MSA

Due to Jerry Coyne, I encountered an interview in the Guardian with Colin Blakemore: "Colin Blakemore: How the human brain got bigger by accident and not through evolution."

The headline is a misnomer, as Blakemore is not denying evolution, he is denying selection. But Blakemore's argument is based completely on a false presentation of the facts. Consider:

The question is: why is it so big compared to the brains of our predecessors, such as Homo erectus? Until 200,000 years ago, there had been a gradual increase in brain size among hominins, starting three million years ago. Then, abruptly, there was a remarkable increase of about 30% or so.

That's Blakemore. Now, here's a chart of endocranial volumes of Pleistocene human fossils:

As you can see, there's no sudden jump 200,000 years ago, or at any other time. The data, such as they are, are consistent with a single pattern of increase over time, as pointed out by Sang-Hee Lee and Milford Wolpoff (2003).

Heck, it's the lack of a sudden jump that has gotten all the attention. Because if "modern" humans suddenly showed up in Africa 200,000 years ago, and all of a sudden had vastly larger brains than any other hominins, wouldn't that be a simple and tidy story? Don't you think we'd all be talking about the sudden origin of modern humans as reflected by their larger brains?

It just didn't happen.

Well, it's one thing to be empirically wrong. That's a simple error that's easily corrected. But Blakemore, relying on the erroneous assumption of a single shift in brain size, asserts that neutral macromutations must be an important mode of human brain evolution:

Genetic studies suggest every living human can be traced back to a single woman called "Mitochondrial Eve" who lived about 200,000 years ago. My suggestion is that the sudden expansion of the brain 200,000 years ago was a dramatic spontaneous mutation in the brain of Mitochondrial Eve or a relative which then spread through the species. A change in a single gene would have been enough.

I hope that the empirical pattern is enough to convince you that this hypothesis is false. The "sudden increase" simply did not happen.

But in case you need more persuasion: Blakemore here assumes that the increase in brain size had no negative consequences. Otherwise it couldn't proceed neutrally. Here is his argument:

The environment of early humans was so clement and rich in resources that this greedy new brain, which would have absorbed even more of the body's energy, could be sustained without danger. Later, when times got hard, during droughts or climate changes, it helped us deal with these crises, which could otherwise have killed us off, by dreaming up novel ideas to problems.

You see the outline: Life was easy, and humans could grow fat-brained, like so many sheep. Fortunately, our fat brains were then useful when times were tough. Blakemore describes this as somehow different from the idea that brains were adaptive -- it's in fact just another adaptive story for larger brains.

But it falls apart, when we consider that assumption -- life was easy. I put it to my students this way: Suppose you lay a lot of sugar beets out on your land. What will happen to the deer population?

The answer is not that the deer will grow fat-brained and later evolve to conquer humanity. The answer is that there will be a lot more deer.

Population growth is much faster than adaptation, and it's hundreds of times faster than a neutral gene can transit through the population. Humans in the past were not a static population, living in peace with an abundant environment. They were repeated faced with Malthusian crises -- on submillennial timescales. That's why a close understanding of climate variability is so relevant to our evolution. The fact that tools and behaviors change so slowly in the Middle Pleistocene is informative -- it shows that humans weren't coming up with dramatically new ways to track shifting ecologies.

And that means that the selection pressures of the energetic and life history constraints on the brain were repeatedly imposed on human populations. A substantial increase in brain size should have immediately been disadvantageous -- if it had no compensatory benefits to fitness.

What remains is testing the hypotheses about those benefits to fitness. Blakemore actually is presenting one such hypothesis -- that a larger brain mostly was adaptive because of its ability to transmit traditions. That's testable, and is consistent with the greater transfer of information apparent in recent archaeological traditions compared to Middle Pleistocene ones. But there are other hypotheses as well, and it is quite difficult to compare them with the available record.

That's why it's so important to state the empirical record accurately.

UPDATE (2010-03-29): A reader points out that Malthusian crises, in terms of resource or food availability, may have been avoided by warfare or predation -- people kill each other instead of starving. I see that point, particularly where we consider the way that epidemic disease can relax competition for food until population growth resumes. Performing well under predation or competition would be one way that brain size might have had compensatory benefits to fitness beyond its energetic and life history costs.

References:

Lee S-H, Wolpoff MH. 2003. The pattern of evolution in Pleistocene human brain size. Paleobiology 29:186-196.

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

Julio Mercader reports in a short Science paper that the MSA stone artifacts from Ngalue cave, Mozambique, preserve thousands of grains of sorghum starch, along with a few other grasses and palm pith.

The role of starchy plants in early hominin diets and when the culinary processing of starches began have been difficult to track archaeologically. Seed collecting is conventionally perceived to have been an irrelevant activity among the Pleistocene foragers of southern Africa, on the grounds of both technological difficulty in the processing of grains and the belief that roots, fruits, and nuts, not cereals, were the basis for subsistence for the past 100,000 years and further back in time. A large assemblage of starch granules has been retrieved from the surfaces of Middle Stone Age stone tools from Mozambique, showing that early Homo sapiens relied on grass seeds starting at least 105,000 years ago, including those of sorghum grasses.

This is another of those very interesting technical developments in archaeology. The use of grass seeds may not be surprising in itself. Some think that australopithecines were eating grass seeds for a substantial amount of their diet; some (notably Clifford Jolly and Jonathan Kingdon) have suggested that grass seeds were one of the resources that prompted the evolution of bipedality. The dental reduction in early humans doesn't argue strongly against seed consumption; they are an important part of the diet for many recent hunter-gatherers including Australians. But it's nice to see a direct confirmation that humans were gathering seeds relatively intensively.

How intensive? Well, there is a slight problem:

It is not clear why the tools should be mostly coated with grass starches and not so much with other types of starch. It is possible that high-starch–bearing grass refuse built up considerably in the cave’s main chamber at times of human occupation, thus coating both tools that were used in the processing of grass seeds and others that were not.

Hmmm. On the one hand, that means pretty intensive grass collection. On the other, if such a substantial fraction of the actual sedimentary debris in the cave was composed of anthropogenic plant waste, it's probably not possible to get an accurate picture of the importance of the seeds as a fraction of the diet. It's a data point: these people, living around this cave, used a lot of Sorghum grasses and processed seeds in some way with stone tools.

It makes me wonder about what non-stone implements they may have used. Winnowing baskets?

References:

Mercader J. 2009. Mozambican grass seed consumption during the Middle Stone Age. Science 326:1680-1683. doi:10.1126/science.1173966

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

This is a complicated story with many interlocking parts. Telling the whole story may well take me fifty posts. There's a lot of new science hiding in here waiting to get out.

I'm starting now because of the new paper by Luke Premo and Jean-Jacques Hublin, titled "Culture, population structure, and low genetic diversity in Pleistocene hominins." This paper is not the final word on its topic, nor is it the first word. But it is very much worth reading.

It makes an excellent point of departure to explain what we know and don't know about the genetics of prehistoric humans. Premo and Hublin propose an interesting model with interaction between culture and natural selection, as an explanation for a 35-year-old problem in human evolution: Our low level of genetic variation.

Their model may be right. I certainly think there's a kernel of truth in it, shared with a number of other models, as I'll describe below. And it's testable -- a project to which we'll be returning in the next few months.

I can understand that National Geographic wants to promote news from researchers who take National Geographic money. It's only natural, and as a publicity organ for paleoanthropology, they haven't done so badly in the past.

But this story titled, "Humans 80,000 Years Older Than Previously Thought?" is just silly.

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

That was the headline of many of last week's stories about the paper by Behar and colleagues, drawing upon the Genographic Project African mitochondrial DNA (mtDNA) data. Here's a quote from the National Geographic Society's press release:

Previous studies have shown that while human populations had been quite small prior to the Late Stone Age, perhaps numbering fewer than 2,000 around 70,000 years ago, the expansion after this time led to the occupation of many previously uninhabited areas, including the world beyond Africa.

And here's project director Spencer Wells' quote in the same release:

Dr. Spencer Wells, National Geographic Explorer-in-Residence and Director of the Genographic Project, said: "This new study released today illustrates the extraordinary power of genetics to reveal insights into some of the key events in our species' history. Tiny bands of early humans, forced apart by harsh environmental conditions, coming back from the brink to reunite and populate the world. Truly an epic drama, written in our DNA."

Well, that certainly sounds dramatic. But is it true?

I've gotten a couple of e-mail questions from readers about this new book, Big Brain: The Origins and Future of Human Intelligence. The authors are Gary Lynch and Richard Granger.

Both Lynch and Granger are experts in neuroscience, with a long list of publications on memory, cortical organization, and chemical regulation of brain activity. Neither of them is an anthropologist or archaeologist.

So I suppose I shouldn't be surprised to see what appears to be complete lunacy in the book description:

Our big brains, our language ability, and our intelligence make us uniquely human. But barely 10,000 years ago--a mere blip in evolutionary time--human-like creatures called "Boskops" flourished in South Africa. They possessed extraordinary features: forebrains roughly 50% larger than ours, and estimated IQs to match--far surpassing our own. Many of these huge fossil skulls have been discovered over the last century, but most of us have never heard of this scientific marvel. Prominent neuroscientists Gary Lynch and Richard Granger compare the contents of the Boskop brain and our own brains today, and arrive at startling conclusions about our intelligence and creativity. Connecting cutting-edge theories of genetics, evolution, language, memory, learning, and intelligence, Lynch and Granger show the implications of large brains on a broad array of fields, from the current state of the art in Alzheimer's and other brain disorders, to new advances in brain-based robots that see and converse with us, and the means by which neural prosthetics-- replacement parts for the brain--are being designed and tested. The authors demystify the complexities of our brains in this fascinating and accessible book, and give us tantalizing insights into our humanity--its past, and its future.

Now, I haven't read the book, and this is not a review. I think a book that puts together the state of the art in neuroscience and tries to relate that to many aspects of human evolution would be a great book. Maybe this book has some of that stuff in it.

But it seems pretty evident from the description that there has been a major misfire. If the description of the book is accurate then they have the evolutionary biology almost entirely wrong. I assume the description is at least in the ballpark, since it is the publisher's description, and it's borne out by this Discover magazine review:

Judging from fossil remains, scientists say the Boskops were similar to modern humans but had small, childlike faces and huge melon heads that held brains about 30 percent larger than our own.

That's what fascinates psychiatrist Gary Lynch and cognitive scientist Richard Granger. "Just as we're smarter than apes, they were probably smarter than us," they speculate. More insightful and self-reflective than modern humans, with fantastic memories and a penchant for dreaming, the Boskops may have had "an internal mental life literally beyond anything we can imagine."

OK, that's a pretty surprising story: an ancient race with unique mental endowments, living in an exotic part of the world. It sounds uncannily like the Atlantis myth. What is the reality here?

