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Tuesday, June 30, 2009

As promised, malaria resistance in baboons

Last week I started to mention a recent paper in Nature on the evolution of malaria resistance in baboons, but then went out and partied instead. Not wanting to be a bastard, I'd better make good. While I'll try to pull a good lesson from this, be warned that I'm about to discuss a topic about which I am no expert.

Malaria sucks, you don't want to get it. There are anti-malaria medications out there, but I understand that they can make you insane, or at least have crazy dreams. Fortunately for millions of humans, there is a genetic basis for malaria resistance, so they don't have to buy the anti-malaria crazy pills. Now, the paper tells me that a polymorphism in part of the FY gene turns the gene off in red blood cells, and that individuals with this variant are then strongly protected from malaria. No Lariam for these folks.

Jenny Tung and colleagues analyzed the homologous region of the FY gene in almost 200 yellow baboons (Papio cynocephalus) from Kenya, as well as tested these baboons for Hepatocystis parasites--relatives of Plasmodium vivax, which don't cause malaria in baboons, but does really suck for them. And wouldn't you know it--this same region on the baboon FY gene is also associated with Hepatocystis infection, where individuals with certain genetic variants have a lower susceptability to infection!

Now, the underlying genetic architecture and subsequent mechanisms of infection resistance are not exactly the same. But here's the take home message from the paper:
"These results suggest that the genetic basis of phenotypic variation in different primate species can exhibit a remarkable degree of parallelism. In this case, not only are the similarities present at the molecular level . . . but they also extend to the mechanism that links molecular and phenotypic variation"
In other words, closely related species are equiped with very similar (or often the same) genetic or developmental "hardware," and so evolution can cause them to come up with similar solutions to the same problem. In this case, there's a similar genetic basis underlying infection resistance in humans and baboons. But I think this is a lesson that can be extended to, or at least kept in mind when considering, phenotypic evolution generally.

I've always (well, for the past three and a half years since I've been studying physical anthropology) thought that such a situation might characterize the "robust" australopithecines of East and South Africa. It is possible that these groups are not each others' closest relatives, but that they evolved many craniodental characters in parallel, in response to selection for a heavy-chewing diet. This becomes even more plausible if it should turn out that many of these cranial and dental features are morphologically integrated--something I'm working on at the moment (if anyone reads this and scoops me, you will pay).

So, interesting paper. Reference
Tung, J. et al. Evolution of a malaria resistance gene in wild primates. Nature, in press.

Monday, June 29, 2009

Cranial robusticity in Homo sapiens

Perusing my AJPA RSS feed, I came across an interesting abstract (see attempt at citation below). This article tests three different hypotheses for cranial robusticity in modern humans: genetic, mastication, and climate, and finds that mastication doesn't seem to explain the robusticity of some populations. I didn't read the article, just the abstract (it's summer, and I was perusing), but it got me thinking. If we find population variation that is not based on climate or diet within modern humans, could this have been the case in more ancient hominids? My memory for australopithecine crania is terrible, but I keep thinking of all the different sized "erectines" and "habilines" we looked at in 565 - that sample definitely represented different levels of robusticity. I'm not really sure where I'm going with this (I probably should have read the article and thought about it for a day or so to collect my thoughts, but I'm impatient and felt like posting). I guess I'm just trying to link what we know about modern humans to what we think we know about other hominids. Thoughts? Did anyone else look at this article? Did you find it interesting or dull or poorly written or irrelevant? Is everyone having a good summer so far?

Baab et al. (2009) Relationship of Cranial Robusticity to Cranial Form, Geography and Climate in Homo sapiens. American Journal of Physical Anthropology - June 25.

Thursday, June 25, 2009

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!

Sunday, June 21, 2009

Australopithecus africanus (?) foot bone, and a small rant

Be forewarned, this summary of a recent article on an A. africanus fifth metatarsal also features a short rant. So feel free to stop reading after I start to sound preachy or crazy.

