Qafzeh

Debbie Guatelli-Steinberg and Donald Reid report on the perikymata spacing of a sample of fourteen anterior teeth from Qafzeh. These are "early modern humans", among the earliest to be located outside of Africa, but their anatomical position relative to Neandertals and other groups has been subject to frequent dispute.

As I've emphasized several times ("Neandertal teeth: the other shoe", "How modern is "modern tooth development"?"), this growth characteristic of teeth is variable among living human populations. What remains totally unclear is why it varies.

Neandertals are at the low end of the human range of variation for perikymata counts on their anterior teeth, and the patterning of packing across the tooth is somewhat different. In particular, Neandertals have fewer perikymata nearer the roots of these teeth (for details, I suggest Guatelli-Steinberg's 2009 review article).

The current paper follows up on earlier work by Janet Monge and colleagues (2006). They emphasized that the Qafzeh anterior teeth fit within the overall human range of variation, but observed that two individuals were very close to Neandertals in their packing patterns. Here, Guatelli-Steinberg and Reid include more specimens in the sample, confirming this similarity.

From their conclusion:

The purpose of this study was to investigate whether Qafzeh teeth are different from those of modern humans in the percentage of perikymata present in their cervical [sic] appear to fall in the lower 50% of the modern human distribution, and a few fall within the lowest 5% of the distribution. Thus, this sample of Qafzeh teeth appears to differ from those of modern humans in the same direction that Neandertals do: with generally lower percentages of perikymata in their cervical regions. As can be seen in the SEM montages in Figure 2, perikymata become much more closely spaced in the cervical relative to incisal halves of the Inupiaq LI2 than they do in either the Neandertal or Qafzeh LI2s. Although sample sizes precluded a similar test between the Qafzeh and Neandertal teeth, plots of the averages for these teeth (Fig. 1a,b) reveal the similarity of the Qafzeh and Neandertal teeth, particularly for the UI2, LC, LI2, and LC. Values for two of the Qafzeh UI1s and a single UC are closer to the modern human than Neandertal means for these tooth types, revealing overlap in the ranges of values, as is also true for Neandertals and modern humans (Guatelli-Steinberg et al., 2007).

It may be worth pointing out that the perikymata packing pattern was a key part of Ramirez-Rossi and colleagues' conclusion that the Les Rois B mandible as well as several other Les Rois dental specimens show affinities to Neandertals.

I think Monge and colleagues are correct in asserting that this packing pattern is not a taxonomic diagnosis. Notwithstanding that the precise Neandertal-like pattern, present at Qafzeh, does not occur in the known human samples, we still don't know why human patterns differ from each other. In their discussion, Guatelli-Steinberg and Reid suggest alternatives for the mechanism forming the straiae, but I'd like to have some kind of genetic answer -- what developmental processes changed, carrying this feature along with them?

Anyway, another contrary observation to the idea of "modern human dental development", I guess.

References:

Guatelli-Steinberg D, Reid DJ. 2010. Distribution of Perikymata
on Qafzeh Anterior Teeth. Am J Phys Anthropol (in press). doi:10.1002/ajpa.21158

Guatelli-Steinberg D, Reid DJ, Bishop TA, Larsen CS. 2005. Anterior tooth growth periods in Neandertals were comparable to those of modern humans. Proc Nat Acad Sci USA 102:14197-14202. doi:10.1073/pnas.0503108102

Guatelli-Steinberg D. 2009. Recent studies of dental development in Neandertals: Implications for Neandertal life histories. Evol Anthropol 18:9-20. doi:10.1002/evan.20190

Monge JM, Tillier A-M, Mann AE. 2006. Perikymata number and spacing on early modern human teeth : Evidence from Qafzeh cave, Israel. Bull Mem Soc Anthropol Paris 18:25-33.

