Why is protista not a clade

Current rules governing validation of new species, from various codes of nomenclature, have become an impediment to naming of new protists. Standard requirements for protist species descriptions and type specimens need to be modernized to accommodate the rapid discovery of new species made possible by modern microscopic and molecular techniques.

Although we agree with the criticisms of the botanical and zoological codes made by proponents of the Phylocode, we did not all agree that the current Phylocode is the solution, nor does it currently address species typification. Accordingly, new guidelines are needed to govern standards in protist species descriptions and classification. Over the past 25 years, molecular phylogenetic studies have led to extensive modification of traditional classification schemes for eukaryotes.

The most dramatic changes have occurred within protists, from which multicellular organisms evolved. The names of many protist groups and the genera they include have been changed so many times that the classification scheme is unclear, and it is difficult to determine which names apply.

Two recent reviews have provided a modern phylogenetic perspective on the overall organization of eukaryote clades Keeling et al. A necessary extension of this phylogenetic research was to establish a new classification that reflected the general consensus on the taxonomic names and their authorities Adl et al. The decision to do so was primarily practical.

Where possible, well-known names referring to recognized monophyletic groups were retained. Although it did not try to follow the Phylocode, groups of named lineages were defined by apomorphies derived characters as much as possible, but node-based and stem-based definitions were used as necessary, even though they were not identified as such in the final presentation. In this classification, name endings that conveyed hierarchical information in a traditional code e.

We believe this scheme to be more utilitarian as it recognizes one name for each clade where multiple names for the same clade were used previously. Furthermore, the classification is intended to facilitate future modification in light of improved phylogenetic information, without requiring a cascade of name changes. Further changes to the classification will no doubt be necessary given that our knowledge of some groups and our geographical sampling are still far from complete.

Several critical issues remain to be resolved and we must continue to work towards a practical consensus. Adl et al. Metazoa Haeckel , Plantae Haeckel , and some Phaeophyceae Hansgirg are recognized as being truly multicellular. The current number of described protist species, including fungi, is widely acknowledged to be a fraction of the total diversity in nature Table 1 ; May, ; Corliss, Many geographic regions have not been sampled at all and most regions and habitats are insufficiently sampled.

The rate of discovery of new species from environmental samples remains high. Indeed, most soil, freshwater, or marine samples collected contain a multitude of undescribed species Foissner, , ; Slapeta et al.

Owing to insufficient environmental sampling and reisolation, the geographical distribution of most species remains unknown. A metadata statistical analysis of species richness indicated that unicellular organisms showed high relative local species richness, which is consistent with most species being locally rare Hillebrand et al. Species composition for protists was statistically less similar between samples with geographical distance, suggesting a regionally restricted distribution for some or many species, likely due to limitations to protist dispersal over long distances.

Interpretation of these results is complicated, however, because species identification is typically based on morphology, which often may not distinguish between species with similar or identical morphologies Hillebrand et al. Approximate number of described species and estimated total number of species in each group. Potential number of species were estimated by authors for each group based on number of unknown DNA sequences found in environmental samples. To give just one example, Diatomea Dumortier and Bacillariophyta Haeckel both describe the same clade: the diatoms.

The ranks within this group received a parallel series of names independently by zoologists and botanists to accommodate rank endings appropriate for each code the so-called ambireginal classification.

These unnecessary duplications introduced a double language throughout protist classification schemes that resulted in confusion. The situation was exacerbated from the s onward, as many genera were reclassified to accommodate new research and discoveries of new taxa. The traditional classification of protozoa and algae collapsed during the s and s as many groups were subsequently shuffled. Many ranks contained genera that were described under one code and other genera under the other code.

More dramatically, it became evident through molecular phylogenies that fungi governed by the ICBN are a sister lineage of animals governed by the ICZN , and novel protists discovered at the base of both of these clades were described following ICZN rules Mendoza et al. Lastly, the recognition of monophyletic groups based on modern phylogenetic concepts forces us to do things that are awkward with the traditional codes.

For example, we would be forced to place classes within classes, and kingdoms within kingdoms, or invent many new ranks.

These issues were elaborated fully elsewhere and will not be repeated here Cantino, ; Pleijel and Rouse, Previous attempts at synthesis of a classification for eukaryotes, based on identifying successive evolutionary steps and providing a Linnaean name for each rank in the hierarchy, required numerous novel rank names Cavalier-Smith, and never became widely used by protistologists. In part, this valiant effort was premature because most of the molecular phylogenetic information necessary became available subsequently.

Several alternative classifications were proposed in this new light, with new competing names for the same groups of organisms Cavalier-Smith, ; Patterson, , , with accompanying changes in ranks and authority as required by the ICBN or the ICZN. As a result, authors resorted to selecting one of several possible names for each group or, more commonly, used informal names without specifying an authority or a definition.

This further added to the confusion. Without a memory of the history of changes associated with a taxon name, rank, and clade, identifying a group and its composition became very difficult for professionals, and almost impossible for those entering the field of protistology. There was simply no common rationale for deciding which name and which classification to use.