Friend and colleague Jerry DeSilva is part of a recent study of the fossil Stw 114/115, the earliest and most complete hominin fifth metatarsal (the bone forming the side “wall” of your foot just before your little toe). Probably it can be attributed to Australopithecus africanus. Lead author is Bernhard Zipfel of the University of the Witswatersrand. On an aside, Bernhard is the curator of the fossil collections at Wits, so if you’re interested in researching their collection, he’s the one to contact. I met him a few weeks ago, and he is very nice and friendly.


Back to the paper, the authors present a thorough description of the fossil foot bone, a thorough comparison of it to human and great ape homologues, and an exploratory multivariate analysis. The conclusion is that the fossil is decidedly human-like, indicating that the individual who possessed this foot (presumably A. africanus) had a lateral foot functionally identical to modern humans (read “obligate biped”). The authors infer from its overall form that feet of A. africanus (or, again, whatever species this fossil belonged to) had both a longitudinal and a transverse arch, just like humans (non-human primate feet only have the transverse arch).


I have to say, this is an excellent paper, especially compared to lots of studies I’ve read over the past few years. The qualitative description and comparison of the fossil points to many differences between human and ape fifth metatarsals, and similarities between the fossil and humans. Observations made with the eye are then corroborated and elaborated with a quantitative analysis. In contrast, many (but of course not all) studies today largely omit qualitative descriptions and comparisons, delving straight into quantitative analyses. I think this is in attempt to be “scientific” and objective. This zeal for being ‘scientific’ with regard to quantitative methods stands in curious opposition to a general lack of actual hypothesis testing in much of the literature. Of course, this is not a jab at exploratory and descriptive studies, which by their nature usually don’t have hypotheses to test.


I think it’s important to remember that not all questions can (or have to) be addressed by strictly quantitative studies (i.e. by numbers). For example, human metatarsals have a groove separating the head from the shaft—this feature relates to our increased ability to “dorsiflex” our toes when we walk (think of how your toes are oriented relative to the rest of your foot when on tip-toes). This groove is absent in apes. How can a quantitative analysis of human vs. ape metatarsals account for this? I suppose it could be scored as ‘present’ or ‘absent,’ or scored by the relative expression of the groove (i.e.0=absent, 1=weak, 2=deep, etc.). But, the former, dichotomizing scoring system fails to account for variation, while the latter can become quite subjective. On the other hand, I suppose a very complex geometric morphometric analysis could use an immense amount of landmarks to describe the shape of the metatarsal, including the groove (or lack thereof) behind the head. But then you get into the issue of comparing biologically non-homologous structures (although Bookstein and others have done a good—or rather ingenious—job developing methods for making ‘geometrically homologous’ semi-landmarks, and Klingenberg has recently described a way to compare features that are variably present or absent). The main point here is that by focusing/relying solely on ‘the numbers’ (or ‘the science’), researchers stand to miss some important anatomical information.


Sorry about the rant. Anyway, the paper doesn’t really miss anything. It’s a great example of the union of qualitative and quantitative analyses. My only comment is on their human reference sample of “Victorian British” people. I don’t know the sample, but they probably wore shoes. A more apt comparison might have been with humans that didn’t wear shoes, since shoes really affect our foot anatomy. Of course if this sample was habitually unshod, then this doesn't really matter. And regardless, the Sts 114/115 Australopithecus africanus (?) fifth metatarsal shows great similarity to those of humans, and probably functioned like those of humans.


Reference

Zipfel B, DeSilva J and Kidd R. Earliest complete hominin fifth metatarsal—Implications for the evolution of the lateral column of the foot. American Journal of Physical Anthropology, in press. DOI 10.1002/ajpa.21103


Saturday, June 20, 2009

SK 62 sketch


Copying John Hawks, here's a picture I drew a few weeks ago while looking at some of the juvenile Australopithecus robustus material from Swartkrans. This cute little bugger is SK 62. On the left it preserves the deciduous (a.k.a. "baby") left second incisor through the deciduous second molar; on the right are the deciduous canine and molars. The permanent ("adult"!) central incisors are in the process of erupting, and the left permanent first molar is visible in its crypt behind the dm2. What I like about its deciduous canines (I think most or all A. robustus juvenile canines are like this) is that they are quite asymmetrical, with the bulk of the crown displaced mesially, and a little lingual tubercle/ridge distally. Looks like a mitten. The corpus is tallest anteriorly but gets shorter as it runs posteriorly--this pattern is slightly less marked in adults. It appears to have a weak 'chin,' huh?

