Rodent evolution: back to the root

Molecular Biology and Evolution
Gennady ChurakovJürgen Schmitz

Abstract

Some 70 Ma, rodents arose along a branch of our own mammalian lineage. Today, about 40% of all mammalian species are rodents and are found in vast numbers on almost every continent. Not only is their proliferation extensive but also the rates of DNA evolution vary significantly among lineages, which has hindered attempts to reconstruct, especially the root of, their evolutionary history. The presence or absence of rare genomic changes, such as short interspersed elements (SINEs), are, however, independent of high molecular substitution rates and provide a powerful, virtually homoplasy-free source for solving such phylogenetic problems. We screened 12 Gb of rodent genomic information using whole-genome three-way alignments, multiple lineage-specific sequences, high-throughput polymerase chain reaction amplifications, and sequencing to reveal 65 phylogenetically informative SINE insertions dispersed over 23 rodent phylogenetic nodes. Eight SINEs and six indels provide significant support for an early association of the Mouse-related and Ctenohystrica (guinea pig and relatives) clades, the Squirrel-related clade being the sister group. This early speciation scenario was also evident in the genomewide distribution pattern of B1-rel...Continue Reading

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