The purpose of classification is to arrange biological diversity in such a way as to facilitate communication and accurate information retrieval. This system must operate within a phylogenetic context and must be able to accommodate modification while retaining name stability. This is a particularly onerous task as there are millions of phylogenetic entities at different hierarchical levels, with thousands more being discovered annually May and Nee, The mess that arose in the classification of protists attests to the failure of the ICBN and ICZN to arrive at a mutually satisfactory accommodation, at accommodating changes in the classification, and providing unambiguous name stability in a modern evolutionary context.

Binomial nomenclature is responsible for much of the instability in the classification, as each time a taxon is moved, its generic name is changed Cantino, This is not problematic for a small number of taxa, but the extent of change required to the classification was unforeseen.

The fundamental division of life into plants versus animals appeared distinct and stable enough at the time, but protists blurred that distinction. The flexibility that would later be required of the traditional schemes, with the rapid expansion of protist taxa and extensive reclassification, simply could not be accommodated while retaining name stability. Other problems with the Linnaean rank-based nomenclature have been the subject of many papers over the past 15 years de Queiroz and Gauthier , ; Cantino et al.

Some of the more problematic issues raised are that 1 rank dictates priority and synonymy under separate codes, instead of clades; 2 rank changes cause a cascade of name changes following even minor changes in phylogenetic hypotheses shifting to a new rank changes both the name, and the authority of a group, even though the organisms it describes and the clade remains the same ; 3 the codes are essentially silent on what is considered today to be the overriding concern in classification—the principle of common descent.

It is permissible for the members of well supported clades to be separated into paraphyletic categories, even if doing so introduces misleading information about evolutionary relatedness; and 4 more emphasis is placed on who named or moved a group than the group and its name.

Several other issues concern outdated approaches to describing species. For example, the requirement for Latin descriptions in the ICBN and what is acceptable as a type specimen and holotype under both codes are impractical for protists and need modernizing, as discussed below. Unfortunately, the Phylocode is not much help on this point.

It has been argued that the traditional codes can be revised to accommodate some of the problems mentioned above, and that many of the identified problems are not serious Barkley et al. That may be true for extant Animalia and Plantae, although some disagree Cantino, , but for protists that is simply not the case.

An example of the many profound difficulties that can be encountered was recently provided for Pneumocystis , a pathogen that was traditionally treated as a protozoan under the ICZN but is now known to be a fungus and must be treated by the ICBN Redhead et al. These difficulties are encountered with well-known isolates that exist in many laboratories.

The problem is insurmountable with isolates that can be fully described but cannot be cultured or cryopreserved. To place the issue in perspective, imagine a situation where plant species descriptions would be acceptable only if the new specimen was domesticated enough to be cultivated!

For example, a protist specimen that is digitally photographed and then used to obtain DNA for phylogenetic information will no longer physically exist to be deposited as a holotype. However, the resulting digital images, sequence data, and DNA sample—which are all necessary, sufficient, and more useful than a microscope slide for subsequent identification—continue to exist. At some point, so much modification is needed that the original code is no longer the same code but becomes something new Cantino, It is impossible to be familiar with the diversity and classification of protists on the one hand and to claim that the ICBN and the ICZN have been stabilizing and accommodating on the other.

By expelling a stream of mucopolysaccharides from the raphe, the diatom can attach to surfaces or propel itself in one direction. Figure Assorted diatoms, visualized here using light microscopy, live among annual sea ice in McMurdo Sound, Antarctica.

Gordon T. During periods of nutrient availability, diatom populations bloom to numbers greater than can be consumed by aquatic organisms.

The excess diatoms die and sink to the sea floor where they are not easily reached by saprobes that feed on dead organisms. As a result, the carbon dioxide that the diatoms had consumed and incorporated into their cells during photosynthesis is not returned to the atmosphere.

The biological carbon pump is a crucial component of the carbon cycle that maintains lower atmospheric carbon dioxide levels. Like diatoms, golden algae are largely unicellular, although some species can form large colonies. Their characteristic gold color results from their extensive use of carotenoids, a group of photosynthetic pigments that are generally yellow or orange in color. Golden algae are found in both freshwater and marine environments, where they form a major part of the plankton community.

The brown algae are primarily marine, multicellular organisms that are known colloquially as seaweeds. Giant kelps are a type of brown algae. Some brown algae have evolved specialized tissues that resemble terrestrial plants, with root-like holdfasts, stem-like stipes, and leaf-like blades that are capable of photosynthesis.

The stipes of giant kelps are enormous, extending in some cases for 60 meters. A variety of algal life cycles exists, but the most complex is alternation of generations, in which both haploid and diploid stages involve multicellularity. Compare this life cycle to that of humans, for instance.

Haploid gametes produced by meiosis sperm and egg combine in fertilization to generate a diploid zygote that undergoes many rounds of mitosis to produce a multicellular embryo and then a fetus.

However, the individual sperm and egg themselves never become multicellular beings. Terrestrial plants also have evolved alternation of generations.

