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Vertebrate Genomes Compared How the Concept of “Model Organism” Has 21 Changed S CIENCE’ S C OMPASS 65 text falls short of what might be expected 64 of an encyclopedia—the author’s lack of 63 expertise in several aspects of meteoritics 62 has resulted in errors. The straightforward 61 text takes the traditional approach of sys- 60 tematically describing stones, stony-irons, 59 and iron meteorites in terms of their clas- 58 sification and properties. The book is not 57 the sort that a nonspecialist would read in 56 order to learn about meteorites; it is much Image not 55 too technical for that. However, it is beau- available for 54 tifully and lavishly illustrated with many 53 pictures of meteorites in thin section as online use. 52 well as of hand specimens. These images 51 should help the work fulfill another of its 50 goals, providing a “guide to assist 49 searchers in the field to recognize the 48 many classes of meteorites.” 47 Meteoritics has come a long way in the 46 208 years since Chladni’s publication. Be- 45 van and de Laeter devote their final chapter 44 to looking to the future, in which they con- 43 sider missions to Mars, comets, and aster- BROWSINGS 42 oids, along with efforts to retrieve interstel- Earth from Above. Revised and Expanded Edition. Yann Arthus-Bertrand. Abrams, New 41 lar dust. Much remains for the next 200 York, 2002. 462 pp. $45.00. ISBN 0-8109-3495-7. Earth From Above. An exhibit at Mil- 40 years; we are still looking for meteorites lennium Park, Chicago, IL, through 30 September 2002. 39 that are indubitably from Mercury, Venus, a With a helicopter as his preferred tripod, Arthus-Bertrand specializes in composing im- 38 cometary nucleus, and a Kuiper belt object. ages on the fly. Ranging from an intimate glimpse at a worker resting on cotton in the 37 Part of the excitement of meteoritics is Côte d’Ivoire to a spectacular panorama of the Himalayan crest, the 190 photographs in 36 knowing that any of these extraterrestrial this oversize volume capture the beauty of natural landscapes and human settlements 35 rocks might already be here on Earth, just alike. Many depict strikingly abstract patterns, such as these formed by crystallized salts 34 waiting to be found, identified, and written on the surface of Kenya’s Lake Magadi (above). Arthus-Bertrand’s project was supported 33 about. In their different ways, both of these by UNESCO, and the book includes 14 new short essays on our beleaguered world and 32 books convey the message that meteoritics steps towards an “eco-economy.” The exhibit, with 120 large (1.2 m by 1.8 m) prints, 31 is a fast-moving field, one in which we still opened in Paris in May 2000 and has appeared in 40 cities and 15 countries. 30 have much to learn. 29 28 27 S CIENCE’ S C OMPASS PERSPECTIVES 26 25 PERSPECTIVES: GENOMICS the underlying evolutionary and genetic 24 mechanisms that shape them. 23 The tiger pufferfish is a good example of 22 Vertebrate Genomes Compared how the concept of “model organism” has 21 changed. Growing up to 70 cm in length, it 20 S. Blair Hedges and Sudhir Kumar is a relatively large marine fish known for its 19 taste, not a laboratory workhorse like the fly 18 t takes two of anything to make a com- account for this difference. Its unusually or mouse. It was introduced as a “genomic 17 parison. With the publication of the draft small genome size, combined with a faster model” organism (3) specifically because of 16 Igenome sequence of the tiger pufferfish method of sequencing (whole-genome its compact genome, permitting efficient 15 (Fugu rubripes) by Aparicio et al. on page shotgun), has yielded a much lower price comparison with the human genome. Other 14 1301 of this issue (1), we are now able to tag—a mere $12 million compared with the genomic models include human parasites, 13 compare the genomes of two vertebrates. hundreds of millions of dollars spent on se- such as Plasmodium and Trypanosoma, and 12 Measuring 365 million base pairs in length, quencing the human genome. The primary species of interest to agriculture, such as rice 11 the Fugu genome is only one-ninth the size incentive for sequencing this and other ver- and corn. Fugu’s relative, the spotted green 10 of the human genome (2) yet contains ap- tebrate genomes lies in better identification pufferfish (Tetraodon nigroviridis), is a 9 proximately the same number of genes. and characterization of human genes and much smaller (up to 17 cm in length) fresh- 8 Shorter introns and a smaller amount of their regulatory elements, especially those water species with a similarly small genome, 7 repetitive DNA in the pufferfish genome that are mutated in human diseases. For ex- and is more accessible to experimental re- 6 ample, nearly 1000 putative human genes search requiring laboratory breeding. The 5 S. Blair Hedges is at the NASA Astrobiology Institute have been discovered by comparing the Tetraodon genome, one of at least 18 verte- 4 and Department of Biology, 208 Mueller Laboratory, Fugu and human genomes (1). Beyond brate genomes being sequenced, is almost 3 Pennsylvania State University, University Park, PA 16802–5301, USA. S. Kumar is in the Department of biomedical applications, the extent of con- complete (see the figure). 