South Africa

Today I was looking through the online data files for the South African genome. Those online files are available from the Data Libraries entry of the Galaxy bioinformatics tool website.

I noted last week that some of the most interesting data -- in particular, the genotypes for new SNPs -- are not yet available to download ("Online toolkits -- the good and the frustrating"). But in the meantime there are some very interesting things there. In particular, the sequencing team has made available a list of amino-acid-coding mutations present in one or more of the five individuals (four Bushmen and Desmond Tutu) for whom the team obtained exome sequence.

If you look at the summary information for this list, it gives the position of amino-acid-coding mutations against the human reference genome (hg18), the position and identity of the amino acid change. It then gives a "prediction" of whether the mutation is damaging to gene function.

This kind of prediction can be very misleading. The categories of effects include "tolerated" and "damaging", but these are based on whether the site tends to be conserved in other mammal lineages, and whether the new amino acid is very different in affinity (and possible conformation) compared to the reference. There's no "beneficial" -- even though some fraction of these polymorphisms are probably retained because of selection on the mutant allele.

I say that because one of the five individuals (TK1) has an amino-acid-coding mutation in FOXP2.

Yeah, that surprised me when I found it.

As you'll remember the coding sequence of FOXP2 is pretty strongly conserved in other mammals. Two amino-acid-coding substitutions in humans separate us from other primates, an additional one separates primates from the mouse genome (Enard et al. 2002). This area of the genome looks like it had undergone a recent sweep in human populations, with relatively little variation and a strong excess of rare mutations surrounding the gene. Coop and colleagues (2008) gave a point estimate of the time of a sweep in humans as 42,000 years ago, which I wrote about at the time ("FOXP2 is really recent, it really did introgress (if it's not contamination)"). That estimate has to be massively too young -- it's not plausible that a sweep could be that recent and fixed worldwide.

Meanwhile, last year, Ptak and colleagues (2009) followed up on my suggestion that there might really have been a recent sweep, but one near FOXP2, instead of involving one of the two human amino acid substitutions. They found statistical linkage between flanking sites immediately around the gene, which would be unlikely after a fixed sweep of FOXP2 itself. That linkage is quite likely if the human-specific substitutions were already fixed, and much later another nearby site underwent a partial sweep. It remains to be demonstrated, however, what nearby site is a plausible candidate for a recent partial sweep.

So, finding variations near FOXP2 is very relevant to the history of this gene region. If there is an ongoing sweep involving some site near the gene, we should expect that some human populations haven't undergone the sweep yet, or have the selected haplotype at a lower frequency than others. The existing datasets from Africa -- mainly HapMap and HGDP sets -- are insufficient to test the hypothesis because they include only common SNP variants at low density. But sequence data from South Africa can give us a direct estimate of the nucleotide diversity around FOXP2, thereby letting us test for the presence of a recent sweep.

The amino acid coding variant in one of these Bushman genomes came to me as a total surprise. Using the alignment with hg18, the location of the mutation is at position 114089380 on chromosome 7. The mutation changes a leucine in the wild-type sequence to a proline in the mutant, and the algorithm classifies it as "damaging" -- probably because the two residues are very different in their hydropathy. This position is not one of the two human-specific amino acid substitution sites. In fact it is in the forkhead box domain of the protein itself, which is the DNA-binding motif. Without going further into the biochemistry, I really can't guess what the effect of the mutation would be. I'm not really sure it's relevant -- after all, if it is a singleton in the population it might well be a recessive with no effect on the carrier phenotype.

Still, the mutation could be common in the Bushman population. Our point estimate of the mutation's frequency is one in eight. Maybe it's a new variant that confers some advantage; maybe it's a result of a founder effect tens of thousands of years ago. It could even be widespread within Africa. We won't know until we have more genomes.

The mutation is not in any of the regions sequenced by Krause and colleagues (2007) in the Neandertals from El Sidrón. I wouldn't expect it to be there -- as a derived variant, it would be unlikely to evolve in parallel in Neandertals and southern African populations. But who knows what else we'll find?