First, if you do a simple Google Scholar search for "Boskop", you will discover that this has not been a going topic in human evolution for nearly fifty years. Most intellectual effort on the topic of "Boskopoids" happened between 1915 and 1930. I want to emphasize how easy it is to discover these things by a simple Google search. This is obscure knowledge, but for a good reason -- it's obsolete and has been for fifty years!

The supposed "Boskop race" was named after a South African skull -- consisting of frontal and parietal bones, with a partial occiput, one temporal and a fragment of mandible -- found on a Transvaal farm in 1913. The skull is a large one, with an estimated endocranial volume of 1800 ml. But it is hardly complete, and arguments about its overall size -- exacerbated by its thickness, which confuses estimates based on regression from external measurements -- have ranged from 1700 to 2000 ml. It is large, but well within the range of sizes found in recent males.

Robert Broom named the skull Homo capensis, emphasizing its differences from recent peoples of the region, and proposing a close relationship with European Cro-Magnons. Other remains found later were also attributed to this "type," and so the "Boskop race" became a category of paleoanthropology. Few people know that before Raymond Dart made his name by analyzing and reporting on the Taung skull, he had written in to Nature with a description of "Boskopoid" crania (Dart 1923).

But this concept of a "Boskop race" did not emerge from any clear understanding of the South African past. In fact, MSA, LSA, and recent archaeological-associated remains were lumped indiscriminately into the category. What provoked the racial category was a confusion about the relationships of recent and historical southern African remains. Anthropologists had attempted to apply primary racial categories such as "Negroid," "Bushman," "Hottentot" and "Strandloper," corresponding to extant or recent tribes or other groups. But the distinctions between these categories did not appear to extend far into the prehistoric past. So anthropologists looked for the origins of these racial types within the sample of prehistoric crania -- constructing a "Boskopoid" type for those with later "Bush" or "Strandloper" resemblances.

This category became untenable as further information about the archaeology of South Africa came to light. Ronald Singer (1958) reviewed the "Boskop race" evidence as it existed by the 1950's. He concluded that there was no reason to maintain that any "big-headed, small-faced group" had existed in prehistory, separate from the current biological variability of "Bushman, Hottentot and Negro." But that view is unsupportable -- in fact, what happened is that a small set of large crania were taken from a much larger sample of varied crania, and given the name, "Boskopoid." This selection was initially done almost without any regard for archaeological or cultural associations -- any old, large skull was a "Boskop". Later, when a more systematic inventory of archaeological associations was entered into evidence, it became clear that the "Boskop race" was entirely a figment of anthropologists' imaginations. Instead, the MSA-to-LSA population of South Africa had a varied array of features, within the last 20,000 years trending toward those present in historic southern African peoples. Singer ends his paper thusly:

It is now obvious that what was justifiable speculation (because of paucity of data) in 1923, and was apparent as speculation in 1947, is inexcusable to maintain in 1958.

That is pretty much where matters have stood ever since. "Boskopoid" is used only in this historical sense; it is has not been an active unit of analysis since the 1950's. By 1963, Brothwell could claim that Boskop itself was nothing more than a large skull of Khoisan type, leaving the concept of a "Boskop race" far behind.

Today, skeletal remains from South African LSA are generally believed to be ancestral to historic peoples in the region, including the Khoikhoi and San. The ancient people did not mysteriously disappear: they are still with us! The artistic legacy of the ancient peoples, clearly evidenced in rock art, is impressive but no more so than that of the European Upper Paleolithic or that of indigenous Australians.

And their brains were not all that big. Boskop itself is a large skull, but it is a clear standout in the sample of ancient South African crania; other males range from 1350 to 1600 ml (these are documented by Henneberg and Steyn 1993). That is around the same as Upper Paleolithic Europeans and pre-Neolithic Chinese. LSA South Africans fit in with their contemporaries around the world.

To be sure, there has been a reduction in the average brain size in South Africa during the last 10,000 years, and there have been parallel reductions in Europe and China -- pretty much everywhere we have decent samples of skeletons, it looks like brains have been shrinking. This is something I've done quite a bit of research on, and will continue to do so, because it's interesting. But it is hardly a sign that ancient humans had mysterious mental powers -- it is probably a matter of energetic efficiency (brains are expensive), developmental time (brains take a long time to mature) and diet (brains require high protein and fat consumption, less and less available to Holocene populations).

So, how did this idea of ancient Boskops make it into a book by two neuroscientists in 2008?

If not through science, then possibly from science fiction. The "Boskop race" was immortalized in popular writing by Loren Eiseley, who included an essay on Boskop Man in his collection, The Immense Journey, first published in 1958. As you can see, by this time the entire concept of a "Boskop race" had fallen into scientific disrepute. But Eiseley was undeterred: he conjured the idea that the Boskopoids were advanced in their large brains and small faces -- the apex of a trend toward paedomorphism, the retention of juvenile characteristics. In this state, they resembled what Eiseley suggested would be the "Future Man":

We can, of course, repeat the final, unanswerable question: What did this tremendous brain mean to the Boskop people? We can marvel over their curious and exotic anatomy. We can wonder at the mysterious powers hidden in the human body, so potent that once unleashed they brought this more than modern being into existence on the very threshold of the Ice Age.

We can debate for days whether that magnificent cranial endowment actually represented a superior brain. We can smile pityingly at his miserable shell heaps, point to the mute stones that were his only tools. We can do this, but in doing it we are mocking our own rude forefathers of a similar day and time. We are forgetting the high artistic sensitivity which flowered in the closing Ice Age of Europe and which, oddly, blossomed here as well, lingering on even among the dwarfed Bushmen of the Kalahari.

What we can say is that perhaps the unloosed mechanism ran too fast, that the biological clock had speeded them out of their time and place -- a time which ten thousand years later has still not arrived. This, then, was the logical end of complete foetalization: a desperate struggle to survive among a welter of more prolific and aggressive stocks.

For Eiseley, Boskop served as a kind of memento mori -- the so-called advanced race had succumbed to "more prolific and aggressive stocks." A theme of the essay is that the entire idea of "Future Man" is anti-evolutionary -- there are no ineluctible trends of progress in evolution, because such progressive populations may always be endangered by their own direction of change.

I hate to think that the theme of a 2008 book was pulled straight from a 1958 essay, but I don't know where else they would have gotten the idea. No anthropologists have written much about the so-called "Boskopoids" since 1958. There is no such thing as an "IQ estimate" for a fossil human; that's entirely nonsensical. There's no question that there have been massive cultural changes in the last 10,000 years. But the idea that our brains' functions have atrophied from some Pleistocene state has been left long behind in the dust of nineteenth-century race studies.

So I'm left wondering: Why would two neuroscientists, after going to all the trouble to write a book about the evolution of the human brain, use completely obsolete anthropological information without doing a simple Google search to see if the facts have stayed the same as in 1923?

I don't have an answer, but I'm interested in reading the book to see if it lives up to its billing.

UPDATE (2010-01-04): Discover magazine has printed a long except from the book. The information about the "Boskop race" is more than fifty years out of date. I reflect on the excerpt ("Return of the 'amazing' Boskops").

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.

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.

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

Edmund Blair Bolles is reporting from the Evolang conference in Barcelona. Unfortunately I had to cancel my presentation there, but it has been great to read these summaries of some of the papers. I wanted to point readers to his account of Francesco D'Errico's talk:

Neanderthals had language comparable to that of Homo sapiens, Bordeaux-based archaeologist Francisco D’Errico told participants in the Evolang conference in Barcelona this morning (Saturday, March 15, 2008). This claim totally discards the older Big Bang theory that said language arose only very recently (40 to 75 thousand years ago), and also challenges the Out-of-Africa theory that proposes Homo sapiens emerged in Africa about 200 thousand years ago and spread over the rest of the world, carrying language and culture with the, beginning about 60 thousand years ago. A new history will have to be written.

If you have been reading here, you have seen many of the new perspectives D'Errico is talking about, but together they make a very compelling package. Consider:

1. We now know that australopithecines had ape-like vocal tracts, complete with pharyngeal air sacs.

2. We now know that Middle Pleistocene humans (Atapuerca) had humanlike hyoids, unlike australopithecines, so modern human vocal tract anatomy was plausibly a derived feature of Homo, including Neandertals.

3. We have good evidence of pigment use from MSA Africa and Mousterian Europe. The Neandertals in particular appear to have been coloring skin with manganese crayons.

4. Decorative/ornamental artifacts were manufactured both by MSA Africans and Neandertals.

5. Neandertals shared the modern human-derived FoxP2 variant.

I have some notes on D'Errico's work (with Maria Soressi) on Neandertal pigment use that I'll post later. Given the confluence of the recent evidence from genetics, archaeology, and anatomy, I do not see how anyone can maintain the hypothesis that Neandertals (and presumably, other Late Pleistocene humans) did not have language.

Now, that is not to say that they (or any Late Pleistocene humans) were identical in their linguistic adaptations to living or recent people. I still think that communication is the most likely focus of evolutionary change in the Late Pleistocene -- but a change based within a pre-existing community of language users, not a newly-sprung linguistic skill. In fact, I think the next constructive step should be to characterize the variation in linguistic adaptations in recent people, who are surely not identical to each other. That verges on the subject of my presentation, which -- if you attend the AAPA meetings this spring, you will still get a chance to hear. That is, if you stick around until Saturday!

I was reading back through Bednarik's "Concept-mediated marking in the Lower Palaeolithic," for some background on the ochre-shellfish post, and I ran across this quote in Bednarik's rejoinder to Randall White:

[A]n estimated 100 tons of iron ore was mined at just one Middle Stone Age site, Ngwenya, carbon-dated to about 43,200 B. P. (Dart and Beaumont 1971)

That seemed striking -- that is, I hadn't seen any other references to that site -- so I tracked down a bit more information about Ngwenya. The LSA/MSA hematite quarry was described in short publications by Raymond Dart and Peter Beaumont (1967, 1969, 1971). In recent years, the quarry had been mined by a modern operation, and had been a locus of iron ore mining since LSA times at least. Dart had some interest in the idea of Stone Age mining for iron ore, having found an LSA mine in Zambia many years before. Some old flaked tools and other artifacts were found at Ngwenya, and Dart got some some archaeologists, including Adrian Boshier, to investigate.

The Swaziland National Trust has an informative, although unreferenced, website discussing the findings:

Boshier found three ancient mines named Lion, Castle and Stag caverns. He collected stone tools in and around them made of dolerite, which is foreign to the area. The tools were unlike those normally found on a stone age site, they were more specialised, consisting of choppers, picks and hammer stones. Professor Dart identified them as mining tools. The tools were not confined to the surface layers but were scattered throughout huge depressions which would have been solid haematite. In one of the mines they were lying among and beneath thousands of tons of red iron oxide known as haematite. Enquiries by Boshier among the Swazis elicited the information that haematite deposits had been mined in historic times and that it was the custom to fill in the excavation to avoid offending the spirits of the underworld. Boshier theorised that if the holes had been refilled with haematite then the mine workers must have wanted something other than haematite.

