  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.
