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?

ResearchBlogging.org
Reference
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

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.
ResearchBlogging.org
References
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

Tooth formation rates – what do species comparisons really mean?

A paper just came out in PNAS, by Tanya Smith and others, in which they estimate tooth-crown formation times in a large sample of modern humans (n=>300 individuals), a modest sample of Neandertals (n=8), and a poor sample of ‘fossil Homo sapiens‘ (n=3). Teeth form by the periodic deposition of enamel (the hard, white part visible in teeth in the mouth) and dentin (forms the tooth root and internal part of the crown). These periodicities are fairly regular (though variable), thus allowing researchers to estimate how long it took for teeth to develop. As previous studies have shown, Smith and colleagues find that Neandertals formed most of their teeth faster than modern humans.

Growth and development are part of an organism’s life history strategy, and so the observation that Neandertals (and other fossil human species/lineages) form their teeth faster than modern people suggests that perhaps they ‘lived faster’ and died younger than us. It has also been used as evidence that Neandertals are a different species from modern humans.
But I don’t know how well the latter taxonomic argument works. Along these lines, I wish the authors had discussed the meaning of the estimated crown formation times for their fossil ‘modern’ humans (Qafzeh 10 & 15 from Israel ~100 thousand years ago, and Irhoud 3 from Morocco ~160 thousand years ago). The boxplot summaries of crown extension rates (above) show that Neandertals are, indeed, generally fast relative to the large modern sample. However the fossil-modern humans (asterisks, which I’ve circled in red) show a bizarre, not easily interpretable pattern. For the central upper incisors (I1), fossil-moderns are either within the Neandertal range or an outlier at the high end of the human sample. For the lower second incisor (I2) the two fossil-moderns are either waaaaaay above the human range, or a little below it -either way it’s outside the human range. In addition, the sole fossil-modern lower first molar has a lower rate than the modern sample – suggesting an even slower development time. Only the fossil-modern canine formation time fits comfortably within the range of modern humans. Given this wide range of variation in tooth crown formation times in the very small sample of fossil-modern humans, I don’t think we can use this information to make taxonomic arguments.
I think these dental histology studies are very interesting, but I don’t know how much stock we can put in any taxonomic interpretations of them. That Neandertal teeth form faster than modern humans’ is old news, and the discussion focused solely on the neandertal-modern human comparison. It’s too bad that the really interesting part of the paper – the variation in formation time displayed by the fossil-moderns – got no discussion.
The paper
Smith TM et al. 2010. Dental evidence for ontogenetic differences between modern humans and Neandertals. Proceedings of the National Academy of Sciences, in press.

Neandertal Nuclear Genome: Multiregional Evolution is the new Out of Africa

Green and colleagues announced the Neandertal nuclear genome in tomorrow’s issue of the journal Science. Hitherto only complete mitochondrial DNA (mtDNA) genomes had been recovered. These are only inherited maternally, and the genetic differences between the Neandertal mtDNA and that of modern humans seemed to suggest that Neandertals and humans didn’t mix, that is that they were replaced by “anatomically modern humans” (whatever that phrase means). mtDNA is special as far as genetic stuff goes – only inherited maternally, so only tells about one strain out of a slew of ancestors; doesn’t recombine; as a result, selection acting on a part results on selection of the entire mitochondrial genome; oh and it’s certainly not selectively neutral.
So should we have been wary when it was suggested by mtDNA that neandertals and humans were separate species (recall the issue was even crazier with the Denisova mtDNA specimen…)?
YES – HUMANS AND NEANDERTALS EXCHANGED GENES (but just Eurasian humans…)

