Evo-Devo

Come hear me talk about brains on Tuesday

/ zcofran / Leave a comment

This coming Tuesday I’ll be giving a talk about the evolution and development of the human brain, as part of the seminar series of the School of Humanities and Social Sciences here at Nazarbayev University. My research doesn’t really fall neatly under the realms of ‘humanities and social sciences,’ so  the talk should be a neat change of pace for these SHSS seminars. I’ll be previewing something I’ve been working on with Dr. Jeremy DeSilva, and that I’ll be presenting at the AAPA conference in a few weeks. So if you can’t make it to Astana, maybe you can catch the shorter show in Knoxville!

Here’s info from the flier (sorry about the title, I’m new to this; also, I won’t be talking for 90 minutes):

Building the Most Powerful Computer: Evo-Devo of the Human Brain


4:20-5:50 pm
Tuesday, 26 March 2013

at Nazarbayev University, Block 7, Room 7-507
53 Kabanbay Batyr Ave.
Astana

Synopsis: Your brain is one of the most remarkable things to emerge in all the history of Life, and has been a critical part of humans’ adaptive success. This talk will examine how this machine came into existence. I will first describe how the brain grows and develops across an individual’s lifetime. Next I turn to the possible ways development was modified during the course of our evolution to result in our singularly powerful brains. Special attention is given to teasing out secrets of brain evolution from the dismal fossil record.

Taking back Epigenetics

/ zcofran / 1 Comment

If I’m good at anything, it’s looking into one topic and then getting distracted by something else during my search. In a recent case, I was scouring the literature on growth and life history. One ribald thing led to another, and next thing I know I’ve stumbled upon Gunter Wagner’s recent review of the book Epigenetics: Linking Genotype and Phenotype in Development and Evolution. WTF is epigenetics, you ask? That’s actually a pretty good question (see here). In the past several years, the term has most often been associated with the causes/effects of structural modifications to chromatin (the DNA-containing stuff that makes up chromosomes). For sure, coincident with Wagner’s review, a paper in last week’s Nature Reviews Genetics defines epigenetics as “the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence.” (Feil and Fraga 2012).

This is an extremely narrow focus for a term that was originally meant to be about basically everything besides genes that contribute to an organism’s phenotype (this idea was developed by the great, rather underrated, 20th century biologist Conrad Waddington). Lotsa epigenetics research by the narrow definition (i.e. modifications to histones and chromatin) focuses on how cells – not organisms – retain their identity/function (or, phenotype). Epigenetics in the narrow sense are important determinants of an organism’s phenotype, but these alone are insufficient to understand how and why organisms’ become the way they are. Yes, the narrow definition leaves room for environmental influences on gene expression (though “environment” could refer to the state of affairs within a cell or an organism, in addition to the outside world). But it nevertheless imparts agency solely to genomes in affecting an organism becomes.

And this is what the aforesaid book and review are about. Wagner asks, “what would be lost if the original perspective of epigentics [as defined by Waddington] was lost to science?” This is important because an organism is not simply a robotic readout of its genes, but people cannot seem to shake this centuries-old biological determinism.

Is that a homunculus
in your [sperm’s]
pocket?

In the early days of ‘modern’ (or let’s say ‘recent’) biology, there was a popular idea of “Preformationism,” that animals grew from these pre-formed miniature versions of themselves (homunculi) in germ cells. It did not take long for this idea to be quashed, but the underlying idea persisted. Wagner recounts, “With the rise of genetics during the 20th century, however, a new form of quasi-preformism arose, basically replacing the old homunculus with the genome, whereas the developmental process creating the phenotype was put in a black box” (emphasis mine). [See Gilbert et al. (1996) for a nice historical overview describing how the rise of population genetics in the early 20th century left embryology and developmental biology by the wayside of the Modern Evolutionary Synthesis]

This latent desire to essentialize biology to some singular determinant (be it an homunculus or a gene) is something people just can’t get away from. Srsly, there’s a persistent sentiment in biology that Real Science is only the high-profile, lab-coated work in genetics. Along these lines, even I adopted the recently popular narrow view of “epigenetics” a while back when I dated a woman who worked at an epigenetics lab, in hindsight probably so I would sound more like a capital-S Scientist (below).

