Chapter 5 - Phylogeny and Evolution of 12S rDNA in Gruiformes (Aves)

Abstract

In this chapter, several observations and inferences about the evolutionary dynamics and character evolution of the 12S rDNA molecule have been presented. These include variation in secondary structure resulting from stem migration and uncompensated insertions and deletions within stems; replication slippage as a mechanism of sequence length variation in loops; differences in per-site substitution rates between birds and mammals; the process of compensatory substitution in stems; and differences in distributions of synapomorphies and homoplasies that are spatially correlated with functional and structural regions of 12S rDNA. A robust but simplified estimate of the instantaneous ratio of rates between transversions to transitions is calculated for the 12S rDNA of Gruiformes. 12S rDNA is not entirely saturated by homoplasious substitutions at the levels of gruiform divergence, because it performs well at resolving much older divergences. Yet it exhibits sufficient noise to hinder the resolution of a phylogeny that may be characterized by relatively short internodal branches. High rates of substitution thus are not confined to particular sites across taxa; they are found in different locations in different lineages.