Phylum

Life Domain Kingdom Phylum Class Order Family Genus Species
The hierarchy of biological classification's eight major taxonomic ranks. A kingdom contains one or more phyla. Intermediate minor rankings are not shown.

In biology, a phylum (/ˈfaɪləm/; plural: phyla) is a level of classification or taxonomic rank below Kingdom and above Class. Traditionally, in 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.[1][2][3] Depending on definitions, the animal kingdom Animalia or Metazoa contains approximately 35 phyla, the plant kingdom Plantae contains about 12, and the fungus kingdom Fungi contains about 7 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 by Haeckel from the Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan."[4] In plant taxonomy, Eichler (1883) classified plants into five groups named divisions, a term that remains in use today for groups of plants, algae and fungi.[1][5] The definitions of zoological phyla have changed from their origins in the six Linnaean classes and the four "embranchements" of Georges Cuvier.[6]

Informally, phyla can be thought of as groupings of organisms based on general specialization of body plan.[7] 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).[8] 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.[8] 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).[9] 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.[10]

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.[8]

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.[8] 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.[8] 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.[11]

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.[12]

Known phyla

Animal phyla

Protostome Bilateria
Deuterostome
Basal/disputed
Others (Radiata or Parazoa)
PhylumMeaningCommon nameDistinguishing characteristicSpecies described
Acanthocephala Thorny head Thorny-headed worms[13]:278 Reversible spiny proboscis that bears many rows of hooked spines approx. 1,100
Annelida Little ring[13]:306 Annelids Multiple circular segment 17,000+ extant
Arthropoda Jointed foot Arthropods Segmented bodies and jointed limbs, with Chitin exoskeleton 1,134,000+
Brachiopoda Arm foot[13]:336 Lampshells[13]:336 Lophophore and pedicle 300-500 extant
Bryozoa Moss animals Moss animals, sea mats, ectoprocts[13]:332 Lophophore, no pedicle, ciliated tentacles, anus outside ring of cilia 5,000 extant
Chaetognatha Longhair jaw Arrow worms[13]:342 Chitinous spines either side of head, fins approx. 100 extant
Chordata With a cord Chordates Hollow dorsal nerve cord, notochord, pharyngeal slits, endostyle, post-anal tail approx. 100,000+
Cnidaria Stinging nettle Cnidarians Nematocysts (stinging cells) approx. 11,000
Ctenophora Comb bearer Comb jellies[13]:256 Eight "comb rows" of fused cilia approx. 100 extant
Cycliophora Wheel carrying Symbion Circular mouth surrounded by small cilia, sac-like bodies 3+
Echinodermata Spiny skin Echinoderms[13]:348 Fivefold radial symmetry in living forms, mesodermal calcified spines approx. 7,000 extant; approx. 13,000 extinct
Entoprocta Inside anus[13]:292 Goblet worms Anus inside ring of cilia approx. 150
Gastrotricha Hairy stomach[13]:288 Gastrotrich worms Two terminal adhesive tubes approx. 690
Gnathostomulida Jaw orifice Jaw worms[13]:260 approx. 100
Hemichordata Half cord[13]:344 Hemichordates[13]:344 Stomochord in collar, pharyngeal slits approx. 100 extant
Kinorhyncha Motion snout Mud dragons Eleven segments, each with a dorsal plate approx. 150
Loricifera Corset bearer Brush heads Umbrella-like scales at each end approx. 122
Micrognathozoa Tiny jaw animals Limnognathia Accordion-like extensible thorax 1
Mollusca Soft[13]:320 Mollusks / molluscs Muscular foot and mantle round shell 112,000[14]
Nematoda Thread like Round worms, thread worms[13]:274 Round cross section, keratin cuticle 25,000–1,000,000[15][16]
Nematomorpha Thread form[13]:276 Horsehair worms, Gordian worms[13]:276 approx. 320
Nemertea A sea nymph[13]:270 Ribbon worms, Rhynchocoela[13]:270 approx. 1,200
Onychophora Claw bearer Velvet worms[13]:328 Legs tipped by chitinous claws approx. 200 extant
Orthonectida Straight swimming[13]:268 Orthonectids[13]:268 Single layer of ciliated cells surrounding a mass of sex cells approx. 20
Phoronida Zeus's mistress Horseshoe worms U-shaped gut 11
Placozoa Plate animals Trichoplaxes[13]:242 Differentiated top and bottom surfaces, two ciliated cell layers, amoeboid fiber cells in between 1
Platyhelminthes Flat worm[13]:262 Flatworms[13]:262 approx. 25,000[17]
Porifera * Pore bearer Sponges[13]:246 Perforated interior wall 5,000+ extant
Priapulida Little Priapus Penis worms approx. 16
Rhombozoa Lozenge animal Rhombozoans[13]:264 Single anteroposterior axial cell surrounded by ciliated cells 75
Rotifera Wheel bearer Rotifers[13]:282 Anterior crown of cilia approx. 2,000
Sipuncula Small tube Peanut worms[13]:310 Mouth surrounded by invertible tentacles 144–320
Tardigrada Slow step Water bears, moss piglets[13]:324 Four-segmented body and head 1,000+
Xenacoelomorpha Strange form without gut — Ciliated deuterostome 2
Total: 34 2,000,000+

