Monday, October 31, 2011

And so the plot thickens

"These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed."

I'm sure it will turn out to be more complex still. Onward and upward!

"Freely available online through the PNAS open access option."


Here you go
Skoglund P and Jakobsson M. Archaic human ancestry in East Asia. Proceedings of the National Academy of Sciences in press. doi:10.1073/pnas.1108181108.

Wednesday, October 26, 2011

Dmanisi Homo erectus: I'll have what she's having

Speaking of diet in fossil humans ... Herman Pontzer and buddies just published a brief analysis of fine-scale tooth wear in the Dmanisi Homo erectus specimens.

Teeth are useful as hell in life. Humans' teeth are critical not only for eating, sporting a sexy smile, and biting people (right), but also for speech and song ("f," "th" and "v" sounds). Some parents even harvest their childrens' exfoliated baby teeth. The things we do with teeth.

Teeth are also really useful for studying long-dead people and animals - teeth may preserve pretty well for millions of years, they can be used to estimate an individual's age-at-death, and their shape and composition can be used to learn about diet. In a vile act of revenge, the food that sustains us also scrawls its Nom Hancock into the surfaces of our teeth. So, scientists can study the microscopic marks (= "microwear") on tooth surfaces to see what kinds of foods were eaten shortly before death. Peter Ungar, an author of the current paper, has done a lot of work here, and his website is worth checking out if you're interested in learning more. Microwear can't really tell you exactly what an animal was eating, but can tell you whether the animal mostly ate grasses, leaves, hard objects like nuts, and so forth.

So Pontzer and colleagues (in press) examined the microwear on some of the lower molars of the youngest members of the nearly 1.8 million year old (Ferring et al. 2011) Homo erectus group from Dmanisi in the Republic of Georgia. To the left is a picture of the jaws, from the paper (from another paper. How meta of me). The microwear patterns of these badass early humans fit cozily within the variation exhibited by other Homo erectus specimens.

Microwear in Homo erectus is pretty variable, but still rather distinct from other fossil groups like robust Australopithecus, and a little less distinct from their putative ancestor H. habilis. This suggests that something special about Homo erectus was the species' great dietary breadth - Homo erectus' key to colonial and evolutionary success might not have been the adoption of a key dietary resource, but rather the ability to utilize a wide range of food resources. Atkins diet be damned. What's neat is that the Dmanisi hominids, though kind of primitive (Australopithecus-like) in terms of brain size and some aspects of skull shape, nevertheless demonstrated key behaviors of H. erectus, namely colonization (Dmanisi is the oldest reliably-dated hominid site outside Africa), and dietary flexibility. This really suggests the success of our ancestors was due to some behavioral innovation, aside from advances in stone tool technology.

Now, these Dmanisi H. erectus kids' teeth wore like other H. erectus, and it would be reasonable to infer that this is because they ate similar foods. This makes it all the more mysterious that the other Dmanisi jaws, from older adults, have teeth completely worn to shit (sorry to swear). D3444/3900 (left) are the cranium/mandible of an individual who was missing all their teeth, except maybe a lower canine - the earliest example of edentulism in the human fossil record (Lordkipanidze et al. 2005). D2600 (below) is a very large mandible with teeth so worn that the pearly-white first-molar crowns were gone and the internal pulp cavity (and nerve) were exposed. (Interestingly, D2600 is so large that some researchers initially argued it represented a different species from the other jaws - yet Adam Van Arsdale presented evidence that this extreme tooth wear may actually be responsible for making jaws relatively taller in early humans).

So what's curious is why the older Dmanisi hominids should show such an extreme amount of tooth wear compared to other H. erectus, but microwear on the young suggests their diet was the same (that is, just as diverse in texture) as others in the species. Was Dmanisi-level tooth wear (and tooth loss) comparable to other H. erectus, and we just happen not to have found them at other sites? (KNM-ER 730 from Kenya is the next-most worn early Homo that next comes to mind) Is there another aspect of diet we don't know about, that caused the Dmanisi teeth to wear especially quickly? Or were these early Homo from Dmanisi actually living longer than other H. erectus? I suspect the second is more likely, but that's a hypothesis that remains to be tested.