Ramirez Rozzi FV, d'Errico F, Vanhaeren M, Grootes PM, Kerautret B, Dujardin V. 2009. Cutmarked human remains bearing Neandertal features and modern human remains associated with the Aurignacian at Les Rois. J Anthropol Sci 87:153-185.

Another of the craniometric stories going around this week (Discovery News) proposes that early Levantine modern humans (Skhul-Qafzeh) and Pleistocene Australians come from an early out-of-Africa dispersal that was later mostly replaced by true modern humans (represented by Upper Paleolithic Europeans and living people everywhere). The study is by Michael Schillaci; here's the abstract:

This study examines the genetic affinities of various modern human groupings using a multivariate analysis of morphometric data. Phylogenetic relationships among these groupings are also explored using neighbor-joining analysis of the metric data. Results indicate that the terminal Pleistocene/early Holocene fossils from Australasia exhibit a close genetic affinity with early modern humans from the Levant. Furthermore, recent human populations and Upper Paleolithic Europeans share a most recent common ancestor not shared with either the early Australasians or the early Levantine humans. This pattern of genetic and phylogenetic relationships suggests that the early modern humans from the Levant either contributed directly to the ancestry of an early lineage of Australasians, or that they share a recent common ancestor with them. The principal findings of the study, therefore, lend support to the notion of an early dispersal from Africa by a more ancient lineage of modern human prior to 50 ka, perhaps as early as OIS 5 times (76-100 ka).

But the Skhul-Qafzeh sample and the Pleistocene Australia + Wadjak sample used in the paper (a subset of all the actual specimens) are all males, and the Upper Paleolithic Europeans and recent skeletal samples are (as you might expect) half female.

Seems like a problem....

References:

Schillaci MA. 2008. Human cranial diversity and evidence for an ancient lineage of modern humans. J Hum Evol (in press) doi:10.1016/j.jhevol.2007.10.010

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

OK, NEWS FLASH: "Out of Africa dispersal was not as simple as once thought."

That's the lede in the press release about the Tianyuan skeleton.

That's very nice and all, but as someone who never thought things were very simple, I have a bit more latitude to talk about why this specimen is interesting.

I have an early edition of the paper by Hong Shang and colleagues. Here is the abstract:

Thirty-four elements of an early modern human (EMH) were found in Tianyuan Cave, Zhoukoudian, China in 2003. Dated to 35,500 -33,500 radiocarbon years before present by using direct accelerator mass spectrometry radiocarbon, the Tianyuan 1 skeleton is the among the oldest directly dated EMHs in eastern Eurasia. Morphological comparison shows Tianyuan 1 to have a series of derived modern human characteristics, including a projecting tuber symphyseos, a high anterior symphyseal angle, a broad scapular glenoid fossa, a reduced hamulus, a gluteal buttress, and a pilaster on the femora. Other features of Tianyuan 1 that are more common among EMHs are its modest humeral pectoralis major tuberosities, anteriorly rotated radial tuberosity, reduced radial curvature, and small talar trochlea. It also lacks several mandibular features common among western Eurasian late archaic humans, including mandibular foramen bridging, mandibular notch asymmetry, and a large superior medial pterygoid tubercle. However, Tianyuan 1 exhibits several late archaic human features, such as its anterior to posterior dental proportions, a large hamulus length, and a broad and rounded distal phalangeal tuberosity. This morphological pattern implies that a simple spread of modern humans from Africa is unlikely.

The paper is largely descriptive (which is certainly appropriate for an initial publication), but there aren't many pictures. I imagine they are holding pictures for a more extensive publication on the skeleton. There are also few comparisons presented. These are all fine; it's not a monograph, it's a short descriptive paper. But the brevity means that there might be interesting comparisons beyond those presented, so this is possibly an abbreviated list.

