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In biology, a phylum (/ˈfaɪləm/; plural: phyla) is a level of classification or taxonomic rank below Kingdom and above Class. Traditionally, i n botany the term division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts the terms as equivalent. Depending on definitions, the animal kingdom Animalia or Metazoa contains approximately 33 phyla, the plant kingdom Plantae contains about 14, and the fungus kingdom Fungi contains about 8 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

The term phylum was coined in 1866 by Ernst Haeckel from the Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan." In plant taxonomy, August W. Eichler (1883) classified plants into five groups named divisions, a term that remains in use today for groups of plants, algae and fungi. The definitions of zoological phyla have changed from their origins in the six Linnaean classes and the four "embranchements" of Georges Cuvier.

Informally, phyla can be thought of as groupings of organisms based on general specialization of body plan. At its most basic, 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). Attempting to define a level of the Linnean hierarchy without referring to (evolutionary) relatedness is unsatisfactory, but a phenetic definition is useful when addressing questions of a morphological nature—such as how successful different body plans were.

Definition based on genetic relation

The most important objective measure in the above definitions is the "certain degree" that defines how different organisms need to be to be members of different phyla? The minimal requirement is that all organisms in a phylum should be clearly more closely related to one another than to any other group. Even this is problematic because the requirement depends on knowledge of organisms' relationships: as more data become available, particularly from molecular studies, we are better able to determine 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) in the middle of the 20th century, but molecular work almost half a century later found them to be a group of annelids, so the phyla were merged (the bearded worms are now an annelid family). On the other hand, the highly parasitic phylum Mesozoa was divided into two phyla, Orthonectida and Rhombozoa, when it was discovered the Orthonectida are probably deuterostomes and the Rhombozoa protostomes.

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.

Definition based on body plan

A definition of a phylum based on body plan has been proposed by paleontologists Graham Budd and Sören Jensen (as Haeckel had done a century earlier). The definition was posited because extinct organisms are hardest to classify: they can be offshoots that diverged from a phylum's line before the characters that define the modern phylum were all acquired. By Budd and Jensen's definition, a phylum is defined by a set of characters shared by all its living representatives.

This approach brings some small problems—for instance, ancestral characters common to most members of a phylum may have been lost by some members. Also, this definition is 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 greater problem is that it relies on a subjective decision about which groups of organisms should be considered as phyla.

The approach is useful because 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. 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. 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.

A classification using this definition may be strongly affected by the chance survival of rare groups, which can make a phylum much more diverse than it would be otherwise. Representatives of many modern phyla did not appear until long after the Cambrian.

Known phyla

Animal phyla

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Plant phyla (divisions)

The kingdom Plantae is defined in various ways by different biologists (see Current definitions of Plantae). All definitions include the living embryophytes (land plants), to which may be added the two green algae divisions, Chlorophyta and Charophyta, to form the clade Viridiplantae. The table below follows the influential (though contentious) Cavalier-Smith system in equating "Plantae" with Archaeplastida, a group containing Viridiplantae and the algal Rhodophyta and Glaucophyta divisions.

The definition and classification of plants at the division level also varies from source to source, and has changed progressively in recent years. Thus some sources place horsetails in division Arthrophyta and ferns in division Pteridophyta, 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), or for conifers alone as below.

Since the first publication of the APG system in 1998, which proposed a classification of angiosperms up 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.

Fungal divisions

Phylum Microsporidia is generally included in kingdom Fungi, though its exact relations remain uncertain, and it is considered a protozoan by the International Society of Protistologists (see Protista, below). Molecular analysis of Zygomycota has found it to be polyphyletic (its members do not share an immediate ancestor), which is considered undesirable by many biologists. Accordingly, there is a proposal to abolish the Zygomycota phylum. Its members would be divided between phylum Glomeromycota and four new subphyla incertae sedis (of uncertain placement): Entomophthoromycotina, Kickxellomycotina, Mucoromycotina, and Zoopagomycotina.

Protista phyla (divisions)

Kingdom Protista (or Protoctista) is included in the traditional five- or six-kingdom model, where it can be defined as containing all eukaryotes that are not plants, animals, or fungi. Protista is a polyphyletic taxon (it includes groups not directly related to one another), which is less acceptable to present-day biologists than in the past. Proposals have been made to divide it among several new kingdoms, such as Protozoa and Chromista in the Cavalier-Smith system.

