Category Archives: South Africa

Echoes from the past (May 17 2013)

Some interesting news I cannot dedicate much effort to:

Human intelligence not really linked to frontal lobe.

New research highlights that the human frontal lobe is not oversized in comparison with other animals. Instead the human intelligence seems to be distributed through all the brain, being the network what really matters → Science Daily

Ref. Robert A. Barton and
Chris Venditti. Human frontal lobes are not relatively large. PNAS, May 13, 2013 DOI: 10.1073/pnas.1215723110

Early hominin ear bones found together in South Africa.

The three bones, dated to c. 1.9 Ma show intermediate features between modern humans and apes → PhysOrg.

New hominin site in Hunan (China).

The sediments of Fuyan cave, in which five human teeth (Homo erectus?) were found, along with plenty of animal ones, are dated to 141,700 (±12,100) years ago. → IVPP – Chinese Academy of Sciences.

The five human teeth

Neanderthal workshop found in Poland.

In Pietrowice Wielkie (Silesia), which is at the end of a major natural corridor from the Danubian basin → PAP.

Ancient Eastern Europeans ritually killed their pets to become warriors.

In the Bronze Age site of Krasnosamarkskoe (Volga region, Russia) more than 50 ritually pieced skulls of dogs have puzzled archaeologists, who have reached the conclusion, after researching Indoeuropean accounts from India, that the animals may have been killed in adulthood rituals: the boys who were to become warriors had to kill their most beloved pet in order to be accepted as such, and did so in a precise and macabre ritual → National Geographic.

Ancient log boat found in Ireland.

In the Boyne river, which was in the past a major artery of the island. Not yet dated: it could be from prehistoric times or the 18th century. → Irish Times.


Khoesan and Coloured autosomal DNA in context

There has been a number of studies coming out recently on Khoesan genetics but this one does not seem to be just redundant, providing some extra information instead.

Desiree C. Petersen et al., Complex Patterns of Genomic Admixture within Southern Africa. PLoS Genetics 2013. Open accessLINK [doi:10.1371/journal.pgen.1003309]


Within-population genetic diversity is greatest within Africa, while between-population genetic diversity is directly proportional to geographic distance. The most divergent contemporary human populations include the click-speaking forager peoples of southern Africa, broadly defined as Khoesan. Both intra- (Bantu expansion) and inter-continental migration (European-driven colonization) have resulted in complex patterns of admixture between ancient geographically isolated Khoesan and more recently diverged populations. Using gender-specific analysis and almost 1 million autosomal markers, we determine the significance of estimated ancestral contributions that have shaped five contemporary southern African populations in a cohort of 103 individuals. Limited by lack of available data for homogenous Khoesan representation, we identify the Ju/’hoan (n = 19) as a distinct early diverging human lineage with little to no significant non-Khoesan contribution. In contrast to the Ju/’hoan, we identify ancient signatures of Khoesan and Bantu unions resulting in significant Khoesan- and Bantu-derived contributions to the Southern Bantu amaXhosa (n = 15) and Khoesan !Xun (n = 14), respectively. Our data further suggests that contemporary !Xun represent distinct Khoesan prehistories. Khoesan assimilation with European settlement at the most southern tip of Africa resulted in significant ancestral Khoesan contributions to the Coloured (n = 25) and Baster (n = 30) populations. The latter populations were further impacted by 170 years of East Indian slave trade and intra-continental migrations resulting in a complex pattern of genetic variation (admixture). The populations of southern Africa provide a unique opportunity to investigate the genomic variability from some of the oldest human lineages to the implications of complex admixture patterns including ancient and recently diverged human lineages.

The array of Khoesan populations senso stricto analyzed in this study is much smaller than that of Schebusch 2010 but this study has the advantage of including Cape Coloureds and their Baster relatives, partially descendants from the otherwise extinct pastoralist Khoekhoe (Hottentots, now considered a derogative term) who lived in much of Southern Africa upon the arrival of Bantu and Europeans, as well as the amaXhosa, a Bantu people which clearly display marked Khoesan admixture.

