Pattern of gene duplication in animal genomes

Duplication of genes, giving rise to multigene families, has been a characteristic feature of the evolution of eukaryotic genomes. It has been proposed that an increase in vertebrate gene number and gene family size has resulted from duplication of the entire nuclear genome by polyploidization (the 2R hypothesis). Herein we have conducted extensive analyses using phylogenetic and other comparative methods of available animal and fungal gene families.; A novel method was developed to test the significance of duplicated blocks in the available annotated genomes. The yeast Saccharomyces cerevisiae genome had a majority of block duplications that occurred between chromosomes, evidence of a polyploidization event over two hundred million years ago; while the nematode Caenorhabditis elegans and the fly Drosophila melanogaster did not show a pattern evident of a past polyploidization event.; Gene families in human, worm, yeast and fly were compiled and separated by size. Phylogenetic analysis was applied to time gene duplications within each gene family size of two to eight. The pattern of gene duplications was inconsistent with 2R. Although the human genome had a higher proportion of recent gene duplications than the other animal genomes, the proportion of duplications after the deuterostome-protostome split was constant across families, with no peak of such duplications in four-member families, contrary to the expectation of the hypothesis of whole genome duplication. Also, a substantial majority of human four-member families showed topologies inconsistent with two rounds of polyploidization in vertebrates.; Recently available mapped human genes allowed a test for duplicated structure in the human genome. Eighteen potentially duplicated blocks were identified and phylogenetic analysis revealed these blocks having been duplicated at widely different times. Sharing of bi-chromosomal families between chromosomes followed a highly unexpected pattern, whereby 18 of the chromosomes formed a set that shared at least 10 of these bi-chromosomal families with at least one other member of the set. This is a pattern inconsistent with whole genome duplication (2R) and consistent with tandem duplication followed by translocation to shuffle the genes about the chromosomes.