articles18.6 per Mb). This suggests that breakpoints may be more likely tooccur or to undergo ®xation in gene-poor intervals than in generichintervals. The occurrence <strong>of</strong> breakpoints may be promoted byhomologous recombination among repeated sequences 359 . When<strong>the</strong> sequence <strong>of</strong> <strong>the</strong> mouse <strong>genome</strong> is ®nished, this <strong>analysis</strong> can berevisited more precisely.A number <strong>of</strong> examples <strong>of</strong> extended conserved segments <strong>and</strong>syntenies are apparent in Fig. 46. As has been noted, almost all<strong>human</strong> genes on chromosome 17 are found on mouse chromosome11, with two members <strong>of</strong> <strong>the</strong> placental lactogen family from mouse13 inserted. Apart from two singleton loci, <strong>human</strong> chromosome 20appears to be entirely orthologous to mouse chromosome 2,apparently in a single segment. The largest apparently contiguousconserved segment in <strong>the</strong> <strong>human</strong> <strong>genome</strong> is on chromosome 4,including roughly 90.5 Mb <strong>of</strong> <strong>human</strong> DNA that is orthologous tomouse chromosome 5. This <strong>analysis</strong> also allows us to infer <strong>the</strong> likelylocation <strong>of</strong> thous<strong>and</strong>s <strong>of</strong> mouse genes for which <strong>the</strong> <strong>human</strong>orthologue has been located in <strong>the</strong> draft <strong>genome</strong> sequence but <strong>the</strong>mouse locus has not yet been mapped.With about 200 conserved segments between mouse <strong>and</strong> <strong>human</strong><strong>and</strong> about 100 Myr <strong>of</strong> evolution from <strong>the</strong>ir common ancestor 360 ,weobtain an estimated rate <strong>of</strong> about 1.0 chromosomal rearrangementbeing ®xed per Myr. However, <strong>the</strong>re is good evidence that <strong>the</strong> rate <strong>of</strong>chromosomal rearrangement (like <strong>the</strong> rate <strong>of</strong> nucleotide substitutions;see above) differs between <strong>the</strong> two species. Among mammals,rodents may show unusually rapid chromosome alteration. Bycomparison, very few rearrangements have been observed amongprimates, <strong>and</strong> studies <strong>of</strong> a broader array <strong>of</strong> mammalian orders,including cats, cows, sheep <strong>and</strong> pigs, suggest an average rate <strong>of</strong>chromosome alteration <strong>of</strong> only about 0.2 rearrangements per Myrin <strong>the</strong>se lineages 361 . Additional evidence that rodents are outlierscomes from a recent <strong>analysis</strong> <strong>of</strong> synteny between <strong>the</strong> <strong>human</strong> <strong>and</strong>zebra®sh <strong>genome</strong>s. From a study <strong>of</strong> 523 orthologues, it was possibleto project 418 conserved segments 350 . Assuming 400 Myr since acommon vertebrate ancestor <strong>of</strong> zebra®sh <strong>and</strong> <strong>human</strong>s 362 , we obtainan estimate <strong>of</strong> 0.52 rearrangements per Myr. Recent estimates <strong>of</strong>rearrangement rates in plants have suggested bimodality, with somepairs showing rates <strong>of</strong> 0.15±0.41 rearrangements per Myr, <strong>and</strong>o<strong>the</strong>rs showing higher rates <strong>of</strong> 1.1±1.3 rearrangements per Myr 363 .With additional detailed <strong>genome</strong> maps <strong>of</strong> multiple species, it shouldbe possible to determine whe<strong>the</strong>r this particular molecular clock istruly operating at a different rate in various branches <strong>of</strong> <strong>the</strong>evolutionary tree, <strong>and</strong> whe<strong>the</strong>r variations in that rate are bimodalor continuous. It should also be possible to reconstruct <strong>the</strong> karyotypes<strong>of</strong> common ancestors.Ancient duplicated segments in <strong>the</strong> <strong>human</strong> <strong>genome</strong>Ano<strong>the</strong>r approach to genomic history is to study segmental duplicationswithin <strong>the</strong> <strong>human</strong> <strong>genome</strong>. Earlier, we discussed examples<strong>of</strong> recent duplications <strong>of</strong> genomic segments to pericentromeric <strong>and</strong>subtelomeric regions. Most <strong>of</strong> <strong>the</strong>se events appear to be evolutionarydead-ends resulting in nonfunctional pseudogenes; however,segmental duplication is also an important mode <strong>of</strong> evolutionaryinnovation: a duplication permits one copy <strong>of</strong> each gene to drift <strong>and</strong>potentially to acquire a new function.Segmental duplications can occur through unequal crossing overto create gene families in speci®c chromosomal regions. Thismechanism can create both small