Protist diversity and eukaryote phytogeny

Abstract

The last quarter century has seen dramatic changes in our understanding of the phylogenetic relationships among protist groups and their evolutionary history. This is due in large part to the maturation of molecular phylogenetics, to geno- mics and transcriptomics becoming widely used tools, and to ongoing and accelerating progress in characterizing the major lineages of protists in the biosphere. As an introduction to the Handbook of the Protists, Second Edition, we provide a brief account of the diversity of protistan eukaryotes, set within the context of eukaryote phylogeny as currently understood. Most protist lineages can be assigned to one of a handful of major groupings ("supergroups"). These include Archaeplastida (which also includes land plants), Sar (including Stramenopiles/Heterokonta, Alveolata, and Rhizaria), Discoba, Metamonada, Amoebozoa, and Obazoa. This last group in turn contains Opisthokonta, the clade that includes both animals and fungi. Many, but not all, of the deeper- level phylogenetic relationships within these groups are now resolved. Additional well-known groups that are related to Archaeplastida and/or Sar include Cryptista (cryptophyte algae and their relatives), Haptophyta, and Centrohelida, among others. Another set of protist lineages are probably most closely related to Amoebozoa and Obazoa, including Ancyromonadida and perhaps Malawimonadidae (though the latter may well be more closely related to Meta- monada). The bulk of the known diversity of protists is covered in the following 43 chapters of the Handbook of the Protists; here we also briefly introduce those lineages that are not covered in later chapters. The Handbook is both a community resource and a guidebook for future research by scientists working in diverse areas, including protistology, phycology, microbial ecology, cell biology, and evolutionary genomics.