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,[18] 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,[19] 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),[20] 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.[21]

Land plants Viridiplantae
Green algae
Other algae (Biliphyta)[18]
DivisionMeaningCommon nameDistinguishing characteristicsSpecies described
Anthocerotophyta[22] Anthoceros-like plant Hornworts Horn-shaped sporophytes, no vascular system 100-300+
Bryophyta[23] Bryum-like plant, moss plant Mosses Persistent unbranched sporophytes, no vascular system approx. 12,000
Charophyta Chara-like plant Charophytes approx. 1,000
Chlorophyta Yellow-green plant[13]:200 Chlorophytes approx. 7,000
Cycadophyta[24] Cycas-like plant, palm-like plant Cycads Seeds, crown of compound leaves approx. 100-200
Ginkgophyta[25] Ginkgo-like plant Ginkgo, maidenhair tree Seeds not protected by fruit (single living species) only 1 extant
Glaucophyta Blue-green plant Glaucophytes 13
Gnetophyta[26] Gnetum-like plant Gnetophytes Seeds and woody vascular system with vessels approx. 70
Lycopodiophyta,[20]

Lycophyta[27]

 Lycopodium-like plant

Wolf plant

 Clubmosses & spikemosses Microphyll leaves, vascular system 1,290 extant
Magnoliophyta Magnolia-like plant Flowering plants, angiosperms Flowers and fruit, vascular system with vessels 295,383
Marchantiophyta,[28]

Hepatophyta[23]

 Marchantia-like plant

Liver plant

 Liverworts Ephemeral unbranched sporophytes, no vascular system approx. 9,000
Pinophyta,[20]

Coniferophyta[29]

 Pinus-like plant

Cone-bearing plant

 Conifers Cones containing seeds and wood composed of tracheids 629 extant
Pteridophyta Pteris-like plant, fern plant Ferns & horsetails Prothallus gametophytes, vascular system approx. 9,000 (not including lycophytes)
Rhodophyta Rose plant Red algae approx. 7,000
Total: 14

Fungal divisions

DivisionMeaningCommon nameDistinguishing characteristics
Ascomycota Bladder fungus[13]:396 Ascomycetes,[13]:396 sac fungi
Basidiomycota Small base fungus[13]:402 Basidiomycetes[13]:402
Blastocladiomycota Offshoot branch fungus[30] Blastoclads
Chytridiomycota Little cooking pot fungus[31] Chytrids
Glomeromycota Ball of yarn fungus[13]:394 Glomeromycetes, AM fungi[13]:394
Microsporidia Small seeds[32] Microsporans[13]:390
Neocallimastigomycota New beautiful whip fungus[33] Neocallimastigomycetes
Zygomycota Pair fungus[13]:392 Zygomycetes[13]:392
Total: 8

Phylum Microsporidia is generally included in kingdom Fungi, though its exact relations remain uncertain,[34] and it is considered a protozoan by the International Society of Protistologists[35] (see Protista, below). Molecular analysis of Zygomycota has found it to be polyphyletic (its members do not share an immediate ancestor),[36] 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.[34]

