This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

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The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

A mechanism for gene conversion is proposed which overcomes many of the difficulties that any copy choice model encounters. It is suggested that along with general genetic pairing of homologous genomes at meiosis, effective pairing over short regions of the genetic material occurs at the molecular level by the separation of the strands of the DNA double helices, followed by the annealing of strands from two homologous chromatids. If the annealed region happens to span a heterozygous site, mispairing of bases will occur. Such a situation may be analogous to that in DNA which is damaged by mutagens; the same or similar repair mechanisms may operate, and these, by adjusting the base sequences in order to restore normal base pairing, would bring about gene conversion in the absence of any genetic replication. The model indicates how precise breakage and rejoining of chromatids could occur in the vicinity of the conversion, so that conversion would frequently be accompanied by the recombination of outside markers. The model also proposes that the distance between two mutant sites on a fine structure map depends not so much on the frequency of a recombinational event occurring between them, but rather on the degree of inhibition of the processes of genetic pairing by the mutants themselves. The model will explain almost all the data in a formal way, and it has the advantage over copy choice mechanisms for gene conversion in (1) being compatible with semi-conservative replication of DNA, (2) not invoking DNA synthesis during or after genetic pairing, (3) providing a molecular mechanism for close specific pairing, (4) making it unnecessary to postulate sister strand exchange or a process akin to this, (5) suggesting why rates of gene conversion in opposite directions are sometimes unequal and (6) providing an explanation of the clustering of mutant sites, a basis for map expansion and for the apparently capricious departure of fine structure maps from additivity. Although the model proposed is a general rather than a specific one, it suggests that the process of conversion and intragenic recombination is more complex than is usually believed, since it depends on several interacting factors. Nevertheless, it is hoped that the introduction of a model with this complexity will help to stimulate specific experiments, and that these will provide definitive information which would never be obtained if simpler models of conversion and intragenic recombination were believed to explain the genetic data sufficiently well.

/pdf/a-mechanism-for-gene-conversion-in-fungi-1tp9iv58rz.pdf

A mechanism for gene conversion in fungi.

The subkingdom Protozoa now inclues over 65,000 named species, of which over half are fossil and approximately 10,000 are parasitic. Among living species, this includes approximately 250 parasitic and 11,300 free-living sarcodines (of which approximately 4,600 are foraminiferids); approximately 1,8000 parasitic and 5,100 free-living flagellates; approximately 5,600 parasitic "Sporozoa" (including Apicomplexa, Microspora, Myxospora, and Ascetospora); and approximately 2,5000 parasitic and 4,700 free-living ciliates. There are undoubtedly thousands more still unnamed. Seven phyla of PROTOZOA are accepted in this classification--SARCOMASTIGOPHORA, LABYRINTHOMORPHA, APICOMPLEXA, MICROSPORA, ASCETOSPORA, MYXOSPORA, and CILIOPHORA. Diagnoses are given for these and for all higher taxa through suborders, and reporesentative genera of each are named. The present scheme is a considerable revision of the Society's 1964 classification, which was prepared at a time when perhaps 48,000 species had been named. It has been necessitated by the acquisition of a great deal of nex taxonomic information, much of it through electron microscopy. It is hoped that the present classification incorporatesmost of the major changes that will be made for some time, and that it will be used for many years by both protozoologist and non-protozoologists.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1550-7408.1980.tb04228.x