References:

Coop G, Bullaughey K, Luca F, Przeworski M. 2008. The timing of selection at the human FOXP2 gene. Mol Biol Evol 25:1257. doi:10.1093/molbev/msn091

Ptak S, Enard W, Wiebe V, Hellmann I, Krause J, Lachmann M, P&aauml;&aauml;bo S. 2009. Linkage disequilibrium extends across putative selected sites in FOXP2. Mol Biol Evol 26:2181-2184. doi:10.1093/molbev/msp143

Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin J-J, Bertranpetit J, Hänni C, Fortea J, de la Rasilla M, Rosas A, Pääbo S. 2007. The derived FoxP2 variant of modern humans was shared with Neandertals. Curr Biol 17:1-5. doi:10.1016/j.cub.2007.10.008

Enard W, Przeworski M, Fisher SE, Lai CSL, Wiebe V, Kitano T, Monaco AP, P&aauml;&aauml;bo S. 2002. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869-872. doi:10.1038/nature01025

Schuster SC and many others. 2010. Complete Khoisan and Bantu genomes from southern Africa. Nature 463:943-947. doi:10.1038/nature08795

Oh, good grief!

[post UPDATED]

I have had an unusual number of hits the past few days, so I went through my logs looking for the source. Turns out people are reading my 2008 review of the "Boskops race"("The 'amazing' Boskops").

Over 10,000 people have read that post since the New Year began. That post has always gotten a recurring readership, because of a 2008 book by Gary Lynch and Richard Granger, Big Brain: The Origins and Future of Human Intelligence.

Evidently the book is about to come out in paperback. And Discover magazine, which gave the book a fairly positive review on its release, has now reprinted an excerpt detailing the wondrous features of the Boskops race ("What Happened to the Hominids Who Were Smarter Than Us?"). Someone copied the whole thing to Richard Dawkins' website. And people reading the excerpt are trying to find out more about this fantastic story, and finding my blog.

Well, to all those seeking the light of paleoanthropology, welcome!

To those who have linked the post: I want to let you all know that your links have directed more than 10,000 people to find some actual true information about the "Boskop race". Good work out there!

What can I do to update people, now that this story is spreading once again? My original post gives a short history, but was not based on a real review of the book. I was just trying to get some accurate information out there.

Now I have read the excerpt, and much (but not all) of the Boskop-related text in the book (courtesy of Amazon).

It's worse than I feared. The excerpt actually presents 1920's-era anthropology as if it were the state of our knowledge about Boskop and the "Boskop race" today. I have not found any passages in the book or chapter notes that contradict the excerpt's portrayal. I cannot find references or citations of post-1940 research on skeletal remains or archaeology from southern Africa. There's no hint of what happened after archaeologists began to use radiocarbon dating, nor do we hear even the identity of any specimens, except for the original (and fragmented) Boskop skull itself.

How can this be? From the book's notes, it appears that the authors didn't find any information on these topics:

One of the oddities in the Boskop story is the disconnect between the rich trove of references from the early twentieth century, and the paucity of references after that time (Lynch and Granger 2008: 218).

I find that very sad, because there is a much richer trove of references after 1958. Archaeologists have developed a deep understanding of the chronology and material culture of LSA and later hunter-gatherers around the Cape and northward. Skeletal biologists have studied the health status, demography, and morphology of Holocene and earlier peoples. Some have even examined the endocranial volumes of southern African skeletal samples, and have tested the hypothesis of trends in brain size over time.

All this work shows a very different picture than that sketched by Lynch and Granger.

I'm going to be very measured, because while I am often snarky, I rarely come straight out and write that something is bunk. The portrayal of "Boskops" in the Discover excerpt is so out of line with anthropology of the last forty years, that I am amazed the magazine printed it. I am unaware of any credible biological anthropologist or archaeologist who would confirm their description of the "Boskopoids," except as an obsolete category from the history of anthropology.

[UPDATE (2010-01-04): I have heard from Amos Zeeberg, the Web editor at Discover. He writes that the excerpt was intended to run identified as a "controversial idea, but that context didn't come across as intended." The web page has been changed to make that context clear, and to link to my discussion here. I think it's great that he responded so quickly, although I think that this case is not controversial, it's non-science. ]

Besides that, the authors make several questionable statements about the relative sizes of parts of the brain and their relation to cognition and behavior in ancient hunter-gatherers.

