the evolution of mammalian gene families哺乳动物的基因家族的进化.pdf

The Evolution of Mammalian Gene Families 1 2¤a 3¤b 4¤c 1 Jeffery P. Demuth , Tijl De Bie , Jason E. Stajich , Nello Cristianini , Matthew W. Hahn * 1 Department of Biology and School of Informatics, Indiana University, Bloomington, Indiana, United States of America, 2 School of Electronics and Computer Science, ISIS Group, University of Southampton, Southampton, United Kingdom, 3 Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America, 4 Department of Statistics, University of California Davis, Davis, California, United States of America Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic ‘‘revolving door’’ of gene gain and loss represents a large number of gen