In the brown algae genus Laminaria , haploid spores develop into multicellular gametophytes, which produce haploid gametes that combine to produce diploid organisms that then become multicellular organisms with a different structure from the haploid form Figure Certain other organisms perform alternation of generations in which both the haploid and diploid forms look the same.

Several species of brown algae, such as the Laminaria shown here, have evolved life cycles in which both the haploid gametophyte and diploid sporophyte forms are multicellular.

The gametophyte is different in structure than the sporophyte. A saprobic oomycete engulfs a dead insect. The oomycetes are characterized by a cellulose-based cell wall and an extensive network of filaments that allow for nutrient uptake. As diploid spores, many oomycetes have two oppositely directed flagella one hairy and one smooth for locomotion. The oomycetes are nonphotosynthetic and include many saprobes and parasites.

The saprobes appear as white fluffy growths on dead organisms Figure Most oomycetes are aquatic, but some parasitize terrestrial plants. One plant pathogen is Phytophthora infestans , the causative agent of late blight of potatoes, such as occurred in the nineteenth century Irish potato famine.

The Rhizaria supergroup includes many of the amoebas, most of which have threadlike or needle-like pseudopodia ammonia tepida, a Rhizaria species, can be seen in Figure Pseudopodia function to trap and engulf food particles and to direct movement in rhizarian protists. These pseudopods project outward from anywhere on the cell surface and can anchor to a substrate.

The protist then transports its cytoplasm into the pseudopod, thereby moving the entire cell. This type of motion, called cytoplasmic streaming , is used by several diverse groups of protists as a means of locomotion or as a method to distribute nutrients and oxygen. These shells from foraminifera sank to the sea floor.

Foraminiferans, or forams, are unicellular heterotrophic protists, ranging from approximately 20 micrometers to several centimeters in length, and occasionally resembling tiny snails Figure As a group, the forams exhibit porous shells, called tests that are built from various organic materials and typically hardened with calcium carbonate.

The tests may house photosynthetic algae, which the forams can harvest for nutrition. Foram pseudopodia extend through the pores and allow the forams to move, feed, and gather additional building materials. Typically, forams are associated with sand or other particles in marine or freshwater habitats. Foraminiferans are also useful as indicators of pollution and changes in global weather patterns. This fossilized radiolarian shell was imaged using a scanning electron microscope.

A second subtype of Rhizaria, the radiolarians, exhibit intricate exteriors of glassy silica with radial or bilateral symmetry Figure Needle-like pseudopods supported by microtubules radiate outward from the cell bodies of these protists and function to catch food particles.

The shells of dead radiolarians sink to the ocean floor, where they may accumulate in meter-thick depths. Preserved, sedimented radiolarians are very common in the fossil record. Red algae and green algae are included in the supergroup Archaeplastida.

It was from a common ancestor of these protists that the land plants evolved, since their closest relatives are found in this group. Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, multicellular, and colonial forms. Red algae, or rhodophytes, are primarily multicellular, lack flagella, and range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category.

The red algae life cycle is an alternation of generations. Some species of red algae contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green tint of chlorophyll, making these species appear as varying shades of red.

Other protists classified as red algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have been detected at depths of meters. Other red algae exist in terrestrial or freshwater environments. The most abundant group of algae is the green algae. The green algae exhibit similar features to the land plants, particularly in terms of chloroplast structure.

That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.

The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas. The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism Figure Volvox colonies contain to 60, cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion.

Individual Volvox cells move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism.

Volvox aureus is a green alga in the supergroup Archaeplastida. This species exists as a colony, consisting of cells immersed in a gel-like matrix and intertwined with each other via hair-like cytoplasmic extensions. Ralf Wagner. Caulerpa taxifolia is a chlorophyte consisting of a single cell containing potentially thousands of nuclei. True multicellular organisms, such as the sea lettuce, Ulva , are represented among the chlorophytes.

In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters Figure Some have rigid cell walls, while others have more flexible cell membranes. Their methods of movement include passive drifting, swimming with flagella, swimming with cilia and creeping along with pseudopods. Even certain very basic criteria that have been used to define the group, such as the presence of nuclei and mitochondria, either don't exist or take on bizarre forms in some protists.

Scientists have tried to classify the organisms within the protists as either plant-like, fungus-like, or animal-like. However, genetic testing and close examination have revealed that these categories often don't hold up, either. For example, Euglena have characteristics of both plant-like and animal-like protists.

Euglena have chloroplasts like plants, in the sense that the chloroplasts allow them to gain energy from the sun through photosynthesis. At the same time, they have a tail or flagella which they use to swim, making them mobile, a very animal-like characteristic.

Many other protists also have characteristics that make it difficult to justify keeping them all in a single group or subgroup. Scientists have begun to use new criteria to sort protists. In fact, the protists can be sorted into between three and ten proposed kingdoms, depending on which researchers are doing the sorting.

Scientists are trying to create these groups based on evolutionary relationships. The goal in forming kingdoms is to group all the descendants from a common ancestor into one group.