turned out to have bigger genomes than humans.

The genome of Gonyaulax polyhedra, for example, is 28 times the size of ours. A solution of sorts emerged in the 1970s: so-called junk DNA. In addition to proteincoding genes, genomes contain stretches of DNA that encode RNA molecules or are just vestiges of old genes. Many genomes, including our own, are dominated by viruslike sequences of DNA called mobile elements that can make new copies of themselves that get inserted in new spots in the same genome. The human genome is 98.5% noncoding DNA. Comparing the genomes of living species, scientists have found that genomes can expand and shrink quickly, with mobile elements spreading like a genomic plague. The cotton EVOLUTION genome, for example, tripled in size over the past 5 million to 10 million years. On the other hand, copying errors can cause cells to snip out large chunks of noncoding DNA by accident, Dinosaur fossils are helping scientists tease apart why the sizes of genomes vary so shrinking their genomes in the process. To test whether natural selection plays a dramatically among species strong role in determining the size of a species Tyrannosaurus rex, it turns out, had a pretty impact on tracing the evolution of bird genome, scientists have compared a wide range small genome. A team of American and genomes. Birds are dinosaurs; theyre the last of species, searching for correlations between British scientists estimates that it contained a vestige, says Organ. Scientists have long genome size and other traits that might be adaprelatively puny 1.9 billion base pairs of DNA, noted that birds have small genomes com- tive. Finding these correlations has been diffia little over half the size of our own genome. pared to reptiles, their closest living relatives, cult, however, because relatively few genomes The scientists who came up with this esti- but it was unclear how and when that change had been measured until recently, and many of matealong with estimates for the genomes of occurred. Organs study suggests that the those measurements turned out to be wrong. 30 other dinosaur specieshad no ancient dinosaur ancestors of birds had evolved small Genome sizes are easy to misjudge, even with DNA to study. T. rex, after all, became extinct genomes long before birds modern genome sequencing 65 million years ago, and its genome is long took to the sky. I think its methods. When scientists Genomes Big and Small gone. Instead, they discovered a revealing cor- very exciting, says T. Ryan sequence a genome, they relation: Big genomes tend to be found in ani- Gregory, an expert on generally break it up into Nematode (Caenorhabditis mals with big bone cells. By comparing the size genome size at the Univerfragments and then try to elegans): 100 million bp of cells in dinosaur fossils to those of living ani- sity of Guelph in Canada. piece them together like a Thale cress (Arabidopsis mals, the scientists got statistically sound esti- Its the kind of paper weve puzzle. Noncoding DNA thaliana): 160 million bp mates for the sizes of the dinosaur genomes. needed for a long time. is loaded with repeating Fruit fly (Drosophila The findings, published by Nature this sequences, which are diffimelanogaster): 180 million bp week, are more than just a curiosity. Chris Giant genomes in lowly cult to reassemble properly. Puffer fish (Takifugu rubripes): Organ, a Harvard University paleontologist creatures Things are improving, 400 million bp and the lead author of the new paper, says the The wide array of genome says Gregory. New techRice (Oryza sativa): 490 million bp estimates shed new light on a big puzzle: Why sizes startled scientists niques are enabling moredo the genomes of living species come in such when it came to light in the precise measurementsfor Human (Homo sapiens): a staggering range of sizes, varying more than early 1950s. Until then, the instance, scientists are 3.5 billion bp 3000-fold in animals? A fruit flys genome is prevailing wisdom had adding DNA-staining comLeopard frog (Rana pipiens): 350 times smaller than ours, whereas the mar- been that complex animals pounds to cells and then 6.5 billion bp bled lungfish genome is 37 times bigger. needed bigger genomes using image-processing softOnion (Allium cepa): Recently, some large-scale comparisons of than simple ones needed. ware to analyze the amount 16.4 billion bp genome sizes have suggested that natural And yet, as one paper of stain. And the results of Mountain grasshopper (Podisma selection may favor big genomes in some explained, a salamanders these studies are now being pedestris): 16.5 billion bp species and small genomes in others. But genome contains 70 times stored in online databases, Tiger salamander (Ambystoma some skeptics argue that genome size may not as much DNA as is found in making possible large-scale tigrinum): 31 billion bp be adaptive at all. Now, with the advent of a cell of the domestic fowl, comparisons. Gregory mainwhat Organ likes to call dinogenomics, sci- a far more highly developed tains a database of animal Easter lily (Lilium longiflorum): 34 billion bp entists can begin to tease out some answers by animal. As researchers genome sizes at the Univeradding extinct species to the emerging picture sized up more genomes, the sity of Guelph (genomesize. Marbled lungfish (Protopterus of genome evolution. paradox grew deeper. Some com), Kew Gardens bioloaethiopicus): 130 billion bp The new study will have its most direct single-celled protozoans gists manage one for plants