families, such as <strong>the</strong> ®ve relatedgenes <strong>of</strong> <strong>the</strong> b-globin cluster on chromosome 11, <strong>and</strong> large ones,such as <strong>the</strong> olfactory receptor gene clusters, which toge<strong>the</strong>r containnearly 1,000 genes <strong>and</strong> pseudogenes.WormFlyHumanPOZ:~143Homeodomain:~90 POZ:~95 Homeodomain:~92POZ:~140Homeodomain:~220MATHPOZC2H2C2H2Paired HD HDPOZPaired HD HDPOZC2H2C2H2C2H2C2H2C2H2C2H2PairedHDHDPOZKPou HD Lim HDPou HD Lim HDPOZ APOZbZipPouHDLimHDPOZNHR:~230Zn LBC4DM:80C4DMC2H2C2H2SAZ (MYB-like):35SAZ SAZ SAZKrabKrab:~220C2H2C2H2C2H2C2H2C2H2C2H2ScanScan:~50C2H2C2H2C2H2C2H2C2H2C2H2bHIHbHLH:53bHIHbHLH:105PAS PAS bHIH bHIH PAS PASUnique <strong>and</strong> shared domain organizations in animalsCG-1C5 TigOlf-1TigP53FankankKIAA0833SSRPSh2STATHMGSSRPPHDP53FP53FP53MeFkdwkTigNFATCGBPYCSmyDEAF-1HfP53FankankankankankHMGTigNFKBHistone foldPOZS SPRy ATPaseSAF-AMTFFlyCDP1AAA A AAAAAAF49E12.6E2FE2FWormHBP-1ATXSAZHMGwdwdwdwdwdwdwdwdC2H2C2H2AND-1HMGHMGUBF-1GHLHMG HMG HMG HMGZHX-1PMS-1RFX5RFXHMGHD HD HD HD HDAAAncient architecturesconserved in all animalsShared byfly <strong>and</strong> <strong>human</strong>Unique t<strong>of</strong>ly or wormUnique to<strong>human</strong>Figure 45 Lineage-speci®c expansions <strong>of</strong> domains <strong>and</strong> architectures <strong>of</strong> transcriptionfactors. Top, speci®c families <strong>of</strong> transcription factors that have been exp<strong>and</strong>ed in each <strong>of</strong><strong>the</strong> proteomes. Approximate numbers <strong>of</strong> domains identi®ed in each <strong>of</strong> <strong>the</strong> (nearly)complete proteomes representing <strong>the</strong> lineages are shown next to <strong>the</strong> domains, <strong>and</strong> some<strong>of</strong> <strong>the</strong> most common architectures are shown. Some are shared by different animallineages; o<strong>the</strong>rs are lineage-speci®c. Bottom, samples <strong>of</strong> architectures from transcriptionfactors that are shared by all animals (ancient architectures), shared by ¯y <strong>and</strong> <strong>human</strong> <strong>and</strong>unique to each lineage. Domains: K, kelch; HD, homeodomain; Zn, zinc-binding domain;LB, lig<strong>and</strong>-binding domain; C4DM, novel Zn cluster with four cysteines, probably involvedin protein±protein interactions (L. Aravind, unpublished); MATH, meprin-associated TRAFdomain; CG-1, novel domain in KIAA0909-like transcription factors (L. Aravind,unpublished); MTF, myelin transcription factor domain; SAZ, specialized Myb-like helixturn-helix(HTH) domain found in Stonewall, ADF-1 <strong>and</strong> Zeste (L. Aravind, unpublished); A,AT-hook motif; E2F, winged HTH DNA-binding domain; GHL, gyraseB-histidine kinase-MutL ATPase domain; ATX, ATaXin domain; RFX, RFX winged HTH DNA binding domain;My, MYND domain; KDWK, KDWK DNA-binding domain; POZ, Pox zinc ®nger domain; S,SAP domain; P53F, P53 fold domain; HF, histone fold; ANK, ankyrin repeat; TIG,transcription factor Ig domain; SSRP, structure-speci®c recognition protein domain; C5,5-cysteine metal binding domain; C2H2, classic zinc ®nger domain; WD, WD40 repeats.NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com © 2001 Macmillan Magazines Ltd909
articlesThe most extreme mechanism is whole-<strong>genome</strong> duplication(WGD), through a polyploidization event in which a diploidorganism becomes tetraploid. Such events are classi®ed as autopolyploidyor allopolyploidy, depending on whe<strong>the</strong>r <strong>the</strong>y involvehybridization between members <strong>of</strong> <strong>the</strong> same species or differentspecies. Polyploidization is common in <strong>the</strong> plant kingdom, withmany known examples among wild <strong>and</strong> domesticated crop species.Alfalfa (Medicago sativa) is a naturally occurring autotetraploid 364 ,<strong>and</strong> Nicotiana tabacum, some species <strong>of</strong> cotton (Gossypium) <strong>and</strong>several <strong>of</strong> <strong>the</strong> common brassicas are allotetraploids containing pairs<strong>of</strong> `homeologous' chromosome pairs.In principle, WGD provides <strong>the</strong> raw material for great bursts <strong>of</strong>innovation by allowing <strong>the</strong> duplication <strong>and</strong> divergence <strong>of</strong> entirepathways. Ohno 365 suggested that WGD has played a key role inevolution. There is evidence for an ancient WGD event in <strong>the</strong>ancestry <strong>of</strong> yeast <strong>and</strong> several independent such events in <strong>the</strong> ancestry<strong>of</strong> mustard weed 366±369 . Such ancient WGD events can be hard todetect because only a minority <strong>of</strong> <strong>the</strong> duplicated loci may beretained, with <strong>the</strong> result that <strong>the</strong> genes