The suspicion, mentioned by Dart and Beaumont (1967), was that specularite (a dark-colored sparkly hematite) was the real objective of the quarrying -- they were also led to this idea by the fact that Castle Cavern had surface exposures of hematite, so it would hardly be worth mining deep into Lion Cavern to get it.

Anyway, once the initial excavations found a substantial antiquity for quarrying at the site, they went deeper to see how old the activity really was:

From six to eight feet, there were undoubted Middle Stone Age artefacts together with some possible Later Stone Age tools. From eight feet to worked bedrock at over eleven feet, the deposit yielded some 23,000 artefacts which belong unquestionably to a middle stage of the Middle Stone Age. Occasional stone mining tools were also found. Well-defined ash levels indicated that the assemblage was in situ. Quartz, white quartzites, grey-and-white dappled quartzite, black indurated shales, and greenish cherts were the main materials used. Most of these rock-types occur on a ridge overlooked by and about a quarter of a mile from the cavern. Some of the exposures there bear clear evidence of having been flaked. The dappled grey-and-white quartzites come from exposures about a mile and more northwest of the site (Dart and Beaumont 1969:127).

The extent of the Middle Stone Age activity at the site suggested that a vast amount of hematite had been removed:

At least 50 tons of haematite rich in specularite must have been removed from Lion Cavern; two-thirds of it during the Middle Stone Age (Dart and Beaumont 1967:408).

Their dating of charcoal nodules (Dart and Beaumont 1967) in the "middle to lower levels of the Middle Stone Age level" were 22,280 +/- 400 BP and 28,130 +- 260 BP. This was later revised (Dart and Beaumont 1971) to a larger number, based on further survey. Likewise, Dart and Beaumont (1971) provided an earlier date at or above the limits of radiocarbon, 43,200 BP.

None of this informs us about the earliest use of red pigments, which is far older, or the earliest evidence of quarrying, which is also far older. It's probably even irrelevant to the development of the MSA in southern Africa, which, again, is far older.

But in the context of the recent literature, highly focused on the "first" evidence of ochre use, or ocher engraving, or "symbolic behavior," a site like this one can get lost in the noise. Systematic utilization of one site for one purpose is not recent in the archaeological record, but when we find evidence of such places, they can be the most informative about the activities of people in the past, their transfer of information with each other, and their acquisition of resources across relatively long distances.

References:

Bednarik RG. 1995. Concept-mediated marking in the Lower Paleolithic. Curr Anthropol 36:605-634.

Dart RA, Beaumont P. 1969. Evidence of iron ore mining in Southern Africa in the Middle Stone Age. Curr Anthropol 10:127-128.

Dart RA, Beaumont P. 1971. On a further radiocarbon date for ancient mining in southern Africa. S Afr J Sci 67:10-11.

Am I really going to wait a week to write about the red-haired Neandertals? No, not quite -- but I'm taking some time to add detail to the story. Meanwhile, here are some of the things I've been reading this weekend around the web:

Some Ebola phylogeography

I've written about Ebola in gorillas and chimpanzees a few times here. Now, Tara Smith describes how genetic analyses of the strains that have killed these primates are adding to our knowledge of the disease's biology and spread:

Over a 5 year time period, researchers found 47 dead animals in the Gabon/Republic of Congo region--17 of these were determined to be infected with Ebola-Zaire. Using the polymerase chain reaction, they were able to amplify portions of the glycoprotein gene (GP) from 6 gorillas and a chimpanzee, and compare the sequences to those previously identified in humans. When they compared the sequence to other EBO-Z GP sequences published to date, they found that these new genes were divergent enough to constitute a new group within the EBO-Z subtype--and that recent human cases from the Republic of Congo during the same time frame also fit into this new group (designated group B; the previous identified groups were group A, which included sequences from the 1976 outbreak and several outbreaks in the mid-1990s, and group R, from outbreaks between 2001-3).

A long post with a review of the recent literature and a lot of details about the virus. Animal-human (zoonotic) pathogen transfer is one of Smith's research topics, and she covers the bases very well.

Nature Conservancy and the Adirondacks

The New York Times has an article discussing the recent purchase of a 161,000-acre tract of the Adirondacks by the Nature Conservancy. The details of the purchase require continued low-intensity logging to supply a paper mill, and the organization will have to sell some parcels to finance the deal.

Naturally, there are conflicting opinions about what should be done with the land.

[T]he most intense pressure is coming from local communities, environmental organizations and special interest groups, all clamoring to stake their interest in the property. Mr. Carr's list of petitioners is long: raft guides, float plane pilots, hunting clubs, loggers, hikers, school superintendents, buffalo ranchers and municipal golf course operators looking to expand. "Mike Carr has created a five-year nightmare for himself in trying to decide how to unload this property," said John Sheehan, spokesman for the Adirondack Council, a nonprofit environmental organization. The impact of those decisions on the Adirondacks and the people who live, work and play there, he said, will be immeasurable.

I have a soft spot for the Nature Conservancy because of their role in preserving tallgrass prairie, but the organization has a lot of critics because of its accommodation to economic pressures. This is an even discussion of the economic and social conflicts facing the organization now that this deal has gone through.

Autumn colors

We've been enjoying some of the autumn colors here during the last couple of weeks. Every year around this time, you see stories about why leaves turn colors. I'll point you to Larry Moran's relatively short explanation, which keys in on both the mechanisms that time leaf senescence and, in this passage, its biochemical consequences:

It has to do with senescence. In the autumn the leaves of deciduous trees fall off the tree to prepare for winter. As the leaves die, the tree attempts to salvage as much nitrogen and carbohydrate as it can. While the photosynthetic apparatus is winding down it is more likely to produce free radicals and oxidative damage. To prevent excess damage the leaves produce pigment molecules that block some of the light and reduce levels of photosynthesis. Red pigments, such as anthocyanins are especially effective (Feild et al. 2002).

He also notes that the availability of nitrogen in the soil influences coloration, which along with species abundances helps to explain why some forests are especially gorgeous this time of year.

Sell your DNA?

If you're interested in DNA patents, biomedical research, and privacy interests, you could do worse than reading this post at Eye on DNA.

Shellfish and ochre

Julien Riel-Salvatore considers some thoughts emerging from the Pinnacle Point paper by Curtis Marean and colleagues:

By and large, what most strikes me about the paper is the discussion of a "behavioral package" that comprises coastal living, shellfish exploitation, ochre use and bladelet production. These elements are unquestionably all there at PP13B, but their varying representation across the LC-MSA stratigraphy strongly suggests that they were far from indissociable in evolutionary time, and this even at a single locale. Interestingly, this very fact emphasizes how dynamic the MSA appears to have been as a form of behavioral adaptation, even in its comparatively early phases. This contrasts with some views of the MSA as a single 'thing' across space and time. That said, it also raises the issue of whether we are, in fact dealing with a discrete "package" and of what elements are its essential features, for lack of a better term. I think that we still have some way to go in highlighting what the advantages provided by each of these different behaviors was, especially in different situational contexts, but it is very intriguing to first find them in association when the coast first appears to become more or less permanently occupied.

This is the missing element in a lot of the Neandertal coverage of the past couple of weeks. As we discover elements of the ancient European genetic package that compare with modern humans in various ways, we are left to consider exactly what is different or unique about the MSA African behavioral evidence.

Tim Jones at Remote Central comes up with a more critical view of the behavioral evidence, noting that much of the habitable coastline of the world more than 150,000 years old is now underwater.

I have been formulating some of my own thoughts (believe it or not, the MSA paper has occupied a lot more of my attention than the Neandertal ones!), and I'll see if I can get them out in the next few days.

In the meantime, read Julien's take, and his previous post may be worthwhile for Tom Tomorrow fans.

More on charities

Dave and Greta at Cognitive Daily polled their readers to find out which charity fundraising methods are most effective. (They're trying to raise money for the Donor Choose campaign). Matching funds work the best to motivate potential donors, according to their polling. Then there's this:

We asked respondents to report their income, so we could then correlate income with the various incentives for giving. We found no significant correlations except in two areas. There was a moderate positive correlation (r=.27) between income and the amount a person donates the first time they give to a charity. There was a small negative correlation (r=-.16) between income and the amount people would pay for candy in charity fundraisers. Apparently you'd be better off selling candy bars for charity in a lower-income neighborhood than in a wealthy neighborhood.

This reminds me of the Arthur, where they're all selling candy bars for their school band, and Buster eats them all himself in a fit of crazed chocoholism. By the way, Googling "Chocolate Fundraiser" is a scary, scary experience. Not as scary as Ebola, but scary.

This week, Johannes Krause and colleagues from the Max Planck Evolutionary Anthropology institute announced that they had tickled FoxP2 out of two Neandertal specimens from El Sidrón, Spain. The bones were excavated in sterile (clean-cave?) conditions, immediately frozen and then shipped to Leipzig, where extracts were taken in clean-room conditions.

Here's an FAQ about what they found.

Why is this paper really important?

Isn't it obvious? It's important because it demonstrates that more than one Neandertal is suitable for nuclear genome recovery. We will know about genetic variation in Neandertals, sooner rather than later. These two bones come from different individuals, because the Leipzig group found two different mtDNA sequences in them. Together with the Vindija Vi 33.16 specimen in the original Neandertal genome papers, this makes three nuclear genome Neandertals. There will be more.

It also shows the possibility of probing ancient skeletons for specific genes. Here, they went in looking for Y-DNA, X-DNA and particular sites on FoxP2, and they found them. That is definitely the way to go if you want to test a biologically significant hypothesis fast -- otherwise, you just have to wait until the sequence comes up in your genome project.

However, I question the value of probing for individual genetic variants in this way. Every probe takes a bit of sample, which might be more efficiently used in whole-genome sequencing. We have 25,000 genes, and every one is potentially interesting. Every small sample used to assay only one of those genes may destroy many sequences from the others. It would be one thing if samples were trivial and easily replaced, but they obviously aren't.

Still, we will certainly see additional probes for genes that are of particular interest. I wouldn't be surprised to see MC1R results soon, to probe whether there were pigmentation variants in Neandertals. The same has already been done for woolly mammoths.

So, Neandertals had the human-specific FoxP2 form. Did they talk?