IQ of fossils

We have no credible way of estimating the IQ of a fossil skull. The excerpt claims:

Even if brain size accounts for just 10 to 20 percent of an IQ test score, it is possible to conjecture what kind of average scores would be made by a group of people with 30 percent larger brains. We can readily calculate that a population with a mean brain size of 1,750 cc would be expected to have an average IQ of 149.

First of all, there never was any human population with a 1750 cc average brain size.

Now, taking the counterfactual: A regression equation within a population can predict an expected value for an individual within that population. But in population genetics, the average IQ that we would predict for a population with a 1750 cc average, depends on how the brain got to be that size. Natural selection on intelligence or brain size would have altered the relation that holds within humans. Nor do we know whether the present-day correlation would have characterized any ancient population -- or indeed most living human populations. The current value in Europeans may be an artifact of Holocene genetic changes.

The authors do not list the specific regression that they use, or its source. The correlation relates to the proportion of variance explained by the relation of brain size and intelligence is irrelevant to this prediction. What we want to know is the slope of the regression. The prediction here would require a slope of 0.14, assuming it had been derived from a population with a mean male volume of 1400 cc and an average IQ of 100. That's a higher slope than I've seen reported in any analysis of the brain size - IQ relationship.

The "inconceivable" prefrontal cortex

We know little about the relative sizes of cortical areas in fossil hominins. The excerpt claims that the prefrontal area of a Boskop must have been "inconceivably large"

Going from human to Boskop, these association zones are even more disproportionately expanded. Boskop’s brain size is about 30 percent larger than our own—that is, a 1,750-cc brain to our average of 1,350 cc. And that leads to an increase in the prefrontal cortex of a staggering 53 percent. If these principled relations among brain parts hold true, then Boskops would have had not only an impressively large brain but an inconceivably large prefrontal cortex.

First of all, there was never any human population with an 1750 cc average brain size.

Again, the example is a misapplication of regression, in this case an among-species regression. The excerpt appears to assume that the evolution of relative prefrontal area among human populations must have followed the same disproportionate pattern of increase as that between humans and chimpanzees. Prefrontal cortex volume is larger, relative to brain size, in humans compared to other primates. But this relation is not very much larger in humans -- recent estimates range from less than 10 to 30 percent compared to chimpanzees (Holloway 2002, Schoenemann et al. 2005). Even if some ancient humans had a second burst of expansion, again as great as that on the hominin lineage leading from apes to us, their prefrontal volume would hardly be "inconceivably large".

And there's no reason at all to assert such a second, bonus expansion of prefrontal area in ancient humans. The prefrontal area ought to scale close to the total brain size, as it does within living people.

Science fiction

The authors actually cite and discuss Loren Eiseley's Immense Journey, which I discussed in my earlier post. Eiseley was a naturalist/anthropologist/science writer, and a very popular essayist -- he's the kind of person we could use more of today. But his reflections on the "Boskop people" were a fictional trope -- and were already, in 1958. He was a great writer, but relying on Eiseley for up-to-date information on anthropology is like relying on Truman Capote as an authority on crime.

Suppose that we take the "Boskops" story just as a science fiction fairy tale -- a story showing that evolution is not synonymous with progress, as the authors imply. I still conclude that much of the other information about brain size in the excerpt is questionable or false.

The authors speculate:

Our big brains give us such powers of extrapolation that we may extrapolate straight out of reality, into worlds that are possible but that never actually happened.

That's Boskop, all right. Extrapolated straight from worlds that never happened!

References:

Broom R. 1918. The evidence afforded by the Boskop skull of a new species of primitive man (Homo capensis). Anthropol Pap Am Mus Nat Hist 23 (2):63-79.

Brothwell DR. 1963. Evidence of early population change in central and southern Africa: Doubts and problems. Man 63:101-104.

Dart R. 1923. Boskop remains from the south-east African coast. Nature 112:623-625.

Dubow S. 1996. Human origins, race typology and the other Raymond Dart. African Studies 55:1-30.