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.[13]:120 Protista is a polyphyletic taxon[37] (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.[38]

Protist taxonomy has long been unstable,[39] 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,[40] adapted from the system used by the International Society of Protistologists.[35]

Chromista
Protozoa
Phylum/DivisionMeaningCommon nameDistinguishing characteristicsExample
Amoebozoa Amorphous animal Amoebas Amoeba
Bigyra Two ring
Cercozoa
Choanozoa Funnel animal
Ciliophora Cilia bearer Ciliates Paramecium
Cryptista
Euglenozoa True eye animal Euglena
Foraminifera Hole bearers Forams Complex shells with one or more chambers Forams
Haptophyta
Loukozoa Groove animal
Metamonada Giardia
Microsporidia Small spore
Myzozoa Suckling animal
Mycetozoa Slime molds
Ochrophyta Yellow plant Diatoms Diatoms
Oomycota Egg fungus[13]:184 Oomycetes
Percolozoa
Radiozoa Ray animal Radiolarians
Sarcomastigophora
Sulcozoa
Total: 20

The Catalogue of Life includes Rhodophyta and Glaucophyta in kingdom Plantae,[40] but other systems consider these phyla part of Protista.[41]

Bacterial phyla/divisions

Currently there are 29 phyla accepted by List of Prokaryotic names with Standing in Nomenclature (LPSN)[42]

  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).[42]

  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

Notes

    References

    1. 1 2 McNeill, J.; et al., eds. (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 2017-05-14.
    2. ↑ "Life sciences". The American Heritage New Dictionary of Cultural Literacy (third ed.). Houghton Mifflin Company. 2005. Retrieved 2008-10-04. 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 2012-07-23.
    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.
    8. 1 2 3 4 5 Budd, G.E.; Jensen, S. (May 2000). "A critical reappraisal of the fossil record of the bilaterian phyla". Biological Reviews. 75 (2): 253–295. PMID 10881389. doi:10.1111/j.1469-185X.1999.tb00046.x. Retrieved 2007-05-26.
    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. PMID 8865666. doi:10.1093/oxfordjournals.molbev.a025675.
    11. ↑ Budd, G. E. (September 1998). "Arthropod body-plan evolution in the Cambrian with an example from anomalocaridid muscle". Lethaia. Blackwell Synergy. 31 (3): 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. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 Margulis, Lynn; Chapman, Michael J. (2009). Kingdoms and Domains (4th corrected ed.). London: Academic Press. ISBN 9780123736215.
    14. ↑ Feldkamp, S. (2002) Modern Biology. Holt, Rinehart, and Winston, USA. (pp. 725)
    15. ↑ Hodda, M (2011). "Phylum Nematoda Cobb, 1932. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness". Zootaxa. 3148: 63–95.
    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 2007-04-09.
    18. 1 2 Cavalier-Smith, Thomas (22 June 2004). "Only Six Kingdoms of Life". Proceedings: Biological Sciences. London: Royal Society. 271 (1545): 1251–1262.
    19. ↑ Mauseth 2012, pp. 514, 517.
    20. 1 2 3 Cronquist, A.; A. Takhtajan; W. Zimmermann (April 1966). "On the higher taxa of Embryobionta". Taxon. International Association for Plant Taxonomy (IAPT). 15 (15): 129–134. JSTOR 1217531. doi:10.2307/1217531.
    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
    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. p. 489
    23. 1 2 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". In A. Jonathan Shaw & Bernard Goffinet (Eds.). Bryophyte Biology. Cambridge: Cambridge University Press. p. 21. ISBN 0-521-66097-1.
    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. 1 2 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. PMID 17572334. doi:10.1016/j.mycres.2007.03.004.
    35. 1 2 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. (Nov–Dec 2006). "Phylogeny of the Zygomycota Based on Nuclear Ribosomal Sequence Data". Mycologia. Lawrence, KS: Mycological Society of America. 98 (6): 872–884.
    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. 1 2 "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. 1 2 J.P. Euzéby. "List of Prokaryotic names with Standing in Nomenclature: Phyla". Retrieved 2016-12-28.

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