I think the genetic observation leans toward that direction, but doesn't really change our understanding. Consider:

Neandertals have a hyoid bone with humanlike anatomy, as did the Atapuerca people at more than 300,000 years ago, even though A. afarensis did not. So something related to vocalization evolved in humans by the Middle Pleistocene. Although Neandertal vocal tracts may not have been identical to recent humans, there is nothing about them that would preclude speech. The only paleoneurological observation about language puts a developed Broca's area on the KNM-ER 1470 endocast, Homo habilis.

Like other Middle Paleolithic/MSA people, their technology required more information to learn than earlier, Lower Paleolithic industries, leading to regional differentiation and more task-specific facies. Late Neandertals made use of some technology otherwise used only by Upper Paleolithic modern humans. Their hunting methods must have required cooperation and may have been impossible without a more sophisticated communication strategy than used by other primates.

All of these things argue for some kind of Neandertal language irrespective of FoxP2.

Then again, most of the arguments against humanlike language facility in Neandertals also have nothing to do with FoxP2, either. The slow technological progress, limited collection strategies, the rarity of any artistic or symbolic expression, their high mortality rate, and -- of course -- the fact that they no longer exist have all been considered as evidence that Neandertals lacked some essential aspect of "behavioral modernity." If language is a prerequisite for the modern human pattern of behavior, then Neandertals may not have talked, at least not in the way we do.

I think the FoxP2 story has really confused people much more than necessary. But in this case, the confusion is the same that results from every other gene study: when the press says we've found a gene "for" something, what it ought to say is that we've found an allele that affects something.

No macromutation happened. Language did not spring full-formed into the mind of some ancient African. All members of Homo used communication systems including some (possibly minimal) elements of language, and the evolution of the human brain, along with technological changes throughout the Paleolithic, reflect the evolution of communication. Human language evolved -- like all things -- over a long time, and like all complex phenotypes it required a series of mutational changes. Many of these mutations became fixed during recent human evolution, some may still be changing in frequency today. Language evolution is probably a continuing process.

That means that it must have involved many more genes than FoxP2 -- which after all experienced only two amino acid substitutions in all of human evolution. I would imagine the number of genes involved in language evolution is more than 500, and I wouldn't be surprised if it were much more. In that context, it seems quite silly to say FoxP2 is the "critical" evolutionary change for anything.

Then you agree with Language Log. They told me that FoxP2 isn't a "language gene."

The case is strong that the two FoxP2 coding substitutions in humans were selected because of their role in language. The gene sequence is strongly conserved in most mammals, and shows similar changes in some other species with unusual vocal adaptations, such as echolocating bats (Li et al. 2007). Its expression pattern delineates areas related to vocalizations in both humans and birds, and the pattern itself differentiates between song-learning versus nonlearning bird species (Haesler et al. 2004, Teramitsu et al. 2004, Webb and Zhang 2005). And of course, mutations to FoxP2 can result in specific language impairment (SLI) in humans.

Still, that case is only circumstantial. We know that FoxP2 was under selection, that it became fixed in humans, probably during the Late Pleistocene, and that breaking the gene changes brain development and damages language skills. But we don't know what a human would be like with the chimpanzee form of the protein. We don't know whether both of the human-specific amino acid substitutions have a different effect than one. Most important, we don't know what other genetic changes may have been necessary backgrounds for selection on FoxP2.

This means Neandertals were really modern humans, right?

This study should put an end to the "sudden mutation" model of modern human origins.

There was not a single mutation that made the critical difference in the ancestry of today's people. There was no cognitive Rubicon leading to modern human evolution. I would analogize the process as a slow-motion avalanche: at first a few small sands began to tumble, and then selection on a large number of genes became inevitable. FoxP2 is one of those genes, and as yet we don't know whether it was near the beginning or near the end of the process.

But it is clear that the process began before the Neandertals were gone. Some aspects of behavioral complexity did begin to evolve rapidly sometime after 70,000 years ago. This rapid evolution was multiregional in context -- it was not limited to a single human population. In particular, it was not limited to Africans: the last Neandertals clearly manifested technological and behavioral strategies otherwise defined as "behaviorally modern" (d'Errico 2003). There's a reason why the Neandertal-produced Châtelperronian industry of France and Spain was historically considered the first Upper Paleolithic industry.

But we have undergone light-years of change since the last Neandertals lived. This is not a question of "modern human origins" anymore. We can now show that living people are much more different from early modern humans than any differences between Neandertals and other contemporary peoples. I think that "modern humans" is on its way to obsolescence. What matters is the pattern of change across all populations. Possibly that pattern was initiated by changes in one region but the subsequent changes were so vast that the beginning point hardly matters.

We all know that the Neandertal genome is riddled with contamination from modern humans. Isn't the null hypothesis that we have a modern human sequence here because it is a modern human?

Well, as you know, I'm not all that convinced that contamination explains the interpretive discrepancies between last year's genome papers. But still, this study has done some things to address the problem of contamination.

It is notable that Green et al. (2006) found 25% modern human mtDNA in one of the El Sidrón bones: this shows that even "sterile" excavation, immediate freezing and extraction under clean-room conditions cannot exclude contamination. There is at the moment nothing more that can be done. We will always have the problem of a contamination fraction in ancient Neandertal skeletons. So we have to judge each study by the extent to which we can exclude contaminants with statistical analysis.

For this study, Krause et al. (2007) developed a test of nuclear DNA contamination: they identified seven gene variants that differ between the recovered Vindija Vi 33.16 nuclear genome and all known living humans. In other words, these are human-derived mutations that are absent from the only known Neandertal nuclear genome. Then, they probed the El Sidrón bones for these sites. They found only the ancestral form in their extracts of both bones -- presumably because no human contaminants were present in their samples.

That seems like a pretty good indication that the other sites in their sample represent the true gene variants of the ancient Neandertals. I wouldn't go so far as to say that contamination is ruled out, but it seems like these are good results.

Did FoxP2 introgress into Neandertals?

It sure looks that way to me. Let's consider the evidence:

FoxP2 recently fixed in humans. According to Enard et al. (2002:871):

Under a model of a randomly mating population of constant size, the most likely date since the fixation of the beneficial allele is 0, with approximate 95% confidence intervals of 0 and 120,000 years.

Now, Enard et al. (2002) noted that human populations have grown over time, and that they are not randomly mating, so that this date estimate might be too recent. Allowing for population growth since "10,000--100,000 years ago," they asserted that fixation of FoxP2 must have happened "during the last 200,000 years of human history." But this is not quite accurate. Unlike genetic drift, positive selection can and often does fix genes rapidly in a growing population. It simply doesn't matter that the human population has been rapidly growing: FoxP2 may still have just become fixed yesterday.

Last year, Green and colleagues (2006) considered that the Neandertal-modern population divergence time might have been quite recent, depending on the ancestral population size. According to the estimates of Wall and Kim (2007), the Green et al. data are consistent with a Neandertal-modern population divergence time as recent as 30,000 years ago. Of course, that date would predict substantial admixture between contemporary Neandertal and non-European populations -- they would have been exchanging genes up to the very lifetimes of the last Neandertals. According to those data there would be nothing surprising about Neandertals and living people sharing the human-derived FoxP2 allele. But as mentioned above, Wall and Kim (2007) used the recent divergence estimate as evidence that the Neandertal genome data from Green et al. must be contaminated.

So, if we cannot trust the data, then we have to fall back on some other estimate of the divergence date. Noonan and colleagues (2006) estimated a divergence date between Neandertals and modern populations between 170,000 and 570,000 years ago. If we accept that, then the confidence intervals of the Neandertal-human divergence and the FoxP2 selective sweep might barely overlap. Might. But I will note that a minimal overlap between the 95% confidence intervals of two point estimates does not mean that they are not significantly different. Only if the expected value of one estimate falls within the 95% confidence interval of the other do they fail to be significantly different. It is pretty unlikely that the most recent FoxP2 sweep is older than 170,000 years ago and the Neandertal-modern population split is as recent as 170,000 years.

That is, unless the "split" time reflects widespread genetic introgression.

The current paper (Krause et al. 2007) goes to some contortions to try to establish that the FoxP2 sweep could really have been older than 300,000 years ago (where they place the lower confidence limit on the N-M split):

The third scenario is that the selective sweep started before the divergence of the ancestral populations of Neandertals and modern humans around 300,000-400,000 years ago

Let me just say that I was surprised to read this explanation in a paper from this group. One of the main arguments they have been posing as a scientific value of the Neandertal genome sequencing is that conventional methods don't detect selection at 300,000-400,000 years ago. But here, they consider such an ancient mutation to be the most likely hypothesis. This seems like quite a shift just to avoid the unpleasant idea of Neandertal introgression. Ooooh -- can't have those Neandercooties!

In reality, there is no reason to think the fixation of FoxP2 happened as early as 300,000 years ago, and indeed the very high frequencies of the linked derived alleles (over 97% for six of the linked alleles) suggest strongly that the sweep probably happened within the last 100,000 years -- otherwise, subsquent genetic drift should have caused these linked derived alleles to show more dispersion in their current frequencies. The same features that make the inference of selection so strong at FoxP2 -- it is far (>286 kilobases) from the nearest gene and it includes many high-frequency derived alleles in addition to reduced polymorphism -- make it very unlikely that the selective sweep was ancient.

So, considering that the El Sidrón samples both share the human-derived amino acid substitutions on the same haplotype as modern humans, complete with all the high-frequency derived SNPs, it seems almost certain that the gene introgressed into Neandertals from modern humans.

Or, there's one other option. One of the El Sidrón bones includes a relatively rare (in humans) ancestral SNP allele at one of those linked sites where the derived allele is at very high frequency in humans. One explanation: the selected mutation arose in Neandertals and introgressed into other humans. That would explain why this Neandertal didn't have a SNP variant on its FoxP2 haplotype that later became very common in humans: Neandertals had the new FoxP2 first.

What about that Y chromosome thing?

The El Sidrón bones both tested positive for the Y chromosome site assayed in the study. That means they were both male (duh!). But more important, the Y chromosomes of both individuals lacked the human-specific derived mutation that the researchers tested for. Since all human males yet surveyed have this human-derived mutation, this means that a Y chromosome variant has fixed in modern humans that Neandertals did not have. Since the entire nonrecombining portion of the Y chromosome is completely linked, we can infer that the entire modern human Y chromosome has undergone at least one fixation not shared with the ancestors of these Neandertals.

Here's the text (from page 2):

Both Neandertals yielded products for Y chromosomal primer pairs, indicating that they were males. Strikingly, all 15 Y chromosomal products for the five assayed positions show the ancestral allele. This includes two polymorphisms that define the deepest split among current human Y chromosomes (Y2 and Y4, Figure S1) as well as two polymorphisms that cover less common African Y chromosomes (Y3 and Y5, Figure S1). These Y chromosome results must derive, then, either from Y chromosomes that fall outside the variation of modern humans or from the very rare African lineages not covered by the assay (Figure S1). For our purposes, this result shows that neither the maternally inherited mtDNA nor the paternally inherited Y chromosome shows evidence of gene flow from modern humans into Neandertals or of subsequent contamination of their mortal remains.

