March 4, 2008, 8:56 pm

Bones Are Not the Only Fossils

By Olivia Judson

(A fossil footprint from Beit Zait, near Jerusalem. (Olivia Judson)

I put my foot beside the footprint. Whatever made it had feet the same size as mine. Almost exactly. I stepped to the next print. But it had longer legs; or, at least, it took longer strides than I usually do. I knelt down to take a photograph. Three toes. Like the foot of a wading bird. But big.

And old. What was once mud has turned to rock. The animal that left a trail of footprints here, in what is now a small, neglected park in the hills outside Jerusalem, did so in the Cretaceous, more than 65 million years ago.

What made them? The scientist who first described these footprints, back in 1962, thought it might have been Elaphrosaurus, a light, bipedal, meat-eating dinosaur related to T. rex. Others have suggested it was an early bird.

The uncertainty isn’t surprising. Different animals often make similar tracks. Moreover, the places where footprints can be preserved aren’t the same as those that preserve bones. Drying mud flats — the scenes of much footprinting — are places where the bones of a dead animal tend to be stolen by scavengers. So fossil footprints and bones are almost never found together; as a consequence, most prehistoric footprint-makers are known only from their tracks.

But even though the identities of trackmakers may be mysterious, fossil footprints give us information about the past — information that can’t be gathered from bones alone. Early analyses of fossil footprints gave important insights into the postures and gaits of dinosaurs, showing that the animals were more upright and less sprawling than the first palaeontologists had thought, and that they usually carried their tails aloft, rather than dragging them on the ground.


Footprints can also tell you how fast dinosaurs moved: if you know the size of the foot and the length of the stride, speed can be calculated from a simple formula (at right; see notes for details). I applied it to the Jerusalem tracks, and discovered that the animal, assuming it was a dinosaur, was going about six kilometers (3.72 miles) an hour — Roman army marching speed. So not a gallop, but not a stroll.

Until a few years ago, I tended to think of fossils as bones and shells — the vestiges of animal skeletons. But all sorts of other things can leave fossils, too. Footprints are one. Feces, another. Impressions of skin and feathers. Leaves and pollen. Growth rings of trees.

All of these open different windows onto the past; together, they help us construct a richer portrait of it than we could glean from skeletons by themselves. Widths of tree rings indicate rainfall, and thus, climate. Fossil leaves can show damage from the maraudings of ancient insects; analysis of leaf damage can thus illuminate the broader dynamics of ecosystems. Fossil feces (“coprolites”) reveal extinct diets; they can also reveal attributes of plants where actual plant fossils are missing. For instance, the early fossil record of grasses is poor, and the tough structures of grass stems have been postulated to have evolved in response to their being eaten by grazing mammals. But bits of grass in coprolites from the Cretaceous show that grasses had begun to diversify earlier than we thought, and that grasses were made of tough stuff before the grazers appeared.

Of the various fossil phenomena I’ve heard of, however, here’s the one I find most surprising: genomes. I hadn’t thought of genomes as being something that could leave a direct, physical mark, a genome-print. But they do.

Genomes are made of DNA, so the bigger the genome an organism has, the more DNA it has in each cell. This, in turn, affects the volume of the cells. And although different types of cells within an organism have different characteristic volumes, all of them are affected by the amount of DNA they contain. So if you compare cells of the same type across a range of related species, you’ll find that differences in sizes reflect differences in how much DNA the cells have. (Some estimates suggest that as much as half of the variation in cell size of a given type can be accounted for by differences in genome size.)

The volumes of some types of cell can be measured from fossil skeletons or leaves. Which gives a method for estimating the genome sizes of organisms long extinct. For instance, the size of osteocytes — bone cells — can be measured from cross sections of fossil bone. Similarly, in plants, you can measure the size of guard cells in fossil leaves. (Guard cells border the pores, known as stomata, through which plants take up carbon dioxide and excrete oxygen and water vapor.)

Genome size is one of the more curious aspects of natural history. Among eukaryotes — organisms, such as animals, plants and fungi, that keep their DNA sequestered in the cell nucleus — differences in genome size can be prodigious. For instance, the amoeba known as Amoeba dubia has only one cell, yet its genome holds the world record for enormity. It’s nearly 200 times larger than ours, and more than 200,000 times larger than that of another single-celled organism, a parasite known as Encephalitozoon cuniculi. Most birds have tiny genomes. Some lilies have gigantic ones. In short, there’s no obvious relationship between genome size and the number of genes you have, or how complex an organism you are.

The reason is that differences in genome size are accounted for not by the numbers or sizes of genes — the stretches of DNA that contain the instructions for making proteins — but by varying amounts of “extra,” non-protein-coding DNA, sometimes known as “junk.” (I don’t like “junk,” which suggests the DNA is useless: even if it doesn’t hold the instructions for making proteins, it may still serve a valuable purpose. For instance, stretches of non-coding DNA between parts of a gene can regulate how fast the protein gets made.)

Again, genome-prints tell us more than the mere facts of genomic bigness. They hold information about metabolism and lifestyle. Larger genomes take longer to copy, and many metabolic processes get slower as well. Conversely, small genomes tend to be accompanied by a high metabolism (animals) or rapid growth (plants). Above a certain genome size, plants are condemned to a perennial lifestyle: they can’t grow fast enough to be annuals. Similarly, it’s been suggested that the small genomes of birds evolved in tandem with the ability to fly — flight being an activity that demands a high metabolic rate. Consistent with this idea, flightless birds have larger genomes than flighty birds, and bats generally have smaller genomes than other mammals.

