Draft:Protist systematics

The systematics of protists includes the study of the evolutionary relationships between protists, as well as the resulting methods and systems of classifying them into biological taxa. In the early history of microbial classification, protists were largely divided between more animal-like protozoa (variously called animalcules or infusoria) and more plant-like algae, depending on certain characteristics associated with the plant (sessile, photosynthetic) and animal (motile, heterotrophic) kingdoms.

Historical overview

Early classifications

Since Ancient history, life was interpreted as divided between the plant and animal kingdoms, primarily distinguished based on the ability to photosynthesize and a sessile lifestyle (plant-like), and the ability to move and a predatory lifestyle (animal-like). However, there have always been ambiguous organisms with characteristics of both, and difficult to assign to either. After the discovery of microbes by Antony van Leeuwenhoek in the 17th century, microbial eukaryotes were incorporated into this dichotomy, but increased the number of organisms that could not fit neatly in either category. For example, miscroscopic motile algae were considered animal-like despite their ability to photosynthesize.

Before the mid-18th century, microscopic life was completely excluded from the framework of biological classification. They were referred to as 'animalcules' or 'infusoria', but never assigned to species. The first inclusion was in 1752 by John Hill, who proposed a separate kingdom for animalcules, but this was disregarded by Linnaeus, who limited them to a type of worms in his Systema Naturae.

Up until the 19th century, taxonomists continued making arbitrary taxonomic decisions to comply with this dichotomy, but it had become increasingly clear that these microbes were not clearly assignable as animals or plants. As Joseph M. Scamardella described it in his historical review, "[n]o clear consensus existed about the systematic nature of these organisms and their evolutionary relationship to one another or to larger plants and animals. Microscopic life became increasingly intertwined and constrained taxonomically within the dichotomy of the plant and animal kingdoms". Notably, in 1820 Georg A. Goldfuss coined the term Protozoa (meaning 'first, or early animals') as a class of animals that included ciliates, motile algae, and cnidarians (corals and jellyfish). In 1845, Carl Theodor von Siebold established a separate phylum of animals under the same name, consisting of ciliates and rhizopods (amoebae), which he regarded as "unicellular animals" with the function and structure of an individual animal cell, but not a complete organism. In contrast, other researchers such as Louis Agassiz considered protozoa to be more plant-like and rejected their placement in the animal kingdom.

Proposals of a separate kingdom

Within a decade, five authors proposed the erection of a separate kingdom for these beings: Richard Owen as Protozoa in 1859, John Hogg as Regnum Primigenum (Protoctista) in 1860, Thomas B. Wilson and John Cassin as the Primalia in 1863, and Ernst Haeckel as the Protista in 1866, although this treatment would not become widespread until the mid-20th century. Each proposal varied in composition and evolutionary significance.

Owen referred to his kingdom Protozoa (including microalgae and sponges) as "numerous beings, mostly of minute size, and retaining the form of nucleated cells" that lacked the "superadditions of true plants and animals". He believed plants and animals were defined by a set of several traits, which protozoa lacked: cellulose, oxygen production, roots, and lack of a digestive system in the case of plants; respiration and heterotrophy in the case of animals). It was rejected by others due to the ambiguity in using the same name as von Siebold's earlier phylum Protozoa. Hogg's Regnum Primigenum ('primigenal kingdom') contained the Protoctista, which he coined as meaning 'first created beings' (from Ancient Greek proto- 'first' and -ctista 'built'), not in an evolutionary sense but a seemingly creationist one. He defined them as "primary" or "lower" organisms; like Owen, he included both unicellular and multicellular organisms, such as sponges. Wilson and Cassin's kingdom Primalia contained the previous protoctists as well as organisms they considered "unicellular aggregations" (fungi, lichens, sponges, and macroalgae), and they interpreted it for the first time as the evolutionary link between inorganic matter and the animal and plant kingdoms. The four authors' proposals remained in obscurity.

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  Hogg's 1860 illustration of the Four Kingdoms of Nature, showing "Regnum Primigenum" (Protoctista) as a greenish haze at the base of the Animals and Plants
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  Haeckel's 1866 tree of life, with the third kingdom Protista including some Monera (bacteria) as ancestors to animals, plants, and most other protists

Ernst Haeckel proposed in 1866 the Protistenreich or kingdom Protista (meaning 'the first of all, primordial, the ones who came first in time'). Inspired by Darwinism, he gave importance to their evolutionary role and to discerning genealogical or, as he coined, "phylogenetic" lineages. He included protozoa, flagellated algae, diatoms, bacteria, and sponges as Protista, while excluding lichens, fungi, and macroalgae as plants, and infusoria as animals. Notably, he believed that most protist lineages evolved independently from the plants or animals, and that the three evolved from bacteria. In a later 1878 revision, he excluded sponges from Protista and included infusoria, following his gastraea theory where he postulated the blastula stage as the unifying trait of animals. In yet another revision in 1892, Haeckel resurrected the Protozoa (ancestral to animals) and Protophyta (ancestral to plants) as subgroups of Protista, with a third one named "Protista Neutralia", meant for those not ancestral to either.

Although Haeckel's Protista eventually became the most widely known of all the proposals, it was criticized by both his contemporaries, including William Saville-Kent and Otto Bütschli, and many future authors, especially due to its ambiguous delimitation. Bütschli agreed that genealogy should be the basis for classification, but saw the kingdoms proposed by Haeckel as artificial and questioned the validity of their specific composition, which seemed at times more arbitrary than the earlier plant-animal dichotomy. According to Herbert F. Copeland, his criticisms influenced the delay in widespread recognition of additional kingdoms. During the 1880s, Bütschli published his own classification based on exhaustive comparative studies on the morphology and life cycles of protozoan cells. He separated the microbes completely as Protozoa ("single-celled animals") and Protophyta and bacteria ("single-celled plants"). He divided the protozoa in broad classes according to morphological and locomotive features, namely: Mastigophora (flagellates), Sarkodina (amoebae), Infusoria (ciliates) and Sporozoa (spore-forming parasites). This view was solidified over the rest of the global scientific community, and by the turn of the century it became the widely accepted framework, with only a few authors such as Clifford Dobell defending the protistan concept.