That's not such a big surprise. Already we knew that the fixation of the human Y chromosome was very recent -- probably within the last 70,000--100,000 years, and possibly even more recently. Every man on earth shares recent Y chromosome mutations that were completely absent in Middle Pleistocene humans. That is one radical recent evolutionary change.

The paper elsewhere suggests that this absence of the human-derived Y chromosome in Neandertals as evidence that they did not contribute other genes to us. I could not disagree more.

The very recent fixation of the Y chromosome in an expanding human population is extremely unlikely to have resulted from genetic drift. Drift does not eliminate rare variants as quickly in an expanding population. Instead, one or more Y chromosome mutations must have been positively selected, resulting in the fixation of the entire NRCY in recent humans.

In that context, the Neandertal result is quite expected: they had an earlier Y chromosome lacking one or more mutations later selected in the other ancestors of living people.

References:

Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Nat Acad Sci USA doi:10.1073/pnas.0704665104

d'Errico F. 2003. The invisible frontier. A multiple species model for the origin of behavioral modernity. Evol Anthropol 12:188-202. doi:10.1002/evan.10113

Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Pääbo S. 2006. Analysis of one million base pairs of Neanderthal DNA. Nature 444:330-336. doi:10.1038/nature05336

Haesler S, Wada K, Nshdejan A, Morrisey EE, Lints T, Jarvis ED, Scharff C. 2004. FoxP2 expression in avian vocal learners and non-learners. J Neurosci 24:3164-3175. doi:10.1523/JNEUROSCI.4369-03.2004

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

Li G, Wang J, Rossiter SJ, Jones G, Zhang S. 2007. Accelerated FoxP2 Evolution in Echolocating Bats. PLoS ONE 2(9): e900. doi:10.1371/journal.pone.0000900

Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Pääbo S, Pritchard JK, Rubin EM. 2006. Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113-1118. doi:10.1126/science.1131412

Wall JD, Kim SK. 2007. Inconsistencies in Neanderthal genomic
DNA sequences. PLoS Genet 3:e175. doi:10.1371/journal.pgen.0030175.eor

Julien Riel-Salvatore figures the Liang Bua "hobbit" tools aren't so complicated after all:

Personally, I have never been especially convinced by the claims for systematic blade technology associated with LB1. The two 'macroblades' (a, b) and two 'microblades' (e, f) illustrated by Morwood et al. (2004: Fig. 5) aren't very regular (the central dorsal ridges are not straight in any of them) and none of their platforms (from what can be seen) are truly 'lipped', unlike the platforms usually generated by soft-hammer production (which is largely employed in true blade production). Furthermore, the illustrated "burin core" really looks to me like a flake core from which a series of small flakes with subparallel edges were knocked off, not a bladelet core. None of this really conforms to the "narrow blades removed sequentially from blade cores" alluded to by some detractors (in Culotta 2007:741) who considers they can only be produced by H. sapiens (a misleading assertion anyway [Bar-Yosef and Kuhn 1999]). Rather, M. Moore and T. Sutkina , who have studied the tools, argue that they represent fairly "simple stone artifacts" (in Culotta 2007:741), which happen to include a few flakes that are twice as long as they are wide - the traditional, if slightly outdated, definition of a blade.

Julien notes that archaeologists often illustrate the "best looking" tools in their papers, and the LB tools aren't all that good looking -- to his mind, they aren't convincing as intentional blades. He connects the idea of rudimentary tools to the wrist morphology, suggesting that the wrist may mean a lack of fine motor control.

As for myself, I agree it's hard to tell. I find Mark Moore's papers on the technology in SE Asia/Australasia to be informative, but it's not entirely clear which direction to interpret them. One consistent point (c.f. Brumm and Moore 2005, Camb Arch J 15:157) is that modern humans in the area did not create anything clearly more "Upper Paleolithic-like" than the LB tools. The abilities of local modern humans don't really address whether a "Homo floresiensis" population might have produced similar artifacts.

Nor is the anatomy of the wrist very convincing on the question of tool manufacture: Until we know about the wrist morphology of late Acheulean/early MSA people, we simply aren't going to know whether "complex" or "sophisticated" tools need any particular wrist architecture.

So, with the tools, I wonder whether people have been trying to connect dots that don't need connecting.

Meanwhile, Leigh Dayton of The Australian reports that the LB tools show "evidence of plant work and butchery":

Working with University of Queensland colleagues Michael Haslam and Gail Robertson, Dr [Carol] Lentfer found evidence of plant work and butchery on stone flakes and cobbles from archeological layers ranging from 12,000 to 55,000 years old.

They identified blood and bone on some tools, but more than 90 per cent of the residues were from woody and fibrous plants.

...

Dr Lentfer said hobbits clearly enjoyed a barbecue, as evidenced by the remains of fires and numerous animal bones, especially of baby stegodons (small elephants), komodo dragons and giant rats. The animal bones were found near tools and hobbit remains, and had cut marks indicative of butchery.

Well, that's more than we knew yesterday...

It is no secret that I really don't like the hypothesis that the massive ancient eruption of Mt. Toba, Sumatra, wiped out much of the worldwide human population 74,000 years ago, possibly allowing modern humans to spread in its wake.

Sure, this eruption was the largest known within the last half-million years. If any ancient volcanic event was going to have an effect on human populations and world climate, it would be this one. And it remains quite possible that there were severe climatic effects lasting a millennium or more.

But there has never been any sign of anatomical or archaeological discontinuity outside Africa at this time. Moreover, no genetic evidence suggests a sudden harsh bottleneck at 74,000 years ago -- most genes are consistent with such a bottleneck only because a recent, sudden, and short bottleneck would have almost no effect on gene diversity. Considering that the Neanderthals in glacial Europe continued right on after the Toba eruption without any hiccup, it always seemed like a very shaky idea.

But still, there seemed to be nothing impossible about a more local effect of the eruption. I mean, if a giant megavolcano spouts off right next door, it has to be bad, right?

Well, maybe on Sumatra itself, but apparently not in some other fairly nearby places. This week's paper by Petraglia and colleagues (2007) appears to have sunk the Toba bottleneck entirely. Very simply, they found a Toba ash horizon in India, and found very similar archaeology both below and above the eruption.

Based on some features of the tools, Petraglia and colleagues speculate that the makers may have been a relatively early sample of modern humans:

Analyses of the archaeological industries recovered from the site indicate a strong element of technological continuity between the pre- and post-Toba assemblages. Together with the presence of faceted unidirectional and bidirectional bladelike core technology, these pre- and post-Toba industries suggest closer affinities to African Middle Stone Age traditions (such as Howieson's Poort) than to contemporaneous Eurasian Middle Paleolithic ones that are typically based on discoidal and Levallois techniques (Fig. 3). The coincidence of (i) evidence of hominins flexible enough to exhibit continuity through a major eruptive event, (ii) technology more similar to the Middle Stone Age than the Middle Paleolithic, and (iii) overlap of the Jwalapuram artifact ages with the earlier end of the most commonly cited genetic coalescence dates (21-23) may suggest the presence of modern humans in India at the time of the YTT event. This interpretation would be consistent with a southern route of dispersal of modern humans from the Horn of Africa (24); the latter, however, will remain speculative until other Middle Paleolithic sites in the Indian subcontinent and Arabian Peninsula (25) are excavated and dated.

I tend to discount point (i) about flexibility, since European Neandertals were apparently flexible enough to survive ice ages with large decade-scale swings from warm to cold. But it is hard to get people to Australia by 50,000 years ago unless they were in India before that.

A dispersal of MSA people from Africa would be an interesting twist on the "modern human origins" problem. If the first "modern" humans outside Africa were MSA users, there is no particular reason to assert that they were different from the population represented at Skhul and Qafzeh. The lack of a full Upper Paleolithic technical kit anywhere in Africa before 50,000 years ago makes an MSA-associated disperal seem more credible. The assembly of the Upper Paleolithic in Eurasia would therefore be a local cultural development, possibly associated with further biological change.

I find that association to be the most important reason to continue investigating these sites. In the meantime, we can forget about the cataclysmic effect of Toba on the poor hominids.

References:

Petraglia M, Korisettar R, Boivin N, Clarkson C, Ditchfield P, Jones S, Koshy J, Lahr MM, Oppenheimer C, Pyle D, Roberts R, Schwenninger J-L, Arnold L, White K. 2007. Middle Paleolithic assemblages from the Indian subcontinent before and after the Toba super-eruption. Science 317:114-116. doi:10.1126/science.1141564

Bouzouggar et al. (2007) report on a series of perforated Nassarius shell beads found in a layer dating to ca. 82,000 years ago in Grotte des Pigeons, Morocco.

The shells are similar to the ones that Marian Vanhaeren found in a drawer of the British Museum last year, from Skhul. Those shells are believed to date to the time of the Skhul fossil series, over 100,000 years ago. At present, they're basically the only evidence of any behavioral difference between the early modern humans from Skhul and Qafzeh and either earlier or later Neanderthal-like people from Tabun, Amud, or Kebara. It's not much, but it's a little.

In last year's paper, Vanharen et al. (2006) also reported a single perforated Nassarius shell from Oued Djebbana, Algeria. The date was unknown, believed by radiocarbon to be older than 35,000 years. That followed after the discovery of 41 Nassarius shell beads from Blombos, South Africa (Henshilwood et al. 2004). Although there were doubts with those finds (expressed in news stories by Michael Balter and Constance Holden), the Blombos finds are quite compelling:

Small objects may easily be displaced through archaeological layers, and perforated tick shells were also recovered at Blombos Cave from the more recent LSA layers. OSL measurements on 1892 individual quartz grains from the aeolian sand layer that separates the LSA and MSA levels (6) indicates no contamination by grains of different ages, contraindicating downward percolation of younger objects. Also, MSA beads are significantly larger (P < 0.0001) than those from LSA levels; the most common MSA perforation type is present on <1% of the LSA shells; LSA beads do not have the wear facets found on MSA specimens; and only 5% of MSA beads have broken lips, compared to 52% of LSA beads, suggesting that the latter were strung in a different way. MSA beads are dark orange or black, whereas those from the LSA are white or pale beige (fig. S1). MSA shells were found in clusters of 2 to 17 beads, with each group clustering in the same or neighboring 50-by-50-cm quadrates. Within a group, shells display a similar size, shade, use-wear pattern, and perforation size. Each cluster may represent beads coming from the same beadwork item, lost or disposed during a single event (Henshilwood et al. 2004:404).

