The divergence of mutation rates and spectra across the Tree of Life

Abstract

Owing to advances in genome sequencing, genome stability has become one of the most scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological, the mutation rate (per nucleotide site per generation) ranges over three orders of magnitude among species and several‐fold within individual phylogenetic lineages. Within all major organismal groups, mutation rates scale negatively with the effective population size of a species and with the amount of functional DNA in the genome. This relationship is most parsimoniously explained by the drift‐barrier hypothesis, which postulates that natural selection typically operates to reduce mutation rates until further improvement is thwarted by the power of random genetic drift. Despite this constraint, the molecular mechanisms underlying DNA replication fidelity and repair are free to wander, provided the performance of the entire system is maintained at the prevailing level. The evolutionary flexibility of the mutation rate bears on the resolution of several prior conundrums in phylogenetic and population‐genetic analysis and raises challenges for future applications in these areas.

GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes

“…longevity, body mass, body length and d N /d S ) significantly correlate with a more direct N e proxy, i.e . the polymorphism-derived N e (Figure 7 ; ( 65 )).…”

“…In Lynch et al. ( 65 ) the per species germline mutation rate (μ) and level of neutral diversity (π s ) was integrated into the equation N e =π s /4μ, to produce what we named a ‘polymorphism-derived N e ’. This more direct estimates of N e was calculated for 65 of the species in our dataset.…”

DNA Damage, Genome Stability and Adaptation: a Question of Chance or Necessity?

“…Another study found a negative correlation between levels of gene heterozygosity and rates of chromosomal speciation, suggesting that rates of speciation increase in populations with small Ne (low heterozygosity) [57]. The only feasible way, however, of estimating Ne is to rely on measures of within-population nucleotide diversity at neutral genomic sites, such as silent sites in codons (dS) [58]. While dependence of heterozygosity on Ne is necessarily true for isolated populations of the same species (same mutation rate per individual), it is not entirely clear whether the use of such measures can be applied to whole taxonomic groups for comparative studies [59].…”

DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity?

“…Another study found a negative correlation between the levels of gene heterozygosity and the rates of chromosomal speciation, suggesting that the rates of speciation increase in populations with a small effective population size (low heterozygosity) [57]. The only feasible way, however, of estimating the effective population size is to rely on measures of within-population nucleotide diversity at neutral genomic sites, such as silent sites in codons (dS) [58]. While the dependence of heterozygosity on the effective population size is necessarily true for isolated populations of the same species (same mutation rate per individual), it is not entirely clear whether the use of such measures can be applied to whole taxonomic groups for comparative studies [59].…”