john hawks weblog

paleoanthropology, genetics and evolution

Shanidar

  • Tartar control and Neandertal plant use

    Tue, 2011-01-04 23:44 -- John Hawks

    Dental plaque is a biofilm made up of bacteria adhering to the enamel surface of the teeth. Plaque is soft but over many days can gradually calcify. The hardened plaque, called calculus (or dental tartar) can build up in layers. This forms an ideal surface for further plaque formation and can damage the connective tissue between the teeth and gums -- so dentists and dental hygienists work hard to remove tartar.

    Despite these risks to dental health, calculus formation is a natural process in populations of humans and animals. Teeth from archaeological sites often have calculus adhering to them. This calculus contains partially mineralized bacteria, organic material, epithelial cells and fragments of foods ingested by the individual during her life.

    Recently, archaeologists and paleontologists have begun to examine calculus samples microscopically to identify the traces of ancient foods. Phytoliths are microscopic structures made of silica or calcium oxalate, many of which are distinctive to species or genera of plants. These durable inorganic structures can persist for hundreds of thousands of years. Many kinds of plants store their starches in granules that can also persist over long periods of time. These granules differ in form among families of plants. Starch granules also display characteristic changes when they are heated or cooked in liquid. Hence they can provide evidence of cooking practices by ancient people.

    Amanda Henry and colleagues [1] scraped a bit of calculus off the teeth of Shanidar 3, from the north of Iraq sometime around 50,000 years ago. This skeleton is housed at the Smithsonian National Museum of Natural History, and figured in the 2009 story about a projectile wound between its ribs ("Real stories of the Neandertal CSI"). The Shanidar skeletal remains are generally called Neandertals on the basis of their morphology. This case is better for Shanidar than for near-contemporaries in the Levant such as Amud or Kebara, and may reflect connections with populations to the north in the Caucasus. No genetic sampling has been done on the Shanidar sample.

    Neandertals are known for a diet stereotype -- they ate a very high proportion of meat. This stereotype is rooted in fact: the majority of Neandertal sites show a clear reliance on large mammal acquisition. Bison, horse, red deer and other large mammals are represented, often with a statistical preference toward one of these species at a given site. The faunal remains from many Neandertal sites are consistent with an ambush hunting strategy, with a higher proportion of prime age adult animals than found among persistence hunters or scavengers. The stable isotope record in Neandertal teeth so far seems consistent with an estimated 90% or more meat consumption, leaving relatively little dietary intake from plant foods.

    This is an odd picture for a hunter-gatherer: all hunting and little gathering. Most living hunter-gatherers rely on plant foods to buffer the risks of hunting. Many eat far more calories from plants than from meat. Plant processing in the archaeological record is well-known from among the earliest archaeological traces ("Plant processing with early Oldowan tools") and continued throughout the Paleolithic. The question at hand is specific to Neandertals -- how dependent were they on plant foods, and how much would they have been specifically adapted to meat acquisition and consumption? Some high-latitude hunting groups, such as the Inuit, do maintain very high meat consumption, and the Neandertals may have relied on this strategy in Europe.

    In contrast to Europe, a pattern of plant exploitation has long been known in the Middle Paleolithic of the Levant, at sites like Amud and Kebara that many argue were occupied by Neandertals. For example, Marco Madella and colleagues [2] describe phytoliths from the soils of Amud Cave. They demonstrated that these people were probably gathering seeds from grasses, systematically enough to concentrate the phytoliths from mature grass panicles in the sediments. Efraim Lev and colleagues [3] described charred plant remains including legumes and pistachio nuts from the Mousterian levels of Kebara Cave. Middle Paleolithic people in the Levant were using plants in quantities as great as can be shown at any contemporary sites anywhere in the world.

    Henry and colleagues help to put the seeds in the mouths of the Shanidar Neandertals. The Shanidar 3 calculus samples yielded substantial evidence of barley consumption. Many of the starch granules were clearly cooked:

    The overall pattern of damage to the starch grains matches most closely with that caused by heating in the presence of water, such as during baking or boiling, rather than “dryer” forms of cooking like parching or popping (38). The finding of cooked Triticeae starches on the Shanidar teeth reinforces evidence from other studies (13) that suggest that Near Eastern Neanderthals cooked plant foods.