Henneberg M, Steyn M. 1993. Trends in cranial capacity and cranial index in Subsaharan Africa during the Holocene. Am J Hum Biol 5:473-479.

Holloway RL. 2002. How much larger is the relative volume of area 10 of the prefrontal cortex in humans? Am J Phys Anthropol 118:399-401. doi:10.1002/ajpa.10090

Pycraft WP. 1925. On the calvaria found at Boskop, Transvaal, in 1913, and its relationship to Cromagnard and Negroid skulls. J Roy Anthropol Inst 55:179-198.

Schauder DE. 1963. The anthropological work of F. W. FitzSimons in the Eastern Cape. S Afr Archaeol Bull 18:52-59.

Semendeferi K, Armstrong E, Schleicher A, Zilles K, Van Hoesen GW. 2001. Prefrontal cortex in humans and apes: a comparative study of Area 10. Am J Phys Anthropol 114:224-241.

Singer R. The Boskop "race" problem. Man 58:173-178.

Singer R. 1962. Presidential Address 1962: The South African Archaeological Society: The future of physical anthropology in South Africa. S Afr Archaeol Bull 17:205-211.

Stynder DD, Ackermann RR, Sealy JC. 2007. Craniofacial variation and population continuity in the South African Holocene. Am J Phys Anthropol 134:489-500. doi:10.1002/ajpa.20696

On occasion, I point out interesting findings from archaeological chemistry and microscopic study of site formation processes. Last month, I pointed to the ability to distinguish animal and plant fat residues on ancient artifacts. Before that, there was the discovery of flax fibers from the Upper Paleolithic of Dzudzuana Cave, Georgia.

In July, a paper by Paul Goldberg and colleagues described the "micromorphology" of the sediments from Middle Stone Age levels of Sibudu Cave, South Africa. The excavations at Sibudu have been able to distinguish many distinct stratigraphic units with distinctive spatial locations and compositions. Micromorphology involves looking at these sediments in microscopic detail, picking out small grains of crushed bone, charcoal, plant fibers, phytoliths, and other materials.

Goldberg and his colleagues were able to make some very cool observations. For one thing, they have charred drips of broiled grease:

Two types of amorphous organic combustion remains were identified in samples from Sibudu: a type with a typically vesicular texture and a type with a cracked texture. The first type was found as isolated bodies, subrounded with a diameter of 10 µm to 1 mm, and they exhibited no evidence of cell structure. Bubbles or vesicles give the bodies a highly porous nature, and they are often thin walled. The microstructure of these homogenous or finely heterogeneous isotropic particles and their droplet-shaped occurrence suggest that these bodies were originally fluid and that they underwent a degassing process but have since hardened. These bodies resemble char and are probably derived from the burning of flesh or animal fat (104-105).

Mmmmm...MSA barbecue. The other type of "amorphous organic combustion remains" are charred resins, from trees or seeds. Mmmm...MSA smokehouse.

Second, they have beds.

Because of its long fibrous nature, it seems that this material consists of herbaceous plants, possibly some type of sedge, reed, or grass. There is no evidence to suggest that this plant would have grown naturally in the rock shelter, and the presence of clay aggregates derived from the river valley found in association with the laminated plant fibers implies that the grass or reed was transported to the cave from the nearby Tongati River by the shelter’s inhabitants.

The compact and laminated structure of the organic fibers in this microfacies also suggests that, once brought to the cave, the grass or reed was subjected to compaction, most likely through trampling. Further evidence supporting the interpretation of trampling is seen in the stringers of charcoal, clay aggregates, and burnt bone that define horizontal and subhorizontal surfaces on top of and within the laminated organic fibrous material. Pieces of éboulis and lithic fragments also define surfaces wi thin the microfacies. The fact that this grass or reed was transported to the cave by humans and that once there it was influenced by human trampling suggests that this microfacies represents a type of constructed bedding. If this is the case, then Sibudu contains the oldest evidence for constructed bedding, significantly older than that reported at the open-air site of Ohalo in Israel (Nadel et al. 2004).

