Substitution rate variation in closely related rodent species

The existence of evolutionary rate variation has previously been demonstrated between different orders, different species and even between different regions of the same gene. To examine rate variation between closely related species of rodents we have sequenced the adenine phosphorybosyltransferase (APRT) gene from Mus spicilegus, Mus pahari, Mastomys hildebrandtii, Stochomys longicaudatus and Gerbillus campestris and compared these sequences with the previously published Mus musculus, Rattus norvegicus and Mesocricetus auratus APRT sequences. The alignment of these eight rodent APRT sequences reveals two large insertions within the introns: an insertion with sequence similar to a B1 repetitive element is found within Mastomys and an insertion with sequence similar to a B2 repetitive element is found within M. pahari. A phylogeny for the rodent APRTs agrees with the previously published rodent phylogeny based on other molecular and morphological data. The relative rate test which is often used to test for variation in rates of evolution in different lineages is shown here to be sensitive to the choice of outgroup and therefore should be used with great caution. This sensitivity is detectable only with closely related species and results from the prevalence of homoplastic substitutions. Rate variation is demonstrated within the APRT exons and introns and between the rodent species (with the most significant difference being a rate difference in M. spicilegus). In addition, some third codon positions are shown to be more prone to substitution than others. This clearly demonstrates that even between very closely related species there is ample evidence of major differences in rates of evolution among species, among regions of the gene and among different positions within the gene. We also demonstrate that standard methods of analysis might not detect this variation.