Wednesday, June 18, 2008

Talk about 'fighting dirty'

Maybe it’s just me, but impressing women is difficult. Nowadays it takes all kinds of tricks—I mean charms—to show a woman that you’re worth even a moment of her time. Wasn’t always like this. Time was, back in the days of Olde, a knight would joust with some other guy, and the victor won the hand of the lady—maybe a princess, or a fishwife or someone. I mean they didn’t chop off her hand and give it to the winner. “Hand” is just an expression. He won her heart. No, not her actual physical heart, he wasn’t trying to acquire her courage. “Heart” is an old-fashioned term used by Shakespeare and others to mean “love,” or something. Point is, men used to physically fight other guys to determine who would end up with the princess or fishwife and sire a lot of kids to work on the farm or swab the deck or something. But what did hominins do to determine who won the hearts of the ladies?

Some animals (let’s focus on primates) don’t fight with lances like in Olden Days. Some fight dirty—they leave the competition up to their sperm. Why? Sometimes it pays not to have to fight off other suitors like Odysseus had to (hey, another Classics reference), and sometimes it can even be beneficial to have other males around. Take chimpanzees and bonobos, for instance. The live in multi-male, multi-female groups, where the males tend to be related and stay in their natal group for life, while females disperse and join a new group once they’re old enough to have their own offspring. Male chimpanzees often cooperate in patrolling their territory’s borders, hunting, and other macho activities. And females mate promiscuously—no one's wearing white at these weddings. So how do males maintain lots of buddies (who are mating competition) while still trying to father lots of offspring—sperm competition.

One thing you might notice superficially about a chimpanzees is that males’ testes are huge relative to body size. This is because part of their mating strategy is to (when mating, mind you) release copious amounts of sperm so that the chance of fertilization is higher. Also, their ejaculate forms a ‘sperm plug,' (theoretically) so that the next male that mates with that female will be less likely to achieve fertilization. Sperm competition like this characterizes species where females are promiscuous. Other species, like the gorilla, which are incredibly sexually dimorphic (males are much, much larger than females) and in which males overtly compete with one another for females do not exhibit this sperm competition. In fact, gorillas have a completely different social structure from chimpanzees see (my earlier post on the robust australopiths): (usually) a single dominant male associates and mates with a few females, and gorilla testes are tiny for their body size. Like it's always cold outside.

A recent study looked at hominoid seminal protein evolution to determine what type of mating systems humans may have evolved in (Carnahan and Jensen-Seaman 2008). The authors looked at coding sequences for three seminal proteins in extant humans, chimpanzees, bonobos, gorillas, orangutans, and gibbons/siamangs to compare the rates of non-synonymous vs. synonymous substitutions. A higher ratio—more non-synonymous substitutions—is usually evidence for some kind of selection: according to Neutral Theory, most genetic mutations should be neutral, that is, they shouldn’t alter fitness. Some substitutions, 'synonymous,' might not change what amino acid is coded; however if the substitution changes the amino acid, there is a high chance that it will be deleterious (i.e. negatively affecting fitness). So if we see a larger-than-expected amount of non-synonymous mutations, then they were likely beneficial, and so were under positive selection, i.e. were selected for.

So what did the authors find? For chimps and bonobos the non-synonymous/synonymous ratio was ‘greater than one,’ (I don’t think the paper gave an actual number other than “>1”). Also there was little variation in the sequences. This indicated that the seminal proteins were under positive selection, consistent with the aforementioned symptoms of sperm competition. Conversely, for gorillas and gibbons, characterized by no sperm competition, and little/no female promiscuity, these seminal proteins were basically non-functional.

But for humans, the ratio was 1.02, with a great amount of protein variation. Also, humans appear to be fixed for two amino acid substitutions where most other mammals are conserved. So what does this mean—is human evolution characterized by a mating system similar to that of gorillas, with overt male-male competition, and sexual body size dimorphism (this is supported by most fossil evidence)? Or is it better characterized by a chimpanzee-like mating system, with promiscuous females and sperm competition? Difficult to say. Here’s the authors’ take (Carnahan and Jensen-Seaman, in press, p. 8):

This could be interpreted in several ways. . . . these genes may have been evolving nearly neutrally with little functional constraint and therefore on their way to becoming pseudogenes, as seen in gorillas who have little or no sperm competition. . . . An alternative interpretation is that since these [non-synonymous/synonymous] ratios are estimated along the entire human lineage since our divergence from the common ancestor of humans and chimpanzees, they may be reflecting an average across fluctuating episodes of positive selection and purifying selection, in turn because of fluctuating mating systems.