How does the skeleton affect the "Out of Africa" story? It dates to 34,430 +/- 510 radiocarbon years, which is approximately the same age as the earliest "modern" European remains, from Pestera cu Oase, Romania. That makes it important, regardless -- but it is also by far the most complete skeleton in China from this early time period. The other remains that may represent the early modern Chinese population generally have some uncertainty about their dates (such as Liujiang) or more fragmentary (and also insecurely dated, like the Salawusu remains). The Upper Cave specimens from Zhoukoudian are substantially later, less than 25,000 and possibly as young as 12,000 years old. So the skeleton's date makes it very important

What about its features? In terms of morphology, it shares much with early modern humans in Europe. I got a chance to discuss the paper very briefly with Dave Frayer and Milford Wolpoff, who know this morphology better than me -- although any errors here are my own. The skeleton is relatively robust, but fits within the range of robusticity of post-Neandertal Upper Paleolithic Europeans. The paper discusses a number of pathological details of the skeleton, mostly age-related.

The abstract says that the anterior-to-posterior dental proportions of the mandible are similar to late archaic humans. Here is what the text says about this feature on page 4:

The buccolingual diameters of the I2 to M3 are similar to those of most Late Pleistocene humans, samples of which differ principally in their anterior dental dimensions (35; Table 4). However, an index of summed anterior (I2, C1) to posterior (M1, M2) crown breadths (Table 5) differentiates the Neandertals from most modern humans. The Tianyuan 1 index of 73.4 is matched among the EMHs only by the Upper Paleolithic Arene Candide 1, Dolni Vestonice 13, and Mladec 54 (11.5% of the EMHs), whereas it is exceeded by 81.3% of the Neandertals, the lowest of which is still 72.9. It is above all of the Middle Paleolithic modern human (MPMH) plus Nazlet Khater 2 values. Tianyuan 1 is even closer to the Neandertal pattern if the premolar breadths are added to the molar breadths; its value of 41.6 is exceeded only by the same three European EMHs and 60.0% of the Neandertals. The Tianyuan 1 dental proportions therefore fall in the overlap zone of late archaic and Upper Paleolithic EMHs and separate from the MPMH.

In other words, this specimen has a big lateral incisor and canine relative to its molars. This particular feature is interesting, but maybe not not all that informative relative to the comparative samples. The data make clear that both the lateral incisor and molars of the specimen are smaller than the average size of the Skhul-Qafzeh hominids; it's just that the molars have reduced more (and the canine is a bit larger, but easily in the range of variation).

About those hand bone features, here is what the paper says on page 5:

The hamulus has the reduced palmar projection of the EMHs (Table 8), but its relative proximodistal length aligns it with the Neandertals (Fig. 3). The one distal manual phalanx, probably from the second ray based on articular and osteoarthritic matching with the left second more proximal phalanges, has a moderately large distal tuberosity that is circular and lacks proximal ungual spines (Fig. 3). The relative breadth of the tuberosity falls between the Neandertals and modern humans (including the MPMH) (Table 8). The form of the tuberosity is the archaic Homo (and Neandertal) pattern, although it is occasionally seen in EMHs.

This is probably more interesting from a biobehavioral perspective than a phylogenetic one. In other words, these help us to infer the behavior of early Upper Paleolithic people, which for the hands appears to match that of the Neandertals in many respects. The strong robusticity of the femur, tibia, and humerus of the skeleton confirm that behavioral interpretation. These may still be informative in a phylogenetic sense -- that is, they may show the retention of genes from earlier Eurasian hominids. But more importantly, they show that the adaptive context of modern humans changed across the time span from 35,000 to 15,000 years ago or so, and modern human anatomy evolved as a consequence.

Probably the most interesting observation along biobehavioral lines is that shoe wear may have influenced the individual's foot development. This is from the BBC article:

The single toe bone which was unearthed seems to suggest the individual wore shoes, pushing back the earliest known evidence for footwear by about 10,000 years.

An earlier study by Professor Trinkaus shows that human small toes became weaker during the stage of prehistory known as the Upper Palaeolithic, and that this can probably be attributed to the adoption of sturdy shoes.