The bedding material was in some instances burned, in some instances swept or trampled in such a way that the regular alignment of the phytoliths was jumbled and disrupted. They interpret this as efforts to "maintain" the site -- in other words, housekeeping:

What seems a likely and reasonable scenario is that the original organic matter of this laminated layer of sedges, grass, or reeds was completely combusted, resulting in total ashing of the organic material. The calcitic ash in this microfacies was transformed through phosphatization, as evidenced by the presence of a few remnant pockets of phosphate in this microfacies. The fact that large crystals of gypsum often form directly below these phytolith layers provides suggestive evidence for the downward leaching of CO₃- or P-rich solutions.

Just an aside -- that is such interesting chemistry, like the organic materials and ash are melting down into the underlying deposits.

The association between microfacies 2 and 4 suggests that the sedges, grass, or reeds that were brought into the cave for bedding were usually burned and probably by humans when they no longer used the bedding. This observation explains the sequence seen in samples SS-6 and SS-5 of laminated nonburnt fibrous organic material grading into laminated burnt fibrous organic material with phytoliths (microfacies laminated type 2B); the sequence is finally capped by a layer of laminated phytoliths.

Why did they burn the stuff? The authors guess that they were trying to cut down on parasites:

Together, this evidence shows that not only were the occupants of Sibudu bringing grass or reeds into the cave—likely for the construction of bedding—but they were periodically burning them, possibly as a means to remove pests or insects that had colonized the beds. (Smoldering goat dung and organic matter can be observed in many parts of the Middle East, including Hayonim, where tick removal is one of the important objectives; P. Goldberg 1992, personal observation.)

The MSA at Sibudu dates to between 45,000 and 65,000 years ago, with the best evidence for bedding in the units that OSL puts around 50,000 years ago. The implications of the "site maintenance" and spatial characteristics of the site are mentioned in the paper's conclusion:

Organization of living space, and particularly a deliberate use of space, has been suggested by Wadley (2001) and also Binford (1996) as an important trait of culturally modern behavior, reflecting a more complex social organization. While the evidence from the laminated units at Sibudu may reflect such organization, the lack of evidence for such spatial organization, such as is the case for the lower homogeneous layers at Sibudu, should not automatically suggest that occupation in these units was any less complex.

If spatial organization of living space is a "modern" behavioral feature, it is one shared by Neandertals (I noted that briefly in a 2006 post). But then, it's shared by any number of invertebrates, also. I think the interpretation of this kind of behavior will have to wait until we have more sites investigated with comparable methods. As the introduction to the current paper points out, a lot of spatial information could be brought out of these micro-scale studies, if they were conducted routinely.

References:

Goldberg P, Miller CE, Schiegl S, Ligouis B, Berna F, Conard NJ, Wadley L. 2009. Bedding, hearths, and site maintenance in the Middle Stone Age of Sibudu Cave, KwaZulu-Natal, South Africa. Archaeol Anthropol Sci 1:95-122. doi:10.1007/s12520-009-0008-1

The Tswaing Crater is around 40 km from Pretoria, South Africa. It was created by an asteroid impact some 200,000 years ago, which released roughly the energy of the Tunguska explosion of 1908. The crater's floor has a salt pan, where people have gone to gather salt since MSA times. The floor has been cored, with analyses of sediment salinity and pollen, giving a record of climate over the last 200,000 years. For example, a 2007 paper by Kristen and colleagues:

Sediments from Lake Tswaing (25°24'30'' S, 28°04'59'' E) document hydrological changes in southern Africa over the last 200 Ka. Using high-resolution XRF- scanning, basic geochemistry (TIC, TOC, TN), organic petrology and rock-eval pyrolysis, we identify intervals of decreased carbonate precipitation, increased detrital input, decreased salinity and decreased autochthonous (algal and bacterial) organic matter content that represent periods of less stable water column stratification and increased rainfall. Between 200 and 80 Ka BP, these intervals appear to be contemporaneous with local summer insolation maxima, indicating a strong influence of precessional variability (~23 Ka) on African subtropical climate. This influence weakens during the last glacial period (~80 to 10 Ka BP), when humid intervals at 73 to 68 Ka, 54 to 50 Ka, 37 to 35 Ka and 15 to 10 Ka BP are largely out of phase with insolation changes, and presumably reflect southward displacement of the ITCZ (Inter Tropical Convergence Zone) and/or changes in ocean circulation.

