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Background  Recent phylogenetic studies have revealed that the mitochondrial genome of the angiosperm  Silene noctiflora  (Caryophyllaceae) has experienced a massive mutation-driven acceleration in substitution rate, placing it among the fastest evolving eukaryotic genomes ever identified. To date, it appears that other species within  Silene  have maintained more typical substitution rates, suggesting that the acceleration in  S. noctiflora  is a recent and isolated evolutionary event. This assessment, however, is based on a very limited sampling of taxa within this diverse genus.    Results  We analyzed the substitution rates in 4 mitochondrial genes ( atp1 ,  atp9 ,  cox3  and  nad9 ) across a broad sample of 74 species within  Silene  and related genera in the tribe  Sileneae . We found that  S. noctiflora  shares its history of elevated mitochondrial substitution rate with the closely related species  S. turkestanica . Another section of the genus ( Conoimorpha ) has experienced an acceleration of comparable magnitude. The phylogenetic data remain ambiguous as to whether the accelerations in these two clades represent independent evolutionary events or a single ancestral change. Rate variation among genes was equally dramatic. Most of the genus exhibited elevated rates for  atp9  such that the average tree-wide substitution rate for this gene approached the values for the fastest evolving branches in the other three genes. In addition, some species exhibited major accelerations in  atp1  and/or  cox3  with no correlated change in other genes. Rates of non-synonymous substitution did not increase proportionally with synonymous rates but instead remained low and relatively invariant.    Conclusion  The patterns of phylogenetic divergence within  Sileneae  suggest enormous variability in plant mitochondrial mutation rates and reveal a complex interaction of gene and species effects. The variation in rates across genomic and phylogenetic scales raises questions about the mechanisms responsible for the evolution of mutation rates in plant mitochondrial genomes.

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae