mainly by two variants of the haplotype A29. This lineage only links to East Asia however, having arrived almost without doubt, via Indonesia from mainland East Asia (either Indochina or China or both).

It is clearly not related to Austronesian expansion and could have arrived either within the early Neolithic of ISEA (arguably Austroasiatic in language) or even earlier. At least one of the papers I checked rather supports a pre-Neolithic introduction and certainly before the archaeologically supported age of c. 3000 years ago.

The Y-DNA of dingos also shows a strong founder effect (only two haplotypes, with overlapping but distinct distributions) and again the most obvious connections seem to be in SE Asia.

See (freely accessible):

• Peter Savolainen et al. 2004, A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA (PNAS).
• Matthias C.R. Oskarsson et al. 2011, Mitochondrial DNA data indicate an introduction through Mainland Southeast Asia for Australian dingoes and Polynesian domestic dogs (Proceedings of the Royal Society B). 
• Arman Ardalan et al. 2011, Narrow genetic basis for the Australian dingo confirmed through analysis of paternal ancestry (Genetica).

Update (Jan 18): It is probably interesting also to mention that Australian Aborigines show no difference with Papuans in their overall amount of Denisovan ancestry. This also appears as contradictory with the idea of significant external admixture, which should have diluted at least minimally that Denisovan component (Indians have none).


Update (Apr 7): A new "working paper" has been published on this matter, sharing my critical stand towards the sloppiness of Puhach's team but still considering plausible a Holocene gene flow from India. I have commented in a new entry.

Puctuated equilibrium, speciation and everything else

I believe it is worth recommending the reading of this new review paper which discusses the various evolutionary theories en vogue, with emphasis in punctuated equilibrium, which is surely a very realistic model:

Jaroslav Fregg, Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution. Biology Direct 2013. Open access → LINK [doi:10.1186/1745-6150-8-1]

Abstract

Punctuational theories of evolution suggest that adaptive evolution proceeds mostly, or even entirely, in the distinct periods of existence of a particular species. The mechanisms of this punctuated nature of evolution suggested by the various theories differ. Therefore the predictions of particular theories concerning various evolutionary phenomena also differ.

Punctuational theories can be subdivided into five classes, which differ in their mechanism and their evolutionary and ecological implications. For example, the transilience model of Templeton (class III), genetic revolution model of Mayr (class IV) or the frozen plasticity theory of Flegr (class V), suggests that adaptive evolution in sexual species is operative shortly after the emergence of a species by peripatric speciation -- while it is evolutionary plastic. To a major degree, i.e. throughout 98-99% of their existence, sexual species are evolutionarily frozen (class III) or elastic (class IV and V) on a microevolutionary time scale and evolutionarily frozen on a macroevolutionary time scale and can only wait for extinction, or the highly improbable return of a population segment to the plastic state due to peripatric speciation.

The punctuational theories have many evolutionary and ecological implications. Most of these predictions could be tested empirically, and should be analyzed in greater depth theoretically. The punctuational theories offer many new predictions that need to be tested, but also provide explanations for a much broader spectrum of known biological phenomena than classical gradualistic evolutionary theories.

I don't dare to evaluate the paper but I do recommend reading it because it can help us to better understand what is going on when we talk of speciation, competition, evolution, dynamic equilibrium, etc. I picked up this quote:

Approximately 35% of the substitutions (20-70%, depending on the studied taxon) was shown to occur in brief periods of speciation. It is worth mentioning that we are not aware of how many speciation events actually occur in the studied, seemingly unbranched lineages. Therefore, the published estimates of speciation associated substitution rates represent only the lower margin of the real figures.

And the only figure, which illustrates how a highly diverse population/species can be stable and how evolution can happen and often does in bottlenecks instead:

Most punctuational theories of evolution, including the evolutionary conceptions of Wright, Mayr, Carson, Templeton and Flegr (for comparison see Table 1), suggest that sexually reproducing species respond evolutionarily to selection (are evolutionarily plastic) only during speciation. The mechanisms of this type of evolutionary behavior of sexual species suggested by the various theories differ, for a review see [1]. For example, the genetic revolution model [2] implicitly and the frozen plasticity theory explicitly [3] suggest that a species is evolutionary plastic when its members are genetically uniform, i.e. only after a portion of the original species has split off, skirted extinction for several generations, and then undergone rapid multiplication (Figure 1).