Protist taxonomy has long been unstable, with different approaches and definitions resulting in many competing classification schemes. The phyla listed here are used for Chromista and Protozoa by the Catalogue of Life, adapted from the system used by the International Society of Protistologists.

The Catalogue of Life includes Rhodophyta and Glaucophyta in kingdom Plantae, but other systems consider these phyla part of Protista.

Bacterial phyla/divisions

Currently there are 29 phyla accepted by List of Prokaryotic names with Standing in Nomenclature (LPSN)

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

Archaeal phyla/division/kingdoms

Currently there are 5 phyla accepted by List of Prokaryotic names with Standing in Nomenclature (LPSN).

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

See also

• Cladistics
• Phylogenetics
• Systematics
• Taxonomy

Notes

References

1. ^ McNeill, J., ed. (2012). ()International Code of Nomenclature for algae(), fungi, and plants (Melbourne Code), Adopted by the Eighteenth International Botanical Congress Melbourne, Australia, July 2011 (electronic ed.). International Association for Plant Taxonomy. Retrieved 14 May 2017. {{cite book}}: Unknown parameter |displayeditors()= ignored (help); line feed character in |title= at position 50 (help)
2. "Life sciences". The American Heritage New Dictionary of Cultural Literacy (third ed.). Houghton Mifflin Company. 2005. Retrieved 4 October 2008. Phyla in the plant kingdom are frequently called divisions.
3. Berg, Linda R. (2 March 2007). Introductory Botany: Plants, People, and the Environment (2 ed.). Cengage Learning. p. 15. ISBN 9780534466695. Retrieved 23 July 2012.
4. Valentine 2004, p. 8.
5. Naik, V.N. (1984). Taxonomy of Angiosperms. Tata McGraw-Hill. p. 27. ISBN 9780074517888.
6. Collins AG, Valentine JW (2001). "Defining phyla: evolutionary pathways to metazoan body plans." Evol. Dev. 3: 432-442.
7. Valentine, James W. (2004). On the Origin of Phyla. Chicago: University Of Chicago Press. p. 7. ISBN 0-226-84548-6. Classifications of organisms in hierarchical systems were in use by the seventeenth and eighteenth centuries. Usually organisms were grouped according to their morphological similarities as perceived by those early workers, and those groups were then grouped according to their similarities, and so on, to form a hierarchy. {{cite book}}: Invalid |ref=harv (help)
8. ^ Budd, G.E.; Jensen, S. (May 2000). "A critical reappraisal of the fossil record of the bilaterian phyla". Biological Reviews. 75 (2): 253–295. doi:10.1111/j.1469-185X.1999.tb00046.x. PMID 10881389. Retrieved 26 May 2007.
9. Rouse G.W. (2001). "A cladistic analysis of Siboglinidae Caullery, 1914 (Polychaeta, Annelida): formerly the phyla Pogonophora and Vestimentifera". Zoological Journal of the Linnean Society. 132 (1): 55–80. doi:10.1006/zjls.2000.0263.
10. Pawlowski J, Montoya-Burgos JI, Fahrni JF, Wüest J, Zaninetti L (October 1996). "Origin of the Mesozoa inferred from 18S rRNA gene sequences". Mol. Biol. Evol. 13 (8): 1128–32. doi:10.1093/oxfordjournals.molbev.a025675. PMID 8865666.
11. Budd, G. E. (September 1998). "Arthropod body-plan evolution in the Cambrian with an example from anomalocaridid muscle". Lethaia. 31 (3). Blackwell Synergy: 197–210. doi:10.1111/j.1502-3931.1998.tb00508.x.
12. Briggs, D. E. G.; Fortey, R. A. (2005). "Wonderful strife: systematics, stem groups, and the phylogenetic signal of the Cambrian radiation". Paleobiology. 31 (2 (Suppl)): 94–112. doi:10.1666/0094-8373(2005)031[0094:WSSSGA]2.0.CO;2.
13. ^ Margulis, Lynn; Chapman, Michael J. (2009). Kingdoms and Domains (4th corrected ed.). London: Academic Press. ISBN 9780123736215.
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16. Zhang, Z (2013). "Animal biodiversity: An update of classification and diversity in 2013. In: Zhang, Z.-Q. (Ed.) Animal Biodiversity: An Outline of Higher-level Classification and Survey of Taxonomic Richness (Addenda 2013)". Zootaxa. 3703 (1): 5–11. doi:10.11646/zootaxa.3703.1.3.