The invention of rugged shoes reduced humans' reliance on strong, flexile toes to grip and balance.

Or, as the paper puts it:

The second proximal pedal phalanx, however, is gracile, similar to MUP humans and distinct from the MPMH and Neandertals (Table 6). Given the apparent tibial robusticity, this suggests, as with MUP humans (43), the reduction of anterior pedal bending stress through the habitual use of footwear.

OK, so what have we learned? The skeleton is certainly important, but some more comparative work will help to place it in a broader context. As it stands, it may be the most important single specimen for interpreting the Late Pleistocene population history of China, but it lacks many of the anatomical areas that would inform us more clearly of its relationships -- in particular, no face, upper teeth, or vault. Some of the most informative observations are relevant to interpreting its behavior. But it would help if we knew for sure whether it was male or female!

For more information on other Chinese Late Pleistocene sites, I can recommend Dennis Etler's excellent table of Chinese fossil hominids.

References:

Shang H, Tong H, Zhang S, Chen F, Trinkaus E. 2007. An early modern human from Tianyuan Cave, Zhoukoudian, China. Proc Nat Acad Sci USA (online early) doi:10.1073/pnas.0702169104

Thank goodness for blogs. Thanks to GNXP and Dienekes, I've been looking at the new paper by Paul Mellars. Here's the title:

Why did modern human populations disperse from Africa ca. 60,000 years ago? A new model

The thing is, this is nearly indistinguishable from Richard Klein's model. There are only two possible distinctions between Mellars and Klein. The first is with regard to the Skhul and Qafzeh hominids: Klein interprets these as "near-modern" samples lacking significant evidence of modern behavior; Mellars accepts evidence for symbolic behavior at Qafzeh including possible grave goods, perforated shells, and pigment use.

The second is that Mellars interprets Klein as supporting a "sudden change in the cognitive capacities of the population involved, entailing some form of neurological mutation" (Mellars 2006:9384) at 40,000 to 50,000 years ago. In contrast, Mellars supports either a sudden change or a gradual change in cognitive capacities, entailing either neurological mutations or environmental changes, at 80,000 years ago.

So I guess the only difference is the timing, since I read Klein as essentially agnostic about the mechanism of cognitive evolution (he mentions mutation as a possible mechanism, but clearly has no specifics on this point).

And if Mellars is willing to accept that the Qafzeh burials are evidence of symbolic behavior, it is hard for me to see how his position can be differentiated from d'Errico, who after all has only pointed out that similar evidence for Neandertal symbolic behavior must be interpreted in similar cognitive terms. Now that seems to me like an impossible coincidence...

The AP reports that high school science labs are poor. The story comes out of a study by the National Research Council.

"For literally 150 years, laboratories have been the sacred cows of science education," said Susan Singer, chairwoman of the committee that wrote the report and professor of biology at Carleton College. "Nobody has stopped to question what the value added is, or how we should go about using labs to improve learning. We haven't asked the right questions."

Of course, there aren't very many (if any) biological anthropology labs in high schools, so this doesn't address us directly. But anthropology is a very popular lab science on many college campuses, including UW. My read is that it's popular because it has a "cool" factor, and it's popular because it isn't as reductionist as many other biological courses. But I've seen my share of uninspiring bio anthropology labs, so I for one take the message about high school labs sciences as both a warning and an opportunity.

The way I see it, the problem with most lab sciences is that they always are set up with a predetermined result. You're "supposed" to see a certain outcome, be it an exothermic reaction, acceleration, similarities between Qafzeh and modern Europeans, or whatever. It's just a way to "get your hands on the materials."

How many problems are there with this? Of course, to start with, half the students would probably rather not have their hands on the materials. You can't believe the number of undergraduates I have who won't put their hands on a skull. Now I'm sure a few are real consciencious objectors, with some kind of ethical problem touching human bone. I've never had a student tell me that, but I can imagine it. But for the most part, they just don't want to --- either because of the "ick" factor, or because they are superstitious, or because they're afraid somehow they'll look like idiots.