The paper uses the "open review" format, including commentaries from the reviewers and the replies by the author - this I find an interesting novelty which adds some value to the paper by pointing possible avenues for discussion or further research.

Ancient tsunamis of Europe

In red the tsunami sediments
Measures: height of the wave at each location

A huge tsunami probably hit the northern parts of Doggerland (the emerged landmass of what is now the North Sea) some 8000 years ago. The evidence from this catastrophic event, which probably affected the earliest inhabitants of NW Europe in a catastrophic way comes from an underwater formation off the Norwegian coast known as Storegga, which was partly demolished by the force of the giant wave, as well as from sedimentary layers at various coastal locations. The wave reached more than 20 meters at the Shetlands, where it left a 30cm-thick revealing layer.

Another possible tsunami may have affected the Southwestern coasts of Iberia in the 7th century BCE. This is currently being researched and could be related to the collapse of the semi-mythical city of Tartessos.

Sources: Meteoweb[it], Paleorama[es] (→ link 1, link 2).

Early Neolithic burials found near Istanbul

Pendik, a suburb of Istanbul on the Asian coast of the Bosporus, has produced a Neolithic settlement dating to c. 8500 years ago, including houses, burials and various tools (spoons, needles, axes). 

One of the Pendik burials

Source: Press TV.

Châtelperronian was made by Neanderthals

Contrary to some rumors and some skepticism, the archaeology and radiocarbon chronology appear to support only Neanderthals as the material authors of the first "mode 4" stone industry of Western Europe: the Châtelperronian.

They still allow for it, and especially the novel behavior of production and use of durable ornaments (on bone mostly), to have been influenced by the penetration of Homo sapiens.

Jean-Jacques Hublin et al., Radiocarbon dates from the Grotte du Renne and Saint-Césaire support a Neandertal origin for the Châtelperronian. PNAS 2012. Open access → LINK [doi: 10.1073/pnas.1212924109 ]

Abstract

The transition from the Middle Paleolithic (MP) to Upper Paleolithic (UP) is marked by the replacement of late Neandertals by modern humans in Europe between 50,000 and 40,000 y ago. Châtelperronian (CP) artifact assemblages found in central France and northern Spain date to this time period. So far, it is the only such assemblage type that has yielded Neandertal remains directly associated with UP style artifacts. CP assemblages also include body ornaments, otherwise virtually unknown in the Neandertal world. However, it has been argued that instead of the CP being manufactured by Neandertals, site formation processes and layer admixture resulted in the chance association of Neanderthal remains, CP assemblages, and body ornaments. Here, we report a series of accelerator mass spectrometry radiocarbon dates on ultrafiltered bone collagen extracted from 40 well-preserved bone fragments from the late Mousterian, CP, and Protoaurignacian layers at the Grotte du Renne site (at Arcy-sur-Cure, France). Our radiocarbon results are inconsistent with the admixture hypothesis. Further, we report a direct date on the Neandertal CP skeleton from Saint-Césaire (France). This date corroborates the assignment of CP assemblages to the latest Neandertals of western Europe. Importantly, our results establish that the production of body ornaments in the CP postdates the arrival of modern humans in neighboring regions of Europe. This new behavior could therefore have been the result of cultural diffusion from modern to Neandertal groups. 

Fig. 1. Calibrated ages and boundaries calculated by using OxCal 4.1 (37) and IntCal09 (36). The Grotte du Renne ages are in black and are compared with the Saint-Césaire human [Neanderthal] bone date in red. Asterisk indicates anthropogenically modified bones. The results are linked with the (NGRIP) δ18O climate record.

Importantly, it is also confirmed that Grotte-du-Renne (Arcy-sur-Cure, Burgundy) is one of the last Chatelperronian, and therefore surely Neanderthal, pockets in  Western Europe, co-existing with Aurignacian North-East and South-West of it, what is suggestive of this latter culture, probably the first settlement by Homo sapiens, expanding to SW Europe via Italy rather than Germany.