I guess there are three things to take away from this study. First, it provided a novel way to integrate genetic and behavioral data to try to infer aspects of hominin behavior when there is little direct evidence, other than sexual dimorphism (or not, depending on who you ask…) in the fossil record. Second, this is another instance where molecular data are really interesting, but equivocal as to what they mean exactly (see one of my earlier posts). Just as there are gaps in the fossil record, molecular data, with all their summary statistics, models and assumptions, have their shortcomings as well. Finally, this provides another caution for using Pan as an analog for the chimp-human common ancestor (haven’t discussed this one lately). Said common ancestor, and basal hominins for that matter, may have been behaviorally similar to extant chimpanzees in some ways, but this study points out one way in which extant Pan may well be derived relative to other hominids/-oids. Oh, and who could resist linking the study’s subject (semen) with half of one of the author’s last names? I could. Grow up, seriously.

Carnahan SJ, Jensen-Seaman MI (2008) Hominoid seminal protein evolution and ancestral mating behavior. American Journal of Primatology 9999(9999):n/a

Tuesday, June 17, 2008

Is Classics really so antiquated?

I'm reading up on morphometrics at the moment, in preparation for a geometric morphometrics summer school I'll be attending at the beginning of July. Basically, morphometrics is the study of shape, how to quantify it and analyze it statistically. Modern morphometrics techniques are currently being used in biology and paleontology to do really neat comparative studies, such as of hominin cranial shape, of ontogeny and morphological integration (i.e. sets of traits that are developmentally and/or functionally related). One important method for comparing shape is what is called a Procrustes analysis, in which one shape is essentially fit onto another. To quote Dryden and Mardia (1998, p. 83), "Procrustes methods are useful for estimating an average shape and for exploring the structure of shape variability in a dataset."

Where does Classical education come in? A little known Zach Fun Fact is that I studied Classics for a considerable part of my earlier undergraduate career. So it is sad that I didn't know the significance of Procrustes. To quote Dryden and Mardia, again (p. 42): 

"In Greek mythology Procrustes was the nickname of a robber Damastes, who lived by the road from Eleusis to Athens. He would offer travellers a room for the night and fit them to the bed by stretching them if they were too short or chopping off their limbs if they were too tall. The analogy is rather tenuous but we can regard one configuration as the bed and the other as the person being 'translated', 'rotated' and possibly 'rescaled' so as to fit as close as possible to the bed."

So one of the most important morphometric methods is a sick Classics joke. I mean that's seriously morbid. And that's why Classical Studies might not be so bad, after all.

Monday, June 16, 2008

Zach, get over the robust australopithecines

Let’s return to my favorite group (though I think they’re not terribly closely related) in the human fossil record, the robust australopithecines. They have popped fairly frequently in the news this year, most recently regarding their possible use of bone tools (Backwell and d'Errico, in press). This group is funny. They first appeared probably some time around 2.7 million years ago, in the controversial form of Australopithecus aethiopicus. No one knows where exactly this enigmatic group came from, save for that the only known, fairly complete cranium (KNM WT 17000) has many primitive features, and is largely similar to the earlier A. afarensis. Around 2.3 million years ago or so, A. aethiopicus appears to be ‘replaced’ by A. boisei, whose face is less protruding, has smaller anterior teeth, and has a derived P3 morphology. This is all in East Africa, mind you. Then, some time probably around 2 million years ago, or a little later, a robust form (A. robustus) appears in South Africa, where erstwhile the only hominin was A. africanus (some argue that there are 2 species in the A. africanus hypodigm). Personally, A. robustus looks like a more ‘robust’ A. africanus: larger posterior teeth, more anteriorly placed cheeks—but there is much overlap in many of traits between these two taxa. And much to the chagrin of many cladists, the South and East African robusts appear fairly different morphologically; a recent study (Gonzalez-Jose et al. 2008) that examined hominoids morphometrically (that is, in terms of aspects of cranial shape) found the two robust taxa to be distinct (but that’s a topic for another post . . .). And all the while these buggers lived right alongside Homo, our ancestors! That’s some effed up stuff.

Now for the recent paper. Blackwell and d’Errico (in press) report on an assemblage of bone tools from the site of Drimolen in S. Africa (~2-1.5 million years ago). Drimolen is very near Swartkrans and Kromdraai, two other cave sites with a wealth of A. robustus, and to a lesser extent Homo, material has been recovered. First, how do they know these bones were tools? The tools were compared to other bones, known to have been worn (down) by other processes, like gnawing or carnivore chewing, and the tools appear quite different from these. Also, experimental studies of actually using bones as digging tools (to dig up underground tubers and especially to dig into termite mounds) have produced the same kind of wear as the fossil bone tools. Finally, many bone tools are known from the site of Swartkrans, which as I mentioned above is also laden with A. robustus remains. So it appears pretty likely that A. robustus (or Homo) was using bone tools to dig for foodstuffs around Drimolen and other cave sites in the early Pleistocene. *Note: our friend and colleague Julie Lesnik is currently finishing up her fieldwork, examining bone tools from Swartkrans, and observing chimpanzees digging for termites in Senegal; perhaps we could get her to write a good post on the topic.