Hipster scientist. H3S10 phosphorylation correlates with 
decreased levels of heterochromatin, possibly regulating
chromosome condensation (Chenet al 2008). Image: bit.ly/zEfPaq

Of course, genes code for how a cell should behave, but we have this tendency to want to extrapolate from the cell to the organism, and this is where developmental biology becomes a critical link. And this is what the new Epigenetics book is about (so far as I can tell, I haven’t yet had a chance to read it all).

It’s abundantly clear that phenotypes arise out of an inextricably complex series of interactions – between genes, proteins, cells, tissues, environments, etc. These interactions do not occur solely at the genetic (or narrow-sense epigenetic) level. Developmental biology helps ‘connect the dots’ between genes and morphology, but cannot do so by focusing solely on genes and chromatin.

ResearchBlogging.org

References
Chen, E., Zhang, K., Nicolas, E., Cam, H., Zofall, M., & Grewal, S. (2008). Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature, 451 (7179), 734-737 DOI: 10.1038/nature06561

Feil, R., & Fraga, M. (2012). Epigenetics and the environment: emerging patterns and implications. Nature Reviews Genetics DOI: 10.1038/nrg3142

Gilbert, S. (1996). Resynthesizing Evolutionary and Developmental Biology. Developmental Biology, 173 (2), 357-372 DOI: 10.1006/dbio.1996.0032

Hallgrímsson B and Hall BK, eds. 2011. Epigenetics: Linking Genotype and Phenotype in Development and Evolution. Berkeley: University of California Press.

Wagner, G. (2011). Epigenetics in all its beauty Trends in Ecology & Evolution DOI: 10.1016/j.tree.2011.09.003

Evo-devo of the human shoulder?

/ zcofran / 1 Comment

It’s a new year, and while my mind should be marred by a hangover, instead all I can think about are fossils and scapulas.


A pretty cool study was published online in the Journal of Human Evolution last week, and I’ve finally gotten to peruse it. Fabio Di Vincenzo and colleagues analyzed the shape of the outline of the glenoid fossa on the scapula (not to be confused with the glenoid on your skull), from Australopithecus africanus to present day humans. The glenoid fossa is essentially the socket in the ball-and-socket joint of your shoulder. The authors found that there is pretty much a single trend of glenoid shape change from Australopithecus through the evolution of the genus Homo: from the fairly narrow joint in Australopithecus africanus and A. sediba, to the relatively wide joint in recent humans. The overall size and shape of the joint influences/reflects shoulder mobility, so presumably this shape change hints that more front-to-back arm motions became more important through the course of human evolution (authors suggest throwing in humans from the Late Pleistocene onward).



The finding of a single predominant trend in glenoid shape evolution is pretty interesting. On top of that, the authors add an ‘evo-devo’ twist by comparing species’ average “shapes” (first principle component scores, on the y-axis in the figure at right) with their estimated ages at skeletal maturity (which appears scaled to the modern human value, on the x-axis). Though it’s not an ideal dataset for running a linear regression, the figure at right shows that there appears to be a fairly linear relationship across human evolution, such that groups with an older age at skeletal maturity tend to have a more rounded (modern human-like) glenoid fossa (note that the individuals in the analysis were all adults). Overall size does not contribute to shape variation among these glenoids.


This work raises two issues, and ultimately leads to a testable evo-devo hypothesis. The first issue is to what extent we can trust their estimates of age at skeletal maturity. These estimates were allegedly taken from a chapter by Helmut Hemmer (2007) in the prohibitively expensive Handbook of Paleoanthropology. Cursorily glancing at this chapter, I can’t find age at skeletal maturation estimated for any hominids. It is possible that in my skimming I missed the estimates, or alternatively that Di Vincenzo and colleagues misinterpreted another variable as skeletal development. Either way, these estimates would still need to be taken with a grain of salt, given that it is almost impossible to know the true age at death of a fossil (but see Antoine et al. 2008), especially if there are no associated cranio-dental elements.


That said, it is perfectly reasonable to suppose that the age at skeletal maturation has increased over the course of human evolution; life-span increased through human evolution, and so all else being equal (which it almost certainly isn’t) we could expect that maturation would occur later over time, too. So this leads to a second issue: given the “evo-devo change” the authors hypothesize, what is the evo-devo mechanism? That is, how was development modified to effect the evolutionary changes we see in the hominid scapula? Because they found adult glenoid shape correlates with estimated age at skeletal maturity, this leads to the hypothesis that postnatal skeletal growth accounts for the shape difference. Indeed, they state:

“If functional and static allometric influences are unlikely, we…interpret the trend…as reflecting growth and developmental factors. A major, albeit gradual, trend of ontogenetic heterochrony occurred in the evolution of the genus Homo… and thus differences within and between taxa in overall growth rates may have produced the pattern of variation between samples, as well as the overall temporal trend observed. The regression of life history variables [they only looked at 1]… with PCA [principle components analysis] scores supports this ‘ontogenetic’ hypothesis.”