Wednesday, June 10, 2009

Programming Update: Resampling procedure

In the last post, I was talking about learning to program in R. I was able to re-program a resampling project that I'd written in Visual Basic, but I could not figure out how to store my resampled test-statistics, so I could plot a histogram of their distribution. Last night, after searching the world wide webs, I stumbled upon an even shorter code for resampling. I was able to tweak that code to the specs of what I wanted it to do, and--voila--I have a program that resamples my comparative sample, takes two specimens and computes a test statistic, compares that to my fossil specimens, and repeats the process as many times as I want. I'll print the code at the end for readers to mess with if they want.

The basic idea of the project is that the "habiline" cranial fossils--early Homo from 1.9-1.6 million years ago are quite variable. Because of this, researchers have tried to fit these square pegs of fossils into round holes of species--H. habilis and rudolfensis. A simple, univariate trait that has been claimed to be evidence of multiple species is cranial capacity variation. For a long time this idea was propagated by comparing ER 1470 with ER 1813, because the two have very different cranial capacities and were thought to date to 1.9 Ma. Turns out, though, that while ER 1470 is 1.9 Ma, and ER 1813 might be closer to 1.65 Ma (Gathogo and Brown 2006). Gathogo and Brown state that a more geologically apt comparison, then, would be between ER 1813 and ER 3733. For the 1.9 Ma interval, the most disparate comparison is between ER 1470 and OH 24. Here's the summary of specimens, ages, and their cranial capacities:
1.9 Ma: ER 1470 (752 cc) and OH 24 (590 cc)
1.65 Ma: ER 3733 (848 cc) and ER 1813 (510 cc)
Ratio of ER 1470/OH24 = 1.274
Ratio of ER 3733/ER 1813 = 1.663
So I wrote a program that tests the null hypothesis that early habiline cranial capacity variation is no different from that of extant gorillas--gorillas being one of the most size-dimorphic living relatives of hominins. If I cannot reject the null hypothesis, this would suggest that I cannot reject the idea that the habiline fossils sample a single species, based on cranial capacities. To test this, I took the ratio of the larger cranial capacity to the smallest, rather than male to female--this makes it easier to compare to the max-min ratio of habilines, without having to assume the sex of the specimens. The resampling program randomly selects two gorilla specimens, takes the ratio of the larger to the smaller, and repeats 5000 times. This way, I can assess the probability of randomly sampling two gorilla cranial capacities that are as different as the two sets of habilines.

The results, displayed in the histogram, show that there is a 25% chance of sampling two gorilla cranial capacities as different as the early habilines (1.9 Ma). However, there is only a 0.006% chance of sampling to gorillas as different as ER 1813 and ER 3733. Thus, we reject the null hypothesis for the comparison of ER 3733 and ER 1813. This means it is very unlikely that these two specimens come from a single species with a level of dimorphism/variation similar to modern day gorillas. This could mean that the two represent two different, contemporaneous species, or that they represent a single species with a level of variation greater than in our extant analog. The test cannot distinguish between these alternatives.Histogram of the resampled gorilla cranial capacity ratios. Notice that it is one-tailed. The red-dashed line indicates the 95th percentile. The early habiline ratio (E) is well within the 95 limit, while the later ratio (L) is outside the 95th percentile.

