Journal of Molecular Evolution

, Volume 57, Issue 3, pp 271-281

Five Hundred Sixty-Five Triples of Chicken, Human, and Mouse Candidate Orthologs

  • Ming OuyangAffiliated withInformatics Institute, University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854
  • , John CaseAffiliated withDepartment of Computer and Information Sciences, University of Delaware, Newark, DE 19716
  • , Vijaya TirunagaruAffiliated withAstrazeneca Pharmaceuticals LP, 1800 Concord Pike, Wilmington, DE 19850
  • , Joan BurnsideAffiliated withDelaware Biotechnology Institute, University of Delaware, Newark, DE 19716 Email author 

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The Human Genome Project has provided abundant gene sequence information on human and important model organisms. The chicken is well positioned from an evolutionary standpoint to serve as a link between higher and lower organisms, particularly mammals, and amphibia and fish. In this study we used stringent criteria to select 565 triples of chicken, human, and mouse candidate orthologs. We analyze the sequences with respect to nucleotide and amino acid similarities. This analysis also allows measurement of evolutionary distances of different proteins. We found that chicken-human and chicken-mouse sequence identities are highly correlated; similarly for chicken-human and chicken-mouse evolutionary distances. With chicken as the out-group, we found that mouse has a higher substitution rate than human, supporting the generation-time effect hypothesis. We also described the transversion bias, which is the preference for some transversions than others in nucleotide substitutions. We demonstrated that there are statistically significant properties in the differences of orthologous sequences. The differential patterns, in combination with sequence similarity analysis, may lead to the identification of genes that are very divergent from the mammalian orthologs.


Comparative genomics Ortholog Alignment Evolutionary distance Transversion bias Generation-time effect