I would guess a lot of the fear of embarrassment comes from past lab experiences --- sometime, somewhere in high school, some lab instructor or lab partner either made them look bad, or just allowed them to be passive observers while someone else did all the work.

Some of the superstition is native. Some of it is probably inspired by my first day warning that if they drop or break a skull, the tortured soul will return to haunt their nightmares (OK, that's a little severe, but I haven't had a dropped skull yet on my watch).

But my worst problem is that most students just don't know how to look at things and think critically, without being told what to think. They are used to having the answers fed to them in advance. Dealing with a lab where the instructor won't tell them the outcome really seems to phase a lot of them.

It usually takes me a couple of sessions to get them comfortable with the idea that I'm not going to tell them the answers. And I'm not going to grade them based on a predetermined result. I want them to observe what is there, systematize it, and use it to make comparisons. When I split them into different stations, I observe an interesting thing: different people observe different things! We talk about the different observations, and how they arrived at them. Students put themselves in the head of their colleagues by seeing them describe the fossils with their own observations. And at that point is the time to introduce terminology, and history, and alternative views.

I'm always looking for ways to make my labs better --- more interesting, more useful, and most importantly, better at getting measurable results. Any suggestions? Let me know, and I'll post some!

Two papers in the in the current (May 13, 2005) Science and an accompanying commentary focus on the mtDNA evidence relating to human dispersals into South and Southeast Asia. One paper, by Vincent Macaulay (University of Glasgow) and colleagues provides mtDNA sequences from aboriginal populations of the Malay peninsula.

Here's the abstract:

A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia 65,000 years ago was rapid, most likely taking only a few thousand years (Macaulay et al. 2005:1034).

The second paper, by Kumarasamy Thangaraj and colleagues, covers the mtDNA variation of Andaman Islanders. The abstract is less informative; here's the conclusion:

Our data indicate that two ancient maternal lineages, M31 and M32 in the Onge and the Great Andamanese, have evolved in the Andaman Islands independently from other South and Southeast Asian populations. These lineages have likely been isolated since the initial penetration of the northern coastal areas of the Indian Ocean by anatomically modern humans, in their out-of-Africa migration 50 to 70 thousand years ago. In contrast, the Nicobarese show a close genetic relation with populations in Southeast Asia, suggesting their recent arrival from the east during the past 18 thousand years (Thangaraj et al. 2005:996).

Nicholas Wade has an article about the paper in the New York Times. Here's a great exchange:

There is no evidence of modern humans outside Africa earlier than 50,000 years ago, said Dr. Richard Klein, an archaeologist at Stanford. Also, if something happened 65,000 years ago to allow people to leave Africa, as Dr. Macaulay's team suggests, there should surely be some record of that in the archaeological record in Africa, Dr. Klein said. Yet signs of modern human behavior do not appear in Africa until 50,000 years ago, the transition between the Middle and Later Stone Ages, he said.

"If they want to push such an idea, find me a 65,000-year-old site with evidence of human occupation outside of Africa," Dr. Klein said.

Of course, there is no chance whatsoever that a 65,000 year genetic date is significantly different from 50,000 years. Both the current papers follow a long and dishonorable tradition of not providing any confidence interval for their date estimates. Both papers do provide standard errors -- without explanation, they report different standard errors for the same clades -- but standard errors do not say anything about the real uncertainty in the age estimates. It is not all that easy to figure out what the full range of uncertainty in the estimates may be, since it owes not only to the distribution of uncertainty in coalescence times (which is assymmetrical and skewed toward the high end) but also in uncertainty coming from assumptions like the human-chimpanzee divergence time and adequacy of the sampling scheme. Based on the standard errors alone (ranging around 7,000 years for the clade ages related to the "dispersal"), the 63,000 year date is not significantly different from 50,000 years. The true range of uncertainty is probably far greater.