2 Biology, Life Sciences 351, Arizona State University, servation and divergence among the puffer- A major motivation behind genome-se- 1 AGENCY,CREDIT:YANN ARTHUS-BERTRAND/ALTITUDE PARIS Tempe, AZ 85287–1501, USA. fish and human genomes will shed light on quencing projects is to generate a better www.sciencemag.org SCIENCE VOL 297 23 AUGUST 2002 1283 S CIENCE’ S C OMPASS 65 Homo sapiens (Human) 64 Pan troglodytes (Common chimpanzee) 63 Macaca mulatta (Rhesus macaque) 62 Mus musculus (House mouse) 61 Rattus norvegicus (Norway rat) Canis familiaris (Domestic dog) 60 Felis catus (Domestic cat) 59 Equus caballus (Horse) 58 Sus scrofa (Domestic pig) 57 To marsupials Bos taurus (Domestic cattle) 56 Ovis aries (Domestic sheep) 55 Gallus gallus (Domestic fowl) Xenopus laevis (African clawed frog) 54 Xenopus tropicalis (Tropical clawed frog) 53 Danio rerio (Zebrafish) 52 Oryzias latipes (Japanese medaka) 51 Tetraodon nigroviridis (Spotted green pufferfish) 50 Takifugu rubripes (Tiger pufferfish or “Torafugu”) 49 Paleozoic Mesozoic Cen. 01234 48 Haploid genome 47 400 300 200 100 0 mass (pg) 46 Million years ago 45 Evolution of vertebrate genomes. The evolutionary tree shows relationships, times of divergence, and genome sizes (in picograms of DNA, pg) of 44 vertebrates whose genomes have been selected for sequencing. Classically, 1 pg of DNA has been considered equivalent to roughly 1 billion base pairs, 43 although the conversion factor for both human and Fugu is 0.91 ×109 base pairs. The position of marsupials is indicated to illustrate their potential im- 42 portance in filling an evolutionary gap in genome projects (12). The relationships and divergence times are largely from a molecular clock study of 658 41 proteins (8), although reflecting current uncertainty in the position of some orders of mammals (9) and supplemented with data on fishes and 40 genome sizes of vertebrates (www.genomesize.com/) (12–15). “Takifugu” is considered by ichthyologists to be the correct genus instead of the more 39 popular “Fugu”(www.fishbase.org/). 38 37 understanding of the genetics of human at evolutionarily conserved positions of the parts where times are unknown (8). Accu- 36 diseases (4). Sequencing of the complete protein sequence, and the alteration in chem- rate species divergence times are needed to 35 Fugu genome, a distant relative of humans, istry is more extreme than that permitted by link biological events with Earth’s geologi- 34 provides an opportunity to compare these natural selection (7). Thus, comparison of cal history and the appearance of charac- 33 two genomes at the level of exons, introns, nonmammalian genomes with the human teristic life forms. Such genomic clocks 32 and the protein sequence. The much short- genome will be crucial for understanding the might determine with better precision 31 er length of Fugu introns will enable se- genetic basis of many human diseases. whether the orders of mammals began 30 quence stretches important for regulating Evolutionary biology also has benefited splitting from one another in the Mesozoic 29 gene expression (5) to be identified, and greatly from genome-sequencing projects. era (80 to 100 million years ago) when 28 the role of noncoding DNA (which makes The wealth of new genome data is helping to continents were breaking apart, or later in 27 up most of the human genome) to be clari- better resolve the tree of life, particularly its the Cenozoic era (65 million years ago) af- 26 fied. The Fugu genome carries a handful of major branches. This has been especially true ter the dinosaurs disappeared, vacating 25 “giant” genes containing long introns, for prokaryotes, where more than 80 genomes ecological niches (8). Robust estimation of 24 which should provide insight into what has have been sequenced so far and the results the timing of gene-duplication events en- 23 driven the change in genome size during have greatly improved our view of the early ables reliable predictions of gene content 22 evolution. Understanding the genome history of life. For vertebrates, many thorny in unsequenced genomes and estimation of 21 structure of Fugu also will foster a clearer issues remain to be resolved, such as the phy- the rate of gene content increase over time 20 picture of the master control genes direct- logeny of families and other major groups in (11).
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