Nucleotide substitutions during speciation may explain substitution rate variation

Although molecular mechanisms associated with the generation of mutations
are highly conserved across taxa, there is widespread variation in
mutation rates between evolutionary lineages. When phylogenies are
reconstructed based on nucleotide sequences, such variation is typically
accounted for by the assumption of a relaxed molecular clock, which is
just a statistical distribution of mutation rates without much underlying
biological mechanism. Here, we propose that variation in accumulated
mutations may be partly explained by an elevated mutation rate during
speciation. Using simulations, we show how shifting mutations from
branches to speciation events impacts inference of branching times in
phylogenetic reconstruction. Furthermore, the resulting nucleotide
alignments are better described by a relaxed than by a strict molecular
clock. Thus, elevated mutation rates during speciation potentially explain
part of the variation in substitution rates that is observed across the
tree of life.