Read more, dammit!
Ferring, R., Oms, O., Agusti, J., Berna, F., Nioradze, M., Shelia, T., Tappen, M., Vekua, A., Zhvania, D., & Lordkipanidze, D. (2011). From the Cover: Earliest human occupations at Dmanisi (Georgian Caucasus) dated to 1.85-1.78 Ma Proceedings of the National Academy of Sciences, 108 (26), 10432-10436 DOI: 10.1073/pnas.1106638108

Lordkipanidze, D., Vekua, A., Ferring, R., Rightmire, G., Agusti, J., Kiladze, G., Mouskhelishvili, A., Nioradze, M., de León, M., Tappen, M., & Zollikofer, C. (2005). Anthropology:  The earliest toothless hominin skull Nature, 434 (7034), 717-718 DOI: 10.1038/434717b

Pontzer H, Scott JR, Lordkipanidze D, Ungar PS. In press. Dental microwear texture analysis and diet in the Dmanisi hominins, Journal of Human Evolution (2011). DOI:10.1016/j.jhevol.2011.08.006

Sunday, October 23, 2011

Data, development and diets

As mentioned briefly but repeatedly on this blog, my dissertation is about growth of the lower jaw in Australopithecus robustus (right), comparing it with jaw growth in recent humans. This is important because we don't really know exactly how skeletal-dental (especially skeletal) maturation of our fossil relatives compares with us today. From a developmental perspective, it is also important to know how and when adult form arises during growth, and how these processes vary within and between species.

It's not easy to examine ontogeny in fossil samples. In a post a few weeks ago I included a drawing of some of the A. robustus juvenile jaws. At the time, I was pointing out variation in dental maturity (which is a nice thing when studying growth), but the picture also reveals a bigger bugbear - variable preservation of features (which is a terrible thing if you're trying to study growth).

For example, the youngest individual in the fossil sample (right, viewed from above, front is at the top of the picture) includes only the second baby molar tooth, a bit of the bone surrounding the sides and back of the tooth, and a small portion of the ascending ramus. The oldest subadult in the sample (SKW 5), on the other hand, is almost entirely complete. In between these ages, jaws variously preserve different parts. Under these circumstances (i.e. lots of missing data), growth cannot be studied by traditional (namely, multivariate) methods (how I will deal with this is a topic for another day).

So while studying the fossils in South Africa, in order to maximize the number of comparisons I could possibly make, I measured just about every single linear dimension conceivable on these jaws. I thus have a spreadsheet with 300 columns of measurements I could take on each specimen. Most of the cells are empty : (

What's a boy to do?! In order to compare A. robustus with humans, I need to take the same measurements on a growth series of human jaws, too. But life is short, and if I want to finish this project before I succumb to some sinister signature of senescence, I really can't take hundreds of measurements on a human sample which is much larger than the fossils. Plus, a lot of the individual measurements are a bit redundant: some of the distances overlap, many of the variables can be taken on the right and the left sides, etc.

If I am to finish collecting data in a reasonable time frame, I need to cull my variables from 300 to however many (a) maximizes the comparisons I can make within the less-complete A. robustus sample, and (b) are not too repetitive. Boo. Plus I have to get these spreadsheets ready to be read and analyzed in the program R, which for whatever reason is always a pain in the ass.

Again, the statistics of the overall comparisons is a topic for another day, and I haven't had the opportunity yet to write the analytical program(s). But I have looked at some individual traits in A. robustus compared with a subsample of humans. For example, at the left is a plot of changes in height of the jaw at the baby second molar or adult second premolar (which replaces the baby molar). Obviously my human sample is way to small at the moment to make any really meaningful statements about how growth compares between the two species. Note also that these are absolute measures and not size-corrected, and that these are stages of dental eruption rather than chronological ages. But from this preliminary view, the two species are very similar up to around when the first adult molar comes in ("stage 4" here). Thereafter, the A. robustus individuals dramatically increase in size rather fast, whereas humans only slowly increase in size.

