An outline of estimation of divergence time and diversification process based on the molecular phylogenetic tree

Abstract

Understanding the process by which life diversifies is one of the central issues in biology. To clarify this process in focal taxa as well as to conduct phylogenetic analyses, a divergence time estimation-an important analysis to determine the timescale of a phylogenetic tree-must be performed. It is thought that the diversification process can be vividly reconstructed by estimating the diversification rate and ancestral geographic area, characterizing ancestral ecology, and mapping ancestral habitats according to a time-calibrated phylogenetic framework. Here we introduce a divergence time estimation method and various other methods for reconstructing the process of diversification based on the time-calibrated phylogenetic framework with some study examples of aquatic organisms, mainly fish.