There is perhaps a question as to whether the holes might represent eating the gastropods inside the shells rather than stringing them, but the Blombos beads appear to have been colored by red ochre or put in contact with other objects that were.

The collection from Grotte des Pigeons is not quite as numerous as the Blombos sample (with only 13 shells recovered), but like Blombos, they are in situ and with fairly clear associations. Also, Bouzouggar et al. can give pretty good detail about why humans had to bring them and how they were made:

The N. gibbosulus shells certainly were brought to the site by humans. The local dolomitic bedrock is too old to be a source, predating the origin of the species (36). The distance from the site to the contemporary coast could not have been <40 km (37), too far for natural processes known to carry marine shells inland, such as animal predators or major stor ms (38). It also is clear that the N. gibbosulus were not intended for human consumption because all show features characteristic of dead shells accumulated on a shore. These features include encrustations produced by bryozoa, tiny shells, and sea-worn gravel embedded into the body whorl and perforations produced by a predator on the ventral side of the shell (SI Fig. 7). Comparison with the perforation pattern recorded on a modern thanatocoenosis of this species reveals that the Taforalt [i.e., Grotte des Pigeons] shells do not represent a random selection from a natural assemblage of dead shells (Fig. 5). None of the archaeological examples is undamaged, whereas almost half of those from the comparative sample are intact, and the perforation type most common on the archaeological specimens is rare in nature. This type, a single perforation on the dorsal side at the center of the last spiral whorl, is observed in only 3.5% of the comparative sample; the probability of randomly collecting a sample of shells like that from Taforalt is extremely low (P 0.0001), which suggests that the shells with a perforation on the dorsal side were either deliberately collected or perforated by humans. Although the latter seems more probable, the agent responsible for the perforations cannot be firmly identified. Microscopic features diagnostic of human intervention in the production of the perforation are absent (39). Hole edges on the dorsal aspect are rounded and smoothed on four shells. The remainder have irregular outlines with chipping of the inner layer, indicating the agent responsible for the perforation punched the shells from the outer dorsal side. Holes with irregular edges may be obtained by punching the dorsal side with a lithic point (2, 11). Smoothed hole edges have been replicated by wearing str ung modern shells (39). Both types of hole edges occur on shells used as beads in Upper Paleolithic sites (40)....

Possible evidence for the stringing of the perforated shells as beads comes from the identification on ten specimens of a wear pattern different from that observed on both the modern reference collection and unperforated specimens from Taforalt. The wear in the latter case homogeneously affects the whole surface of the shells and consists of a microscopic dull smoothing associated with micropits and rare short, randomly oriented striations. The wear on the presumed strung examples is found on the perforation edge and on spots of the ventral and lateral side, and it is characterized by an intense shine associated with numerous random or consistently oriented striations (Bouzouggar et al. 2007:9966-9967).

Like the Blombos shells, a number of those from Grottes des Pigeons preserve "residue" of pigment on their surfaces:

The most likely explanation for the presence of pigment on the shells is their rubbing against material embedded with ocher, such as hide, skin, thread, or other substance. We can rule out accidental causes because in two specimens colorant is stuck in microcracks that cross the worn area, indicating that wear and coloring werre intertwined processes. No other objects (e.g., artifacts or bones) from these deposits carry similar pigments, nor are there obvious particles of natural ochres/ores in the sediments (Bouzouggar et al. 2007:9968).

So here, the critical evidence is that (a) the shells were dead when collected; (b) they were transported by people over 40 km from the shore to the cave; (c) they were worn by stringing; and (d) they were colored with pigment, directly or by contact with something also worn and pigmented.

I don't know that you can do much better than this, unless you find them draped across the neck vertebrae of a skeleton.

What is notable about this? I would say, more important than the date (with now three sites clearly over 70,000 years) is the geographic extent of the perforated shells. Africa is a big continent, and now there are shell beads from the three furthest corners of it (Israel being just above the northeast corner). This suggests a very widespread diffusion or dispersal of shell bead-making; yet the Middle Stone Age was a time of increasing regional distinctiveness of technological industries within Africa. If North, South, and East Africa had different traditions, why did they share beads made from these particular shells -- and in two instances, at least, colored red?

References:

Balter M. 2006. First Jewelry? Old shell beads suggest early use of symbols. Science 312:1731. doi:10.1126/science.312.5781.1731

Bouzouggar A and 14 others. 2007. 82,000-year-old shell beads from North Africa and implications for the origins of modern human behavior. Proc Nat Acad Sci USA 104:9964-9969. doi:10.1073/pnas.0703877104

Henshilwood C, d'Errico F, Vanhaeren M, van Niekirk K, Jacobs Z. 2004. Middle Stone Age shell beads from South Africa. Science 304:404. doi:10.1126/science.1095905

Holden C. 2004. Oldest beads suggest early symbolic behavior. Science 304:369. doi:10.1126/science.304.5669.369

Vanhaeren M, d'Errico F, Stringer C, James SL, Todd JA, Mienis HK. 2006. Middle Paleolithic shell beads in Israel and Algeria. Science 312:1785-1788. doi:10.1126/science.1128139

JOHN: Now, that's a frightening headline.

GRETCHEN: What's that?

JOHN: Regrown arms just around the corner?

GRETCHEN: Whoa, yeah!

JOHN: Can you imagine, just walking around the corner, and, hey, there they are waving at you?

GRETCHEN: I want one growing out of my chest!

The Research Council of Norway has issued a press release about Sheila Coulson's work in the MSA of Botswana:

A startling archaeological discovery this summer changes our understanding of human history. While, up until now, scholars have largely held that man's first rituals were carried out over 40, 000 years ago in Europe, it now appears that they were wrong about both the time and place.

Associate Professor Sheila Coulson, from the University of Oslo, can now show that modern humans, Homo sapiens, have performed advanced rituals in Africa for 70,000 years. She has, in other words, discovered mankind’s oldest known ritual.

...

When they saw the many indentations in the rock, the archaeologists wondered about more than when the work had been done. They also began thinking about what the cave had been used for and how long people had been going there. With these questions in mind, they decided to dig a test pit directly in front of the python stone.

At the bottom of the pit, they found many stones that had been used to make the indentations. Together with these tools, some of which were more than 70,000 years old, they found a piece of the wall that had fallen off during the work.

There are no real details, but I know that some people are interested so I thought I would post. A story at YubaNet has pictures of the "python stone" and of the points from the cave, which make up the evidence for ritual behavior:

"Stone age people took these colourful spearheads, brought them to the cave, and finished carving them there. Only the red spearheads were burned. It was a ritual destruction of artifacts. There was no sign of normal habitation. No ordinary tools were found at the site. Our find means that humans were more organised and had the capacity for abstract thinking at a much earlier point in history than we have previously assumed. All of the indications suggest that Tsodilo has been known to mankind for almost 100,000 years as a very special place in the pre-historic landscape." says Sheila Coulson.

I can't wait to see how they know the date.

UPDATE (12/1/2006): Apparently, neither can Julien Riel-Salvatore...

Brooks and colleagues (2005) describe evidence for distance weaponry from late MSA contexts in eastern and southern Africa. They discuss the size of points from Aduma, Ethiopia, and ≠Gi, Botswana, which are small enough that the most credible explanation is hafting on projectiles such as small thrown spears, atlatl darts, or (probably less likely) arrows.

The article begins with some consideration of why African MSA should show a pattern of regional variability in point morphologies. Explaining variability on a regional scale first requires an explanation of uniformity on a local scale:

Projectile armatures must be able to replace broken armatures, so the haft into which they are placed also imposes limitations on projectile size and form. Having a system of exchange within social networks further encourages similarity of point form so that the product remains interchangeable within a cultural group. Wiessner (1983) argued from ethnographic data that even where forms were extremely limited by raw materials regional styles emerged (e.g., fence wire in Wiessner's ethnographic example). Men hunt well for only a few years but continue to make arrow points for most of their lives; consequently, arrows are frequently given to hunters in exchange for a claim on the evntual kill. Hunting success is influenced by the hunter's familiarity with an armature; this kind of social trade network would therefore be expected to encourage homogeneity in the size and shape of projectile points. Thus social organization, especially the development of exchange networks, constrains point styles and creates sharp discontinuities at social boundaries, whether these boundaries are linguistic, ethnic or simply a result of an empty buffer zone between group ranges (Brooks et al. 2005:234-235).

This is important: if local forms were not standardized, there would be no way to recognize regional variations. Instead, we would see great variability within local samples, with relatively little additional variability between regions -- and much of that regional variation might be attributable to raw material differences.

It is worth noting that this passage makes a functional argument for local standardization, not a purely informational one. One reason to emphasize the functional argument is that regional variability is most notable for points, and less so for other elements of regional assemblages.

They compare the points from two sites, Aduma (here, considered older than 70,000 BP) and ≠Gi (with MSA levels at around 77,000 BP), to those from Tabun, Israel (through layers B, C, and D overlapping the MSA sites). The pattern of change in point dimensions at Tabun suggests that the hafting requirements were in fact a constraint on point dimensions -- in particular, the points are very conservative in the width of their bases, while the length of the point and angle of the point change over time. Against this pattern, the Aduma points decrease in thickness and width over time, but maintain the same point geometry. Brooks and colleagues suggest that the point geometry is the more functionally constrained element in the Aduma sequence, while the hafting requirements constrained the Tabun points.

Also, the weight of points decreased over time through the Tabun, Aduma, and ≠Gi samples, with the decrease most marked in the African sites. Brooks et al. relate this decline in point size and weight to the balance requirements of projectiles -- smaller projectiles demand smaller points. Also, the increased use of obsidian at Aduma tends to decrease weight further, as it is "ligher than the quartzite and silcrete of the ≠Gi points" (p. 248).

They suggest the possibility of contact between the populations that generated the Aduma and Tabun assemblages:

Marginal retouch is another area in which Aduma MSA points are distinguished from Tabun points. Each piece was divided into six retouch areas, three per side, and the presence, position and nature of the retouch, if any, were noted fore each area. While some points from the earliest Tabun sample are retouched, a greater portion of Aduma points are retouched in every level. The pieces that are retouched at Aduma are more completely retouched (retouched in more areas of each piece) than the Tabun points. While inverse, or vental, retouch is rare throughout, it is actually most common in Tabun D. Bifacial retouch, on the other hand, is virtually absent in the Tabun sample and present at significant freuqencies throughout the Aduma sample, except for the uppermost level. Invasive retouch, a hallmark of the classic MSA, is found at low levels in Tabun D (alhtough not it B or C), but at Aduma, it rises along with the frequency of classic MSA points to a maximum in the Ardu II silt sites, then decreases slightly at the top.