Again, this is a very preliminary result, and only for a single measurement. But it is interesting in light of a recent study by Megan Holmes and Christopher Ruff (2011). These researchers compared jaw growth recent humans who differed in the consistency of their diets. They found that kids in the two populations were not too different, but the samples became more different with age to become fairly different as adults. Now, A. robustus seems to have eaten a diet with lots of hard objects (see recent review by Peter Ungar and Matt Spohneimer), but humans' diet (and technology) really obviates the need for chewing as powerful as seen in A. robustus. So this dietary divergence may well be reflected in the growth difference suggested above, but it may not be the sole factor. PLUS I NEED TO INCREASE MY HUMAN SAMPLE.

Stay tuned for more analyses and results!

ResearchBlogging.orgReferences to make you smarter and stronger
Holmes, M., & Ruff, C. (2011). Dietary effects on development of the human mandibular corpus American Journal of Physical Anthropology, 145 (4), 615-628 DOI: 10.1002/ajpa.21554

Ungar, P., & Sponheimer, M. (2011) The Diets of Early Hominins. Science 334(6053), 190-193. DOI: 10.1126/science.1207701  

Thursday, October 13, 2011

Genetic basis of disgusting

The genome of the naked mole rat (Heterocephalus glaber, below right) has been sequenced (Kim et al. 2011), shedding insight into how mammalian evolution made gross.
Here are some factoids about these murine monsters, from a nice editorial accompanying the research paper in Nature. These critters live in underground colonies - because who could suffer to see them on the surface? These bald rats are unique among mammals in that they are "eusocial" like bees or ants. Also like bees and ants, a colony has a single, breeding "queen" in the group, whose mere presence prevents other female mole rats from becoming sexually mature. When a queen dies, females fight for the vacant throne. When one wins and becomes the new queen, she subsequently undergoes a "growth spurt," becoming up to 80% heavier and dramatically lengthening her lower spine (Dengler-Crish and Catania 2007; figure below) - a marvel of phenotypic plasticity. These rats dwell in crowded, dirty tunnels low in light and oxygen; it's kind of like Los Angeles. Plus, they can live for up to 30 years, which is an amazingly long time for an animal so small you can hold in it your hand. They are also apparently resistant to cancer and to some kinds of pain and itching. So, so strange.

With only one female contributing half a generation's genes, you can imagine the shamelessly-naked mole rats are a little more inbred than most of us. In spite of this potential drag to genetic variation (and thereby natural selection), the naked mole rat genome demonstrates a number of adaptations to the species' peculiar lifestyle. For example, the genes TEP1 and TERF1, which have been implicated in determining the lengths of the ends of chromosomes ("telomeres"), show evidence of positive natural selection in the mole rat. Kim and colleagues (2011: 2) say their analyses "point to altered telomerase function ... which may be related to its evolution of extended lifespan and cancer resistance." Cancer resistance!? I think the paper's final paragraph (p. 4) lays out nicely what's most important about research into the genome of this most ghastly rodent:
To summarize, sequencing and analysis of the [naked mole rat] genome revealed numerous insights into the biology of this remarkable animal. In addition, this genome and the associated data sets offer the research communities working in ageing, cancer, eusociality and many other areas a rich resource that can be mined in numerous ways to uncover the molecular bases for the extraordinary traits of this most unusual mammal. In turn, this information provides unprecedented opportunities for addressing some of the most challenging questions in biology and medicine, such as mechanisms of ageing, the role of genetic makeup in regulating lifespan, adaptations to extreme environments, hypoxia tolerance, thermogenesis, resistance to cancer, circadian rhythms, sexual development and hormonal regulation.
ResearchBlogging.orgIt's not news that Life on Earth can be pretty weird sometimes. Understanding how Life became and becomes weird can provide us with tools to make life better for people.