Here's the code (the first two lines tell the program where to find the data, since I haven't posted these, in order to run this program you'll need a) to reset the directory to where you store your data [use the setwd() command] and b) a data file with cranial capacities listed in a single column, the first four of which are the habilines, and the remainder your comparative sample)

setwd("C:/Users/zacharoo/Documents/Data")
get <- read.csv("CranCaps.csv")

habs <- get[1:4,2]
OH24 <- habs[1]; ER1470 <- habs[2]; ER1813 <- habs[3]; ER3733 <- habs[4]
early <- ER1470/OH24; late <- ER3733/ER1813

gors <- get[5:105,2]

p = 0 # incremented if G1/G2 >= "early"
q = 0 # incremented if G1/G2 >= "late"

n = 5000 # <-- NUMBER OF ITERATIONS !!!

gor.boot <- numeric(n) # x-number vector containing test statistics
for (i in 1:n) {
sub.samp <- gors[sample(101,2, replace = FALSE)] # sub.samp = 2 randomly sampled gorillas
G1 <- sub.samp[1]; G2 <- sub.samp[2]
if (G1 >= G2) {ratio <-G1/G2} else {ratio <-G2/G1}
gor.boot[i] <- ratio

if (gor.boot[i] >= early) {p = p +1} else {p = p} #frequencies
if (gor.boot[i] >= late) {q = q +1} else {q = q}
}
pval <- p/i
qval <- q/i
qntl <- quantile(gor.boot, .95)

hist(gor.boot, col = 3, xlab = "Resampled Gorilla ratio", ylab = "Frequency", main = "Frequency Distribution")
points(early,25, pch = "E", col = 2, cex = 1.25); points(late,25, pch = "L", col = 2, cex = 1.25)
abline(v = qntl, col = 2, lty = 6) # line marking the 95% limit

print(pval); print(qval)
summary(gor.boot)


Reference
Gathogo PN, and Brown FH. 2006. Revised stratigraphy of Area 123, Koobi Fora, Kenya, and new age estimates of its fossil mammals, including hominins. Journal of Human Evolution 51(5):471-479.

Tuesday, June 9, 2009

Programming

I'm no wiz when it comes to computers, but lots of really smart people have told me I'd do myself an academic favor by learning to write programs. In Paleobiology last year, Phil Gingerich introduced me to programming in Visual Basic. While I did not become so proficient to find it as useful he did, it still got me interested. Then last semester, Milford urged me and other lawnchair anthropologists to take a course in the department of Ecology and Evolutionary Biology taught by George Estabrook, where we learned to write resampling programs for Excel in Visual Basic. It was a bit stressful at times--reading and writing computer codes at first was like learning to read and write Japanese with little training. But overall I thought it was a very useful class, and I'll certainly be writing more resampling programs in the future (i.e. for my Australopithecus robustus projects...).

But the computer language that everybody's been abuzz about in the past year or so is R. To quote the website (see the link), "R is a language and environment for statistical computing and graphics." The software and codes for it are available FOR FREE on the website. I've been meaning to sit down and figure out how to use it for a year now, and now that I'm all alone at the museum in the evenings, I've begun learning to use R.

At first I had quite a difficult time simply loading data into the program. But once I figured it out (I had the idea, I just wasn't typing it correctly--"syntax" errors), it was quite easy to run. With some datasets supplied from the Paleobiology class, I was able quite easily to compute and plot statistics like principle components analysis and linear models. It's really easy! There are even built-in boostrap (resampling) programs, although I could not figure out how to use them as I wanted.

But that isn't programming--I wasn't making a custom program that would do what I wanted it to do. So I decided to give it a shot. For the programming class last semester (and Milford's "Evolution of the Genus Homo" course), I wrote a resampling program that gave the probability of randomly sampling two gorilla cranial capacities as different as some early habilines. So I decided to try to rewrite that program in R. It took about two evenings of reading manuals and fiddling with commands (and drinking red wine and watching Roadhouse). The R code is much simpler than the original one I wrote in Visual Basic--this is largely because R has a built-in command that permutes rows/columns. Plus, it runs much, much faster--I was able to resample 100,000 times in a few seconds, whereas in the original (VB) program it took a few minutes to do 5,000. I think after a few more evenings of tinkering, I can figure out how to also plot the distribution of resampled test-statistics (although if anyone can tell me how I'd love to hear).

If I can figure out how to do it, I'll post the code so other people can tinker with it if they want. Lesson: use R!

