0000000000181235
AUTHOR
Robert Belshaw
The Phylogenetic Analysis of Variable-Length Sequence Data: Elongation Factor–1α Introns in European Populations of the Parasitoid Wasp Genus Pauesia (Hymenoptera: Braconidae: Aphidiinae)
Elongation factor-1alpha (EF-1alpha) is a highly conserved nuclear coding gene that can be used to investigate recent divergences due to the presence of rapidly evolving introns. However, a universal feature of intron sequences is that even closely related species exhibit insertion and deletion events, which cause variation in the lengths of the sequences. Indels are frequently rich in evolutionary information, but most investigators ignore sites that fall within these variable regions, largely because the analytical tools and theory are not well developed. We examined this problem in the taxonomically problematic parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) using con…
Viral Mutation Rates
Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 108 to106 s/n/c for DNA viruses and from 106 to 104 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mut…
Viral mutation and substitution: units and levels.
Viruses evolve within a hierarchy of organisational levels, from cells to host species. We discuss how these nested population structures complicate the meaning and interpretation of two apparently simple evolutionary concepts: mutation rate and substitution rate. We discuss the units in which these fundamental processes should be measured, and explore why, even for the same virus, mutation and substitution can occur at very different tempos at different biological levels. In addition, we explore the ability of whole genome evolutionary analyses to distinguish between natural selection and other population genetic processes. A better understanding of the complexities underlying the molecula…