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Eukaryotes. This tree is derived from a consensus of several different studies that are cited in the Discussion of Phylogenetic Relationships and the individual pages for each lineage shown. Discussion of Phylogenetic Relationships. Our understanding of eukaryotic relationships has been transformed by the use of molecular data to reconstruct phylogenies (Sogin et al., 1. Prior to that, the diversity of microbial eukaryotes was vastly underestimated, and the relationships between them and multicellular eukaryotes were difficult to resolve (Taylor, 1. Early molecular phylogenies based on small subunit ribosomal RNA (SSU r. RNA) gene sequences suggested a ladder of basal lineages topped by a .
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A great number of the relationships revealed by SSU r. RNA phylogeny have stood the test of time, but subsequent analyses based on protein coding genes and more recently very large datasets composed of hundreds of protein coding genes have led to a revision of the overall structure of the tree. The current view of eukaryotic phylogeny is of a small number of large . Some of these supergroup hypotheses are well supported, while others remain the subject of vigorous debate (see (Keeling et al., 2.
Below we summarise the main members of each supergroup, the evidence for its monophyly, and emerging hypotheses for inter- supergroup relationships. Archaeplastida (Plantae)The Archaeplastida, or Plantae, comprises glaucophytes, red algae, green algae and plants. They are united by the possession of a plastid derived from primary endosymbiosis (see Symbiosis section). There has long been strong support for the monophyly of plastids in Archaeplastida based on molecular phylogeny and also plastid genome structure (Turner, 1.
Turner et al., 1. Burki et al., 2. 00. Moreira et al., 2. Reyes- Prieto et al., 2.
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Excavata. Excavata is a large and diverse grouping that has been proposed based on a synthesis of morphological and molecular data. Many excavates share a similar feeding groove structure (from which the name is derived) (Simpson and Patterson, 2. Simpson and Patterson, 1. Many others lack this structure, but are demonstrably related to lineages that possess it in molecular phylogenies (Simpson, 2.
Simpson et al., 2. Simpson et al., 2. Putting this evidence together led to the suggestion of shared ancestry, and some recent multi- gene phylogenies in fact provide tentative support for the monophyly of the whole group (Burki et al., 2. Rodriguez- Ezpeleta et al., 2.
Chromalveolata. Chromalveolates comprises six major groups of primarily single celled eukaryotes: apicomplexans, dinoflagellates and ciliates are members of the alveolates, they are hypothesised to be related to stramenopiles, cryptomonads, and haptophytes (Cavalier- Smith, 2. Keeling, 2. 00. 9). The basis for this hypothesis is the widespread presence of plastids in these groups that are all derived from secondary endosymbiosis with a red alga.
It was therefore proposed that all chromalveolates share a common ancestor where this endosymbiosis took place (Cavalier- Smith, 1. The monophyly of the plastids has been demonstrated with limited sampling (Hagopian et al., 2. Rogers et al., 2. Yoon et al., 2. 00. Chromalveolata are monophyletic with the Rhizaria nested within (see below) (Hackett et al., 2.
Additional support comes from two genes with unusual evolutionary histories involving lateral gene transfer and/or re- targeting to the plastid that are most consistent with a common origin of chromalveolate plastids (Fast et al., 2. Harper and Keeling, 2. Patron et al., 2. Many of these will not be familiar to many readers, but they are ubiquitous in nature and important predators in many environments. Major lineages include Cercozoa, Foraminifera, and Radiolaria. Rhizaria is the most recently recognized supergroup, having been identified exclusively from molecular phylogenetic reconstruction (Cavalier- Smith, 2. Cavalier- Smith, 2.
Nikolaev et al., 2. Prior to this, there was little reason to anticipate this grouping, because there is no major structural character that unites them. Analyses of multiple protein coding genes have further supported the monophyly of Rhizaria, and suggested a relationship to chromalveolates (see below).
They have been proposed to be a clade called . The root of the tree of eukaryotes has been proposed to be somewhere near this lineage, so it is possible the ? There has long been very strong evidence from several kinds of data for the monophyly of alveolates.
Multi- gene trees have also consistently and strongly supported a relationship between alveolates and stramenopiles (Burki et al., 2. Burki et al., 2. 00. Hackett et al., 2. Patron et al., 2.
Rodriguez- Ezpeleta et al., 2. Rodriguez- Ezpeleta et al., 2.
Simpson et al., 2. There is now also very strong evidence from molecular phylogenies and a shared lateral gene transfer for the monophyly of cryptomonads, haptophytes, and their relatives (Burki et al., 2. Hackett et al., 2.
Patron et al., 2. Rice and Palmer, 2.
In addition there is evidence from the plastid genome and plastid targeted proteins for the monophyly of chromalveolates and their plastids (Fast et al., 2. Hagopian et al., 2. Harper and Keeling, 2. Patron et al., 2.
Rogers et al., 2. Yoon et al., 2. 00.
However, multi- gene trees also consistently show that the entire rhizarian supergroup is closely related to alveolates and stramenopiles (Burki et al., 2. Burki et al., 2. 00. Hackett et al., 2.
Rodriguez- Ezpeleta et al., 2. Rhizaria nested within the group. These relationships will doubtless be refined with further data, but for now we follow the consensus of the available evidence and place the Rhizaria within the Chromalveolata. References. Adl, S.
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