The Kingdoms of Life

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(From the General Principles of Biology page.)

See also The Definition of Life and the Synopsis of the Evolution of Life on Earth pages.

All extant, present-day organisms either possess cell membranes that contain a homeostatic protoplasm ("Cytota") or exist without cell membranes ("Acytota") and depend completely upon a host organism for their metabolism and reproduction. For purposes of this outline, only the former, Cytota, are considered to be truly living. Therefore, we define life according to the criteria set forth in the Definition of Life page. The most widely accepted categories used for the classification of life are set forth below. This outline uses a combination of genotypic and phenotypic classifications for its taxonomy. Although the genotypic categories predominate and are always described in some manner, some of the conventional, morphologic classifications are maintained because of their continued convenience. Because of the large number of recent genetic discoveries, the classification used in this outline results in many categories that cannot easily fit within the conventional order of empire/domain-kingdom-phylum/division-class-order-family-genus-species. In cases where the classification does not fit within the conventional scheme, the category is simply labeled "clade."

Contents

Super-Empire/Super-Domain Acytota (non-cellular "life"[1] - prions, viroids and viruses)

  • Probably, although not necessarily, Acytota are degenerate forms of organisms that devolved from the earlier-evolved prokaryotes.[2]

  • Acytota are entirely dependant upon a host organism for metabolism and reproduction.


Super-Empire/Super-Domain Cytota (cellular life)

The Two Empire System[3]

A recent hypothesis that seems to be gaining ground among biologists is that all living organisms in Cytota may be grouped into one of two empires which are hypothetically entirely monophyletic (i.e., all the organisms in one grouping trace their evolutionary origin to one common ancestor):




The Three Domain System

Until recently, the general consensus of biologists had been to group all living organisms ("Cytota") into one of three domains:[4]



  • Domain Archaea (the archaebacteria that are prokaryotic but that are closely related to eukaryotes)



The Four/Five/Six Kingdom System[5]

Despite the aforementioned attempts at monophyletic classifications, some biologists still find it useful, at least as a pedagogical tool for demonstrating morphologic similarities, to classify the largest groupings of Cytota into six polyphyletic "kingdoms":


Kingdom Prokaryota ("before nuclei")

  • Single-celled, living[6] organisms without nuclei and usually containing a peptidoglycan cell wall external to the cellular membrane.

  • The Last Universal Common Ancestor (LUCA) of life (most likely a primitive bacterium) probably appeared somewhere around 3.5 billion years ago,[7] approximately one billion years after the Earth's formation, when water covered the Earth and the "reducing" atmosphere was composed primarily of ammonia, methane, carbon monoxide, hydrogen sulfide, sulfur dioxide, and water vapor.[8] Consequently, and due to the effects of lightning and/or geothermal heating, the primordial oceans were extremely rich in naturally formed amino acids, nitrogenous bases, lipids, and simple sugars. These compounds reacted naturally with each other over time and, after billions of trillions of reactions, self-replicating combinations of polymerized amino acids (prions) and nucleic acids (viroids) became arbitrarily grouped together in spontaneously formed, lipid bilayer vacuoles, approximately 200 million years before the evolution of LUCA (i.e., about 3.7 billion years ago).[9] The self-replicating molecules that were encapsulated in membranes fared better than those without and, eventually, mechanisms for maintaining the membrane evolved - the first cells were born. Subsequently, there developed mechanisms for the metabolism of nutrients via ATP (or something like it), rather than a reliance on purely exothermic chemical reactions of environmental substances, and for the development and replication of an hereditary, genetic material, further greatly enhancing the survival of those species which developed these faculties.

  • The photosynthetic cyanobacteria (blue-green "algae") evolved around 2.5 billion years ago.[10]

  • Bacteria may have become symbiotic with each other, forming the first mitochondria (possibly due to the endosymbiosis of the rickettsia family of alpha-proteobacteria containing hydrogenosomes), photosynthetic plastids (from the endosymbiosis of cyanobacteria and then the secondary endosymbiosis of the descendant species), and nuclei in the later-evolving "eukaryotes" (a term literally meaning "true nuclei").

  • Although the so-called "archaebacteria" ("old bacteria") are "prokaryotes" (i.e., without nuclei), eukaryotes and archaebacteria are now grouped together in the new clade "Empire Neomura" ("new walls") because a closer, genetic relationship exists between archaebacteria and the eukaryotes than to the prokaryotes due to the fragmentation of eukaryotic genes found only in archaebacteria.[11] This newly discovered sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an α-proteobacterium,[12] which also fails to account for other numerous features shared specifically by eukaryotes and actinobacteria.

