Superphylum

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In biology, a phylum (/ˈfaɪləm/; plural: phyla)^{[note 1]} is a taxonomic rank below kingdom and above class. Traditionally, in botany the term division is used instead of "phylum", although in 1993 the International Botanical Congress accepted the designation "phylum".^[1][2] The kingdom Animalia contains approximately 35 phyla; the kingdom Plantae contains 12 phyla. Current research in phylogenetics is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta.

General description and familiar examples

Concepts of animal phyla have changed importantly from their origins in the six Linnaean classes and the four "embranchements" of Georges Cuvier.^[3] Haeckel introduced the term phylum, based on the Greek word phylon.^[4] In plant taxonomy, Eichler (1883) classified all plants into five groups, named divisions. ^[5] Informally, phyla can be thought of as grouping organisms based on general specialization of body plan.^[6] At the most basic level, a phylum can be defined in two ways: as a group of organisms with a certain degree of morphological or developmental similarity (the phenetic definition), or a group of organisms with a certain degree of evolutionary relatedness (the phylogenetic definition).^[7] Attempting to define a level of the Linnean hierarchy without referring to (evolutionary) relatedness is an unsatisfactory approach, but the phenetic definition is more useful when addressing questions of a morphological nature—such as how successful different body plans were.

Definition based on genetic relation

The largest objective measure in the above definitions is the "certain degree"—how unrelated do organisms need to be to be members of different phyla? The minimal requirement is that all organisms in a phylum should be related closely enough for them to be clearly more closely related to one another than to any other group.^[7] However, even this is problematic, as the requirement depends on our current knowledge about organisms' relationships: As more data becomes available, particularly from molecular studies, we are better able to judge the relationships between groups. So phyla can be merged or split if it becomes apparent that they are related to one another or not. For example, the bearded worms were described as a new phylum (the Pogonophora) when described in 1914, but molecular work almost a century later found them closely related to annelids and merged the phyla, so that the bearded worms are now an annelid family.^[8] Likewise, the highly parasitic phylum Mesozoa was divided into two phyla Orthonectida and Rhombozoa, when it was discovered the Orthonectida are deuterostomes and the Rhombozoa protostomes.^[9]

This changeability of phyla has led some biologists to call for the concept of a phylum to be abandoned in favour of cladistics, a method in which groups are placed on a "family tree" without any formal ranking of group size.^[7] So as to provide a handle on the size and significance of groups, a "body-plan" based definition of a phylum has been proposed by paleontologists Graham Budd and Sören Jensen. The definition was posited by paleontologists because extinct organisms are typically hardest to classify; they can be off-shoots that diverged from a phylum's line before the characters that define the modern phylum were all acquired.

Definition based on body plan

By Budd and Jensen's definition, phyla are defined by a set of characters shared by all their living representatives. This has a couple of small problems—for instance, characters common to most members of a phylum may be secondarily lost by some members. It is also defined based on an arbitrary point of time (the present). However, as it is character based, it is easy to apply to the fossil record. A more major problem is that it relies on an objective decision of which group of organisms should be considered a phylum.

Its utility is that it makes it easy to classify extinct organisms as "stem groups" to the phyla with which they bear the most resemblance, based only on the taxonomically important similarities.^[7] However, proving that a fossil belongs to the crown group of a phylum is difficult, as it must display a character unique to a sub-set of the crown group.^[7] Furthermore, organisms in the stem group of a phylum can possess the "body plan" of the phylum without all the characteristics necessary to fall within it. This weakens the idea that each of the phyla represents a distinct body plan.^[10]

Based upon this definition, which some say is unreasonably affected by the chance survival of rare groups, which vastly increase the size of phyla, representatives of many modern phyla did not appear until long after the Cambrian.^[11]

Lists

Animal phyla

Groups formerly ranked as phyla

Plant divisions

Divisions into which living (extant) plants may be placed are shown in the table below. The classification of plants at this level varies from source to source. Thus some sources place horsetails in division Arthrophyta and ferns in division Pteridophyta,^[14] while others place them both in Pteridophyta, as shown below. The division Pinophyta may be used for all gymnosperms (i.e. including cycads, ginkgos and gnetophytes),^[15] or for conifers alone as below.

Since the first publication of the APG system in 1998, which proposed a classification of angiosperms to the level of orders, many sources have preferred to treat ranks higher than orders as informal clades. Where formal ranks have been provided, the traditional divisions listed below have been reduced to a very much lower level, e.g. subclasses.^[16]

Fungal divisions

Protista phyla

Bacterial Phyla/Divisions

Currently there are 29 phyla accepted by LPSN^[27]

1. Acidobacteria, phenotipically diverse and mostly uncultured
2. Actinobacteria, High-G+C Gram positive species
3. Aquificae, only 14 thermophilic genera, deep branching
4. Bacteroidetes
5. Caldiserica, formerly candidate division OP5, Caldisericum exile is the sole representative
6. Chlamydiae, only 6 genera
7. Chlorobi, only 7 genera
8. Chloroflexi,
9. Chrysiogenetes, only 3 genera (Chrysiogenes arsenatis, Desulfurispira natronophila, Desulfurispirillum alkaliphilum)
10. Cyanobacteria, also known as the blue-green algae
11. Deferribacteres
12. Deinococcus-Thermus, Deinococcus radiodurans and Thermus aquaticus are "commonly known" species of this phyla
13. Dictyoglomi
14. Elusimicrobia, formerly candidate division Thermite Group 1
15. Fibrobacteres
16. Firmicutes, Low-G+C Gram positive species, such as the spore-formers Bacilli (aerobic) and Clostridia (anaerobic)
17. Fusobacteria
18. Gemmatimonadetes
19. Lentisphaerae, formerly clade VadinBE97
20. Nitrospira
21. Planctomycetes
22. Proteobacteria, the most known phyla, containing species such as Escherichia coli or Pseudomonas aeruginosa
23. Spirochaetes, species include Borrelia burgdorferi, which causes Lyme disease
24. Synergistetes
25. Tenericutes, alternatively class Mollicutes in phylum Firmicutes (notable genus: Mycoplasma)
26. Thermodesulfobacteria
27. Thermomicrobia
28. Thermotogae, deep branching
29. Verrucomicrobia

Archaeal Phyla/Division/Kingdoms

1. Crenarchaeota, Second most common archaeal phylum
2. Euryarchaeota, most common archaeal phylum
3. Korarchaeota
4. Nanoarchaeota, ultra-small symbiotes
5. Thaumarchaeota

See also

• Cladistics
• Phylogenetics
• Systematics
• Taxonomy

Notes

References

External links

• Are phyla "real"? Is there really a well-defined "number of animal phyla" extant and in the fossil record?
• Major Phyla Of Animals

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