The New Tree of Eukaryotes

Abstract

For 15 years, the eukaryote Tree of Life (eToL) has been divided into five to eight major groupings, known as 'supergroups'. However, the tree has been profoundly rearranged during this time. The new eToL results from the widespread application of phylogenomics and numerous discoveries of major lineages of eukaryotes, mostly free-living heterotrophic protists. The evidence that supports the tree has transitioned from a synthesis of molecular phylogenetics and biological characters to purely molecular phylogenetics. Most current supergroups lack defining morphological or cell-biological characteristics, making the supergroup label even more arbitrary than before. Going forward, the combination of traditional culturing with maturing culture-free approaches and phylogenomics should accelerate the process of completing and resolving the eToL at its deepest levels. The Eukaryote Tree of LifeResolving the evolutionary tree for all eukaryotes has been a long-standing goal in biology. Inferring an eToL that is both accurate and comprehensive is a worthwhile objective in itself, but the eToL is also the framework on which we understand the origins and history of eukaryote biology and the evolutionary processes underpinning it. It is therefore a fundamental tool for studying many aspects of eukaryote evolution, such as cell biology, genome organization, sex, and multicellularity. In the molecular era, the eToL has also become a vital resource to interpret environmental sequence data and thus reveal the diversity and composition of ecological communities.Although most of the described species of eukaryotes belong to the multicellular groups of animals (Metazoa), land plants, and fungi, it has long been clear that these three 'kingdoms' represent only a small proportion of high-level eukaryote diversity. The vast bulk of this diversity -including dozens of extant 'kingdom-level' taxa -is found within the 'protists', the eukaryotes that are not animals, plants, or fungi [1][2][3][4][5][6]. To a first approximation, inferring the eToL is to resolve the relationships among the major protist lineages. However, this task is complicated by the fact that protists are much less studied overall than animals, plants, or fungi [7]. Molecular sequence data has accumulated slowly for many known protist taxa and numerous important lineages were completely unknown (or were not cultivated, hence challenging to study) when the molecular era began. Thus, resolving the eToL has been a process where large-scale discovery of major lineages has occurred simultaneously with deep-level phylogenetic inference. This makes the task at hand analogous to a jigsaw puzzle, but one where a large and unknown number of pieces are missing from the box and instead are hidden under various pieces of the furniture. The Supergroups ModelBy the early 2000s, a model of the tree emerged that divided almost all of known eukaryote diversity among five to eight major taxa usually referred to as 'supergroups ' [8-12]. The category of supergroup was a purely informal one...

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