Wednesday, December 29, 2010

Iron Chef: Middle Paleolithic

New evidence suggests Neandertals ate cooked foods, and plants at that.

Amanda Henry and colleagues (in press) extracted phytoliths - small mineralized parts from plants - and starch grains from dental calculus found on 2 Belgian (Spy) and 1 Iraqi (Shanidar) Neandertal fossils. I've never seen a study look at this kind of evidence before, I have to say it's pretty neat. Calculus, not just a badass type of mathematics, is mineralized plaque that can build up on teeth. As the Neandertals chewed their foods, the small food particles got trapped in their plaque and this gross matrix hardened onto their teeth. So, if you want to obliterate traces of your diet, and otherwise conform to Western norms of dental hygiene, one thing you can do is be sure always to brush. And floss.
Microscopic barley grains. Top row are examples of grains from Shanidar calculus, and beneath each are examples of modern barley to which they are probably related. Fig. 1 from Henry et al. (in press)
Types of plants eaten by the Shanidar individual include relatives of modern wheat, barley (see figure), and rye, and what looked like beans and date palm, too. In addition, some of the starch grains bear strong resemblance to plant remains after cooking, probably either by boiling or baking. The Belgian samples provided less broad evidence, indicating presence mainly of some type of underground storage organ (like a tuber) and grass seeds. Many phytoliths and grains were unable to be identified, leaving open the chance that future research on these will uncover utilization of a greater breadth of plants.

This is pretty neat, since studies of the isotopes in Neandertal teeth indicated a strong meat component to the diet. In fact, Neandertals have often been referred to as 'top carnivores.' This new study supports other evidence of a large plant component as well. After all, isotope studies are only one form of evidence of diet. Neandertals weren't just big game hunters, they were hunter-gatherers. What's more, they improved the edibility and nutritive value of their plant (and probably also animal) foods by cooking them. So, this study presents another way in which Neandertals were probably no different from contemporaneous humans.

One has to wonder what these paleolithic meals would have been like. Especially what with claims of cannibalism in some Neandertal sites - perhaps "liver with some fava beans and a nice chiaaanti...fhfhfhfhfhfhfh," to quote Hannibal Lecter. And who would win Iron Chef - the classic Neandertals, or their more 'modern' looking contemporaries?

Henry, A., Brooks, A., & Piperno, D. (2010). Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium) Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1016868108

Thursday, December 23, 2010

Denisova the Menace II: Nuclear story

Earlier this year, I discussed the publication of a mitochondrial DNA study from a 50,000 year old pinky bone from Denisova in Siberia. The big story there was that the mtDNA of this specimen was twice as divergent (different) from modern humans as Neandertal mtDNA. This suggested to researchers that there was this rogue human group (some [not I] might say 'species') running around Eurasia around the time of the Upper Paleolithic.

Well now they've sequenced the nuclear genome of one of a Denisova denizen. The picture painted is that a Denisova-Neandertal 'lineage' split off from that of modern humans some time in the distant past, then the Denisovans split from Neandertals some time later. Most interesting, modern-day Melanesians seem to derive about 4% of their genes from this 'archaic' Denisovan lineage, whereas this archaic genetic baggage isn't present in other modern human populations.

AMAZING! Think back to the draft of the Neandertal nuclear genome, also published earlier this year. Green and colleagues (2010) reported that the Neandertal nuclear genome revealed that Neandertals contributed up to 4% of the genomes of modern-day non-Africans. Now, the Denisova genome shows that a different and more specific group of modern humans (Melanesians) appears to uniquely share a different set of nuclear genes from an 'extinct' human group.

But if they contributed their genes to modern people, are they really extinct? Of course not! I'm admittedly not a geneticist, but I think what we're seeing here are the genetic signatures of a single, ancient structured population of modern humans. That is to say, all modern humans derive different amounts of their genes from various ancient subpopulations of 'archaic' humans (for 'archaic,' think 'people that lived a long time ago'). There was just little enough contact between these populations for them to have diverged slightly from one another, but still enough contact for them all to have contributed different parts and amounts of genes to people today.

It is weird, then, to see the ancient DNA geneticist Svante Pääbo (out of whose lab this ancient genetic work is done) say this to BBC News:
"It is fascinating to see direct evidence that these archaic species did exist (alongside us) and it's only for the last few tens of thousands of years that is unique in our history that we are alone on this planet and we have no close relatives with us anymore."
Why are these 'archaic species...alongside us"? The fact that these groups were mixing means that they are a single species - the ability (and propensity) to interbreed is the standard definition of 'species' used in modern biology.

So contrary to Pääbo's quote, I'd say we do have close relatives with us, it's just that modern humans are much more closely to one another related than ancient human populations were to one another. Probably there is more contact between modern human populations, beginning a few tens of thousands of years ago, because population sizes explode to the some 7 billion people we have on earth today. This greater contact means less chance for populations to diverge from one another.

