The Genom of Homo sapiens.pdf

EVOLUTION OF EUKARYOTIC GENES AND INTRONS 295bidopsis, and minimal in the microsporidian (Fig. 1). Anotable difference was observed in the representation ofeukaryotic genomes in KOGs with different numbers ofspecies. The three unicellular organisms are representedlargely in highly conserved seven- or six-species KOGs;in contrast, in animals and Arabidopsis, a much largerfraction of the genes is accounted for by LSEs and byKOGs that include three or four genomes, e.g., animalspecificones (Fig. 1).The phyletic patterns of KOGs reveal a substantial,conserved eukaryotic gene core, but also notable diversity(Fig. 2). The “pan-eukaryotic” genes, which are representedin each of the seven analyzed genomes, comprise~20% of the KOGs, and approximately the samenumber of KOGs include all species except for the microsporidian,an intracellular parasite with a highly degradedgenome (Katinka et al. 2001). Among the remainingKOGs, a large fraction consists of representatives ofthe three analyzed animal species (worm, fly, and human),but ~30% are KOGs with unexpected patterns, e.g.,one animal, one plant, and one fungal species (seehttp://www.ncbi.nlm.nih.gov/COG/new/shokog.cgi).During manual curation of the KOGs, those with unexpectedpatterns were specifically scrutinized to identifypotential highly diverged members from one or more ofthe analyzed genomes, and the KOGs were modifiedwhen such diverged orthologs were detected. Some ofthese unexpected patterns probably indicate that a gene isstill missing in the analyzed set of protein sequences fromone or more of the included eukaryotic species. Largely,however, the unexpected phyletic patterns seem to reflectthe extensive, lineage-specific gene loss that is apparentlycharacteristic of eukaryotic evolution.A PARSIMONIOUS SCENARIO OF GENE LOSSAND EMERGENCE IN EUKARYOTICEVOLUTION AND RECONSTRUCTION OFANCESTRAL EUKARYOTIC GENE SETSAssuming a particular species tree topology, methodsof evolutionary parsimony analysis can be employed toconstruct a parsimonious scenario of evolution; i.e., map-ping of different types of evolutionary events onto thebranches of the tree such that the total number of theevents is minimal. As discussed above, with prokaryotes,the problem is confounded by the fact that both lineagespecificgene loss and HGT apparently have made majorcontributions to genome evolution, with the relative ratesof these processes remaining unknown (Snel et al. 2002;Mirkin et al. 2003). Since HGT between major lineagesof eukaryotes apparently can be safely disregarded, anunambiguous parsimonious scenario including only geneloss and emergence of new genes as elementary eventscan be constructed. The phylogenetic tree of the eukaryoticcrown group seems to have been established withnear complete confidence. In particular, some conflictingobservations notwithstanding, the majority of phylogeneticstudies point to an animal–fungal clade, grouping ofmicrosporidia with the fungi, and a coelomate (chordate–arthropod)clade among the animals (Blair et al.2002; Hedges 2002; Y.I. Wolf et al., unpubl.). Assumingthis tree topology and treating the phyletic pattern of eachKOG as a string of binary characters (1 for the presenceof the given species and 0 for its absence in the givenKOG), the parsimonious scenario of gene loss and emergenceduring the evolution of the eukaryotic crown groupwas constructed. For this reconstruction, the Dollo parsimonyapproach was adopted (Farris 1977). Under this approach,gene loss is considered irreversible; i.e., a gene (aKOG member) can be lost independently in several evolutionarylineages but cannot be regained. The use of thisassumption is justified by the negligible rate of HGT betweeneukaryotes (the Dollo approach is not valid for thereconstruction of prokaryotic ancestors).In the resulting scenario, each branch was associatedwith a unique number of losses and gains, with the exceptionof the plant branch and the branch leading to thecommon ancestor of the fungi–microsporidial clade andthe animals, to which gene losses could not be assignedwith the current set of genomes (Fig. 3). Undoubtedly,once genomes of early-branching eukaryotes are included,gene loss associated with these branches will becomeapparent. The reconstructed scenario includes massivegene loss in the fungal clade, with additional85819472711881421109Figure 2. The phyletic patterns of KOGs. (All-Ec) KOGs represented in all analyzed genomes with the exception of Encephalitozooncuniculi; (All animals, All fungi) KOGs represented exclusively in the three animal species or the two fungal species, respectively.921186AllAll-EcAnimals+FungiPlant+fungiPlant+animalsAll animalsAll fungiOther patterns