Figure 1. Map of southern Africa
showing distribution of sampling per population identifier and
significant historical events that likely shaped ancestral

There is brief mention of maternal and paternal DNA. Just to mention that mtDNA being mostly aboriginal (L0d/L0k) among the Khoesan (86-100%), the Coloureds (68%) and even the Xhosa (47%, all L0d), while aboriginal Y-DNA (essentially A2b and A2c2, plus occasional B2) is concentrated among the Ju/’hoan, with the !Xun being instead dominated by E1b1-M275, of putative East African (Nilotic?) origins. This is consistent with the !Xun being historically pastoralists. European patrilineages, notably R1b, are dominant among the Baster (92%) and Cape Coloured (71%).
Coloureds only make up some 9% of South African population but they dominate the countryside in much of the former Cape Province. Namibian Basters are a subset of them who migrated northwards in 1868.

Figure 2.  PCA and STRUCTURE analysis (click to expand)
We can see in the graphics above how the North Cape Coloured and Baster only display minor Bantu admixture, being essentially a variable mix of European and Khoesan ancestry, with probably also some Malay input (apparent in the increase of the blue component relative to the European reference). Instead East Cape and Cape Town (D6) Coloured appear to have greater apportion of Bantu ancestry and, especially the later, a notable increase of the East Asian input.
The STRUCTURE graph, particularly at K=9, is also informative about other African populations but I won’t dwell in that here. 
The authors also made an interesting exercise of analysis using Ancestry Informative Markers with the !Xun and Xhosa:

Figure 4. Ju/’hoan-Yoruba ancestry
informative markers (AIMs) defined ancestral contributions to the !Xun
and amaXhosa, providing evidence for two distinct !Xun lineages with
differing ancestral contributions.
It seems evident that much of the !Xun ancestry (up to 70%) does not fall in either (Ju/’hoan-Yoruba) category but it is something else, probably specific to this people. The Xhosa Khoesan ancestry also seems closer to the pastoralist !Xun than to the (likely more genuinely ancient) Ju/’hoan. 

There is some more info in the paper but I feel that the essentials are sufficiently covered here. 

See also:

Khoe-San matrilineages and prehistory

A most interesting study has just been published that reconstructs the prehistory of the Khoe-San peoples of Southern Africa primarily using mitochondrial DNA analysis but with very important reliance on archaeological data as well.
Karina M. Schlabusch et al., MtDNA control region variation affirms diversity and deep sub-structure in populations from Southern Africa. BMC Evolutionary Biology 2013. Open accessLINK [doi:10.1186/1471-2148-13-56]

Abstract (provisional)


The current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka (ka = kilo annum [thousand years] old/ago) and sea-borne immigrants within the last 350 years. Here we use mitochondrial DNA (mtDNA) to examine the population structure of various San and Khoe groups, including seven different Khoe-San groups (Ju/’hoansi, !Xun, /Gui+//Gana, Khwe, =Khomani, Nama and Karretjie People), three different Coloured groups and seven other comparative groups. MtDNA hyper variable segments I and II (HVS I and HVS II) together with selected mtDNA coding region SNPs were used to assign 538 individuals to 18 haplogroups encompassing 245 unique haplotypes. Data were further analyzed to assess haplogroup histories and the genetic affinities of the various San, Khoe and Coloured populations. Where possible, we tentatively contextualize the genetic trends through time against key trends known from the archaeological record.


The most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) that can be traced back in time to ~100 ka, found at high frequencies in Khoe-San and sampled Coloured groups. Furthermore, the L0d/k sub-haplogroups were differentially distributed in the different Khoe-San and Coloured groups and had different signals of expansion, which suggested different associated demographic histories. When populations were compared to each other, San groups from the northern parts of southern Africa (Ju speaking: !Xun, Ju/’hoansi and Khoe-speaking: /Gui+//Gana) grouped together and southern groups (historically Tuu speaking: =Khomani and Karretjie People and some Coloured groups) grouped together. The Khoe group (Nama) clustered with the southern Khoe-San and Coloured groups. The Khwe mtDNA profile was very different from other Khoe-San groups with high proportions of Bantu-speaking admixture but also unique distributions of other mtDNA lineages.


