Knibbe, Coulon, et al. (2007) showed that organisms with spatial genomes can adapt to a given mutation rate by changing their genome size and coding density, whereas de Boer and Hogeweg (2010) found that early genome expansion, limited by the per base mutation rate, determines the success rate of evolving abstract pathways for resource consumption.
This equates to a per base pair mutation rate of 2.95 (± 0.21 SE) × 10−8 mutations/site/generation and a genomic mutation rate of 0.18 (± 0.01 SE) mutations/genome/generation.
We identified 31,106 base-substitution mutations, across the 45 sequenced MA lines, which yields a base-substitution mutation rate of 2.34 × 10− (SE: 0.01 × 10−) per site per cell division (table 1 and supplementary table S1, Supplementary Material online).
With spontaneous mutations accumulated in the mutator strain P. fluorescens ATCC948 for almost 2 years, we have established the base-substitution mutation rate of this strain to be 2.34 × 10− per site per generation, dominated by AT → GC transitions.
For a bacterial genome consisting of about a thousand genes of comparable size, this corresponds roughly to a few hundred million years of evolution (based on a mutation rate of 0.003 per genome per replication [24] and a generation time of 0.001 year [25]).
Based on a mutation rate of 1.3%/bp/million years (combined cytochrome b (1.38% MY) [37] and NADH5 (1.22% MY) [38], 601 bp of sequence (NADH5 and cytochrome b) and τ values between 2.605 and 4.24 (Table 6), our estimates of the range expansion for jungle cat in India dates to the mid Pleistocene (166,709 to 271,342 years ago).
The youngest splits in the tree (common ancestors for haplotypes 6 7 and 60 61) were dated even closer to the LGM: with a mean of 29 34 ka (1 76 ka) from the coalescent estimation in BEAST; when based on the mutation rate of 7.6% per site per Ma (for transitions in third-codon positions of cytochrome b in Littorina [28]), the average time for these mutation events is 33 ka.
Based on a mutation rate of 10−7/base-pair/generation (Coller et al., 2001; Hudson and Chinnery, 2006), this leads to an average ∼1 homoplasmic mutation for every 1000 cell generations.
The estimate of divergence was derived from the mode Ks of binned values, based on a mutation rate of 5.17× 10-3 substitutions/synonymous site/Myr for the legume lineage [ 34].
Based on the mutation rate of 0.033 s/s/Myr for the ITS marker, population growth started at approximately 200,000 years before present (BP) in the sampled isidiate taxa, M. elegantula and M. exasperatula.
