Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S rRNA, 16S rRNA, and tRNA-valine

A recent analysis of amino acid sequence data (Graur et al.) suggested thatthe mammalian order Rodentia is polyphyletic, in contrast to mostmorphological data, which support rodent monophyly. At issue is whether thehystricognath rodents, such as the guinea pig, represent an independentevolutionary lineage within mammals, separate from the sciurognath rodents.To resolve this problem, we sequenced a region (2,645 bp) of themitochondrial genome of the guinea pig containing the complete 12Sribosomal RNA, 16S ribosomal RNA, and transfer RNA(VAL) genes forcomparison with the available sciurognath and other mammalian sequences.Several methods of analysis and statistical tests of the data all showstrong support for rodent monophyly (91%-98% bootstrap probability, or BP).Calibration with the mammalian fossil record suggests a Cretaceous date(107 mya) for the divergence of sciurognaths and hystricognaths. An olderdate (38 mya) for the controversial Mus- Rattus divergence also issupported by these data. Our neighbor-joining analyses of all availablesequence data (25 genes) confirm that some individual genes support rodentpolyphyly but that tandem analysis of all data does not. We propose thatthe conflicting results are due to several compounding factors. The uniquebiochemical properties of some hystricognath metabolic proteins, largelyresponsible for generating this controversy, may have a single explanation:a cascade effect resulting from inactivation of the zinc-binding abilitiesof insulin. After excluding six genes possibly affected by insulininactivation, analyses of all available sequence data (7,117 nucleotidesites, 3,099 amino acid sites) resulted in strong support for rodentmonophyly (94% BP for DNA sequences, 90% for protein sequences), whichlends support to the insulin-cascade hypothesis.