This is a big deal, because for the past several decades researchers have debated the nature of modern human origins. On morphological and shaky mtDNA evidence, several researchers have argued that modern humans emerged from a small African population, which then spread throughout the world between 100-200 thousand years ago and replaced all other ‘archaic’ human populations. Intuitively this doesn’t make sense, and today’s neandertal announcement renders the Out of Africa with Replacement model for human origins absolutely untenable.
So, were Neandertals and (even then-modern) humans the same species? Yes! If Neandertals were a different species, we would expect all humans to be equally genetically divergent from neandertals. But this is not what Green and colleagues found. Rather, the genomes of a French person, a Chinese person, and a Papua New Guinean were actually more similar to the Neandertal genomes than the two African human representatives were to the Neandertals. Such disparate divergences mean we’re dealing with genetic variation within a species, rather than between species.
In fact, the authors estimate that about 1-4% of modern, non-African genomes are derived from Neandertals. Plagnol and Wall (2006) estimated around 5% of human genes come from ‘archaic’ humans, so it is good to see corroborating evidence from two sources. It is interesting, however, that earlier candidates for introgression from archaics, such as the microcephalin haplogroup D, do not appear to have come from Neandertals (maybe another archaic population, then?).
The authors were also able to use these neandertal and modern human genomes to estimate regions of the human genome that have been under recent and accelerated evolution, including:
  • SPAG17 is associated with sperm motility – is this evidence for sperm competition and recent sexual selection?
  • Regions in which, among modern humans, mutations are associated with social-cognitive diseases like schizophrenia and autism
  • RUNX2, again where misexpression in humans is associated with dysgenesis of frontal bone (forehead), shoulder and rib-cage shape morphology
Interesting…
I think the only things I would have loved to have seen in this study are simple logistical issues, things that are probably simply not practical at the moment because of technological constraints. First, I’d love to see a much larger set of modern human reference genomes. The study included only 2 human nuclear genomes from sub-Saharan Africa, 1 from Europe, 1 from China and 1 from Papua New Guinea. Yes, this samples variation from all over the world, but it’s 5 out of nearly 7 billion genomes out there today. At the moment, however, it’s just not that easy to acquire and handle genomic data for many individuals.
Second, I’d like to see nuclear genome comparisons using Upper Paleolithic modern humans – ‘modern human’ contemporaries of Neandertals. The Denisova mtDNA was surprising because, at some 40 ka, its genome was about twice as different from modern humans as the neandertal mtDNA sequences were. Just what kind of genetic diversity are we looking at in ancient (anatomically both ‘archaic’ and ‘modern’) humans?
Green and colleagues should be lauded because of how meticulously they went about this project. They took major pains to circumvent issues of contamination, they maximized the DNA they could obtain in spite of preservation issues, they came up with some clever tests. And their results are really interesting.
References
Green RE et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710 – 722.
Plagnol V and Wall JD. 2006. Possible Ancestral Structure in Human Populations. PLoS Genetics 2(7): e105

Denisova the Menace

Johannes Krause and colleagues reported yesterday in Nature‘s advance online publication, on a new hominin mitochondrial DNA (mtDNA) genome. The genetic material is derived from a finger bone which lacks diagnostic morphology, from a southern Siberian site called Denisova dating to between 30 – 50 thousand years ago. Of note, the authors describe that the mtDNA is about twice as different from humans as any neandertal mtDNA is from modern humans. If the human-neandertal mtDNA divergence is accurately estimated at around 450 thousand years ago, that means this mystery specimen’s mtDNA lineage diverged from the human-neandertal line around 1 million years ago.

This is really interesting, because also around 40 thousand years ago, but from a site some 100 km to the west of Denisova, bones that were morphologically non-diagnostic yielded mtDNA basically identical to Neandertals.
Does this speak to the presence of at least 3 human species running around the Old World around 40 thousand years ago? Not necessarily. Most claims of a speciose recent human fossil record are based on cranial morphology. For example, modern human skulls are fairly different from “classic” neandertal skulls of western Europe (which is why the Skhul and Qafzeh hominins which display characteristics of both groups are so interesting). However, the mtDNA we have of most of these specimens comes from non-diagnostic specimens. The first Neandertal mtDNA studied came from a piece of tibia (shin bone); this bone is basically non-diagnostic morphologically between recent hominins, and the site it came from (Vindija, Croatia) has both human and Neandertal remains. The Denisova finger, similarly, is non-diagnostic in morphology so far as I can tell, and the archaeological layer contains both Middle and Upper Paleolithic cultural materials: we have no idea what these mtDNA bearers looked like.
I think people thinking “new species at Denisova” (NB: Krause and colleagues never make this claim!) would be shocked if it turns out that the Denisova remains, or those from which the Vindija specimens came, were morphologically modern humans, but this is entirely possible.
Humans today are not so diverse genetically as superficial appearances may suggest to many people. I wouldn’t be surprised if humans simply displayed more genetic diversity in the past. It is certainly interesting just how different the Denisova genome is from both humans and Neandertals. What exactly this difference means is just not clear. It is further interesting to note that the coding regions of the Denisova mtDNA show signs of strong purifying selection. Assumptions of neutrality are so important for genetic studies that I think people often forget that mtDNA actually serves functions necessary to survival, and is not actually neutral. Maybe this ancient mtDNA lineage lasted so long because the mitochondria provided some selective advantage, hence the purifying selection? Who knows?!
The authors make a funny deduction that I can’t quite follow, that because the Denisova specimen’s mtDNA diverged from humans-neandertals some 1 million years ago, “it was distinct from the initial radiation of H[omo] erectus that first left Africa 1.9 million years ago, and perhaps also from the taxon H. heidelbergensis,” which is the name given to mainly European but also African fossils between 1 and 0.5 million years ago. I just don’t follow this. We don’t know what mtDNA diversity was like at any of these times, so there is no reason to think that this specimen’s ancestors were from some undocumented dispersal from Africa. The implicit assumption is that mtDNA lineages arise sporadically and discretely from Africa and then spread to different parts of the world, repeatedly over the course of human evolution. If there’s gene flow all around from the get-go, then the Denisova specimen simply represents an especially ancient mtDNA lineage – not necessarily an ancient population (recall that mtDNA is only inherited from mothers).
Oh well, should be interesting to see the nuclear DNA from this specimen, surely to be described in the near future…
Reference
Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Paabo S. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature, in press.

