Nature research paper: Somatic mutation rates scale with lifespan across mammals
), using the ‘buildref’ function in dNdScv. For each species, the ‘dndscv’ function was applied to the list of somatic substitutions called in samples of that species, after de-duplicating any substitutions that were shared between samples from the same individual to avoid counting shared somatic mutations multiple times. In addition, the analysis was restricted to genes that were fully contained in the analysable genomes of all samples from the species .
For each sample, sequencing coverage was measured in non-overlapping 100-kb bins along the reference genome of the species, using the coverageBed tool in the bedtools suite . For each bin, the coverage per base pair was calculated by dividing the number of reads mapping to the bin by the bin length, and multiplying the result by the read length .
Estimates of total and allele-specific CN per bin were merged into CN segments, which were defined as contiguous segments composed of five or more bins with identical CN states. Segmentation was performed separately for total and allele-specific CN estimates in each sample. After this process, any pair of adjacent segments with the same CN assignment, and separated by a distance shorter than five bins, was merged into a single segment.
The total genome size of a species was estimated as the total size of its reference genome assembly. Across species, the mean genome size was 2.67 Gb, ranging between 2.41 Gb and 3.15 Gb and with a standard deviation of 221 Mb . This suggests that inter-species variation in genome size should not have a substantial influence on the somatic mutation rate estimates.
To determine the fraction of inter-species variance in mutation rate explained by each life-history variable individually, the LME model described above was used to produce predictions of the mean mutation rate per species; only fixed effects were used when obtaining these predictions, random effects being ignored.
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