The Effect of Secondary Loss on Our Views of Eukaryotic Evolution.

Abstract

Traditionally, phylogenetic relationships among eukaryotes have been inferred using morphological information. In prokaryotes, morphology is not very useful for this purpose and other approaches have been preferred. The morphological bias among those of us who study eukaryotes has led us into a number of traps. Even with the advent of molecular sequence data, we have failed to break some of our bad habits in interpreting phylogenetic trees. The common false assumption, in all its guises, can be boiled down to one phrase-simple equals primitive. The fundamental flaw that has been ignored time and time again is that simple can also mean derived. Misinterpreting the absence of a character as a sign of an organism’s primitive nature often results in a false view of eukaryotic evolution. Secondary loss is a pervasive characteristic of eukaryotic evolution. Parasites appear to be particularly susceptible to secondary simplification or loss of structure. This can be illustrated from our studies of the evolution of eukaryotic organelles. A popular choice as paradigm for the ancestral eukaryote, especially among those who worked with the organism, was for many years Entamoeba histolytica, the agent of amoebic dysentery. This organism lacks many typical eukaryotic features-mitochondria, Golgi apparatus, flagella, rough endoplasmic reticulum-and has other unusual characteristics that could be interpreted as primitive. However, when ribosomal RNA-based phylogenetic trees that included Entamoeba species became available, the branch leading to these organisms was not basal to other eukaryotes, as had