The take-home: We all have multiple ancestors, from various times and places. For more comprehensive and better-informed coverage, check out John Hawks's post on the topic.
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M., Hansen, N., Durand, E., Malaspinas, A., Jensen, J., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H., Good, J., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V., Golovanova, L., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E., Falush, D., Birney, E., Mullikin, J., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Paabo, S. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, & Pääbo S (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161

Monday, December 20, 2010

Iliac spines and cannibal hominids: together at last?

For various reasons I'm reviewing last year's publications on Ardipithecus ramidus, namely the pelvis paper (Lovejoy et al. 2009). I also found a recent review of the hominid spine & pelvis by Lovejoy and McCollum (2010). Both papers discuss the anterior inferior iliac spine (AIIS) - a bump on your pelvis just above your acetabulum (hip socket), to which attaches rectus femoris, a muscle that both flexes the hip and extends the knee. In apes and monkeys (quadrupeds), this 'spine' is generally negligible or absent, whereas in humans and other (extinct) hominids it is quite protuberant. This is because our upright posture necessitates this muscle insertion to be large and protuberant in order to be effective.
Pelvic comparison, yellow arrow points to AIIS. Lovejoy et al. 2009: 71.
Let's see if this discrepancy between these two papers won't drive you nuts:

The form and size of the AIIS in [Ardipithecus ramidus], as well as its projection anterior to the acetabular margin, indicate that this structure had already begun to appear and mature via a novel physis (from Lovejoy et al. 2009: 71e3, emphasis mine)

What distinguishes the AIIS in hominids from those in apes is not its protuberance (those of Gorilla are often very prominent), but rather its emergence from a novel, separate physis, a hominid adaptation that is almost certainly associated with dramatic expansion of iliac isthmus breadth (Lovejoy et al. 2009b) (from Lovejoy & McCollum 2010: 3295, emphasis original)

Now, the second quote tells us we can't use the size and protuberance of the AIIS to completely infer its function (biped-like or ape-like), but rather that its origin of growth tells us whether it is hominid. But the first quote tells us that the size and projection of Ardi's pelvis tells us it did come from a unique growth center. So... I'm confused. Do the prominent Gorilla AIISes arise from a unique growth center as well? (another thing that drives you nuts is that the reference in the second quote, to "Lovejoy et al. 2009b," is to the Ardipithecus hand paper, probably an accident, but not helpful nonetheless)

Scheuer and Black (2000: 357-361) state that "accessory [growth] centers" including the AIIS tend to be variable. That is, the AIIS may have its own center, but often the epiphysis of the upper acetabulum 'reaches' up to form the AIIS. The subadult skeleton in our lab here has billowy-looking bone int he region of the AIIS, but this seems to connect with the rest of the unfused acetabulum. So far, then, the jury's (my jury, at least) out on whether the AIIS is its own growth center in hominids; the uniqueness of it we'll have to wait and see (such as those gorillas described above, or possibly Oreopithecus...).

Lovejoy et al. 2009 (the pelvis paper, not the hand) also reference this novel growth center, citing the great Raymond Dart's description (1953) of the MLD 25 ilium, attributed to Australopithecus africanus from Makapansgat in South Africa. Now, I knew Dart was a clever man, indeed it was he who coined terms like Australopithecus and 'osteodontokeratic.' Very smart guy, Dart, but I'd also read something lo these past several years of graduate school, in which he was described as 'bloodthirsty.' An odd descriptor, I'd thought. But, reviewing Dart's 1953 paper, I came across the following passage, wherein he discusses how unlikely it is that this australopithecine ilium should be so closely associated with another at the site (MLD 7):
Further it is an extraordinary occurrence that two adolescent ilia of apparently opposite sex but virtually identical age should be found in close company in this deposit. The boy [MLD 7] was killed by a bone-smashing blow on the chin from a club or fist. Were they brother and sister [MLD 25] twins, that shared in death the same cannibalistic fate? (Dart 1953: 75)
Possibly. I'll let you know what I uncover about the ontogeny of the AIIS in other animals. NB: this post isn't meant to disparage any of the references. In fact I rather respect these authors, and their work (McCollum's especially) has been quite influential to me.

Dart RA. 1953. The second adolescent (female) ilium of Australopithecus prometheus. Journal of the Palaeontological Society of India 2: 73-83.

Lovejoy CO, Suwa G, Spurlock L, Asfaw B, White TD. 2009. The pelvis and femur of Ardipithecus ramidus: The emergence of upright walking. Science 326: 71.

Lovejoy CO and McCollum MA. 2010. Spinopelvic pathways to bipedality: Why no hominids ever relied on a bent-hip - bent-knee gait. Philosophical Transactions of the Royal Society B: 365: 3289-3299.

Scheuer L and Black S. 2000. Developmental Juvenile Osteology. New York: Elsevier Academic Press.