17. Species Register. "Flatworms — Phylum Platyhelminthes". Marine Discovery Centres. Retrieved 9 April 2007.
18. ^ Cavalier-Smith, Thomas (22 June 2004). "Only Six Kingdoms of Life". Proceedings: Biological Sciences. 271 (1545). London: Royal Society: 1251–1262. {{cite journal}}: |access-date= requires |url= (help)
19. Mauseth 2012, pp. 514, 517.
20. ^ Cronquist, A.; A. Takhtajan; W. Zimmermann (April 1966). "On the higher taxa of Embryobionta". Taxon. 15 (15). International Association for Plant Taxonomy (IAPT): 129–134. doi:10.2307/1217531. JSTOR 1217531.
21. Chase, Mark W.; Reveal, James L. (October 2009), "A phylogenetic classification of the land plants to accompany APG III", Botanical Journal of the Linnean Society, 161 (2): 122–127, doi:10.1111/j.1095-8339.2009.01002.x {{citation}}: Unknown parameter |lastauthoramp= ignored (|name-list-style= suggested) (help)
22. Mauseth, James D. (2012). Botany : An Introduction to Plant Biology (5th ed.). Sudbury, MA: Jones and Bartlett Learning. ISBN 978-1-4496-6580-7. {{cite book}}: Invalid |ref=harv (help) p. 489
23. ^ Mauseth 2012, p. 489.
24. Mauseth 2012, p. 540.
25. Mauseth 2012, p. 542.
26. Mauseth 2012, p. 543.
27. Mauseth 2012, p. 509.
28. Crandall-Stotler, Barbara; Stotler, Raymond E. (2000). "Morphology and classification of the Marchantiophyta". Bryophyte Biology. Cambridge: Cambridge University Press. p. 21. ISBN 0-521-66097-1. {{cite book}}: Unknown parameter |editors= ignored (|editor= suggested) (help)
29. Mauseth 2012, p. 535.
30. Holt, Jack R.; Iudica, Carlos A. (1 October 2016). "Blastocladiomycota". Diversity of Life. Susquehanna University. Retrieved 29 December 2016.
31. Holt, Jack R.; Iudica, Carlos A. (9 January 2014). "Chytridiomycota". Diversity of Life. Susquehanna University. Retrieved 29 December 2016.
32. Holt, Jack R.; Iudica, Carlos A. (12 March 2013). "Microsporidia". Diversity of Life. Susquehanna University. Retrieved 29 December 2016.
33. Holt, Jack R.; Iudica, Carlos A. (23 April 2013). "Neocallimastigomycota". Diversity of Life. Susquehanna University. Retrieved 29 December 2016.
34. ^ Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, et al. (May 2007). "A higher-level phylogenetic classification of the Fungi" (PDF). Mycological Research. 111 (Pt 5): 509–47. doi:10.1016/j.mycres.2007.03.004. PMID 17572334.
35. ^ Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; et al. (29 April 2015). "A Higher Level Classification of All Living Organisms". PLOS One. 10 (6). Retrieved 28 December 2016.
36. White, Merlin M.; James, Timothy Y.; O'Donnell, Kerry; et al. (November–December 2006). "Phylogeny of the Zygomycota Based on Nuclear Ribosomal Sequence Data". Mycologia. 98 (6). Lawrence, KS: Mycological Society of America: 872–884. {{cite journal}}: |access-date= requires |url= (help)
37. Hagen, Joel B. (January 2012). "Five Kingdoms, More or Less: Robert Whittaker and the Broad Classification of Organisms". BioScience. 62 (1): 67–74.
38. Blackwell, Will H.; Powell, Martha J. (June 1999). "Reconciling Kingdoms with Codes of Nomenclature: Is It Necessary?". Systematic Biology. 48 (2): 406–412.
39. Davis, R. A. (19 March 2012). "Kingdom PROTISTA". College of Mount St. Joseph. Retrieved 28 December 2016.
40. ^ "Taxonomic tree". Catalogue of Life. 23 December 2016. Retrieved 28 December 2016.
41. Corliss, John O. (1984). "The Kingdom Protista and its 45 Phyla". BioSystems. 17: 87–176.
42. ^ J.P. Euzéby. "List of Prokaryotic names with Standing in Nomenclature: Phyla". Retrieved 28 December 2016.

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

• Misplaced Pages articles that are too technical from August ()2016
• Use dmy dates from July 2011
• Phyla
• Plant divisions