Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution

Paralogous genes from several families were found in four human chromosomeregions (4p16, 5q33-35, 8p12-21, and 10q24-26), suggesting that theircommon ancestral region underwent several rounds of large- scaleduplication. Searches in the EMBL databases, followed by phylogeneticanalyses, showed that cognates (orthologs) of human duplicated genes can befound in other vertebrates, including bony fishes. In contrast, within eachfamily, only one gene showing the same high degree of similarity with allthe duplicated mammalian genes was found in nonvertebrates (echinoderms,insects, nematodes). This indicates that large-scale duplications occurredafter the echinoderms/chordates split and before the bony vertebrateradiation. It has been suggested that two rounds of gene duplicationoccurred in the vertebrate lineage after the separation of Amphioxus andcraniate (vertebrates + Myxini) ancestors. Before these duplications, thegenes that have led to the families of paralogous genes in vertebrates musthave been physically linked in the craniate ancestor. Linkage of some ofthese genes can be found in the Drosophila melanogaster and Caenorhabditiselegans genomes, suggesting that they were linked in the triploblastMetazoa ancestor.