The authors suggest that humans’ slower growth rates but longer growth period “led to longer periods of bone deposition along the inferior-lateral edge of the [glenoid fossa]”  The heterochronic process they suggest is “peramorphosis” – the descendant reaches a shape that is ‘beyond’ that of the ancestor.

The figure above is from a seminal “heterochrony” paper by Pere Alberch and colleagues (1979), portraying how peramorphosis can occur. In each, the y-axis represents shape and the x-axis is age. A the descendant’s peramorphic shape (“Ya”) could result from accelerated growth (left graph) or from an extension of growth to later ages than in the ancestor (right graph).


And so this leads to a testable hypothesis. Di Vincenzo and colleagues cite (dental) evidence that humans’ overall body growth rates are slower than earlier hominids’, undermining the hypothesis that acceleration is responsible for humans’ glenoid peramorphosis. Rather, they hypothesize that humans’ slower growth rates coupled with a longer period of skeletal development, to result in a relatively wider glenoid, due to increased development of the secondary growth centers (e.g. the graph at right, above). This developmental scenario predicts that subadult human glenoids should resemble earlier hominid adults’, that “ontogeny recapitulates phylogeny” as far as glenoid shape is concerned. Analyzing glenoid growth can even be extended to include fossils – the >3 million year old human ancestor Australopithecus afarensis has glenoids preserved for an infant (DIK-VP-1; Alemseged et al. 2006) and 2 adults (AL 288 “Lucy” and KSD-VP-1; Johanson et al. 1982, Haile-Selassie et al. 2010). An alternate hypothesis is that species’ distinct glenoid shapes are established early during life (i.e. in utero), and/or that no simple heterochronic process is involved.


ResearchBlogging.orgDi Vincenzo’s and colleagues’ study points to the importance of development in understanding human evolution, and their hypothesized “evo-devo change” in glenoid shape is ripe for testing.


References
Pere Alberch, Stephen Jay Gould, George F. Oster, & David B. Wake (1979). Size and shape in ontogeny and phylogeny Paleobiology, 5 (3), 296-317


Alemseged, Z., Spoor, F., Kimbel, W., Bobe, R., Geraads, D., Reed, D., & Wynn, J. (2006). A juvenile early hominin skeleton from Dikika, Ethiopia Nature, 443 (7109), 296-301 DOI: 10.1038/nature05047


Antoine, D., Hillson, S., & Dean, M. (2009). The developmental clock of dental enamel: a test for the periodicity of prism cross-striations in modern humans and an evaluation of the most likely sources of error in histological studies of this kind Journal of Anatomy, 214 (1), 45-55 DOI: 10.1111/j.1469-7580.2008.01010.x


Di Vincenzo, F., Churchill, S., & Manzi, G. (2011). The Vindija Neanderthal scapular glenoid fossa: Comparative shape analysis suggests evo-devo changes among Neanderthals Journal of Human Evolution DOI: 10.1016/j.jhevol.2011.11.010


Haile-Selassie, Y., Latimer, B., Alene, M., Deino, A., Gibert, L., Melillo, S., Saylor, B., Scott, G., & Lovejoy, C. (2010). An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia Proceedings of the National Academy of Sciences, 107 (27), 12121-12126 DOI: 10.1073/pnas.1004527107


Hemmer, Helmut (2007). Estimation of Basic Life History Data of Fossil Hominoids Handbook of Paleoanthropology, 587-619 DOI: 10.1007/978-3-540-33761-4_19


Johanson, D., Lovejoy, C., Kimbel, W., White, T., Ward, S., Bush, M., Latimer, B., & Coppens, Y. (1982). Morphology of the Pliocene partial hominid skeleton (A.L. 288-1) from the Hadar formation, Ethiopia American Journal of Physical Anthropology, 57, 403-451 DOI: 10.1002/ajpa.1330570403

A poor depiction, indeed

/ zcofran / Leave a comment

As I’ve alluded to in some previous posts, in the Spring semester of 2012, I’ll be teaching “Anthrbio 297: Human Evo-devo” at the University of Michigan. It should be a really fun and interesting class, examining the role of development in human evolution.

