Widespread Genomic Signatures of Natural Selection in Hominid Evolution

• Published in: PLoS genetics Vol. 5; no. 5; p. e1000471
• Main Authors: McVicker, Graham, Gordon, David, Davis, Colleen, Green, Phil
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.05.2009; Public Library of Science (PLoS)
• Subjects: Animals; Biological diversity; Chromosomes, Human, X - genetics; Computational Biology; Computational Biology/Comparative Sequence Analysis; Computational Biology/Evolutionary Modeling; Computational Biology/Genomics; Computational Biology/Molecular Genetics; Computational Biology/Population Genetics; Confidence Intervals; Conserved Sequence; Evolution; Evolution, Molecular; Evolutionary Biology/Bioinformatics; Evolutionary Biology/Evolutionary and Comparative Genetics; Evolutionary Biology/Genomics; Evolutionary Biology/Human Evolution; Genetic aspects; Genetics; Genetics and Genomics; Genetics and Genomics/Bioinformatics; Genetics and Genomics/Comparative Genomics; Genome, Human; Genomes; Hominidae - genetics; Hominids; Humans; Likelihood Functions; Markov Chains; Models, Genetic; Molecular Biology/Bioinformatics; Molecular Biology/Molecular Evolution; Molecular evolution; Natural selection; Pan troglodytes; Pan troglodytes - genetics; Polymorphism, Single Nucleotide; Population; Primates; Primates - genetics; Recombination, Genetic; Selection, Genetic; X Chromosome - genetics; United States
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1000471

Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites. To illuminate the selective forces that shaped hominid evolution, we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species relative to the locations of conserved sequence features. Neutral sequence diversity in human and ancestral hominid populations is substantially reduced near such features, resulting in a surprisingly large genome average diversity reduction due to selection of 19-26% on the autosomes and 12-40% on the X chromosome. The overall trends are broadly consistent with "background selection" or hitchhiking in ancestral populations acting to remove deleterious variants. Average selection is much stronger on exonic (both protein-coding and untranslated) conserved features than non-exonic features. Long term selection, rather than complex speciation scenarios, explains the large intragenomic variation in human/chimpanzee divergence. Our analyses reveal a dominant role for selection in shaping genomic diversity and divergence patterns, clarify hominid evolution, and provide a baseline for investigating specific selective events.