The phylogenetic reconstruction adopted in this book is intended to be more or less speculative because most of the evidence has been lost and many organisms have left no trace in the fossil records. Normally, systematic groups and categories arranged in a hierarchical system on the basis of similarities between organisms replace it. Each of these natural groups consists of a set of organisms that are more closely related to each other than to organisms of a different group. This interrelationship is inferred from the fundamental similarities in their traits (homologies) and is thought to reflect fundamental similarities in their genomes, as a result of common descent. Historically, the major groups of algae are classified into Divisions (the equivalent taxon in the zoological code was the Phylum) on the basis of pigmentation, chemical nature of photosynthetic storage product, photosynthetic membranes’ (thylakoids) organization and other features of the chloroplasts, chemistry and structure of cell wall, number, arrangement, and ultrastructure of flagella (if any), occurrence of any other special features, and sexual cycles.