Finally, striking platforms of complete pieces are virtually unmodified in the Tbaun assemblage but up to 50% are thinned or removed on the Aduma points. Overall, the earliest Aduma points from A-1 are most similar to the Tabun points from Level D. If one were to argue that the points for a moment of contact or expansion in either direction, this time period represents the most likely candidate. The later points in both areas dating to late OIS 5 and early OIS 4 are increasingly divergent in style (Brooks et al. 2005:248-249).

I quoted extensively to focus on the difference between the technologies and their different trajectories over time. Brooks and colleagues suggest that if the Tabun and Aduma samples were ever connected (informationally), then it was likely early -- before OIS 5. Through time, Tabun points remained relatively static in overall size but shortened, while Aduma (and ≠Gi) points got smaller and smaller.

Here is the concluding paragraph with respect to the projectile argument:

The Aduma points tend increasingly toward the dimensions of spear thrower darts or arrows, and hold point angle constant. Although ethnographic and archaeological examples of spear throwers are not known from any African site, spear throwers are present at a much later date on all the other inhabited continents and begin to appear at a time when African LSA armatures already fall within the size range of modern arrowheads (at <1.5 g). The early diminution of African stone armature may indicate that Africa passed through a spear thrower state at an earlier date (Brooks et al. 2005:251).

All of these arguments are functional rather than stylistic. The retouch observations fall into an interesting category, because these are (possibly) the strongest evidence concerning the attention of the point makers to their final form. Brooks and colleagues conclude that the functional stasis of the Tabun tools may be reflective of those aspects of early modern humans that inhibited their dispersal further into Eurasia.

Also, the paper includes some cool closeup photos of points to show impact damage on the tips.

References:

Brooks AS, Yellen JE, Nevell L, Hartman G. 2005. Projectile technologies of the African MSA: Implications for modern human origins. In Hovers E, Kuhn SL, eds. Transitions Before the Transition: Evolution and Stability in the Middle Paleolithic and Middle Stone Age. Springer, New York, pp. 233-256.

Considering the paper by Evans and colleagues, I've come up with a list of questions and answers:

What is introgression?

Introgression is the transfer of alleles across species or subspecies boundaries. In other words, it describes gene flow between populations that are partially isolated. For archaic humans, there is no test of the strength or permeability of boundaries between populations; it is common to use the term "introgression" to describe gene flow in such situations, even if such gene flow is fairly common.

The paper by Evans and colleagues describes a scenario of adaptive introgression. In such cases, an allele with a selective advantage moves from one population to another.

Adaptive introgression must be a very unusual event, right? I mean, I've never heard of it before!

If you haven't heard of adaptive introgression, you haven't been reading the literature. Adaptive introgression across species boundaries is very common in mammals, and is almost ubiquitous where closely related species are sympatric. It has long been known to happen on the basis of morphological characters that spread through hybrid zones into adjacent populations. But now that molecular surveys have become common, introgressive genes have been found moving out of current hybrid zones, and also in the areas where hybrid zones likely occurred long in the past.

Hybrid zones themselves are often quite obvious. But introgression is not about hybrids. It occurs when backcrosses spread alleles into the other parental species. Hybrids may have a mixture of many genes and characters. Introgression involves a small number of genes, which are much more likely to spread if alleles are adaptive. Where different populations are in reproductive contact, adaptive introgression may often be the most important source of adaptive alleles -- it provides a way for a species or population to benefit from the adaptive evolution of neighboring species.

There is one thing that impedes introgression: linkage to deleterious alleles. Species separated for longer times are more likely to have alleles that are bad on the genetic background of related species, and so potential adaptive alleles must have advantages outweighing all the deleterious alleles they are linked to. In these situations, adaptive introgression may only occur after enough recombination has broken the adaptive allele apart from some or all of its linked deleterious neighbors.

But I thought that "species" means "no interbreeding!"

Get with the times, man! Mammal species just don't establish reproductive barriers very quickly. Comparing mammals, postzygotic isolating mechanisms take between 2 and 10 million years to evolve. No primate species pairs have evolved postzygotic isolation on the timescale represented by the evolution of Homo. When archaic and modern humans were in contact, they certainly interbred.

OK, but why is this gene introgression? Why couldn't it just have originated in ancient Africans?

The current evidence for introgression comes from the mismatch between the ancient coalescence time for all haplogroups of the microcephalin gene, compared to the very recent selection on the D haplogroup. Now recent selection on an ancient variant could occur within a single population, for example, if the allele was formerly neutral and gained a new advantage with some difference in the genetic background. And an ancient coalescence date would not be unusual in a single population -- several other loci match the 1.7 million years estimated for the microcephalin genealogy.

Two things make this case especially persuasive. First, there is almost no evidence of recombination between the D and non-D haplogroups. If they existed within the same population for 1.7 million years, they should have recombined a lot with each other, and we should see some of those recombinants today. We don't. The best explanation is that the alleles were in different ancient populations, somewhat isolated from each other so that recombination was very rare.

Second, the D haplogroup is common in Europe and Asia, but is very rare in Africa. If it increased under selection from its origin in some ancient African population, then it ought to be most common in Africa now. We might also expect a deeper origin for the D haplogroup in Africa, similar to the structure of many other genetic loci. We observe neither.

Hey, why should this gene be so unique? There's never been any evidence for archaic genes before!

Now, this is clearly where I have let you down, by not blogging about these papers as they have been coming out. What can I say, I have to make a living somehow! If I give away all my research, how can I stay a step ahead?

The most similar locus to microcephalin is the region around MAPT on chromosome 17. Hardy and colleagues (2005) suggested that this locus is a Neandertal introgression. Like microcephalin, the locus has an ancient coalescence (>2 million years), and like microcephalin, an allele is under selection, with its highest current frequency in Europe. Like microcephalin, MAPT is brain-active, with most research centered on its possible role in Alzheimer's and Parkinson's disease. Unlike microcephalin, there are no recombinants between the major (H1 and H2) haplogroups; this is due to a chromosomal inversion between them. Evans and colleagues (2006) note that balancing selection might not be statistically ruled out when there is such an inversion preventing recombination. Still, balancing selection doesn't easily explain the recent positive selection, nor the geographic distribution of variation.

Garrigan et al. (2005b) found evidence for an ancient Asian allele being retained in living Asians. This allele was from a non-coding locus, so it seems unlikely that adaptive introgression is the cause, which might suggest even more widespread genetic survival of archaic DNA. Some loci suggest the survival of archaic lineages within Africa, including another X chromosome noncoding region (Garrigan et al. 2005a) and the dystrophin gene (Zietkiewicz et al. 2003). These would presumably be attributable to partial isolation of Middle Pleistocene African populations, with introgressive gene flow among them.

The widest survey for introgression thus far was by Plagnol and Wall (2006), who conclude that around five percent of human genes show some evidence for introgression from archaic humans. Their statistical test was looking for loci with ancient divergence times and in particular divergent alleles centered in Eurasian (non-African) populations. So this is a kind of estimate under the assumption of relatively great genetic differentiation among archaic human populations.

I'll end with Templeton (e.g., 2005), who found that human autosomal variation supports a broad ancestry of living humans among Eurasian and African archaics, with evidence of genetic dispersals from Africa several times during the Pleistocene. Under this model, intermixture among archaic populations would have been fairly common, at least intermittently. This is the argument that I made with Milford Wolpoff several years ago (Hawks and Wolpoff 2001) -- we just don't see a lot of evidence for genetic differentiation among archaic humans.

This kind of model would imply that genes like microcephalin -- with strong evidence for some isolation of populations -- might be fairly rare. The fact that several of them have now cropped up (the 5 percent estimate from Plagnol and Wall, 2006, being the most informative on this score) means that we have a lot about archaic human population structure yet to discover.

But notice the nature of this uncertainty. We have a difference between substantial introgression among populations structured like hominoid subspecies on one side, and ubiquitous genetic exchanges among populations structured like human races on the other side. Complete replacement is completely out. "Mostly" replacement, or "assimilation" is still in, but with the observation that archaic human genes had substantial evolutionary importance in the adaptation of modern humans.

In other words, we have moved the ball down the field. Time to line up for the next play.

What is all this about microcephalin possibly not being from Neandertals?

Well, the D haplogroup is common in many areas outside of Africa in addition to Europe. So it isn't possible to really specify in what archaic population it may have originated. There is some chance that it may be found in the Neandertal genome sequence, when that becomes available. In fact, that would be the ultimate test for many candidate introgressive alleles.

But there is a good chance that it won't be found in the Neandertal sequence. After all, Neandertals were probably pretty thin on the ground -- especially in Europe. A sampling of their genes would be sort of unlikely to yield a high proportion of archaic alleles that may have survived to the present day. So there is hope that we will find and document such alleles, but the best evidence for many of them may remain their current pattern of variation in living people.

Now, bear with me here. Neandertals were stupid, right? So why would one of their brain genes be advantageous in modern humans?

There are so many possibilities here.

1. Late Neandertals certainly weren't stupid. Consider the Châtelperronian. And the European Mousterian includes basically all the elements that are thought to represent cognitive sophistication in MSA Africans.

2. Neandertal brains were big, and their heat generation requirements means that energetic constraints were very different from other archaic populations. The brain doesn't function in isolation -- its development, growth, and ongoing maintenance depend on metabolic constraints. So Neandertals might easily have had brain development alleles that had different responses to their high-energy lifestyles. Considering that early Upper Paleolithic people had much more effective foraging strategies than Neandertals, high-energy brain development may have had an even greater advantage than it had previously enjoyed.

3. Modern humans are variable in brain morphology and cognition. That variability certainly includes alternative strategies (for example, personality types) that may be maintained by frequency-dependent selection. An archaic population that had particular constraints on its behavioral strategies might have given rise to strategies that worked within the modern human mix. In that context, Neandertals are fairly unique in having a very strong dietary dependence on meat, and their means of hunting was both risky and required cooperation. That adaptation may have led to behavioral strategies that succeeded in modern humans, even as Neandertal anatomies disappeared.

Those are some possibilities we are working on. There are probably many others. The key is that we are looking at the function of some genes that survived, through our reconstruction of the total phenome of a population that no longer survives. We are limited by the evidence, but there are many suggestive hypotheses.

Neandertals went extinct! Their features disappeared in later humans! How can any of their genes have survived?

This is my favorite one to answer, because it invokes the true paradox of introgression. The features that we recognize as Neandertal features, were defined as Neandertal features by virtue of the fact that they are mostly gone! That means that any alleles correlated with Neandertal morphological features were almost certainly selected against, or were at best neutral. That means that those recognizably Neandertal genes are gone!

But here we have a gene that looks to have come from some archaic population. Adaptive introgression occurs when adaptive alleles are selected, and broken apart from their genetic background. So even as many (perhaps most) Neandertal alleles disappeared, some of their alleles began to increase in frequency -- slowly at first, then very rapidly.

