Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes

Many phylogenetic studies have used nuclear introns or coding exons, but few have included untranslated regions (UTRs). Here we compare the phylogenetic utility and patterns of molecular evolution for 3′-UTRs and introns from five unlinked loci in Galliformes (Aves). 3′-UTRs evolved at slower rates and exhibited greater spatial clustering of sites with similar evolutionary rates than associated introns, though they exhibited similar overall model complexities. Base compositions differed between the 3′-UTR and associated intron for two of five loci, suggesting that base composition was not exclusively driven by isochore structure. Phylogenies estimated using individual and concatenated 3′-UTRs were more similar to an independent reference tree than those based upon introns, though all phylogenies were largely congruent. However, some 3′-UTRs were difficult to amplify, potentially limiting their use in phylogenetic studies. This study suggests that 3′-UTRs and introns can exhibit distinct patterns of molecular evolution and that they provide useful phylogenetic signal.