in duplicated segmentscannot be aligned in a one-to-one correspondence but ra<strong>the</strong>rrequire many gaps. In addition, duplicated segments may besubsequently rearranged. For example, <strong>the</strong> ancient duplication in<strong>the</strong> yeast <strong>genome</strong> appears to have been followed by loss <strong>of</strong> more than90% <strong>of</strong> <strong>the</strong> newly duplicated genes 366 .One <strong>of</strong> <strong>the</strong> most controversial hypo<strong>the</strong>ses about vertebrateevolution is <strong>the</strong> proposal that two WGD events occurred early in<strong>the</strong> vertebrate lineage, around <strong>the</strong> time <strong>of</strong> jawed ®shes some 500 Myrago. Some authors 370±373 have seen support for this <strong>the</strong>ory in <strong>the</strong> factthat many <strong>human</strong> genes occur in sets <strong>of</strong> four homologuesÐmostnotably <strong>the</strong> four extensive HOX gene clusters on chromosomes 2, 7,12 <strong>and</strong> 17, whose duplication dates to around <strong>the</strong> correct time.However, o<strong>the</strong>r authors have disputed this interpretation 374 ,suggesting that <strong>the</strong>se cases may re¯ect unrelated duplications <strong>of</strong>speci®c regions ra<strong>the</strong>r than successive WGD.We analysed <strong>the</strong> draft <strong>genome</strong> sequence for evidence that mightbear on this question. The <strong>analysis</strong> provides many interestingobservations, but no convincing evidence <strong>of</strong> ancient WGD. Welooked for evidence <strong>of</strong> pairs <strong>of</strong> chromosomal regions containingmany homologous genes. Although we found many pairs containinga few homologous genes, <strong>the</strong> <strong>human</strong> <strong>genome</strong> does not appear tocontain any pairs <strong>of</strong> regions where <strong>the</strong> density <strong>of</strong> duplicated genesapproaches <strong>the</strong> densities seen in yeast or mustard weed 366±369 .We also examined <strong>human</strong> proteins in <strong>the</strong> IPI for which <strong>the</strong>orthologues among ¯y or worm proteins occur in <strong>the</strong> ratios 2:1:1,3:1:1, 4:1:1 <strong>and</strong> so on (Fig. 49). The number <strong>of</strong> such families fallssmoothly, with no peak at four <strong>and</strong> some instances <strong>of</strong> ®ve or morehomologues. Although this does not rule out two rounds <strong>of</strong> WGDfollowed by extensive gene loss <strong>and</strong> some unrelated gene duplication,it provides no support for <strong>the</strong> <strong>the</strong>ory. More probatively, if twosuccessive rounds <strong>of</strong> <strong>genome</strong> duplication occurred, phylogenetic<strong>analysis</strong> <strong>of</strong> <strong>the</strong> proteins having 4:1:1 ratios between <strong>human</strong>, ¯y <strong>and</strong>worm would be expected to show more trees with <strong>the</strong> topology(A,B)(C,D) for <strong>the</strong> <strong>human</strong> sequences than (A,(B,(C,D))) 375 .However,<strong>of</strong> 57 sets studied carefully, only 24% <strong>of</strong> <strong>the</strong> trees constructedfrom <strong>the</strong> 4:1:1 set have <strong>the</strong> former topology; this is not signi®cantlydifferent from what would be expected under <strong>the</strong> hypo<strong>the</strong>sis <strong>of</strong>r<strong>and</strong>om sequential duplication <strong>of</strong> individual loci.100Occurrences101 2 3 4 5 6 7 8 9 10 11 12100 10 20 30 40 50 60 70 80 90 100Genes per conserved segmentFigure 47 Distribution <strong>of</strong> number <strong>of</strong> genes per conserved segment between <strong>human</strong> <strong>and</strong>mouse <strong>genome</strong>s.10013 14 15 16 17 18 19 20 21 22 X Y1 2 3 4 5 6 7 8 9 10Occurrences1011 12 13 14 15 16 17 18 19 X YFigure 46 Conserved segments in <strong>the</strong> <strong>human</strong> <strong>and</strong> mouse <strong>genome</strong>. Humanchromosomes, with segments containing at least two genes whose order is conserved in<strong>the</strong> mouse <strong>genome</strong> as colour blocks. Each colour corresponds to a particular mousechromosome. Centromeres, subcentromeric heterochromatin <strong>of</strong> chromosomes 1, 9 <strong>and</strong>16, <strong>and</strong> <strong>the</strong> repetitive short arms <strong>of</strong> 13, 14, 15, 21 <strong>and</strong> 22 are in black.105 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90Conserved segment length (Mb)Figure 48 Distribution <strong>of</strong> lengths (in 5-Mb bins) <strong>of</strong> conserved segments between <strong>human</strong><strong>and</strong> mouse <strong>genome</strong>s, omitting singletons.910 © 2001 Macmillan Magazines Ltd NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com