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.
Chemosynthetic, cold-seep-dependent fossil assemblages occur at five fossil localities in the riverside cliffs along the Sagami River, Sagamihara City, central Japan, where the upper part (2.5 ‒ 2.0 Ma) of the marine Nakatsu Group is exposed. The upper Nakatsu Group is marked by coarsening-upward and subsequent fining-upward sequences as follows (in ascending order): mudstone (Lithofacies A), mudstone and sandy mudstone (B), sandy mudstone (C), alternations of sandy mudstone and muddy sandstone (D), sandy mudstone (E), and mudstone (F). The fossil assemblages are dominated by the bivalve molluscs Lucinoma and/or Conchocele that show high rates (79.2 % ‒ 100 %) of valve articulation, occur in clusters, and are frequently preserved in life positions. The fossils are commonly associated with authigenic carbonate concretions consisting
of high-magnesian calcite and/or dolomite that are greatly depleted in 13C (δ13C = -33.31 ‰ to -22.60 ‰ VPDB), suggesting the influence of anaerobic oxidation of methane. These observations indicate that the fossil assemblages are chemosynthetic and cold-seep-dependent. The bathymetric ranges of extant molluscan species and the water temperature inferred from the stable oxygen isotope ratios of the authigenic carbonates suggest that lithofacies E was deposited in water depths of 150 ‒ 240 m.