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and algae (www.kew.org/genomesize/ homepage.html), and biologists at the Estonian University of Life Sciences run a database for fungi (www.zbi.ee/fungal-genomesize). Together, the databases contain information on more than 10,000 species. One of the first correlations scientists noticed was between the size of genomes and the size of cells. It cropped up in a study on red blood cells in vertebrates. Later studies also found a link between cell size and genome size in other groups of species, such as plants and protozoans, and in other types of cells in vertebrates, although not all. Some scientists have argued that natural selection favors big or small genomes because they produce big or small cells. Take the case of Trichomonas vaginalis, a sexually transmitted protozoan that lives in the human vagina. When a multi-institute group led by Jane Carlton, who is now at New York University, published the organisms genome in the 12 January issue of Science (p. 207), they observed that T. vaginalis is padded with far more mobile elements than are found in related protozoans that live elsewhere in the body. The scientists suggest that when T. vaginalis moved into its current ecological niche, its genome expanded rapidly. The protozoan itself became bigger as a result, which made it more effective at chasing and engulfing its bacterial prey. Changing cell size may benefit other kinds of species in other ways. In some groups of animals, species with high metabolic rates tend to have small genomes, for example, whereas species with slow metabolisms have big ones. One possible explanation is that small genomes give rise to small blood cells, which have a high surface-to-volume ratio and can transport oxygen faster across their membranes. If a warm-blooded animal needs to use a lot of oxygen to fuel its metabolism, a small genome might give it an evolutionary edge. The fossil record Consistent with this hypothesis, birds have much smaller genomes than those of their reptilian relatives. But if birds evolved smaller genomes for their high metabolism, the question naturally arises, when did that shrinkage take place? Organ realized that dinosaur fossils might hold the answer. Some dinosaur fossils are so well preserved that they still have the cavities that once held their bone cells (known as osteocytes). But no one had ever established a link between genome size and osteocyte size. That was our first step, says Organ. They examined bones from 26 species of birds, reptiles, mammals, and amphibians. With colleagues at Harvard and the University of Reading, U.K., he

2.8 billion bp 3.1 billion bp

Iguana

Crocodile

1.6 billion bp 1.2 billion bp

Emu

Crow

0 mya

Triceratops
3.2 billion bp

Tyrannosaurus
1.9 billion bp

Deinonychus
1.58 billion bp

100 mya

Apatosaurus
2.15 billion bp

Ornithischians Theropods Dinosaurs

200 mya Small Medium Large

CREDITS (TOP TO BOTTOM): JUPITER IMAGES; DORLING KINDERSLEY/GETTY IMAGES; TOM SCHIERLITZ/GETTY IMAGES; SOURCE: ADAPTED FROM CHRIS ORGAN/HARVARD UNIVERSITY

Dinogenomics. Scientists have come up with a method to estimate the sizes of dinosaur genomes. They conclude that todays birds got their small genomes from their dinosaur ancestors.

mapped his measurements onto an evolutionary tree. The correlation was good enough that they could use the size of a speciesosteocytes to accurately predict its genome size. The scientists then added to the tree branches for 31 species of dinosaurs and used the size of their osteocytes to estimate the size of their genomes. From that information, they inferred how the size of dinosaur genomes had evolved over time. Their analysis suggests that the common ancestor of dinosaurs, a small four-footed reptile that lived about 230 million years ago, had a relatively big genome about the same size as an alligators. That common ancestor gave rise to several major branches of dinosaurs. One of those branches, the ornithischians, included big herbivores such as stegosaurs and Triceratops. Their genomes did not change much. These guys have a typical reptilian-sized genome, says Organ. But another branch of dinosaursbipedal predators known as theropodsevolved significantly smaller genomes. Theropods would ultimately give rise to birds. This blows out of the water the idea that small genomes coevolved with flight, says Organ. Organ suggests that theropods evolved to have higher metabolic rates than other dinosaurs had, and as a result, natural selection favored smaller genomes and smaller cells. Other paleontologists have also found evidence for bird biology in bipedal
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dinosaurs, including feathers, rapid growth, and nesting behavior. You dont decide youre going to fly and be warm-blooded like a bird and then make all these changes, says Organ. Theyre all small cumulative things that go way, way back, and they come together to produce this end form. Although Gregory and others praise Organs paper, some scientists are not as impressed. Its a cute paper, but Im not terribly confident in the outcome, says Michael Lynch of Indiana University, Bloomington, who questions whether natural selection is responsible for driving genomes to different sizes to fine-tune metabolism. Theres a correlation of the two, but I dont know of any direct demonstration of causality. Gregory concedes that even if metabolism can account for the small genomes of animals such as dinosaurs and birds, it wont explain all the patterns scientists find. Plants, for example, have a similar correlation between cell size and genome size, for example, but they dont have an animal-like metabolism. Its possible that plants have different genome sizes because genome size changes the way their cells capture sunlight or transport fluids. Any one feature isnt really going to cover it, Gregory says. You have to look from the bottom up and the top down in every case.
CARL ZIMMER
Carl Zimmers latest book, on E. coli and the meaning of life, will be published next spring.

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Birds