    They report that 42% of the starch granules on these teeth are consistent with damage from cooking, suggesting that cooking was a systematic strategy for plant exploitation in these people. They also find other plants besides grains -- including legume seeds and tubers of some kind, and phytoliths from date palms.

    In addition to the Shanidar 3 skeleton, Henry and colleagues examined calculus samples from the two skeletons from Spy, Belgium. This gave them the opportunity to examine plant consumption in a European context. These teeth included starch molecules in relatively large numbers, mostly derived from some kind of plant underground storage organs (USOs) which the authors tentatively identify as a water lily. At least one starch granule of a sorghum or related grass seed is also present, along with a few other unidentifiable starches and no phytoliths.

    The authors cannot conclude much about the importance of these plant foods to the overall diet. The remains of starch grains and phytoliths tell us about diet breadth but not the proportions of different foods. They do note that nitrogen stable isotopes are most informative about protein-rich food sources, so that a substantial consumption of starchy plants such as grains and USOs might be hidden by isotope analysis. Their main conclusion is about dietary flexibility and the sophistication of Neandertal foraging strategies:

    These lines of evidence [cooking and processing of grains] indicate Neanderthals were investing their time and labor in preparing plant foods in ways that increased their edibility and nutritional quality (24, 45). It should also be noted that date palms and possibly other un- identi␣ed plants have different harvest seasons than barley and legumes, a factor that may suggest that the Shanidar Neanderthals practiced seasonal rounds of collecting and scheduled returns to harvest areas. Overall, these data suggest that Nean- derthals were capable of complex food-gathering behaviors that included both hunting of large game animals and the harvesting and processing of plant foods.

    I expect that quite a bit more evidence from dental calculus will be forthcoming. The study of microfossils from a broader range of sites will help to give a picture of the local resource exploitation. It may not be possible to get an estimate of dietary proportions from these kinds of evidence, but I imagine that similar comparisons of calculus samples from other animals will provide some useful context for the human numbers. In addition, calculus has become a promising source of DNA recovery, from the epithelial cells trapped in its calcified matrix. This has a good chance of recovering ancient DNA from specimens that have not previously yielded any successful extraction.


    References

  • Neandertal CSI revisited

    Thu, 2010-01-07 07:30 -- John Hawks

    Discover has put an article online that they ran in the November issue, which features Steven Churchill's research ("Did we mate with Neanderthals, or did we murder them"). It's a good "present status" article about possible human-Neandertal interactions, pretty much as summarized in the headline. It would be a good link for intro classes.

    For more information about almost every one of the topics in the article, you could do worse than searching my archives:

    The Shanidar impact wounds: "Real stories of the Neandertal CSI"

    Les Rois: "Another Aurignacian Neandertal, or just dinner?", and "Les Rois revisited, and dental classification of other Aurignacian individuals"

    Mary Stiner and Steven Kuhn's social structure hypothesis: "Barbaric yawping about Neandertal women"

  • Real stories of the Neandertal CSI

    Thu, 2009-07-23 22:56 -- John Hawks

    GRRRRRR! Why do I have to keep reading about how spearchucky modern humans went around killing Neandertals?

    It's all over the science news this week -- Shanidar 3, a 50,000-year-old Neandertal from Iraq, has a partially-healed deep cut to one of its ribs. The kind of cut that gets there when you're stabbed with a knife or spear, or shot with an arrow.

    That's pretty interesting in itself, although not news -- the wound has been known and listed as an example of ancient interpersonal violence since the 1960's. It may be the oldest clear example of a wound to a living person from a stone implement, because all earlier cutmarked human remains (there are many) may be post-mortem. Still, not news.

    The "news" part is that Churchill and colleagues (2009) have shown that the wound is most consistent with a small projectile, as opposed to a large thrusting spear. In their discussion, they suggest that modern humans may be the culprits:

    The nature of the lesion to the left 9th rib of the Shanidar 3 Neandertal is most consistent with injury from a low kinetic energy, low momentum weapon. While this does not rule out accidental injury or attack by a conspecific wielding a hand-held weapon, the nature of the traumatic damage, combined with the wound track suggested by the placement and orientation of the rib lesion, is consistent with injury by a long-range projectile weapon traveling along a ballistic trajectory. Given the possible sympatry of this Neandertal with early modern humans, and given possible assymetries in weapon technology between the two species, the case of Shanidar 3 is a good candidate for an instance of Neandertal-modern human interspecific violence (14, emphasis in original).