I'm pointing to this study because it is one that documents wetter periods during the span between the Howieson's Poort (roughly 60,000 years ago) and the Last Glacial Maximum (around 18,000 years ago). There are some who have claimed that this was a long span of aridity in southern Africa -- but more recent evidence makes it clear that the climate was not unimodal but fluctuated as in earlier and later time frames. Also, the climate was simply not arid, compared to "megadrought" periods documented in East Africa before 70,000 years ago.

Thanks to a reader, I've been reading an excellent 2008 paper by Peter Mitchell, which documents archaeological sites and paleoclimate data leading to the conclusion that habitation in southern Africa was not significantly interrupted during late MSA times. I'll refer to it more extensively later, but in the meantime I'm noting some recent work that Mitchell may not have had available when he was writing his article.

In a similar vein, I can point to an article by Louis Scott and colleagues (2008), which examined pollen records from Tswaing Crater as well as the Wonderkrater spring, and speleothem isotope evidence from Lobatse Cave, Botswana. Correlating the records from different sites in the same general area -- in this case, all from the savanna biome of southern Africa -- is very important. Distant climate records, such as the Greenland or Vostok ice cores, give some indication of global climate fluctuations, but it is not usually obvious how these fluctuations will affect specific regions of the world. One lake sediment core from southern Africa helps to show the local climatic fluctuations, but some may be highly localized, while others may reflect regional water and temperature variations. Hence, the correlations among many sites in a single region allow us to talk about climate fluctuations on a scale relevant to human populations.

Again, the region-wide picture in southern Africa between 60,000 and 20,000 years ago does not yield a picture of static, arid or cool conditions. The time period covers almost two full precessional cycles of insolation in southern Africa, and thus covers a wide range of local climate variation. To sum up, I'll cite Mitchell (2008:54), who relied on some earlier work from the Tswaing Crater record:

Peak annual precipitation may have reached 650–720 mm, with the late MIS 3 peak at the low end of this range. The minimum precipitation experienced was about 535 mm; today’s figure for comparison is 630 mm. Thus, although there were certainly periods when rainfall was reduced compared to the present , such reductions still exceeded by some margin the levels experienced by much of Limpopo Province or the highveld today, and for about a third of the time rainfall was actually higher than at present. Moreover, a generally cooler climate should have reduced evapotranspiration, and thus enhanced effective precipitation, more than these raw estimates suggest.

These sources are relevant for the savanna of the northern and eastern parts of South Africa. The region is ecologically diverse, and Mitchell considers different parts of the region in turn.

References:

Kristen I, Fuhrmann A, Thorpe J, Röhl U, Wilkes H, Oberhänsli H. 2007. Hydrological changes in southern Africa over the last 200 Ka as recorded in lake sediments from the Tswaing impact crater. S Afr J Geol 110:311-326. doi:10.2113/gssajg.110.2-3.311

Mitchell P. 2008. Developing the archaeology of marine isotope stage 3. S Afr Archaeol Soc Goodwin Ser 10:52-65.

Scott L, Holmgren K, Partridge TC. 2008. Reconciliation of vegetation and climatic interpretations of pollen profiles and other regional records from the last 60 thousand years in the Savanna Biome of Southern Africa. Palaeogeography, Palaeoclimatology, Palaeoecology 257:198-206. doi:10.1016/j.palaeo.2007.10.018

Zenobia Jacobs and colleagues have a paper in this week's Science that provides age estimates for two of the MSA industries of Southern Africa: the Howieson's Poort and Still Bay industries. Here's the abstract:

The expansion of modern human populations in Africa 80,000 to 60,000 years ago and their initial exodus out of Africa have been tentatively linked to two phases of technological and behavioral innovation within the Middle Stone Age of southern Africa—the Still Bay and Howieson's Poort industries—that are associated with early evidence for symbols and personal ornaments. Establishing the correct sequence of events, however, has been hampered by inadequate chronologies. We report ages for nine sites from varied climatic and ecological zones across southern Africa that show that both industries were short-lived (5000 years or less), separated by about 7000 years, and coeval with genetic estimates of population expansion and exit times. Comparison with climatic records shows that these bursts of innovative behavior cannot be explained by environmental factors alone.