Finally, according to our results, the CP Neandertals of the Grotte du Renne, Saint-Césaire, and Les Cottés clearly postdate the earliest likely modern humans remains documented in western Europe (43) and largely overlap in time with the early Aurignacian in the Swabian area (44) and in southwestern France (42).

 

Fig. S1. Geographical distribution of the Châtelperronian assemblages and location of the three main Châtelperronian sites discussed in the text.

Hat tip to Linear Population Model.

Eye color, face shape and perception of trustworthiness

An old popular Galician song said:

Ollos verdes son traidores...
azules son mentireiros,
os negros e acastañados son firmes e verdadeiros.

Translated:

Green eyes are treacherous...
blue ones are deceitful,
the black and brown ones are loyal and truthful.

Just word of a silly mariner song? Intriguingly science confirms now, in a way, part of this perception (at least for blue and brown eyes).

But notice please that it is the precisely the perception what is being confirmed: people seem to perceive blue eyes in general as somewhat less trustworthy. The study says nothing about people with blue eyes being untrustworthy in fact, just that we tend to distrust them more than people with brown eyes.

Karel Kleisner et al., Trustworthy-Looking Face Meets Brown Eyes. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0053285]

Abstract

We tested whether eye color influences perception of trustworthiness. Facial photographs of 40 female and 40 male students were rated for perceived trustworthiness. Eye color had a significant effect, the brown-eyed faces being perceived as more trustworthy than the blue-eyed ones. Geometric morphometrics, however, revealed significant correlations between eye color and face shape. Thus, face shape likewise had a significant effect on perceived trustworthiness but only for male faces, the effect for female faces not being significant. To determine whether perception of trustworthiness was being influenced primarily by eye color or by face shape, we recolored the eyes on the same male facial photos and repeated the test procedure. Eye color now had no effect on perceived trustworthiness. We concluded that although the brown-eyed faces were perceived as more trustworthy than the blue-eyed ones, it was not brown eye color per se that caused the stronger perception of trustworthiness but rather the facial features associated with brown eyes.

So the authors conclude that it is not eye color but associated face shape what drives untrustworthiness because the phenotype associated with blue eyes is more angular, less rounded, at least for males:

Figure 2. Shape changes associated with eye color and perceived trustworthiness.
Thin-plate spline visualizations of the way face shape correlates with eye color (a–f) and trustworthiness (g–i). Generated face shapes of blue-eyed woman (a) and brown-eyed woman (c) compared to average female face (b). Generated face shapes of blue-eyed man (d) and brown-eyed man (f) compared to average male face (e). Generated face shapes of untrustworthy-looking man (g) and trustworthy-looking (i) man compared to average male face (h). The TPS grids of perceived trustworthiness for women are not shown because shape analysis did not meet statistical significance. The generated facial images (a–f) were magnified 3x for better readability.

They claim that they found no correlation with facial shape for women but I find in the image above almost exactly the same pattern for men and women and not only what they detected: notably the blue eyed people (both genders) and the less trusted men all have in my opinion:

• Smaller eyes
• More serious (defiant, analytic, unsympathetic) expression
• Proportionally broader face or at least jaws

In general the faces to the left look significantly colder, less empathic, a perception that blue eyes can only enhance.

The authors ponder if there is a phenotype linkage disequilibrium associating face and eye color, what seems plausible. But then go on speculating about sexual selection and what not. 

In this sense Razib has an interesting critical analysis questioning if selection is behind the blue eye incomplete sweep in West Eurasia or Europe. If I understand him correctly he seems to suggest, never clearly naming it, that blue eye may have been favored because of the associated skin pigmentation trait, a key adaptive value in the dark winters of Europe and very especially the northern half of it.


Update: is this a peculiarity of Central Europe or the Czech Republic?

A reader sent me an email in which it was questioned if this association is peculiar of the Czech Republic, where the study was performed, and can't be extended for example to Britain. Examples of soft-faced blue-eyed Britons mentioned were Hugh Grant and Alec Baldwin (I'm not sure if Baldwin is such a good counter-example but Grant is for sure one such case). 

I find it a very good criticism and hope that entices debate.



See also: Causes of skin and hair color variance in Europeans remain undetermined.