    So what do I think? I guess anything is possible. But any good murder case hinges on motive and opportunity. Churchill and colleagues don't really give us a way to place modern humans at the scene at the crime.

    The authors point to the only radiocarbon dates available for Shanidar 3, which at 46,000 and 50,000 radiocarbon years are in a range that we probably should not trust for old, non-AMS dates (as they point out). There's no indication of a non-Mousterian industry in the immediate region before 35,000 radiocarbon years, although an earlier presence of non-Neandertals is possible.

    As it stands, what are the odds that the Neandertal Shanidar 3 individual (setting aside the question of whether it or other West Asian specimens really are the same as European Neandertals) would ever have encountered a "modern" human (setting aside the question of whether the two populations were distinct)?

    Well, we don't really know. Probably pretty low. Maybe impossible. But that probability is very important to this "forensic" question.

    Do we know that Shanidar 3 wasn't hit by a Neandertal weapon? The study shows very well that seven blows from a Mousterian point-hafted spear are not enough to guarantee a wound like the one on the ribs of Shanidar 3. That wound has a clear cut to one rib but little involvement of the adjacent rib. The seven experimental blows from a "high-energy" weapon resulted in five wounds with significant slices in two adjacent ribs, and two that affected no ribs at all. In contrast, the "low-energy" trials generated a high fraction of wounds that involved slices to only one rib. Meanwhile, two of those "low-energy" trials were from a Neandertal-associated tool, stabs with a Levallois point.

    But what does this tell us, really? If we just treat the probability of a Shanidar 3-type injury as a binomial with 7 trials in this study, we can't reject the hypothesis that it occurs at a true likelihood of 35 percent. I think the authors have done a cool study, and did a great job evaluating the wounds. The problem is that 7 trials just isn't enough to yield a high confidence. We don't really know that a weapon known to be associated with Neandertals couldn't have made the wound.

    So it comes down to opportunity. Can we place modern humans at the scene of the crime?

    We may not be able to estimate this probability, but we can use Bayes' theorem to evaluate what the likelihood would have to be to satisfy our jury. Let's say our jury is stacked with Neandertals, and is willing to convict a modern human if there is just a five percent chance he committed the crime.

    1. We don't know the probability that Shanidar 3 encountered modern humans. We'll assume that Shanidar 3 would have been attacked with equal probability by whomever he encountered. Hence, the encounter rate with modern humans, the chief unknown, directly determines the chance of being wounded by a modern human.

    2. We do know something about the probability that a random injury from a high-energy Neandertal-made weapon would have the characteristics of the Shanidar 3 wound -- it's something less than 35 percent.

    3. We'll assume the probability of Levallois point stabs is zero, thereby stacking the deck in favor of a modern human killer.

    4. We know that a random wound from a modern human projectile weapon would generate a wound having those characteristics with something like a 50 percent probability.

    Plugging into Bayes' theorem, that means that an encounter rate of 1 modern human for every 28 Neandertals would yield a five percent chance that a modern human was the culprit. Did Shanidar 3 encounter one modern human for every 28 of his own? If not, we have to conclude its very unlikely -- less than five percent -- that his wounds were caused by a modern human.

    At the moment, the best evidence from the site suggests that Shanidar 3 lived fifteen thousand years before any archaeological transition to the "low-energy" impactors. Which tilts the scales in favor of the alternative -- a slightly lower probability impact from a much higher probability weapon.

    References:

    Churchill SE, Franciscus RG, McKean-Peraza HA, Daniel JA, Warren BR. 2009. Shanidar 3 Neandertal rib puncture wound and paleolithic weaponry. J Hum Evol (early online) doi:10.1016/j.jhevol.2009.05.010

  • Mmmm...that's good Neandertal protein in them bones

    Wed, 2005-03-09 11:11 -- John Hawks

    A press release from Washington University describes recent work in extracting and sequencing a bone protein from two of the Shanidar Neandertals. The work is a collaboration of Erik Trinkaus, Ivor Karavanic, and scientists at the Max Planck Institute for Evolutionary Anthropology.

