Analysis of among-site variation in substitution patterns

AUTOR(ES)

Krishnan, Neeraja M.

FONTE

Biological Procedures Online

RESUMO

Substitution patterns among nucleotides are often assumed to be constant in phylogenetic analyses. Although variation in the average rate of substitution among sites is commonly accounted for, variation in the relative rates of specific types of substitution is not. Here, we review details of methodologies used for detecting and analyzing differences in substitution processes among predefined groups of sites. We describe how such analyses can be performed using existing phylogenetic tools, and discuss how new phylogenetic analysis tools we have recently developed can be used to provide more detailed and sensitive analyses, including study of the evolution of mutation and substitution processes. As an example we consider the mitochondrial genome, for which two types of transition deaminations (C⇒T and A⇒G) are strongly affected by single-strandedness during replication, resulting in a strand asymmetric mutation process. Since time spent single-stranded varies along the mitochondrial genome, their differential mutational response results in very different substitution patterns in different regions of the genome.

Documentos Relacionados

• An examination of phylogenetic models of substitution rate variation among lineages
• Patterns of morphologic variation among isolates of Trichosporon beigelii.
• Modeling the site-specific variation of selection patterns along lineages
• Pollinator visitation patterns strongly influence among-flower variation in selfing rate
• Allelic variation in human mitochondrial genes based on patterns of restriction site polymorphism.