Now, why wouldn't a reader of the papers know anything about this range of uncertainty? Not only do the papers not report confidence intervals in the text, but also the entire presentation of the data is relegated to the supplementary information online, which for both papers is substantally longer than the text. These are not just data tables, but relatively full literature reviews (as full as they get for these papers) and methods sections. This is a disturbing new trend for Science: reporting only results in the journal, and putting the information necessary to evaluate the results into a secondary source. What if you are asked by a reporter to comment on an article, and they send you an embargoed draft? You don't know enough about the paper even from the full text to evaluate it.

I've been thinking today about "media packaging" of research results, and this strikes me as a pretty stark example. Two papers on a single theme, packaged together with a commentary. Both of the papers make relatively cautious (although not cautious enough in my estimation) interpretations; the commentary is more daring. Media reports focus on the issue raised in the commentary, quoting other scientists who haven't seen enough of the research to be informedly critical. Good science reporters know enough to be skeptical; look where the preceding exchange goes:

Geneticists counter that many of the coastline sites occupied by the first emigrants would now lie under water, because the sea level has risen more than 200 feet since the last Ice Age. Dr. Klein expressed reservations about that argument, noting that people would not wait for the slowly rising sea levels to overwhelm them but would build new sites farther inland.

Dr. Macaulay said genetic dates had improved in recent years, now that it is affordable to decode the whole ring of mitochondrial DNA, and not just a small segment.

But he said he agreed "that archaeological dates are much firmer than the genetic ones" and that it was possible his 65,000-year date for the African exodus was too old.

So in other words, there's no result here. But this only applies to the young end of the range of dates for possible "Out of Africa" migrations -- the end that Richard Klein has been so active in examining. There is no word at all about the older end of the time range in any of the articles, commentaries, or press reports. But just as there is no chance these dates aren't significantly different from 50,000 years, there is likewise no chance they are significantly different from 80,000 years, or probably even 100,000 years. Let's cover the scenario for the initial Out-of-Africa colonization:

The very similar ages of haplogroups M, N, and R indicate that they were part of the same colonization process [see (23)]. This most likely involved the exodus of a founding group of several hundred individuals (27) from East Africa, some time after the appearance of haplogroup L3 85,000 years ago, followed by a period of mutation and drift during which haplogroups M, N, and R evolved and the ancestral L3 was lost. Although the details of this period remain to be elucidated, the next stage is much clearer. The presence in each region of the same three founder haplogroups, but differentiated into distinct subhaplogroups, indicates that there was a rapid coastal dispersal from 65,000 years ago around the Indian Ocean littoral and on to Australasia (Macaulay et al. 2005:1036).

Thus, the initial timing of this putative migration is bounded on the lower end by the 65,000 year dates, and on the upper end by the 85,000 year estimate for haplogroup L3. The standard error on this estimate as reported in the supplementary information is 8,400 years, which means that this date could easily be 20,000 or more years higher than it is. So an ancestry by Skhul and Qafzeh is not excluded by these analyses, either. But the paper does not even raise this issue. More strikingly, the commentary puts the two facts in adjacent sentences without adding them together:

Early humans even ventured out of Africa briefly, as indicated by the 90,000-year-old Skhul and Qafzeh fossils [HN9] found in Israel. The next event clearly visible in the mitochondrial evolutionary tree is an expansion signature of so-called L2 and L3 mtDNA types in Africa about 85,000 years ago, which now represent more than two-thirds of female lineages throughout most of Africa. The reason for this remarkable expansion is unclear, but it led directly to the only successful migration out of Africa, and is genetically dated by mtDNA to have occurred some time between 55,000 and 85,000 years ago (Forster and Matsumura 2005:965).