Second, how do they know who used these tools? This an excellent question, which similarly plagues the postcranial material from these S. African sites (and even E. African sites, cf. the OH 7 hand and the OH 8 foot, again another topic for another post on another day . . .). The basic argument, similar to that for the postcrania, is that where these bone tools are found, the hominin assemblage is dominated by A. robustus remains; well, at least there are more A. robustus teeth and cranial material relative to comparable Homo fossils. So it’s guilt by association for the bone tools and postcrania here. Of course the only real way to test the hypothesis that most S. African postcrania and bone tools are to be associated with A. robustus and not Homo would be to find a complete skeleton of either, and to find bone tools in strong association (i.e. almost still in the clutches) of a certain taxon. Another argument used in support of robustus as the bone tool user is the fact that stone tools—the hallmark of early humankind?—are relatively absent at these sites. So it’s probable, but certainly not unequivocally proven, that A. robustus was the user of these stone tools (note that the authors never make any claim of such proof).

The authors use the bone tool assemblages from Swartkrans and Drimolen to infer ‘cultural’ behavior patterns for A. robustus. A recent paper claimed that since larger (male) A. robustus cranial specimens tended to be older than smaller ones, that this was evidence for extended male growth in the taxon (Lockwood et al. 2007). This, coupled with the pronounced sexual dimorphism in this taxon (and all hominins until only fairly recently), suggested Lockwood et al. that A. robustus had a social structure similar to that of gorillas, in which one or two males associate with a number of females and their offspring (a simpler answer is that selection favored larger males, and so they were living longer, but Mary and I had trouble trying to demonstrate this). So Blackwell and d’Errico figure that this evidence, along with data from chimpanzee termite-foraging behavior, suggests that females were the predominant practitioners of termiting using bone tools.

Why do I think this is interesting? I think this shows a potentially very important ecological divergence between the robust australopithecine lineages on the on hand, and between A. robustus and Homo on the other. Could the disparate toolkits of these hominins have played an important part in the evolution of these lineages? It is debated whether robust australopithecine hands were physically capable of actually making stone tools (which is quite difficult). Part of this stems from the fact that it’s hard to find a complete hand (damned beetles…) and then to attribute it to a specific taxon. For instance, the OH7 partial hand, which was supposed to be part of the H. habilis holotype, was recently found to be most similar morphologically to A. robustus from S. Africa, and functionally not adapted to tool-making (Moyà-Solà et al. 2008). Of course, this relies on assumptions about whether hand material from Swartkrans represents A. robustus or Homo. Nevertheless, it may well be that part of the adaptive divergence of A. robustus and Homo was the former’s use of bone tools to dig for termites, while the latter was able to manipulate stone to exploit higher quality resources. Cool.

Also significantly, I think this points to more evidence against uniting A. robustus and boisei into the genus Paranthropus. Yes, they both had large posterior teeth (though boisei’s were generally larger) and faces built to house large chewing muscles. But other than that they appear pretty different. As noted above, a recent study looking at modularized traits in crania found that the two robust groups were not monophyletic, which is a criterion when making taxonomic decisions (Gonzalez-Jose et al. 2008). A. robustus has striking affinity with the earlier A. africanus, while A. boisei has striking affinity, to the exclusion of A. robustus, with A. aethiopicus, suggesting that A. robustus and boisei didn’t share a common ancestor. It has also been argued that sharing an ecological space is another criterion for generic membership (Wood and Collard 1999). But isotopic and dental microwear evidence show A. robustus and boisei to have been distinct. Also, (shame on me) I’m not sure the extent to which A. boisei is associated with bone tools, but to my knowledge it is not. So here we have morphological, geological, temporal, and ecological discontinuity between the two main ‘robust’ taxa. That pretty much sinks Paranthropus for me. I don’t know why I am so adamant about these taxa’s paraphyly, but I am. I feel that taxonomy should reflect important biological and phylogenetic reality. And it seems to me that because there isn’t compelling evidence that A. robustus and boisei share the same ancestor, or interbred, that they shouldn’t be taxonomically separated from the other australopithecines. And that’s my two cents.