On the whole, the research reported here presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa.

From the reading of the paper, I gather the following chronology (which should be always taken with some caution because of the uncertainty of “molecular clock” methods but in this case they seem reasonably backed from the material/cultural evidence record):
  1. L0d coalescence time estimate may correlate with the arrival of MSA to the region c. 100 Ka ago (I estimated once ~90 Ka, so it is consistent with my thought).
  2. Its sublineage L0d1’2 might have expanded c. 50 Ka ago (I would rather think of a more ancient chronology, soon after the L0d node – they can’t correlate it properly with any obvious archaeological pattern, so it might be, I guess, more related to the apogee of MSA c. 75 Ka ago).
  3. Some L0d1 subclades (notably L0d1a, L0d1b) would have expanded with the transition to LSA (40-20 Ka ago).
  4. L0d2a shows an star-like expansion that they estimate to have happened c. 7-8 Ka ago and would be related to an Epipaleolithic (with microlithic industry) that is also notable for the increase of the density of archaeological findings in South Africa and Lesotho. This lineage also shows secondary expansion with pastoralism later on.
  5. The introduction of herding c. 2000 years ago may have affected the correlations between the various L0d lineages. However most lineages show signs of expansion in this period. The main exception is L0d1a (decrease instead) and to some extent L0d1c (first decrease, later increase probably related to the !Xun late adoption of pastoralism, affecting especially to L0d1c1).
    1. L0d3 is too old to have expanded with pastoralism, so the authors reject  Tatiana Karafet’s hypothesis that it expanded in this period and that it could be related (to most unlikely) linguistic relation between Sandawe and Khoe-San. Instead they suggest (as I did in the past) that L0d3 had an East African distribution instead with only minor spreading to the Khoe-San in relation with pastoralism.
  6. The recent Iron Age (last millennium) arrival of Bantu-speakers absorbed primarily L0d2a, which is the most common lineage of Khoe-San peoples (including Coloureds, with the partial exception of Cape Coloured, where it is second to L0d2b).
The paper only briefly mentions L0k1, which is most concentrated towards Katanga (D.R. Congo) and may therefore have arrived to Southern Africa only with Bantu or pastoralist flows.
Frequencies and estimated timelines of major Southern African L0d and L0k lineages (from fig. 4):

See also:


Advanced lithic tech 70,000 years ago in South Africa

A new paper argues for the importance of ill-researched early African stone technologies in human techno-cultural evolution, based mostly on the heat-treated microlithic technology used at Pinnacle Point and its persistence through time. 
Kyle S. Brown et al., An early and enduring advanced technology originating 71,000 years ago in South Africa. Nature 2012. Pay per view ··> LINK [doi:10.1038/nature11660]

There is consensus that the modern human lineage appeared in Africa before 100,000 years ago1, 2. But there is debate as to when cultural and cognitive characteristics typical of modern humans first appeared, and the role that these had in the expansion of modern humans out of Africa3. Scientists rely on symbolically specific proxies, such as artistic expression, to document the origins of complex cognition. Advanced technologies with elaborate chains of production are also proxies, as these often demand high-fidelity transmission and thus language. Some argue that advanced technologies in Africa appear and disappear and thus do not indicate complex cognition exclusive to early modern humans in Africa3, 4. The origins of composite tools and advanced projectile weapons figure prominently in modern human evolution research, and the latter have been argued to have been in the exclusive possession of modern humans5, 6. Here we describe a previously unrecognized advanced stone tool technology from Pinnacle Point Site 5–6 on the south coast of South Africa, originating approximately 71,000 years ago. This technology is dominated by the production of small bladelets (microliths) primarily from heat-treated stone. There is agreement that microlithic technology was used to create composite tool components as part of advanced projectile weapons7, 8. Microliths were common worldwide by the mid-Holocene epoch, but have a patchy pattern of first appearance that is rarely earlier than 40,000 years ago9, 10, and were thought to appear briefly between 65,000 and 60,000 years ago in South Africa and then disappear. Our research extends this record to ~71,000years, shows that microlithic technology originated early in South Africa, evolved over a vast time span (~11,000years), and was typically coupled to complex heat treatment that persisted for nearly 100,000years. Advanced technologies in Africa were early and enduring; a small sample of excavated sites in Africa is the best explanation for any perceived ‘flickering’ pattern.
Supplementary materials (PDF) are freely available.
Supplementary Figure 2. Artifacts including crescent shaped backed blades (A-L) and notched blades (M-U) from the DBCS at PP5-6 show affinities with the Howiesons Poort industry. Backed blades are oriented with backed edge up and unmodified edge down. Notched blades are oriented parallel with axis of flake removal.

