BACKGROUND: The uncoupling protein (UCP) genes belong to the superfamily of electron transport carriers of the mitochondrial inner membrane. Members of the uncoupling protein family are involved in thermogenesis and determining the functional evolution of UCP genes is important to understand the evolution of thermo-regulation in vertebrates. RESULTS: Sequence similarity searches of genome and scaffold data identified homologues of UCP in eutherians, teleosts and the first squamates uncoupling proteins. Phylogenetic analysis was used to characterize the family evolutionary history by identifying two duplications early in vertebrate evolution and two losses in the avian lineage (excluding duplications within a species, excluding the losses due to incompletely sequenced taxa and excluding the losses and duplications inferred through mismatch of species and gene trees). Estimates of synonymous and nonsynonymous substitution rates (dN/dS) and more complex branch and site models suggest that the duplication events were not associated with positive Darwinian selection and that the UCP is constrained by strong purifying selection except for a single site which has undergone positive Darwinian selection, demonstrating that the UCP gene family must be highly conserved. CONCLUSION: We present a phylogeny describing the evolutionary history of the UCP gene family and show that the genes have evolved through duplications followed by purifying selection except for a single site in the mitochondrial matrix between the 5th and 6th alpha-helices which has undergone positive selection.
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