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This has been noted in previous phylogenetic reconstructions and different explanations have been proposed, including differences in generation times and longevity, but recent analyses suggest that mutation rates differ for mtDNA between different mammal lineages [73].
We are just beginning to understand how mutation rates differ among mitochondrial, plastid, and nuclear genomes.
However, the mutation rates differ among loci and among alleles, and also between species [ 21].
Although mutation rates differ between taxa, we apply this rate to S. polychroa for a preliminary estimate.
It could be that the mutation rates differ across cell lineages; it could be that selection pressures shape the number of mutations; or the number of mtDNA genome generations could differ across cell lineages.
Gao et al. (2011) reported an analysis of the mutation patterns from a large-scale experiment for screening recessive lethal or nearly lethal mutations and found that mutation rates differ substantially in the germline lineage.
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The model allows for mutation rates differing among loci by using the number of alleles per locus to estimate locus specific relative mutation rate modifiers.
For a given allele length, mutation rate differed among motif types.
However, the heritable mutation rate differed between the genes (78% in DsRed2 and 22% in ey).
Together with the above observation that mutation rate differs at different genomic locations, it is clear that mutations do not occur randomly, but are influenced by both local nucleotide context and genomic position.
First, mitochondrial mutation rate differs substantially across species; for example, mammals tend to have high rates and Drosophila have low rates (Montooth and Rand 2008).
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