The earliest flute, and malaria resistance in baboons

Yesterday, two articles of interest to anthropologists were published in the the journal Nature‘s advance online publication. First is the announcement of a very complete bone flute, and fragments of other flutes, dating to around 35,000 thousand years ago from Germany. The finds come from the site of Hohle Fels in Southern Germany; a few months ago it was announced that the site produced the earliest Venus figurine. Venus figurines are some of the earliest pieces of carved art produced by humans, and are figures of corpulent women with corpulent lady-parts. This latter fact captures the popular imagination as the earliest ‘porn,’ but in truth no one’s sure what exactly they mean, although many researchers think they’re related to fertility. Anyway, the flutes are found in Aurignacian deposits, which by and large are attributed to ‘anatomically modern’ humans, as opposed to the contemporaneous Neandertals. The final sentences of the paper sum things up nicely:

“…early Upper Paleolithic music could have contributed to the maitenance of larger social networks, and thereby may have helped facilitate the demographic and territorial expansion of modern humans relative to culturally more conservative and demographically more isolated Neanderthal populations.”

I like their use of “culturally more conservative” description of Neandertals, whereas in the past the phrasing probably would have been “culturally primitive” or “…less advanced.” “Conservative” is certainly an interesting way to describe cultural differences between Neandertals and other Upper Paleolithic populations. I wonder if Neandertals were also more God-fearing and homophobic, as I understand ‘conservative’ to mean nowadays…

The second topic will have to wait. I just got invited to have dinner and drinks and watch soccer, which I’d be silly to pass up. Go South Africa!

Tabūn Pelvis Reconstruction

News: Weaver and Hublin (2009) virtually reconstructed the Tabūn C1 female Neandertal pelvis using CT scans.

Background: This is the closest we have to a complete female Neandertal pelvis, so a lot of the discussion centers around obstetrics. When a modern human woman gives birth, the infant enters the birth canal facing sideways so that the head will fit through the transversely oval inlet, then turns 90 degrees so it is facing the back so that the head will fit through the AP oval midplane and outlet, and finally turns another 90 degrees after the head passes through the outlet so that the shoulders can also fit through the outlet.

Tabūn conclusions: Neandertal infants (based on Tabūn’s inlet, midplane, and outlet diameters) only required two rotations: the initial turn so the head faces laterally, and the last turn so the shoulders fit through the transversely oval outlet. This means the infant comes out with the head facing sideways and the shoulders facing front (this is also how australopithecines are thought to give birth). This, the authors suggest, means that Neandertals were more primitive than modern humans. Furthermore, the transversely oval birth canal reflects the cold-adapted wide pelvis associated with Neandertals.

Problems:

  1. Methods: There is no sacrum for Tabun. None. It is possible to predict sacral width and thus reconstruct the inlet, but it is improbable for the outlet to be reconstructed accurately without knowing the sacrum’s length, curvature, and orientation.
  2. Sexual dimorphism: They confuse this throughout the paper. First, they female-ize Kebara (a complete male Neandertal pelvis) by assuming that Neandertals were as sexually dimorphic as modern humans. This has been shown to be wrong previously, so it was a dumb assumption. They also find that this is not the case, making me wonder why they bothered with it in the first place. Then, they claim that the difference between Neandertals and modern humans is that Neandertals are like modern males (who have short pubic rami) when really they’re like modern females (who have long pubic rami). See Rosenberg (2007) for more discussion of this.
  3. Cold- and warm-adaptations: They say that Neandertals were cold-adapted because of the wide birth canal, in contrast to warm-adapted modern humans from Africa. First, wide birth canals do not go hand-in-hand with wide pelves. Second, Tabūn lived in the Levant and thus did not need to be cold-adapted. Third, the Busidima female Homo erectus pelvis from Gona is also wide and also not cold-adapted. Fourth, modern humans in Africa evolved a narrow pelvis to be better adapted to the warm environment is based on… uh… KNM-WT 15000? No, wait, that’s also a H erectus, and Gona has already shown that they have wide pelves despite their climate. But what else is there to support this long-held idea? Answer: Not much.

Citations:

  • Weaver, TD and JJ Hublin (2009) Neandertal birth canal shape and the evolution of human childbirth. PNAS Early Edition: 1-6.
  • Rosenberg, KR (2007) Neandertal Pelvic Remains From Krapina: Peculiar or Primitive? Periodicum Biologorum 109(4).