Ernst Haeckel’s drawing of embryonic stages in some vertebrates. Taken from Richardson et al. 1997

My department recommends I create a flier that can be posted around campus. One of my first ideas was to adapt a Haeckel’s classic illustration of embryos of different animals passing through similar stages in utero (which we know today isn’t exactly correct; Richardson et al. 1997), but spin it to include primates and fossil humans. I started sketching it out (very crudely), but kept getting distracted with my pitiful attempts at multitasking. When I stopped zoning out, I was aghast to find my adaptation had taken a peculiar turn.

ResearchBlogging.orgI won’t quit my day job.
More about vertebrate embryology
Richardson, M., Hanken, J., Gooneratne, M., Pieau, C., Raynaud, A., Selwood, L., & Wright, G. (1997). There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development Anatomy and Embryology, 196 (2), 91-106 DOI: 10.1007/s004290050082

Pictures worth thousands of words and dollars

/ zcofran / 2 Comments

ResearchBlogging.orgLooking into subdural empyema, which is a meningeal infection you don’t want, I stumbled upon a study from the roaring 1970s – the glorious Nixon-Ford-Carter years – using computerized axial tomography (hence, CAT scan) to visualize lesions within the skull (Claveria et al. 1976). Nowadays people refer to various similar scanning techniques simply as “CT” (for computed tomography, though this is not exactly the same as magnetic resonance imaging, MRI).

It’s pretty amazing how medical imaging has advanced in the 35 years since this study. For example, to the right is a CAT scan from Claveria et al. (1976, Fig. 4). These are transverse images (“slices”) through the brain case, the top of the images corresponding to the front of the face. You can discern the low-density (darker) brain from the higher density (lighter) bone – the sphenoid lesser wings and dorsum sellae, and petrous pyramids of the temporal bones are especially prominent in the top left image. In the bottom two images you can see a large, round abscess in the middle cranial fossa. Whoa.

What makes this medical imaging technique so great is that it allows a view inside of things without having to dissect into them. Of course, the downside is that it relies on radiation, so ethically you can’t be so cavalier as to CT scan just any living thing. If I’d been alive in 1976, CAT scanning would’ve blown my mind. Still, the image quality isn’t super great here, there’s not good resolution between materials of different densities, hence the grainy images.

But since then, some really smart people have been hard at work to come up with new ways to get better resolution from computerized tomography scans, and the results are pretty amazing. To the left is a slice from a synchrotron CT scan of the MH1 Australopithecus sediba skull (Carlson et al. 2011, Supporting on line material, Fig. S10). You’re basically seeing the fossil face-to-face … if someone had cut of the first few centimeters of the fossil’s face. Just like the movie Face Off.

Quite a difference from the image above. Here, we can distinguish fossilized bone from the rocky matrix filling in the orbit, brain case and sinuses. Synchrotron even distinguishes molar tooth enamel from the underlying dentin (see the square). The post-mortem distortion to the (camera right) orbit is clear. It also looks as though the hard palate is thick and filled with trabecular bone, as is characteristic of robust Australopithecus (McCollum 1999). Interesting…

Even more remarkable, the actual histological structure of bone can be imaged with synchrotron imaging. Mature cortical bone is comprised of these small osteons (or Haversian systems), that house bone cells and transmit blood vessels to help keep bone alive and healthy. Osteons are very tiny, submillimetric. To the right is a 3D reconstruction of an osteon and blood vessels, from synchrotron images (Cooper et al. 2011). The scale bar in the bottom right is 250 micrometers. MICROmeters! Note the scan can distinguish the Haversian canal (red part in B-C) from vessels (white part in B). Insane!

Not only has image quality improved over the past few decades, but CT scanning is being applied outside the field of medicine for which it was developed; it’s becoming quite popular in anthropology. What I’d like to do, personally, with such imaging is see if it can be used to study bone morphogenesis – if it can be used to distinguish bone deposition vs. resorption, and to see how these growth fields are distributed across a bone during ontogeny. This could allow the study the proximate, cellular causes of skeletal form, how this form arises through growth and development. If it could be applied to fossils, then we could potentially even see how these growth fields are altered over the course of evolution: how form evolves.