Things I cited
Anonymous (2011). More than teeth. Nature, 478 (7368), 156-156 DOI: 10.1038/478156a

Dengler-Crish, C., & Catania, K. (2007). Phenotypic plasticity in female naked mole-rats after removal from reproductive suppression Journal of Experimental Biology, 210 (24), 4351-4358 DOI: 10.1242/jeb.009399

Kim, E., Fang, X., Fushan, A., Huang, Z., Lobanov, A., Han, L., Marino, S., Sun, X., Turanov, A., Yang, P., Yim, S., Zhao, X., Kasaikina, M., Stoletzki, N., Peng, C., Polak, P., Xiong, Z., Kiezun, A., Zhu, Y., Chen, Y., Kryukov, G., Zhang, Q., Peshkin, L., Yang, L., Bronson, R., Buffenstein, R., Wang, B., Han, C., Li, Q., Chen, L., Zhao, W., Sunyaev, S., Park, T., Zhang, G., Wang, J., & Gladyshev, V. (2011). Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature DOI: 10.1038/nature10533

Tuesday, October 11, 2011

Variation 2: The female with the flamboyant and massive male

Continuing my investigation into stages of individual development, I've stumbled upon a study of the maturation of semi-wild mandrills (Mandrillus sphinx). Mandrills are one of the most visually striking species of Primates (check out this beastly male to the right), and exemplars of the power of Sexual Selection.

Sexual selection is a special subtype of Natural Selection, where the within-species competition here isn't so much for survival (as in natural selection) but more specifically for reproduction. Sexual selection is believed to be responsible for many differences between the sexes: male primates often (but not always!) have much larger bodies and canine teeth than females, traits that can be beneficial when competing with other males for access to female mates. And/or females may prefer larger-bodied or -canined males for whatever reason. In accord with the power of female preferences, sexual selection is invoked to explain why males of many species are so wildly colored or ornamented.

So mandrills are perhaps the best example of sexual selection in primates. Males' faces, butts and genitals are brightly colored, spanning the spectrum from blood-red to nearly bioluminescent blue. Conceivably, at some point in mandrills' evolutionary history most males were drab-colored, but then who comes riding into town on a silver stallion but a mutant male who was more colossal and colorful than the rest, and females were like, "OMG did you see that variegated guy? I want him so bad," and as a result, this male reproduced more, and the rest of the story writes itself. Coloration may actually communicate information to females about the health or dominance status of the male (e.g. Setchell 2004). I wish I had the time to investigate the physiological bases of how their hair and skin can produce such colors. To revolutionize the tattoo industry.

Mandrills are also remarkable in how much larger males are than females, in terms of canines (Plavcan and van Schaik 1992), molars (Scott et al. 2009) and body size (Wickings and Dixson 1992). And this brings me to my original thought.

The plot to the right tracks growth in body mass (in kilograms) of male and female mandrills (Wickings and Dixson 1992: 132, fig. 1). The male is the top line and the females the bottom one. The arrows indicate timing of sexual maturity. Holy crap, by the time males are sexually mature, they are about 3 times the body mass of females.

The union of the ~25 lb female with the seemingly-paint-splattered, 75 lb male must be a truly terrifying sight.

Things I cited

Plavcan, J., & van Schaik, C. (1992). Intrasexual competition and canine dimorphism in anthropoid primates American Journal of Physical Anthropology, 87 (4), 461-477 DOI: 10.1002/ajpa.1330870407

Scott JE, Schrein CM, & Kelley J (2009). Beyond Gorilla and Pongo: alternative models for evaluating variation and sexual dimorphism in fossil hominoid samples. American journal of physical anthropology, 140 (2), 253-64 PMID: 19358294

Setchell, J. (2005). Do Female Mandrills Prefer Brightly Colored Males? International Journal of Primatology, 26 (4), 715-735 DOI: 10.1007/s10764-005-5305-7

Wickings, E., & Dixson, A. (1992). Development from birth to sexual maturity in a semi-free-ranging colony of mandrills (Mandrillus sphinx) in Gabon Reproduction, 95 (1), 129-138 DOI: 10.1530/jrf.0.0950129

Monday, October 10, 2011

Variation: a blessing and a curse

Trying to start on finishing my dissertation, I'm thinking about the issue dental development and how it relates to skeletal growth. Specifically I'm trying to decide whether I want to analyze my human and Australopithecus robustus samples based on estimates of "dental age," or if I want to be a bit more cavalier and divide the sample into rougher age categories.

