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P APER AND B IBLIOGRAPHY FOR P ITT -L ON S EPT . W ORKSHOP : ‘R ECONSTRUCTING THE C ONCEPT OF H OMOLOGY FOR G ENOMICS Catherine Kendig Birkbeck College, University of London email address: <[email protected]> I. Introduction Much of the understanding which has been gained within the biological sciences has been based upon the traditional account of the phylogenetic lineages of organisms. Evolution, understood as a series of splits, or speciation events, has been the accepted model. The causal relationship between the information contained within the genome and the morphology or ancestry of the organism is thought to be sufficiently close such that given knowledge of one, the others can be inferred. On this account, the phylogenetic inference of an organism’s ancestral lineage is thought to be sufficiently justified by the belief that there is one common cause (or shared ancestor) of each taxon which permits only one true ancestral lineage or ‘true tree’. This means that morphology and ancestry are derivable given the information contained within the genome. And further, that the information contained within the genome can be predicted given the morphology of the organism. However, the phylogeny of genomes has a level of detail which is absent from the traditional organismal account of phylogenetics. The phylogenetic tree which has been relied upon to trace organismal lineage as a series of splits, signifying speciation events, does not work for genome (or gene) lineages. The traditional form of the species (or organismal) tree diagram represents the ancestral history of the organism as a continuous lineage. This lineage can be traced by following the progression of the two-pronged forks which compose the tree and represent the speciation events. Dendrograms start with one initial type of organism which is represented by the root of the tree and represents the shared ancestor of all other organisms within a particular dendrogram which have branched from that tree, making a new species. 1
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The traditional organismal phylogenies fail to preserve this level of detail of genomic phylogenies in two ways. Firstly, the history of a genome includes both the movement of genes from parent to offspring in reproduction, but also the transfer of genetic material in gene duplication events occurring within the genome itself. Secondly, unlike the dendrogram model of organismal phylogeny, the model of genomic lineage is more reticulate. This is because organismal phylogeny traces only the reproductive lineage of one taxon. Whereas the phylogeny of genomes can trace the reproductive lineage as well as either the history of gene duplications within the genome, or the acquisition of genes from horizontal gene transfer. One cannot simply ‘read off’ the phylogenetic lineage of genomes from the phylogenetic lineage of organisms. In light of this distinction, it no longer makes sense to take the organism as the primary
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