Posted by on November 7, 2012 in Africa, Middle Paleolithic, MSA, South Africa, stone tech


Khoesan genetics helping to understand the evolutionary history of Humankind as a whole

A reader sent me a copy of this letter or short paper on South African autosomal genetics:
Carina M. Schlebusch, Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. Science 2012. Pay per view ··> LINK [doi:10.1126/science.1227721]
[Note-update (Oct 2): the supplemental material is free and very very extensive: a must read for genetic data-miners and all those interested in getting deeper and more extensive info, even if just on the ethno-historical background of the populations considered in the study, something that most people, including myself, only know rather shallowly].

The paper has several points of interest but is specially useful, complemented by previous studies like Pickrell 2012, to better understand the aboriginal and modern genetics of Southern Africa, which is analyzed, for example as principal component (and other) analysis relative to geography.

Fig. 1. (click to expand)

(A) Sampling locations.
(B) Principal components analysis (PCA) of African individuals showing PC1 and PC2 rotated to fit geography.
(C) PCA for Khoe-San populations (∼ 2.3M SNPs).
(D) Pairwise FST for sub-Saharan populations (excluding Hadza, see fig. S24 for comparison)
(E) Prediction of the genetic components from geographic, linguistic and subsistence covariates. The predictive error relative to geography is given for each combination of covariates (values < 1 show improved predictive capacity compared to geography).
Also an Admixture analysis with an estimate divergence tree that is off in chronology by about 100% or even more. When will geneticists learn to calibrate their “molecular clock” speculations on archaeology? When?!
Here you have it, annotated by me (in red):
Fig. 2.(click to expand)
(A) Rooted population topology from a concordance test approach (14). Nodes with bootstrap support < 50% are collapsed (dashed lines), all other nodes have bootstrap support > 85%.
[Annotations in red by Maju]
(B) Clustering of 403 sub-Saharan African individuals (∼ 270k SNPs), assuming 2 to 11 clusters.
(C) Clustering of 118 southern African individuals (∼ 2.3M SNPs), assuming 2 to 8 clusters. Compare with fig. S16 that include recently admixed individuals.

Additionally the authors think that they have located a number of key genes that appear to have been selected for among some Khoesan groups and/or diversified around the time of the first human split c. 100 200 millennia ago, such as:
  • MYPN (myopalladin) – associated with muscle growth and function
  • ACTN3 – associated with “fast twitching” muscles and elite athletic performance
  • MHC – major histocompatibility comple
  • PRSS16 and POM121L2 – thought to protect against infectious diseases
  • ERCC4 regulators – related to pigmentation
  • ROR2 – involved in regulating bone and cartilage development
Also the following regions appear to have suffered intense selective pressures among early Homo sapiens in general, always according to the authors:
  • SPTLC1 – involved in hereditary sensory neuropathy
  • SULF2 – that regulates cartilage development
  • RUNX2 – related to morphological differences with other Homo species, notably Neanderthals (frontal bossing, clavical morphology, bell-shaped rib cage, and regulating the closure of the fontanel which is crucial for brain expansion)
  • SDCCAG8 – involved in microcephaly
  • LRAT – associated with Alzheimer’s disease 


Thus, three of the top five regions contain genes involved in skeletal development, and syndromes associated with mutations in these genes display similar morphological features.

While also:

Including SULF2, three of the top five candidate regions are thus associated with neuronal function.

All this falls within expectations, I’d say, but nevertheless most interesting to know in such detail and precision.