References
Carlson KJ, Stout D, Jashashvili T, de Ruiter DJ, Tafforeau P, Carlson K, & Berger LR (2011). The endocast of MH1, Australopithecus sediba. Science (New York, N.Y.), 333 (6048), 1402-7 PMID: 21903804

Claveria, L., Boulay, G., & Moseley, I. (1976). Intracranial infections: Investigation by computerized axial tomography Neuroradiology, 12 (2), 59-71 DOI: 10.1007/BF00333121

Cooper, D., Erickson, B., Peele, A., Hannah, K., Thomas, C., & Clement, J. (2011). Visualization of 3D osteon morphology by synchrotron radiation micro-CT Journal of Anatomy, 219 (4), 481-489 DOI: 10.1111/j.1469-7580.2011.01398.x

McCollum, M. (1999). The Robust Australopithecine Face: A Morphogenetic Perspective Science, 284 (5412), 301-305 DOI: 10.1126/science.284.5412.301

Teaching next summer

/ zcofran / 2 Comments

When I was working at Dmanisi this summer, I used a lot of my free time to develop a course on human evolutionary developmental biology, or evo-devo. I submitted this to my department, and I’m excited to announce that I’ll be teaching this class at U of M in Spring 2012. So if you’re at UM and want to take a badass class exploring the evolution and development of the human body, keep an eye out for this new anthropology offering (NB I need to come up with a catchy title for the class still).

The tentative textbook for the class will be Lewis Held’s Quirks of Human Anatomy: An Evo-Devo Look at the Human Body, which I just got in the mail yesterday. It got very good reviews and should be an interesting read, and with just under 3000 references it has a pretty useful bibliography, too. I’m really looking forward to reading this, and even the first page of the preface points to something promising:

“In Chapter 13 of Origin, Darwin asserted that the evidence from embryology alone was strong enough to convince him of the principle of common descent. Human embryos make many structures we don’t need, and we destroy others after we’ve gone to the trouble of making them. No engineer in his right mind would ever allow such idiocy.”

I can’t wait to read about these idiocies.

Teaching is an important part of my work, but I’ll admit that sometimes I’d rather be doing other things than preparing lessons, assignments and such. I have to say, though, I’ve had a lot of fun preparing this class so far. I’ll keep you posted about what I think of the book and how the course-planning comes along.

[insert clever quip about australopithecus hips]

/ zcofran / Leave a comment

A week and a half ago, Kibii and colleagues (2011) published reconstructions and re-analyses of two hips belonging to the 1.98 million-year old Australopithecus sediba. As with many fossil discoveries, these additions to the fossil record raise more questions than they answer. Unless the question was, “did A. sediba have a pelvis?” It did. Here’s a good summary from the paper itself:

Thus, Au. sediba is australopith-like in having a long superior pubic ramus and an anteriorly positioned and indistinctly developed iliac pillar…[and] Homo-like in having vertically oriented and sigmoid shaped iliac blades, more robust ilia, and a narrow tuberoacetabular sulcus…and the pubic body is upwardly rotated as in Homo. (p. 1410, emphases mine)

So far as I can tell, the main way the hips are ‘advanced’ toward a more human-like condition is that the iliac blades are more upright and sweep forward more than in earlier known hominid hips. Here’s the figure 2 from the paper (more sweet pics of the fossils are available here). NB that in both A. sediba hips much of the upper portions of the iliac blades are missing (reconstructed in white; this region is missing in lots of fossils), so it’s possible they were more flaring like the australopith in the center photo.

The authors’ bottom-line, take-home point is that the A. sediba pelvis has features traditionally associated with large-brained Homo – but belonged to a small-brained species (based solely on the ~430 cc MH1 endocast). They argue that this means that many of these unique pelvic features did not evolve in the context of birthing large-brained babies, as has often been thought. They state that these features are thus “most parsimoniously attributed to altered biomechanical demands on the pelvis in locomotion,” and suggest that this hypothetical locomotion was mostly bipedalism but with a good degree of climbing. Maybe, maybe not. This interpretation is consistent with the analysis of the A. sediba foot/ankle (Zipfel et al. 2011).