    The paper has been published in the
    PNAS Early Access bin. Apparently they attempted to extract protein from Shanidar 2, 4, and 6, as well as Vindija Vi-76/228, but only succeeded in Shanidar 2 and 6. The protein was osteocalcin, which is the second-most abundant protein in bone. The Neandertal amino acid sequences were identical to the human sequences, which themselves do not differ from chimpanzees or orangutans. It is not reported whether there are allelic differences among humans or any of those other species. Gorillas have a sequence that differs from other hominoids at one position, similar to monkeys.

    This study is a first, because protein sequence recovery from fossils this ancient has never succeeded, although previous attempts were made to obtain bone collagen from fossil remains. Apparently the chemical characteristics of osteocalcin in particular aided in its preservation by resisting diagenetic breakdown.

    This study has sort of a "gee, who'd a thunk it" interest, but otherwise it seems to me like a waste of good samples. There is really no hypothesis that are likely to be tested by protein sequences taken from Neandertal fossils. Consider:

    1. The proteins preserved in bone are by and large structural proteins like collagen and this protein, osteocalcin. These structural proteins have essentially the same function in the bones of all hominoids, so there is little chance that there will be important adaptive changes among them.
    2. Human functional genes tend to have genealogies extending back a million years or more. This means that for most functional genes, Neandertals almost certainly would have had alleles within the modern human range of variability. This is more true for protein sequences than for nucleotide sequences, since the possibility of rare neutral variants is substantially lower for amino acid changes.
    3. Unlike genes, proteins appear only in the tissues where they are active. Functional protein differences between humans and Neandertals are very likely either to be developmental signalling proteins active early in ontogeny, or structural and regulatory proteins of the central nervous system. Neither of these classes of protein is likely to be preserved in Neandertal fossil bone.
    4. It is still not known how most differences in amino acid sequence between protein products arise. Considering that there are only 20,000 or so human genes and many more proteins, it follows that there must be several similar proteins created by each gene through posttranslation processing. So for proteins that are substantially rarer and less bound than structural proteins, there will likely be doubt about whether the same gene product is being compared when differences occur.

    When people have talked about fossil protein sequences before, they have usually had in mind the potential recovery of dinosaur proteins or other similarly ancient groups. In that case, the recovery of a structural protein might potentially be helpful for phylogeny, because the relationships with living taxa are so distant that many amino acid changes will have occurred. Likewise, there is some possibility (albeit slim) that a structural protein from a dinosaur might give some information about dinosaur metabolism, such as whether they grew quickly or were warm-blooded.

    For Neandertals or any other ancient human group, there is really no information like this to be had. And even in this case, the human and chimpanzee osteocalcin protein are the same, so there is every expectation that the Neandertal protein would also be the same. One may point to the osteocalcin difference between gorillas and the other hominoids as an exception, but it is far from clear that this is an adaptive difference or that it speaks to the presence of adaptive differences in structural proteins generally. The story presented in the paper is that the gorillas may have more dietary vitamin C, and so retain the amino acid sequence of most mammals, while the other hominoids needed the ability to synthesize the protein in the absence of vitamin C. As yet, it is unclear what has to be explained here, since the sequence in most mammals is obviously unavailable (this study presents only "monkey" and "cow". Even so, most mammals do not have a gorilla-like diet -- including the monkey in the study (Macaca fascicularis). And chimpanzees and gorillas in regions where they are sympatric eat mostly the same species, differing mainly in fallback foods.

    And if this is the kind of hypothesis that can be tested with this work, then clearly the answer is to find out how the protein functions in living mammals first. This means going beyond the comparisons of living hominoids, monkeys and cows, to sequence mammals that present phylogenetic contrasts in diet. We can almost certainly predict beforehand that no fossil specimen of Homo is going to be different from living humans or chimpanzees. If we can show phylogenetic contrasts between other mammals in this amino acid sequence based on diet, then there is some reason to think that some australopithecines might show a difference. In which case it would be worthwhile to grind some australopithecine bone samples to find the answer. But this shouldn't be done on a whim, but only after comparative studies in mammals show that there is some reasonable chance of an interesting result.

    This has turned into a bit of a rant, but please stop letting graduate students grind up our fossils! It is not worth losing rare organic samples just to explore every empirical unknown. Every empirical unknown is not a theoretical unknown, and this case in particular is one where the result could have been predicted in advance.

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.