Around the mid-20th century, through newer techniques in microscopy, it became clear that the anucleated organisms, the prokaryotes, were completely different from the nucleated ones, eukaryotes. During this time, Copeland kept the Protista concept alive through a four-kingdom system (with Monera/Mychota and Protista/Protoctista separated), and persuaded the scientific community to abandon the traditional dichotomy. These efforts culminated in a 1956 publication that defined the limits of plants and animals as organisms with advanced cell, tissue, and organ differentiation, leaving protoctists as all other "lower" eukaryotes (including fungi). Subsequently, the kingdom Protista was more widely adopted through the works of Raymond C. Moore and others. Robert H. Whittaker, influenced by his ecological background, was discontent with the focus on taxonomic definitions over coherent evolutionary themes, and developed his own approach, which culminated in 1969 as the popular five-kingdom system: the multicellular forms along nutritional lines (photosynthetic Plantae, decomposing Fungi, and ingesting Animalia), and the unicellular Protista and Monera. Still, Whittaker admitted issues of polyphyly with this system and recognized that red and brown algae probably arose from different ancestors than green algae and true plants.

Electron microscopy revolution

Starting in the late 1950s, electron microscopy allowed for more detailed observations of the inner structure of cells and their organelles (or ultrastructure), leading to a revolution in the understanding of relationships between protists. Many traditional categories (e.g., algae, fungi, protozoa, amoebae, heliozoa, phytoflagellates, zooflagellates...) became obsolete, shown to be polyphyletic. New and more accurate monophyletic relationships (clades) were established based on finer differences in the chloroplasts, mitochondria, flagella, reproductive cycles, and the cell behavior during mitosis.

By the 1980s, most protist groups ("phyla") were confirmed as clades early on through ultrastructural analysis alone, amounting to 45 in 1984: ciliates, dinoflagellates, several lineages of algae (e.g., rhodophytes, chlorophytes, chrysophytes, diatoms, dinoflagellates), apicomplexans, kinetoplastids, euglenids, parabasalids, diplomonads, and microsporidians. By the beginning of the 1980s, there was a consensus on the monophyly of most groups, but the broader relationships between them was harder to define, partly due to the ancient and rapid radiation of protists. This left some 30 to 45 phyla of protists with loose or absent affinities to other branches, including the animal branch, whose closest relatives were still unknown. Still, some broader assemblages were created, uniting superficially dissimilar protists. For example, the presence of straw-like tubular structures (mastigonemes) on one of the two flagella of chrysophytes, gametes of brown algae, oomycetes, and hyphochytrids, led to the establishment of the Stramenopiles or Heterokonta. The photosynthetic euglenophytes and the largely parasitic kinetoplastids were grouped as the Euglenozoa, both with disc-shaped mitochondrial cristae.

The limitations complicated the appearance of phylogenetic schemes in the first two decades, except for a few attempts. Among these attempts was the hypothesis that eukaryotes evolved from an amoeboid photosynthetic ancestor, which gave rise to all the modern groups of algae and, through secondary losses of chloroplasts, to the protozoa, fungi, and animals. Another was the Archezoa hypothesis, which proposed that the "amitochondriate" protozoa (e.g., archamoebae, parabasalians, microsporidia) were the first eukaryotes, and all other eukaryotes (Metakaryota) evolved from a branch that acquired a mitochondrion. Another notable example was the unification of all algae with chlorophylls a and c (i.e., xanthophytes, chrysophytes and brown algae) as one group, known as the chromophyte algae, separate from those with chlorophylls a and b (i.e., the green algae and plants).

Molecular era

Early molecular sequencing

Since the 1980s, the eukaryotic tree was further developed through the use of molecular phylogenetics, with preliminary analyses using the universal small subunit ribosomal RNA sequence and occasionally some protein-coding genes to infer evolutionary relationships. Even from the first analyses it was demonstrated that the molecular diversity within protists was remarkable, exceeding the one found between plants and animals.

By the 1990s, the trees had resolved a stepwise emergence of successive protist phyla, beginning with the amitochondriate protozoa as most basal, a result that confirmed the earlier Archezoa hypothesis. This notion was further developed by several authors, who proposed a stepwise acquisition of each eukaryotic organelle, starting from the archamoebae at the very bottom with their simpler cytoskeleton: a more complex cytoskeleton, a Golgi apparatus, and lastly the mitochondrion would have been acquired in the following steps. However, their basal position was a result of long branch attraction, a methodological artifact caused by the large deviation of these sequences. The presence of mitochondrial genes in these organisms, and the discovery that their hydrogenosomes and mitosomes originated from mitochondria, made the Archezoa concept obsolete.

Among the broader relationships confirmed by early molecular analyses, some were expected, such as the Stramenopiles based on the mastigoneme-bearing flagella, while others were surprising. A diverse assemblage containing the ciliates, dinoflagellates and apicomplexans was revealed in 1991, and later confirmed to be characterized by the shared presence of cortical alveoli, vesicles underneath the cell membranes; the group became known as Alveolata. Another assemblage grouped animals and fungi, together known as the Opisthokonta; also included were the choanoflagellates as the sister group of animals, confirming a 19th century hypothesis.