A Newly Revised Classification of the Protozoa

are those who consider questions in science which have no unequivocal , experimentally determined answer scarcely worth discussing. Such feeling, along with conservatism, may have been responsible for the long and almost unchallenged dominance of the system of two kingdoms-plants and animals-in the broad classification of organisms. The unchallenged position of these kingdoms has ended, however; alternative systems are being widely considered (1-18) and are appearing in many introductory biology texts (19-24). My purpose in this article is to discuss the merits of two classifications which depart from the traditional two kingdoms, the systems of Copeland (1-3) and Whittaker (4, 5). Two-Kingdom System Man is terrestrial, and he sees around him two major groups of organisms of very different adaptation to nutrition on land-the photosynthetic, rooted, higher plants, and the food-ingesting, motile, higher animals. So distinct in way of life, direction of evolution, and kind of body organization are these groups that a concept of dichotomy-plants versus animals-is almost inescapable if they are considered by themselves. The two groups became the nuclei around which concepts of the plant and animal kingdoms were developed by early naturalists. The kingdoms have been part of the formal classification of living things since Linnaeus (25). Mosses, liverworts, and macroscopic algae are clearly plants in their photo-synthetic and nonmotile way of life, and (though the photosynthetic process itself was not understood by early naturalists) these forms were grouped 150 with the higher land plants. The higher fungi on land are nonmotile, and their apparently \"rooted\" manner of growth suggested the plants. It thus seemed reasonable to assign fungi to the plant kingdom, and some students believed that they had evolved from algae. The wealth of unicellular life discovered by microscopists offered greater difficulty. Some forms were motile and ingested food, however, and were naturally regarded as one-celled animals or proto-zoans. Others were nonmotile and photosynthetic, hence one-celled plants. There remained a wide range of uni-cellular forms in which nonmotility and flagellate or pseudopodial motility, and ingestive, photosynthetic, and absorp-tive nutrition, were combined in various ways which were neither clearly plant-like nor animal-like. In a number of cases plant-like and animal-like unicells were connected by a series of closely related intergrading forms within the same major taxon. There remained also the bacteria which, though few are pho-tosynthetic and many are motile, seemed better treated as plants because of their walled cells. The plant and animal kingdoms …

https://science.sciencemag.org/content/sci/163/3863/150.full.pdf

New concepts of kingdoms of organisms

Colletotrichum - current status and future directions.

Numerous collections of the orange-colored Pocheina have been obtained in North Carolina and other areas of the United States, and in Australia and England. All but one were found on bark of live gymnosperm and frondose trees. A single collection from a dead Juniperus virginiana tree most closely resembles the type collection of P. rosea. Further studies may reveal that the majority of our collections of P. rosea represent a new variety. The new species, P. flagellata, found on the bark of live gymnosperm trees in Wisconsin and North Carolina, has sorocarps that resemble those of our common P. rosea collections but differs in having flagellate cells, spores with more abundant punctations, and nuclei that, during mitosis, lack divided nucleolar parts at the polar areas, which are present in the mitotic nuclei of P. rosea. Pocheina and Acrasis are considered related genera that are unrelated to other acrasid cellular slime molds. As previously noted by Loeblich and Tappan (1961), Guttulina Cienkowsky (1873), a cellular slime mold genus, was antedated by Guttulina d'Orbigny, a foraminiferan genus. Since we have considered both groups of organisms as members of the Kingdom Protista, reclassification of the cellular slime mold genus as Pocheina Loeblich & Tappan and the single known species as P. rosea (Cienk.) Loeblich & Tappan was accepted but retained in the Class Acrasea, Subphylum Mycetozoa, and Phylum Gymnomyxa of the Kingdom Protista (Olive, 1975). At the same time, the acrasid and dictyostelid cellular slime molds were classified separately because of a number of major differences among them. Also, as will be indicated later, Pocheina appears to be related to the genus Acrasis but to no other genus of cellular slime molds presently known. Cienkowsky discovered his cellular slime mold on dead wood containing lichens in a part of Russia that is now Poland, and he described the rose-colored sorocarp as having a round mass of spores at the top of a stalk composed of rows of wedge-shaped cells. In the presence of water the sorocarp cells germinated, yielding amoebae with lobose pseudopodia. The organism was not discovered and described again until it was found on bark of a live cypress tree sent to K. B. Raper from the Netherlands by Nannenga-Bremekamp. Raper (1973) found it to be very similar to the one described by Cienkowsky, although the spores failed to germinate. Our numerous collections of Pocheina in the past several years have turned out to comprise more than a single species. In the following discussion, we will describe what may be two varieties of P. rosea and a new species of the genus. Both species have been grown in culture.

Descriptions of acrasid cellular slime molds: Pocheina rosea and a new species, Pocheina flagellata

Echinosteliopsis, a New Genus of the Mycetozoa

CHAPTER 7 – Labyrinthulina (Labyrinthulas and Thraustochytrids)

Acrasiales of the West Indies

(1954) Taxonomic Differentiation Between Ascobolus Stercorarius and A Furfuraceus Mycologia: Vol 46, No 1, pp 105-109

Lindsay S. Olive

Papers

Descriptions of acrasid cellular slime molds: Pocheina rosea and a new species, Pocheina flagellata

Echinosteliopsis, a New Genus of the Mycetozoa

CHAPTER 7 – Labyrinthulina (Labyrinthulas and Thraustochytrids)

Acrasiales of the West Indies

Taxonomic Differentiation Between Ascobolus Stercorarius and A. Furfuraceus