Some adaptive introgressions may already have been fixed, particularly in Europe (from Neandertals). Others, like microcephalin, are still growing in frequency. The key is to remember Mendel -- this is not blending inheritance of Neandertal traits, it is the extinction of many alleles and the proliferation of some others.

The reduction in frequency of Neandertal-like morphological traits over time is entirely consistent with this scenario. In fact, it shows the widespread importance of Neandertal-modern matings, which led to the emergence of a modern population with many Neandertal traits. The widespread genetic contact is documented by the distribution of the traits -- with different Neandertal-like traits in different specimens. That kind of contact is most likely to enable adaptive introgression to proceed.

UPDATE (11/8/2006): Fixed some citations.

References:

Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, Lahn BT. 2006. Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Proc Nat Acad Sci (early edition) DOI link

Garrigan, D., Mobasher, Z., Kingan, S. B., Wilder, J. A., Hammer, M. F. 2005a. Deep haplotype divergence and long-range linkage disequilibrium at Xp21.1 provides evidence that humans descend from a structured ancestral population. Genetics 170:1849-1856.

Garrigan, D., Mobasher, Z., Severson, T., Wilder, J. A., Hammer, M. F. 2005b. Evidence for archaic Asian ancestry on the human X chromosome. Mol. Biol. Evol. 22:189-192. DOI link.

Hardy, J., Pittman, A., Myers, A., Gwinn-Hardy, K., Fung, H. C., de Silva, R., Hutton, M. and Duckworth, J. 2005. Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens. Biochemical Society Transactions 33:582-585.

Hawks, J., Wolpoff, M. H. 2001. The accretion model of Neandertal evolution. Evolution 55:1474-1485.

Plagnol, V., Wall, J. D. 2006. Possible ancestral structure in human populations. PLoS Genet. 2:e105. DOI link.

Templeton AR. 2005. Haplotype trees and modern human origins. Yrbk Phys Anthropol 48:33-59. DOI link

Zietkiewicz, E., Yotova, V., Gehl, D., Wambach, T., Arrieta, I., Batzer, M., Cole, D. E., Hechtman, P., Kaplan, F., Modiano, D., Moisan, J. P., Michalski, R., Labuda, D. 2003. Haplotypes in the dystrophin DNA segment point to a mosaic origin of modern human diversity. Am. J. hum. Genet. 73:994-1015.

I was looking through some MSA literature, and ran across a paper earlier this year by Negash and Shackley (2006) concerning long-distance movement of obsidian in Ethiopia. Here's the conclusion:

Obsidian is an excellent raw material for stone tool production, and because of its source-specific chemistry, it is an ideal candidate for the tracing of its movement from the source to archaeological sites. Our main objective here was to chemically characterize the obsidian artefacts of Porc Epic, and we have determined that at least some of the artefacts were being transported from a distance as far as 250 linear kilometres away. This is in keeping with other previous investigations in East Africa that have demonstrated MSA movement of obsidian over similar distances from sources to archaeological sites (Merrick et al. 1994).

The citation to Merrick and colleagues (1994) references obsidian transport in Kenya and northern Tanzania.

The transport at the present site (Porc Epic) was dated to older than 77,000 years ago. The paper considers trade versus non-contact long-distance movement:

As indicated above, the source of Kone was occupied during the MSA times. Similarities between Kone and Porc Epic artefacts have been surmised on technological and stylistic grounds (Clark and Williamson 1984; Clark 1988). Clark and Williamson (1984) also argue that Porc Epic was a seasonal hunting camp-site, hypothesizing its inhabitants to have been moving from the Afar Rift following the migration of game. We further hypothesize here that such technological similarity, coupled with the artefacts of Porc Epic being derived from Kone, can be taken as an indication that at least part of the obsidian from Porc Epic was transported by the people of Kone, assuming that the sites were contemporaneous. Alternatively, the inhabitants of Porc Epic may have transported the obsidians. Another equally possible explanation is that the obsidians from Kone reached Porc Epic through direct or intermediate trade or contact. Unfortunately, we do not have radiometric dates for Kone, and such inferences have to await further investigation of MSA sites that may be located between Kone and Porc Epic.

Spatial distributions of artifacts make up a sort of second-order data source; it takes a fairly dense sampling of sites to make inferences about movement networks in this way. So a denser sampling of African MSA sites will yield more information about raw material movement. On the other hand, obsidian is a very high-value raw material, with a bonus of being highly noticeable in assemblages, so it may not be quite comparable to flint movement patterns in the European Middle Paleolithic, for example. Hmm....

References:

Negash A, Shackley MS. 2006. Geochemical provenance of obsidian artefacts from the MSA site of Porc Epic, Ethiopia. Archaeometry 48:1-12. DOI link

I got the Neanderthals on the Edge volume by interlibrary loan to follow up the Barton shellfish consumption reference. Here is the relevant passage from the discussion of that chapter:

Until recently any discussion of shellfish exploitation by Neanderthals or other archaic humans would have been restricted to just a few exceptional examples. However, following publication of work on the Italian Mousterian by Mary Stiner and others, there are now a growing number of instances where evidence has been documented for deliberate harvesting of marine shellfish resources by Neanderthals. These include cave sites and rockshelters in the Ligurian Riviera (Costa dei Balzi Rossi, Riparo Mochi, Barma Grande), further south in Latium (Grotta dei Moscerini) and in the southern Italian province of Puglia (Grotta dell'Alto, Grotta del Cavallo, Grotta Uluzzo C, Grotta Mario Bernadini, Grotta dei Giganti) (Stiner 1994, fig 6.9). Further afield in Africa similar occurrences have been reported from Middle Stone Age deposits at Blombos Cave in the southern Cape (Henshilwood and Sealy 1997) and at the Haua Fteah in Cyrenaica (Klein and Scott 1986). To these can now be added the localities of Vanguard and Gorham's Caves and the Devil's Tower, Gibraltar. The Gibraltar examples indicate that mussels and otehr shellfish probably contributed regularly to the Neanderthal diet. Furthermore they show that selective use was made of the larger shells collected from estuarine habitats and these small packages of food were carried up to four kilometres to the caves to be prepared and consumed. Much larger accumulations of shellfish in association with the Mousterian deposits are also known from unpublished sites north of Gibraltar near Torrelmolinos, in teh Spanish Costa del Sol (Miguel Cortés Sánchez pers. comm.).

The presence of thin in situ ashy hearth horizons in Vanguard Cave has helped establish that the use of the site by Neanderthals was generally episodic with individual occupation events usually being short-lived. Ephemeral use of this cave is exemplified by the upper hearth and midden which probably represented a single episode of use of no more than a few hours duration. Further down the sequence more intensive evidence of occupation is indicated by accumulations of butchered bones of ibex and red deer but here too the data are consistent with short-term occupational use. In both the upper and middle section of this cave it was noticeable that te hearths were positioned in proximity of hte soutehrn cave wall. Similar juxtapositions have been noted at other Mousterian sites (e.g. Tor Faraj, south Jordan; Henry 1998), but unlike Tor Faraj there is no suggestion of multiple individually spaced hearths. Indeed it is noreworthy that the single hearth in the middle section of Vanguard was re-used at least three times. This may reflect the generally lower density of human groups occupying the site at one time. The position of the hearths near the cave wall and the extensive ash spread in the upper part of the cave may also have been partly connected with sleeping or resting activities. For example in ethnographic contexts, it has been noted that ashy spreads between the hearth and the rock wall may coincide with places where bedding was laid down (Parkington and Mills 1991) (Barton 2000:218-219).

McBrearty and Brooks (2000:511-512) give a long list of MSA and associated sites with shellfish remains (taken broadly to include land snails and tortoises). This is a very long passage, and so I won't quote it, except for the conclusion:

Evidence from coastal Italy (Stiner, 1993, 1994; Stiner et al. 1999) and Gibraltar (Barton et al., 1999) shows that Neanderthals did sometimes eat marine shellfish, but the impressive escargotière at Mumba [Rock Shelter, Tanzania] and the numbers of coastal African sites containing quantities of shellfish seem to indicate a more regular intensive use of small scale resources in the MSA (McBrearty and Brooks 2000:512).

This is certainly one of those where I wouldn't want to have to be the graduate student to test that assertion -- after all, how many coastal Neandertal sites are there? And the occurrence of a unique site where land snails were intensively exploited doesn't seem like the best evidence. Notice how Barton described the relatively nonintensive occupation of the Gibraltar Mousterian caves. It would take some pretty sophisticated sampling to work out whether Neandertals and MSA Africans were significantly different in use of these resources.

Common sense suggests they wouldn't be, at least not without some reason. After all, the other protein-rich foods they had available were vastly more dangerous and risky to acquire. Finding shellfish at coastal sites would seem more like filling an obvious archaeological blind spot than saying something distinctive about resource collection abilities.

But then, the use of shellfish in particular figures into the "coastal dispersal" hypothesis for out-of-Africa. The idea that archaic humans were incapable of exploiting coastal resources is inconsistent with the data. But Paul Mellars (2006) presents a curious alternative view:

The second major factor in stone tool technology lies in the specific functions for which the tools were required. If, as most of the current models suggest, the initial colonization of southeastern Asia and Australasia followed a primarily coastal route (12, 18, 20, 21, 61), then the technologies would be likely to adapt primarily to the exploitation of coastal resources, such as fish, shellfish, and marine mammals (together with tropical plant foods) with perhaps only a minor component of hunting larger land mammals, of the kind that clearly formed a major part of the human economy in both Africa and the whole of western Asia and Europe (21, 59). This would presumably have involved much less emphasis on various forms of hunting equipment (such as spears, meat-processing tools, etc.), as well as equipment involved in the manufacture of elaborate skin clothing, or the construction of tents and other living structures, that were essential to survival in much colder, more northerly environments (59, 62).

In other words, Mellars proposes that southeast Asia and Australasia lost stone tool complexity that would have been present in their African ancestors, because they didn't eat many large land mammals.

This takes shellfish-dependence full circle -- hunters that once took African big game found instead that they could live the easy life following the coast and eating marine resources. Well, maybe -- it still seems like a lot of arm-waving based on distributions that may not be different from each other in any real way.

References:

Barton N. 2000. Mousterian hearths and shellfish: late Neanderthal activities on Gibraltar. In Stringer CB, Barton RNE, Finlayson JC, eds., Neanderthals on the Edge: Papers from a conference marking the 150th anniversary of the Forbes' Quarry discovery, Gibraltar. Oxbow Books, Oxford. pp. 211-220.

McBrearty S, Brooks AS. 2000. The revolution that wasn't: a new interpretation of the origin of modern human behavior. J Hum Evol 39:453-563.

Mellars P. 2006. Going East: new genetic and archaeological perspectives on the modern human colonization of Eurasia. Science 313:796-800. DOI link