Use of Paleontological and Phylogenetic Data in Comparative and Paleobiological Analyses: A Few Recent Developments

Abstract

Comparative biology has progressed tremendously but unevenly in the last decades, through incorporation of methodological progress in phylogenetics and in statistical methods that incorporate phylogenetic data into statistical analyses of character correlation or evolution. This review presents a few methods of general interest to comparative biologists, such as phylogenetic independent contrasts (PIC) and variance partition with phylogenetic eigenvector regression. In evo-devo, heterochrony detection has usually been done using event pairing, in the last decade. That method uses a topology, but does not exploit branch length information. A recently proposed method based on squared-change parsimony and PIC exploits both topology and branch lengths, and it outperforms event pairing. Molecular evolution can also benefit from a phylogenetic perspective, as shown in recent studies on genome size evolution. In paleobiology, phylogenies are still rarely and often incompletely incorporated in analyses. Recent developments facilitate time-tree compilations and the combination of paleontological and molecular age data, and new branch length transformation methods can help to standardize PIC, to determine if the characters evolved according to a Brownian motion model, and to deal with clades about which no age information is available.