It's a dating paper, and I like the dating parts. The review of why these two MSA industries are important, I think, overstates the issues to a considerable extent. Yes, there are some interesting elements of the two industries, but these are paralleled in some other MSA industries, both earlier and later, in East and North Africa -- not to mention the Neandertal-associated Middle Paleolithic industries of the Near East and Europe. There is no reason at all to suppose that Howieson's Poort (or the earlier Still Bay) was made by people who embarked from southern Africa on an "out of Africa exodus." The southern African sites are important enough for what they tell us about cultural variability; I don't see the need to exaggerate their significance to the global story.

In many ways, the paper relies on similar methods as found in the 2007 paper by Michael Waters and Thomas Stafford, "Redefining the age of Clovis." In that paper, the authors applied a statistical model to new and existing radiocarbon dates, which allowed them to conclude that the age interval represented by Clovis sites is relatively narrow -- probably as little as 200 years.

That conclusion has not gone unchallenged (e.g., Haynes et al. 2007), in particular on the basis of some earlier dates which might indicate an initially rare Clovis lasted for some time before a brief florescence. Anytime we have to deal with dates from different methods or different laboratories, there is the potential that some will be systematically different. Should we dismiss outliers? Or are they essential evidence of a more extensive time range, during which an industry was relatively rare? Hamilton and Buchanan (2007) found a spatial gradient in Clovis radiocarbon dates, suggesting that they represented a wave of advance from north to south. That observation doesn't refute the short chronology, it refines our notion of how long an industry should persist, and shows that it need not represent a spatially uniform population.

In the current paper on Howieson's Poort and Still Bay dating, Jacobs and colleagues took the approach of systematically providing new OSL dates for nine sites. That deals with ambiguity about earlier dates and different methods quite simply: The authors did not rely on dates from other labs and sources. They do present a figure that puts other labs' dates in the context of their own results (they are consistent with the paper's conclusions), but these do not form the main interpretive context.

The essential picture from the paper is figure 4:

This shows the cluster of dates that fit into Howieson's Poort phase, all consistent with a range from around 60,000 to 65,000 years ago, a cluster for the initial post-Howieson's Poort deposits, most consistent with a date around 57,000 years ago, and a smaller cluster of earlier, Still Bay levels. Considering the problems that have plagued OSL dating up to now, this is an impressive level of consistency. Comparing many dates from different sites gives a solid impression of a short time span for the technology.

Unlike the case of Clovis, Jacobs and colleagues found no spatial pattern in the dates, even though they did look. The figure also shows paleoclimate evidence from ice cores; the Howieson's Poort appears to correspond to a long warming period, but it spans the range of climate from cold to warm. That's what the abstract means when it says that environmental factors do not suffice to explain the industry.

I think the dates are important because of what they can tell us about cultural and biological variability within the MSA. From genetics, we know that the MSA African population was apparently structured, with a clear possibility that the genetic differentiation was once higher than today. If so, we might expect long-lasting cultural differences between African regions. We will need better dates across Africa---not just southern Africa---to really compare regions with each other. Howieson's Poort and Still Bay cultures are a start in this process.

The short duration of the two industries is a very important fact. It was already suspected that the two existed for only a short time -- they are not found in every well-stratified site, and their recognition depends on a few relatively rare artifacts. A rare, high-information artifact is useful as a type fossil, but it is not likely to have persisted for very long in the cultural history of an ancient people.

The data seem to indicate that Howieson's Poort lasted around 5000 years, and spanned an area of between 1.5 and 2 million square kilometers. That falls well within the ranges of time span and duration for the industries of the European Upper Paleolithic, and for that matter the later Middle Paleolithic of Europe. The Still Bay, even shorter and smaller, is also within this range. It will be important to assess whether other MSA variants and earlier Neandertal-associated industries of Europe and West Asia also fall within a cohesive distribution of time and space.