The weird mix of ancient (australopith-like) and newer (Homo-like) pelvic features in A. sediba really raises the question of how australopithecines moved around. More intriguing is that the A. sediba pelvis has different Homo-like features than the ~1 million year old Busidima pelvis (Simpson et al. 2008), which has been attributed to Homo erectus (largely in aspects of the iliac blades). This raises the question of whether A. sediba is really pertinent to the origins of the genus Homo, and whether the Busidima pelvis belongs to Homo erectus or a late-surviving robust australopithecus (e.g. boisei, Ruff 2010).

Also interesting is that the subpubic angle (in the pic above, the upside-down “V” created by the pubic bones just above the red labels) is pretty low in MH2. This is curious because modern human males and females differ in how large this angle is – females tend to have a large angle which contributes to an enlarged birth canal, whereas males have a low angle like MH2. But MH2 is considered female based on skeletal and dental size. This raises the additional questions of whether human-like sexual dimorphism had not evolved in hominids prior to 1.9 million years ago, and whether the sex of MH2 was accurately described.

Finally, though the authors did a great job comparing this pelvis with those from other hominids, I think a major, more comprehensive comparative review of hominid pelves is in order. How does the older A. afarensis hip from Woranso (Haile-Selassie et al. 2010) inform australopithecine pelvic evolution? What about the possibly-contemporary-maybe-later hip from the nearby site of Drimolen (Gommery et al. 2002)? Given the subadult status of the MH1 individual, it would be interesting to compare with the WT 15000 Homo erectus fossils, or A. africanus subadults from Makapansgat, to examine the evolution of pelvic growth.

ResearchBlogging.org

Lots of interesting questions arise from these fascinating new fossils. “The more you know,” right?

References
Gommery, D. (2002). Description d’un bassin fragmentaire de Paranthropus robustus du site Plio-Pléistocène de Drimolen (Afrique du Sud)A fragmentary pelvis of Paranthropus robustus of the Plio-Pleistocene site of Drimolen (Republic of South Africa) Geobios, 35 (2), 265-281 DOI: 10.1016/S0016-6995(02)00022-0

Haile-Selassie Y, Latimer BM, Alene M, Deino AL, Gibert L, Melillo SM, Saylor BZ, Scott GR, & Lovejoy CO (2010). An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. Proceedings of the National Academy of Sciences of the United States of America, 107 (27), 12121-6 PMID: 20566837

Kibii, J., Churchill, S., Schmid, P., Carlson, K., Reed, N., de Ruiter, D., & Berger, L. (2011). A Partial Pelvis of Australopithecus sediba Science, 333 (6048), 1407-1411 DOI: 10.1126/science.1202521

Ruff, C. (2010). Body size and body shape in early hominins – implications of the Gona Pelvis Journal of Human Evolution, 58 (2), 166-178 DOI: 10.1016/j.jhevol.2009.10.003

Simpson, S., Quade, J., Levin, N., Butler, R., Dupont-Nivet, G., Everett, M., & Semaw, S. (2008). A Female Homo erectus Pelvis from Gona, Ethiopia Science, 322 (5904), 1089-1092 DOI: 10.1126/science.1163592

Zipfel, B., DeSilva, J., Kidd, R., Carlson, K., Churchill, S., & Berger, L. (2011). The Foot and Ankle of Australopithecus sediba Science, 333 (6048), 1417-1420 DOI: 10.1126/science.1202703

And I thought I had it bad (or, "Toad terrors")