But it now looks as though small genomes preceded flight in birds by more than 200 million years. Analysis of the size of bone cells from fossils shows that the saurischian dinosaurs — the branch of dinosaurs from which birds are descended — evolved small genomes (and, presumably, high metabolisms) early on. Small genomes may have permitted the evolution of flight; but they did not, it seems, evolve in response to it.

A gust of wind sends leaves skittering across the ground and, interrupting my reverie, brings me back to this place, where feet walked ages before we built Jerusalem. In comparison to the megatrackways of the western United States, which extend for miles and contain tens of thousands of footprints from all manner of different beasts, the series of twenty or so prints in front of me is paltry. But I’ve never seen wild footprints before — up to now the only fossil footprints I’ve seen have been behind glass in museums — and I can’t help feeling moved as I contemplate these tangible traces of a long vanished world.



The tracks outside Jerusalem are described in Avnimelech, M. 1962. “Dinosaur tracks in the lower Cenomanian of Jerusalem.” Nature 196: 264. Their possible identity as bird footprints is raised in Lockley, M. G., Yang, S. Y., Matsukawa, M., Fleming, F., and Lim, S. K. 1992. “The track record of Mesozoic birds: evidence and implications.” Philosophical Transactions of the Royal Society of London B 336: 113-134.

For insights that the study of dinosaur footprints has led to, see Farlow, J. O. and Chapman, R. E. 1997. “The scientific study of dinosaur footprints.” In: Farlow, J. O. and Brett-Surman, M. K. (editors), “The Complete Dinosaur,” Indiana University Press, pp. 519-553, and, in the same book, Lockley, M. G. “The paleoecological and paleoenvironmental utility of dinosaur tracks.” pp. 554-578.

The formula for dinosaur speeds is given in Alexander, R. McN., 1976. “Estimates of speeds of dinosaurs.” Nature 261: 129-130.

If anyone wants to check my calculation of the speed of the Jerusalem animal,

s = .25g0.5?1.67h-1.17

where s is speed in meters / second, g is the gravitational constant (9.8 m/s/s), ? is stride length (in this case, 1.6 m), and h is hip height (~4*foot length, which in this case is 26 cm, giving an h of 1.04.). This gives 1.63 meters/second, or approximately 6 km/hour. I didn’t have a measuring tape with me; the measurements are taken from Avnimelech, M. 1962. “Dinosaur tracks in the lower Cenomanian of Jerusalem.” Nature 196: 264. The marching speed of the Roman army is given in Vegetius, “The Military Institutions of the Romans (De Re Militari)”, translated by Lt. John Clarke in 1767. This is available online. Note that Roman miles are shorter than modern miles.

For an example of the insights that can be gained from fossil leaves, see Wilf, P., Labandeira, C. C., Johnson, K. R., and Ellis, B. 2006. “Decoupled plant and insect diversity after the end-Cretaceous extinction.” Science 313: 1112-1115. For coprolites and grasses, see Prasad, V., Strömberg, C. A. E., Alimohammadian, H., and Sahni, A. 2005. “Dinosaur coprolites and the early evolution of grasses and grazers.” Science 310: 1177-1180.

For estimates of the fossil genome sizes of dinosaurs and birds, and for the extent to which differences in genome size explain differences in cell size, see Organ, C. L., Shedlock, A. M., Meade, A., Pagel, M., and Edwards, S.V. 2007. “Origin of avian genome size and structure in non-avian dinosaurs.” Nature 446: 180-184. For estimates of fossil plant genome sizes, see Masterson, J. 1994. “Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms.” Science 264: 421-424.

For a recent survey of genome sizes and their effects, as well as a discussion of the relationship with cell volume, see Gregory, T. R. 2001. “Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma.” Biological Reviews 76: 65-101. For plants with large genomes being forced to be perennials, see Bennett, M. D., and Leitch, I. J. 2005. “Genome size evolution in plants.” In: Gregory, T. R. (ed) “The Evolution of the Genome.” Elsevier, pp 89-162. For the relationship between flight and genome size in birds, see p. 203 of Hughes, A. L. 1999. “Adaptive Evolution of Genes and Genomes.” Oxford University Press. For small genomes in bats, see Burton, D. W., Bickham, J. W., Genoways, H. H. 1989. “Flow-cytometry analyses of nuclear DNA content in four families of neotropical bats.” Evolution 43: 756-765.

Many thanks to Dan Haydon, Alon Lazarus, Nathan Myhrvold, Dmitri Petrov and Jonathan Swire for insights, comments and suggestions.

Author notes:

Olivia Judson's The Wild Side Blog

Olivia Judson, an evolutionary biologist, is the author of “Dr. Tatiana’s Sex Advice to All Creation: The Definitive Guide to the Evolutionary Biology of Sex,” which was made into a three-part television program. Ms. Judson has been a reporter for The Economist and has written for a number of other publications, including Nature, The Financial Times, The Atlantic and Natural History. She is a research fellow in biology at Imperial College London.

Related links:

Red Gulch Dinosaur Tracksite Wyoming

Miocene Epoch Elephant footprints in Abu Dhabi

The Miocene Epoch

Overview of Dinosaur Tracking Research

Origins Controversies