Ignoring this one, the paper leaves us with these options:

Three possible hypotheses can be distinguished using these data. If modern non-Africans are descendants of populations that dispersed along both northern and southern routes, then mtDNA lineages belonging to relict populations (including Orang Asli, Papuans, and Aboriginal Australians) should diverge from founder types that are distinct from those leading to the main continental Eurasian groups. If there were just a single dispersal, then all non-African populations should diverge from the same set of founders, which would coalesce to 45,000 to 50,000 years ago if the Levantine corridor model were correct, or 60,000 to 75,000 years ago if they were all the result of the proposed earlier single southern route (4). At this time, a northern passage was most likely blocked by desert and semi-desert (26) (Macaulay et al. 2005:1035, citations therein).

Okay, hmm...let me get this straight: modern humans had uber-technology to float across the Red Sea, kill mammoths, and outcompete every archaic human in every ecology they had occupied for a half million years or more, but they couldn't manage to move in 10,000 years across a semi-desert? And let's not forget the "modern" humans that get thrown under the bus in this scenario -- Skhul, Qafzeh, Liujiang -- either they don't qualify as "really" modern, or they've been misdated. Oh, and, there is the slight problem that no other locus provides any evidence of this pattern of population movement -- even the Y chromosome -- and many are not consistent with it.

There is a strategy to deal with these evidentiary problems:

Firm archaeological age estimates are more recent [more ancient dates are simply disregarded in this paper] -- 50,000 years for Australia and ~45,000 years for southeast Asia -- but early evidence may have been lost to sea level rises. Moreover, human populations may then have diffused from the coast into the continental interiors more gradually, leaving a greater archaeological signature on the landscape as they grew in size (Macaulay et al. 2005:1036).

This is always possible, but it can't be a good sign when your hypothesis depends on the same logic as the aquatic ape theory.

A short word about the bottleneck

From the commentary:

One intriguing question is the number of women who originally emigrated out of Africa. Only one is required, theoretically. Such a single female founder would have had to carry the African L3 mtDNA type, and her descendants would have carried those mtDNA types (M, N, and R) that populate Eurasia today. Macaulay et al. use population modeling to obtain a rough upper estimate of the number of women who left Africa 60,000 years ago. From their model, they calculate this number to be about 600. Using published conversion factors, we can translate this estimate into a number between 500 and 2000 actual women. The authors' preferred estimate is several hundred female founders. All such estimations are influenced by the choice of parameters and by statistical uncertainty; hence, it is understood that the true number could have been considerably larger or smaller. Improved estimates will involve computer simulations based on informed scenarios using additional genetic loci (Forster and Matsumura 2005:966).

Gee, are there any other genetic loci that have been examined with this issue in mind? Do any of them agree with a bottleneck reducing human population size to "between 500 and 2000 actual women"? Considering that the answers to these questions are, "yes, many have been examined" and "no, most of them don't agree with that number," what does the full pattern of genetic data say about mtDNA variation?

Earth to Science: what about selection?

Along with the failure to provide confidence limits on estimates, both papers and commentary join another long and dishonorable tradition of completely neglecting the possibility that mtDNA has been affected by natural selection.

There are several ways that selection could affect the interpretations of these papers. My own inclination is to think that an episode of positive selection on human mtDNA explains the its recent coalescence date and the appearance of a rapid dispersal out of Africa. This would be the pattern expected if an advantageous allele appeared within the African population and spread from there through a global human population. The strength of this explanation is that it accounts for why mtDNA looks so different from most autosomal genes in its pattern of variation (c.f. Templeton 2002; Wall and Przeworski 2000).

Now, you don't have to buy into this hypothesis of positive selection to understand that some kind of selection may have severely weakened the ability of human mtDNA to accurately portray ancient population movements. Purifying selection alone would affect these estimates, particularly since they are based on coding region sequences. At the least, small isolated populations may be observed to have a higher effective rate of mutations because of an increased effect of genetic drift against weak purifying selection. At the worst, different environments affecting human groups in the past may have had differential selective effects, with unpredictable effects on the mtDNA phylogeny.