My inclination is to interpret these cultural distributions in terms of information exchanges. In that regard, it is essential to consider smaller units of information transfer. An entire culture is inherited by no one. A stone tool manufacturing technique, on the other hand, may be manifested in multiple artifacts and may have been learned by many individuals over thousands of years. I would be very interested in the temporal patterning within the Howieson's Poort; a question that the dates may now allow archaeologists to answer.

References:

Jacobs Z, Roberts RG, Galbraith RF, Deacon HJ, Grün R, Mackay A, Mitchell P, Vogelsang R, Wadley L. 2008. Ages for the Middle Stone Age of Southern Africa: Implications for human behavior and dispersal. Science 322:733-735. doi:10.1126/science.1162219

Hamilton MJ, Buchanan B. 2007. Spatial gradients in Clovis-age radiocarbon dates across North America suggest rapid colonization from the north. Proc Nat Acad Sci USA 104:15625-15630. doi:10.1073/pnas.0704215104

Haynes G and 14 others. 2007. Comment on "Redefining the age of Clovis: Implications for the peopling of the Americas." Science 317:320. doi:10.1126/science.1141960

Waters MR, Stafford TW, Jr. 2007. Redefining the age of Clovis: Implications for the peopling of the Americas. Science 315:1122-1126. doi:10.1126/science.1137166

I was just taking notes on this paper by Sealy and Pfeiffer (2000), and found some good quotes about body size in the Bushmen, both historically and in archaeological samples:

Historical and ethnographic sources consistently indicate that Khoisan peoples were and continue to be petite. A group of early-20th-century San studied by Dart (1937a, b) had mean statures of 155.8 cm (males) and 146.1 cm (females). Decades later, the Harvard Kalahari study found mean statures of 160.9 cm (males) and 150 cm (females). These values are comparable to the fifth centile of adult stature for contemporary North Americans (Abraham 1979). Adult weights reported for the more recent individuals are 47.9 kg (males) and 40.1 kg (females) (Truswell and Hanson 1976).

It has been claimed that environmental stressors, especially shortages of food, affected growth (Dornan 1975:80; Almeida 1965:6). The secular trend towards increasing stature among mid-20th-century Khoisan (Tobias 1978) could be seen as evidence for the influence of environmental factors.

At the same time, there is a genetic component. Low stature persists even under apparently favourable health conditions. The small body size and lean physique of living Khoisan peoples are often cited in human population biology texts as exemplary of adaptation to a hot, sometimes specifically desert, climate. Their low body-mass index is portrayed as support for Bergmann's and Allen's rules (cf. Molnar 1998, Relethford 1997). Through study of archaeologically derived materials, these hypotheses can be explored.

That's on the historic record. They examine a number of skeletons from archaeological sites and report this:

Dimensions of selected bones from the southern Cape sample are summarized in table 2. Data from one exceptionally small skeleton (UCT 345, probably a dwarf) and the three most recent skeletons with anomalous isotope values (Sealy 1997) are not included in the summary statistics for body size. The mean stature calculated from 20 male femora is 157.8 cm (s.d. = 7.9). Twenty-three female femora have a mean estimated stature of 146.9 cm (s.d. = 10.5). Greater variability among females results from some very small individuals between 4,000 and 2,000 B.P. (see fig. 4). Body size, represented by femoral head diameter to maximize sample size and divided into five sex categories, is plotted against radiocarbon date in figure 5. This figure illustrates that the smallest individuals (femora < 375 mm, therefore < 139 cm tall; femoral head diameters < 34 mm) are "probable" females, classified as female only on the basis of body size and gracility. Hence it may be inappropriate to include them in the calculation of mean female stature. Excluding the four very petite probable females, mean female stature is 149.9 cm (s.d. = 8.5). The four smallest adults appear to be of normal proportions. Only eight males and five females are sufficiently complete for living body mass to be estimated, as this requires both femoral length and bi-iliac diameter. The estimated value is 42.8 ± 6.6 kg for males, 38.3 ± 4.4 kg for females.

That's 4'10'' for females; 5'2'' for males in the archaeological sample. Bi-iliac diameter for males was 214.6 ± 16.8, for females 209.0 ± 12.3.