Antiquity of Laughter

There's a quick blurb in ScienceNOW about a study showing that great ape tots laugh when tickled--hey, just like us! And for all the cuteoverload-lovers (Dana), the story also has footage of an orangutan being tickled.

In the study, researchers tickled baby apes and recorded their responses. The acoustics of the laughs were then compared to humans-being-tickled laughs. The results indicate that tickle-induced laughter in humans, chimpanzees, gorillas, and orangutans is homologous, that is it has the same evolutionary origin. [A siamang (essentially a large gibbon) was also included in the study, and while its response to tickling was similar to the orangutans', it somehow did not display full-fledged laughter]. Nevertheless, the quite vocal human laugh is distinct from the apes' laugh. Quite probably the difference in vocalization is related to the fact that humans speak and apes don't.

In the ScienceNOW states that the study "challenges the notion that exhaled and voiced laughter are 'a uniquely human trait'" (me quoting the commentary, which quotes the lead author of the study). I immediately cringe when I hear/read the phrase "challenge(s) the notion," or often, "widely-held notion." How trite. But I do think it is an interesting study (not like the one wherein they fed cooked foods to great apes...). For starters, researchers can begin to look into why exactly the acoustic patterns differ between humans and apes.

But more importantly, it opens the issue of why humans and animals laugh when tickled. Being tickled is an interesting feeling, because even though it makes you laugh, it also makes you uncomfortable and vulnerable--no one when tickled exclaims, "yes, keep tickling me!" (I've even heard urban legends of people wetting themselves when tickled). Unless tickle-laughter is a secondary result of selection on other things, I would imagine that the phenomenon evolved because of its value in social interactions--interactions which the study suggests are as old as the great apes.

Thursday, June 4, 2009

Epochal Monkey Business

How's that for an overstated amalgam of topics? Two things of interest to biological anthropologists on ScienceNOW today. First is movement toward redefining the Quaternary time period, second is capuchin monkeys who (knowingly?) deceive their peers to get food. Sneaky bastards.

It looks as though there's going to be a slap-fight between geologists and 'quaternists' over the geological time scale, specifically regarding the status of the Quaternary period. Here's a great quote from someone fighting for the Quaternary: "They [The International Commission on Stratigraphy] tried to suppress it [the Quaternary] while no one was looking. . . . They nearly got away with it, [but] we were not going to have it" (1). HA! It's like a story about a church conspiracy, the Elders are afraid of change so they're hiding the truth! The commentary is full of such quotes. Anyway, while I never use the term, I suppose technically much of what I study is Quaternary (~2.6 million years ago to the present, the beginnings of the Human Empire). The main implication for me is that the Pliocene and Pleistocene boundary has moved. The Pliocene is a bad-ass epoch starting around 5.5 Ma (maybe a little less)--this is when we get the later Ardipithecus kadabba, Ar. ramidus, and the origins of Australopithecus. Next is the Pleistocene around 1.8 Ma--at about this time, we have the earliest humans outside Africa (Dmanisi in the Republic of Georgia, possibly Java, and I think some teeth from China). But now the boundary may be pushed back to 2.6 Ma--this is when we have the earliest (evidence of) stone tools, from Gona in Ethiopia. Will this be the end of "Plio-Pleistocene hominins"?

There's also a story about capuchin monkeys that cry wolf to get their comrades' food. Sometimes when a subordinate (in the group under study) sees a higher-ranking individual with some food that he wants, the lower-ranking one will fake a predator-warning, tricking the other into thinking there's danger afoot and running off without its food. Also he craps himself and all the others laugh at and humiliate him. This apparently has implications about the cognitive capabilities in animals--can non-human animals predict how others will respond to certain scenarios? The real lesson for me is that if I'm ever around a capuchin in the wild, and it starts hiccupping (that's the predator alarm), I'd better book it. But I won't leave my food. I'll be damned if I'll let some little platyrrhine walk all over me, I'm a human being, dammit--I help define the Quaternary.

Reference

1. Kerr, R.A., GEOLOGY: A Time War Over the Period We Live In. Science, 2008. 319(5862): p. 402-403.