/ zcofran / 3 Comments

The world can be a terrible place. Sure, there are the finer things that make life worth living – puppies, spooning, hoppy beer, etc. – but there are also things that make you wonder, ‘Now why should anyone ever have to endure this?‘ I recall being a child, growing up on the mean streets of Kansas City, MO, it was a struggle just to get an education. There were bandits that set up a ‘toll’ to cross the bridge to get to the school, and if we didn’t have any pence to put in their pouches, well we’d have to fight our way into the classroom (see map below, of Lincoln College Prep middle school). Getting home in the afternoon was even worse. There was an Iron Maiden. And this thing.
I thought my midwest urban childhood was tough, until today when I read about “cane toads” (Rhinella marina) (below, right). Now, toads in general are odd animals. They’re vertebrates, with a sweet bony spine and skeleton, like us humans and wicked-pisser mammals. But they’re also not like us (“NLU,” as my sweet, politely diabolical grandma would say). Not like us at all. When a human is a baby, she or he looks more or less like an adult, albeit much smaller and cutely misproportioned. But a toad – well, amphibians just have a totally different life plan. Toad babies are these “tadpoles” (or “pollywogs” if you’re feeling especially cavalier and sassy) that don’t have a body with a head and four limbs that can be used for being awesome. Instead, pollywogs are these fat embryo-ish bodies trailing along a slithering tail. Limbs eventually form from tiny buds and the tail is lost. But superficially, the panning out of toad ontogeny looks like giant sperm deciding to become frog-like abomination unto something. So toads are already not quite right from the get go.
But this one species, the cane toad, has tadpoles that EAT THEIR EGG SIBLINGS and EMIT A CHEMICAL THAT STUNTS THE DEVELOPMENT OF THEIR BROTHERS and SISTERS. In the history of human society there have been a number of stories of family eating family, but there is nothing quite like this. It’s a mix between the child-eating Kronos (or Roman “Saturn”) or Thyestes (though his was accidental), and Cain and Abel from the Bible that’s such a smash with the Judeo-Christians, or Romulus and Remus from the mythic founding of Rome. [Hey I guess my Classics BA has come in handy after all!]
So next time you’re feeling down and out, upset with the hand the great Dealer has dealt you, just be glad you weren’t a cane toad. Because then you’d’ve either been eaten/murdered by your older sib, or you’d’ve eaten/murdered your siblings. Yikes.
Feelings aside, this toad presents a very interesting case study. It will be interesting to uncover the biochemistry and genetics behind how the older pollywogs stunt the development of their little brothers and sisters. I can see this really helping with an understanding of how growth and development are controlled and inhibited, and possibly even how they can be manipulated. It would also be interesting to see if in the evolution of these species, there arose any biochemical defenses expressed in eggs and young larvae against older sibs’ fratricidal fragrances, or if it was simply a 1-sided battle.
Life is a funny, funny thing.
Works Ci-toad [sorry for the terrible pun 😦 ]
PS

eFfing Fossil Friday (another late edition)

/ zcofran / 2 Comments
ResearchBlogging.orgI’m sitting at a cafe in Tbilisi, departing at 4:00 am tomorrow for America. Readers will notice that I’ve been MIA while working with the second annual Dmanisi Paleoanthropology Field School. I hate to say it but I’m glad I was too busy to blog all the goings-on (though sorry if it disappointed anyone). All in all it was another great year, and we found some great fossils (about which I don’t think I have permission to say anything at all). Here’s this year’s class with their certification of badassery at the site on the last day:
But Dmanisi won’t be the subject of this belated eFfing Fossil Friday. I’d like instead to turn to the question of just what fossils are good for. I’m told that in China, fossil teeth were once interpreted as dragons’ teeth, and so pulverized and sold as medicine. But what good are they to non-medical science? My recent research interests have come to focus on the relationship between evolution and development. Evolutionary developmental biology (“evo-devo”) research has been dominated by studies of genes, gene expression, and model organisms like fruit flies and mice. In such an environment, the question of the relevance of fossils is especially poignant.
But this morning, while planning a human evo-devo course I hope to teach next summer, I stumbled upon a review paper by Rudolf Raff, titled “Written in Stone: Fossils, genes and evo-devo” (2007). I think the abstract sums things up pretty well:

Fossils give evo-devo a past. They inform phylogenetic trees to show the direction of evolution of developmental features, and they can reveal ancient body plans. Fossils also provide the primary data that are used to date past events, including divergence times needed to estimate molecular clocks, which provide rates of developmental evolution. Fossils can set boundaries for hypotheses that are generated from living developmental systems, and for predictions of ancestral development and morphologies. Finally, although fossils rarely yield data on developmental processes directly, informative examples occur of extraordinary preservation of soft body parts, embryos and genomic information.

It seems often that fossils are falling by the wayside. There’s a sentiment that there’s not much information to be gotten from fossils – they’re too incomplete, too few, too inconvenient, at least as compared with extremely high-output data such as that coming from genomics. But Raff is right – we need fossils. Beyond the excellent points Raff raises in the review, I’m working on getting the most out of these seemingly data-poor fossil samples. Because modern computers are so powerful nowadays, I’m using their sheer processing power to test hypotheses about growth and development in fossil samples. These battered bunches of bones are too tiny to be analyzed by traditional methods. But one thing I think is important to take away from this computer-crazy Information Age, is that we now have machines that can handle almost any kind of question one can think to ask, and it’s really inspiring. The sequencing and analyses of ancient Neandertal and Denisova genomes (Green et al. 2010, Reich et al. 2010) are excellent examples of the amazing research that can be done with computers and creativity (and probably also a horde of hard-working math majors).
So this eFFF (or Sunday) is not dedicated to any specific fossil or set of fossils, but rather to all fossils, even the crappy fragments. Gaumarjos, fossils: your secrets are not safe from us.
Reference
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