Backwell L, d'Errico F Early hominid bone tools from Drimolen, South Africa. Journal of Archaeological Science In Press, Accepted Manuscript

Gonzalez-Jose R, Escapa I, Neves WA, Cuneo R, Pucciarelli HM (2008) Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution. Nature 453(7196):775-778

Lockwood CA, Menter CG, Moggi-Cecchi J, Keyser AW (2007) Extended male growth in a fossil hominin species. Science 318:1443-1446

Moyà-Solà S, Köhler M, Alba DM, Almécija S (2008) Taxonomic Attribution of the Olduvai Hominid 7 Manual Remains and the Functional Interpretation of Hand Morphology in Robust Australopithecines. Folia Primatologica 79(4):215-250

Wood B, Collard M (1999) The changing face of genus Homo. Evolutionary Anthropology 8(6):195-207

Sunday, June 15, 2008

Bigger Problem:

Beetles. I recently heard on Nature podcast (24 April 2008; sometimes work is super boring, and I’m sick of all my music) that beetles are contributing to global warming. North American forests are being pillaged by fungus-bearing Mountain Pine beetles, which render ruddy pine-trees that should be green. They are killing the trees, making the forests massive carbon repositories. Trees are our friends because they clean up carbon emissions for us, and can be climbed on. But these voracious Mountain Pine beetles infesting forests are killing our trees, which means less trees to clean up our carbon. Insult to injury: as the dead trees decay they release more carbon into the atmosphere. So now humans and coleopterans are major contributors to Global Warming. Researchers estimate (Kurz et al. 2008) that these beetles will have caused the release of almost a billion tons of CO2 into the atmosphere between Y2k and the year 2020 (hey, remember the big Y2k fiasco?). Dammit! It would be nice to be able to place a substantial amount of the blame for Global Warming on these dendrophagous coleopterans, absolving humans of their environmental sins. But humans are probably at least partly responsible for the current Mountain Pine beetle outbreak: their northward expansion is due in part to rising temperatures in recent years, and we’re the bastards that have been heating up the planet.

So beetles are already on the list. But apparently beetles have been eating fossils, too. Paleontologists recently identified thousands of dinosaur fossils that ‘bore’ (pun!) traces of beetle feeding activity (Britt et al. 2008). To quote from the abstract:

The traces include mandible marks, pits, and shallow bores on cortical bone, and deep, meandering furrows and tunnels (borings) on articular surfaces. The interiors of bones are intensely mined, and the cavities and borings are filled with fine bone fragments (insect frass). . . . Examination of more than 5,000 bones . . . shows insect traces on bone are common but overlooked and that many bones are substantially damaged by insect mining (Britt et al. 2008, my emphasis).
So how much of the fossil record have these detrivores altered or destroyed? Hard to say, though I have not heard of any known cases of insect damage in the human fossil record. Oh, and “frass” is a funny word for insect excrement.

So what’s the take-home message here? It seems to me that too often beetles’ shortcomings are overlooked by their positive attributes: they’re an unforgivably speciose and evolutionarily ‘successful’ group (the great population geneticist JBS Haldane is credited to have said humans could easily divine that the Creator had “an inordinate fondness for beetles”); they released many great records and #1 singles; some of them like to play with poop, etc. But what are we to do with the ones that destroyed our fossils (arguably making paleontology more interesting) and are helping us microwave our planet? I do not think that drastic punitive action should be taken against the largest order of insects. But the next time you see a beetle, even if it’s not of the Mountain Pine or dermestid persuasion, you tell it, “Shame on you.”


Britt BB, Scheetz RD, Dangerfield A (2008) A Suite of Dermestid Beetle Traces on Dinosaur Bone from the Upper Jurassic Morrison Formation, Wyoming, USA. Ichnos 15(2):59 - 71

Kurz WA, Dymond CC, Stinson G, Rampley GJ, Neilson ET, Carroll AL, Ebata T, Safranyik L (2008) Mountain pine beetle and forest carbon feedback to climate change. Nature 452(7190):987-990

Monday, June 2, 2008

The problem:

Spiders. Or at least one rather large, fast-moving, and intent on web-building spider that successfully terrorized Kristen and I out of the lab this afternoon. Yes, that's the other problem: at 4:30 in the afternoon in the summer, Kristen and I are the only ones around, and neither of us are quite brave enough to deal with little Boris. To be fair, Kristen did almost manage to get him onto a board, which she claims she would then have left in the hallway for a less arachnophobic individual to deal with. Sadly, Boris was too smart for the board trick and instead escaped into a box under the table. I, meanwhile, was doing a trendy new dance in the hallway to the tune of "oh gross oh gross oh gross" - the hot dance number involves much jumping up and down and shuddering in repugnance. As such, we have both sworn off touching, moving, and certainly cleaning any of the boxes under the tables until someone brave enough to squish and/or extract spiders and other creepy crawlies is in the room.

If anyone is interested, we're going to attempt to reclaim our territory tomorrow at 1:30, so as to continue the work we are getting paid to do. If anyone wants to show up as spider protection, I at least would be grateful (I don't want to drag Kristen into my pathetic woe). Alternately, if someone would like to lie and tell us that they were in the lab tonight and saw poor Boris, and "rescued" him to outside West Hall, I will enthusiastically believe the falsehood in favor of my mind's well-being. Hint, hint!

Oh, and this might put a damper on the camping plans proposed in the last post's comments...