Khoisan autosomal genetics

There is a new major paper at arXiv on Southern African autosomal genetics, with emphasis on pre-Bantu aboriginal peoples (usually known as Khoisan, even if the phylogenetic unity of their languages is not anymore accepted).
Joseph K. Pickrell et al., The genetic prehistory of southern Africa. arXiv 2012. Open access ··> LINK.

The hunter-gatherer populations of southern and eastern Africa are known to harbor some of the most ancient human lineages, but their historical relationships are poorly understood. We report data from 22 populations analyzed at over half a million single nucleotide polymorphisms (SNPs), using a genome-wide array designed for studies of history. The southern Africans-here called Khoisan-fall into two groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. All individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began 1,200 years ago. In addition, the Hadza, an east African hunter-gatherer population that speaks a language with click consonants, derive about a quarter of their ancestry from admixture with a population related to the Khoisan, implying an ancient genetic link between southern and eastern Africa.  

Unlike most other African (or global) genetic studies, here the Southern African natives are not undersampled and that way a more realistic genetic structure, with Khoisan peoples occupying their distinct position in the overall human structure, is more evident.

Selected images (from the supplementary material):

Locator map and legend for all PCA graphs:

Color code is as follows:

  • Dark grey: non-Khoisan Africans (incl. Hadza)
  • Blue: Khoe-Kwadi
  • Green: Kx’a
  • Red: Tuu
  • Light grey: Eurasians

Global PCA (SF 2):

The PC1 sets apart Khoisan (specially the Kx’a and the Tuu) from Eurasians, while the PC2 defines the non-Khoisan African dimension (including some Khoisan, specially the Damara).

Africa-only PCA (PC1-2) (SF 3):

Excluded Eurasians, the PC1 is taken by the Khoisan-other African dialectics, while the PC2 contrasts the Ju|’hoan versus the Nama specially. 

Africa-only PCA (PC2-3 with the inclusion of the ǂKhomani) (SF 17):

+ ǂKhomani samples (excluded in previous graphs)

Interestingly enough, here the Damara and the Himba contrasting with other Africans, specially the Dinka, take over PC2. Meanwhile PC3 is monopolized by the contrast between Ju|’hoan and the ǂHoan.

Admixture clustering (SF 7):

Click to expand

As in most previous PC analysis (excepted African PCA 2-3) the most neatly distinct Khoisan populations are the Kx’a (green cluster) and Tuu (purple one). At K=6, two other clusters are taken by the two distinct Pygmy populations, while the fifth one describes Eurasians (or West Eurasians). The remainder indistinct African is shown as blue component but it seems to hide important substructure in fact.

Arguably K=5 may be a better description, or at last one we are more familiar with: differentiating between Khoisans (green), Pygmies (orange), Hadza (purple), other Africans (blue) and Eurasians (red). But something of the order of K=13 or 16 is probably a better description in any case for such a varied bunch.

Special thanks to Millán.


Acheulean use of fire confirmed

That is what Francesco Berna and colleagues argue in a new paper:
The findings are dated to at least one million years ago and correspond to the Acheulean period, characterized by bifacial axes and generally attributed to Homo erectus or H. ergaster.
Partly charred bone from Wonderwerk
As the authors explain, previous claims of fire use in this period in East Africa,  the Levant or China have been plagued with controversy. In most cases the controversy stems from the relatively low resolution of the research and the possibility of the fires being natural occurrences. In the case of Zhoukoudian, near Beijing, what was once claimed as product of fire ended being sedimentary deposits. 
This research actually continues the findings of Peter B. Beaumont last year, who claimed (JSTOR, pay-per-view) that the South African cave hosted evidence of fire dated to c. 1.7 Ma.
The evidence included charred vegetal remains and animal bones, these last not completely calcinated, meaning that combustion was under 700 °C. Also remains of ironstone brought intently to the cave and worked in situ (main material of artifacts) show signs of manipulation under heat above 500 °C.
Apparently the fires were produced almost exclusively with light materials such as dry grasses and leaves. While it is not impossible that they might have used wood and then the evidence got lost, the data from bones indicates combustion under 700 °C, what is compatible with fire produced with lighter materials exclusively.
See also: Boston University’s site, BU Today.