Raff, R. (2007). Written in stone: fossils, genes and evo–devo Nature Reviews Genetics, 8 (12), 911-920 DOI: 10.1038/nrg2225
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

Stimulating the drunk on the platform

/ zcofran / Leave a comment

Gotcha! I mean “simulating” in the title, not “stimulating.” This one’s about programming.

I’m interested, for various reasons, in how evolution might bring about change over time. Recall from my Evolution Overview that evolutionary changes could occur by drift or natural selection. Drift means random change, because a given polymorphism has no effect on fitness. Natural selection, on the other hand, is what my advisor likes to call the 900-lb gorilla: it does whatever the eff it wants. Selection can take existing variation in a population and mold it into all kinds of oddities. Within Primates, natural selection has fashioned inquisitive apes that walk on two legs and go to the moon, and sexual selection has festooned male mandrills in variegated visage (right). Selection can be gentle and allow gradual change (what I like to call sensual selection), or it could be strong and cause rapid change.
Selection can seem random for various reasons (e.g. why is it acting as intensely as it does when it does?), so it is hard to tell whether a given evolutionary scenario can be explained by selection for a given behavior, or if it reflects totally random change (drift).
Monte Carlo statistical methods allow one to simulate a given scenario, to test competing hypotheses. A simple null hypothesis that can be simulated is drift – change is completely random in direction, and if I reject this hypothesis I could argue that an alternative explanation (selection) is appropriate

The random walk is the oft-used analogy for this null hypothesis of random change. Now, if I’d ever been so imperfect as to have succumbed to the siren-song of spirits, maybe I’d corroborate the analogy. But using the extent of your limited but unadulterated imagination, pretend there is a drunk kid who happened to go to Loyola Chicago (like myself), and who walks onto the L platform (like I often did; left, looking north from the Lawrence Red Line stop). As booze takes the reins, he stumbles randomly between the edges of the train platform. This random walk down the train platform could result in the drunkard making it safely to the end, or he could fall off either side to a gruesome doom awaiting on the tracks below.

Thinking about limb proportions, and how to program this hypothesis/scenario, I stumbled upon the useful cumsum() function for the R statistical program. This function allows me to indicate how much change to occur for how many steps (i.e. generations), thus effectively simulating the random walk. For example (right), say I want to ask if the tibia (shin bone) gets long relative to the femur (thigh bone) in human evolution, because of drift vs. natural selection. I start with a given proportion of [tibia/femur] and simulate change in a random direction in tibia and femur length, over a quarter million years (or 18,000 15-year generations).

The figure is a bird’s eye view of a random walk: at each generation the drunken tibia/femur ratio steps forward (to the right in the picture) and randomly right or left (toward the top or bottom of the picture). This took literally 2 seconds to program and graph. The dashed black line represents the relative tibia/femur relationship at the beginning of the evolutionary sequence, and the red line is the ratio 250,000 years (18,000 generations) later. Note that in this particular random scenario, not only is the final tibia/femur ratio exactly that observed, but that over the time span this ratio was reached about 20 different times. Do this randomization 500 or more times to see how often random change will result in the observed difference between time periods. Assuming the simulations realistically model reality, the observed change in limb proportions could easily be explained by drift (i.e. climate or efficiency adaptations did not have so strong a selective advantage as to be detected by this test). That is, the change in proportions could have been effected by random change or by weak directional selection.
I’m currently looking for any ways to make the model more realistic, for example:
  1. how much evolution (e.g. change) could occur per generation. Currently, each generation changes by plus or minus a given maximum. I would like to be able to simulate any amount of change between zero and an a priori maximum.
  2. it’s easier to let the tibia and femur change randomly with respect to one another. However, this is unrealistic because the thigh and leg are serially homologous, their variation is not independent of one another. I would like to model each element’s change per generation to reflect this covariance.
Anyway, I’ve only begun looking into the topic of how to analyze evolutionary change, but it looks like testing evolutionary hypotheses might not be impossible?