Special Issue "Modern Phylogeny: The Three Domains of Life"

Guest Editor
Dr. Kathleen Scott
Department of Biology, University of South Florida, 4202 E. Fowler Avenue, SCA 110, Tampa, Florida 33620, USA
Website: http://biology.usf.edu/ib/faculty/kscott/
E-Mail: kmscott@usf.edu
Interests: physiological ecology of chemolithoautotrophs; marine and freshwater biogeochemistry

Dear Colleagues,

Many physiological capabilities (e.g., glycolysis; phototrophy via bacteriorhodopsin) are shared among more than one of the three great domains of life, either due to inferred presence in a common ancestor, or horizontal gene transfer subsequent to domain differentiation. However, many major capabilities (eg., photosynthesis; methanogenesis; the Calvin cycle) are limited to one domain, or perhaps one phylum, and seem recalcitrant to broader distribution on the tree of life. The purpose of this issue is to provide a venue for adventuresome, yet well-reasoned, speculation about the forces driving and limiting the distribution key physiological capabilities on the tree of life. Are certain lifestyle/phylogenies inherently incompatible (methanogenic bacteria? Photosynthetic or pathogenic archaea?)? Or, is it likely that these organisms exist, but have not been detected yet? Where might we find them, if they do exist? Minireview/perspective format is welcomed.

Dr. Kathleen Scott
Guest Editor

Type of Paper: Article
Title: Trees beyond the Tree
Author: Guillaume Lecointre
Affiliation: UMR 7138 « Systématique, Adaptation, Evolution », Département Systématique & Evolution, Muséum National d’Histoire Naturelle, CP 39, 57 rue Cuvier, 75005 PARIS, France; E-Mail: lecointr@mnhn.fr
Abstract: The term "tree" is commonly used for objects very different in terms of epistemology. We will list several categories of « trees » according to various meanings given to nodes and to links. We will do the same for the « tree of life » (TOL). The distinctions made are useful to clarify assumptions required by certains tools of tree reconstruction. We will show that nine kinds of « trees » are distributed across four levels: the theoretical level, the technical level, the epistemological level, and the synthetic level. Avoiding confusions, it appears that networks are not obligarory representations of the TOL.