To avoid copyright issues, here's a crappy picture I drew a few years ago, of the youngest A. robustus jaws. The youngest, "SK 438" is erupting its last baby tooth (bottom right), while the others have their full set of baby teeth, and none of them has its first adult tooth yet. I don't think I can estimate ages accurately enough to capture the true chronological difference between SK 438 and the rest. Would I be better off just dividing the group into "younger" (SK 438) and "older" (the rest) infants, or even lumping them all together as simply "infants"?

On the one hand, I could assign individuals a chronological age based on a modern referent of known age, at similar stages of dental development. This could allow me to get more fine-scale glimpses into patterns of growth in my samples, but that's assuming I've accurately estimated their ages. Individuals vary in the ages and sizes at which their teeth erupt; a person's first molar, for example, may erupt at anywhere from 4-8 years of age. How can I estimate an individual's age in light of such variation? And what if I'm as poor a judge of ages as Dennis Duffy?! Conceivably I could program my analysis to account for error estimation (which in itself could be educational and interesting, but is it worth the trouble?), but this would also add a further source of uncertainty. And it's like Dwight Schrute said (Michael Scott said), "K-I-S-S: keep it simple, stupid. Great advice, hurts my feelings every time."

On the other hand, I could divide my sample into coarse age categories - say, putting specimens who've attained a given level of dental development in the same group, such as 'infant, child, juvenile, adolescent, and young adult.' This method loses the temporal resolution of the first method, but also avoids the possible errors of assigning strict ages I'm pretty sure I would not infer accurately. But, tooth development does not show a clean 1-to-1 relationship with other systems in the body, such as hormonal axes or the bony skeleton. It's uncertain how accurately kids can be put in any of the above categories (based on general life history variables; Bogin 1999) based on dental development.

Choices, choices.

Variation is a problem for biologists. The theory of evolution was conceived as a way to explain the conundrum of why there is such remarkable variation in the forms of life that Earth is lucky to have harbored. The problem of within-species variation in the relative timing of skeletal and dental development isn't just a bug-bear for paleoanthropologists. It's important to medical doctors and pathologists investigating genetically-based developmental disorders, and to epidemiologists looking at aspects of population health, such as the prevalence of growth stunting. It's also important for forensics specialists who need to use biological clues about the age and identity of crime victims and defendants. I mean, how else would we know whether Jon Voight bit both Kramer and this pencil?

The silver lining, I suppose, on this storm-cloud of biological of variation is that without variation there cannot be evolution. And stasis is boring. If nothing changed since the Cambrian, none of us would be here today. We'd probably be some gross stupid monstrous thing, like this Hallucigenia to the right. It's the quirks and weird variants that arise randomly, that make evolution possible. If individuals all developed exactly the same, then all organisms through all time would be the exact same, and probably all would have gone extinct as they succumbed to some sinister fate, no new variants would have arisen that may have been able to survive the devastation.
So variation is a blessing and a curse. Individual and population variation make it difficult to state norms such as what is "average" or "healthy," and nothing to be concerned about. Variation is also the magic ingredient of adaptation, without which Life could not survive the randomness inherent in any environment.

Things I cited
Bogin, B. (1999). Evolutionary perspective on human growth Annual Review of Anthropology, 28 (1), 109-153 DOI: 10.1146/annurev.anthro.28.1.109

Also 30 Rock, The Office and Seinfeld. Well done, NBC.