Is this a serious problem? On the one hand, even the maximum degree of purifying selection affecting nonsynonymous substitutions probably affects the apparent diversity of the coding region of the global mtDNA by a factor of two or less. So on the surface, although this might be a fairly big problem, it is somewhat limited in its possible impact. On the other hand, this kind of selection almost certainly occurred. Selected sites in the coding region of the mtDNA are increasingly recognized and known to be common within many human populations. Within just the last week, there has been a new announcement of a common mtDNA variant (haplogroup U) related to cancer risk, and one survey associating mtDNA genotypes with performance in elite athletes (Niemi and Majamaa 2005). Mitochondrial dysfunctions (not all caused by mtDNA genes) are known to increase the risk of Alzheimer's, Parkinson's, ALS, and other neurodegenerative disorders (Zhu 2004). Purifying selection has been an important force on the global distribution of mtDNA (Wise et al. 1998). The presence of mutational variants with such a high selective cost may suggest countervening selective advantages to thse mutations that have not yet been discovered -- in other words, suggesting that not only purifying but also balancing selection may be affecting the frequencies of these mtDNA alleles. So the problem is likely serious, and its full extent is not yet known.

A basic cautionary attitude would indicate that it is no longer tenable to assert that the history of the mtDNA of a population is the same as the history of the population. There are just too many unaccounted variables to believe that methods that assume complete neutrality for mtDNA are giving accurate dates for population movements, expansions, or other events. My favorite quote on the issue is from Razib at Gene Expression:

I am not totally discounting all elements of the narrative pressed forward above, but, genes serve as flexible instructions to shape and mold a human's phenotype, the lineages are all their own, and the concordance of the gene lineages with "individual" lineages, let alone populations, is I think an often tenditiously assumed axiom in many of these research papers. The authors above make the identity of genes:individuals, groups of genes:groups of people. Working back over 2,000 generations with such assumptions is I think a somewhat sketchy proposition unless your variables are controlled for (eg; at least the Andamans are islands, which are noted for fostering relatively genetically isolated people. For example, Sardinia is situated in the rather populous Mediterranean, but it often is an outlier in Principal Component Analysis diagrams of European genetics). Or, if your facts are so crystal clear, the narrative so compelling, the predictions so spot on, than the model is simply self-evidently true. But at this point I think that Recent-Out-of-Africa has depleted all the parsimony capital it had saved up, at least from where I stand.

Selection on mtDNA is not a moribund backwater of research; it is being pursued by groups studying some of the highest-profile diseases. We don't know yet how selection may have affected the full pattern of human variability, but we know enough to know that the answer isn't zero. So why have human geneticists studying global mtDNA variability completely ignored the issue? And what will it take for them to hear the message over the buzz of their own voices?

References:

Forster P and Matsumura S. 2005. Did early humans go north or south? Science 308:965-966. Science Online

Macaulay V, et al. 2005. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034-1036. Science Online

Niemi A-K and Majamaa K. 2005. Mitochondrial DNA and ACTN3 genotypes in Finnish elite endurance and sprint athletes. Eur J Hum Genet advance online publication. Nature Online

Templeton AR. 2002. Out of Africa again and again. Nature 416:45-51.

Thangaraj K, et al. 2005. Reconstructing the origin of Andaman Islanders. Science 308:996. Science Online

Wall JD and Przeworski M. 2000. When did the human population size start increasing? Genetics 155:1865-1874.

Wise CA, Sraml M, and Easteal S. 1998. Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees. Genetics 148:409-421.

Zhu X, Smith MA, Perry G, and Aliev G. 2004. Mitochondrial failures in AlzheimerÕs disease. Am J Alzheimer's Dis Other Dement 19:345-352.