  • Current theoretical consensus states that the eubacteria did not necessarily evolve later than the archaebacteria, and that the archaebacteria are genetically distinguishable from the bacteria as a whole. Therefore, the archaebacteria should not be called such and should rather be called "Archaea" ("old ones") and grouped with the eukaryotes entirely outside of the bacteria group, in a new empire called "Neomura" (meaning "new walls"). However, Biology's taxonomy will probably continue to use the prokaryote/eukaryote distinction since the Archaea group, although a more precise and accurate genetic grouping (i.e., by evolutionary heredity), is still prokaryotic and can be easily rationalized as a kind of morphological exception to the genetic schema.


Superkingdom Eukaryota ("true nuclei" - cells containing a membrane-enclosed nucleus)

  1. Kingdom Protista[13] ("first ones")
    • Single-celled eukaryotes - i.e., containing a membrane-enclosed nucleus.

    • Probably first appeared approximately 2.2 billion years ago (with fossilized forms predominating no earlier than 1.6 billion years ago).

    • Thought to have evolved from Bacteria, with the major changes being the replacement of peptidoglycan contained in the cell walls (where present) with other glycoproteins and the development of mitochondria and nuclei.

    • Current theoretical consensus states that a separate group of eukaryotes, "Clade Unikonta" ("one flagellum"), should be distinguished from Protista and placed in their own taxonomic group as genetically more "animal-like," with Unikonta broken down further into "Subkingdom Amoebozoa" ("changing-shape animal") - protists utilizing pseudopodia and moving without the use of flagellae - and clade "Clade Opisthokonta" ("flagellum behind") - protists possessing flagellae. "Fungi" and "Animalia" are then subgroups of Opisthokonta, with the Choanoflagelates existing as an ancestral intermediate group between the Animals and their common ancestor with the Fungi in the larger group, and with the Kingdom of Plantae grouped separately in the new "Clade Bikonta" ("two flagellae"). The remaining eukaryotic protists are either unclassified or exist in two groupings called either Excavata or Rhizaria, depending on whether the cells contain "non-classical" or more typical mitochondria.

    • Other well-known eukaryotic groups, which more often have two emergent flagellae (although there are many exceptions), are often referred to as "Clade Bikonta," which include all the plants, algae, and a few bacteria. However, the unikonts have a triple-gene fusion that is lacking in the bikonts. The three genes that are fused together in the unikonts, but not in the bacteria or bikonts, encode enzymes for synthesis of the pyrimidine nucleotides (found in all living organisms but not necessarily in acytota), with the triple-gene fusion found only in the animals, fungi, and choanoflagelates. Formation of the triple-gene fusion must have involved a coincident double fusion of the genes - a rare pair of events to occur simultaneously - supporting the shared ancestry of Opisthokonta and Amoebozoa.


  2. Kingdom Chromista/Chromalveolata ("with little colored cavities")
    • Chromalveolata are single-celled organisms with pigment-containing plastids.

    • This clade includes all algae whose chloroplasts contain only chlorophyll a (red) or only chlorphyll c (brown), as well as various, closely-related, colorless forms.

    • Symbiotic cyanobacteria may have evolved into the first chloroplasts, the photosynthetic cell organelles of eukaryotes.

    • Chromalveolae cells are surrounded by four membranes believed to have been inherited from some of the earliest chromalveolata "red algae."

    • All chromalveolae are eukaryotes and therefore must have evolved sometime after the first appearance of eukaryotic cells, not earlier than 2.2 billion years ago, after those cells became symbiotic with primitive plastids.


  3. Kingdom Fungi (Latin for "mushrooms," "spongy," or "moldy")
    • Fungi are eukaryotic heterotrophs and are generally non-motile, except during spore dispersal and in the chytrids, which produce flagellated gametes.

    • Fungi utilize chitin rather than cellulose for for the composition of their cell walls, which is some evidence of the closer genetic relationship fungi bear to animals, as opposed to plants.

    • Fungi probably first appeared in marine environments, no earlier than 1.5 billion years ago, becoming terrestrial about 635 million years ago, and then evolving into the "higher fungi" (Glomerales) about 570 million years ago.


    Sexual differentiation first appeared in the eukaryotes (in both fungi and the common ancestor of plants and algae) approximately 1.2 billion years ago, about the same time as the first appearance of Chromalveolata. Sexual differentiation allowed for the recombination of genetic traits that greatly accelerated the evolution of living organisms.


  4. Kingdom Animalia/Metazoa ("animals"/"higher animals")
    • Animals are multicellular, eukaryotic heterotrophs whose anatomies do not utilize cell walls (unlike plants, fungi, or bacteria), are generally motile in at least one stage of development, and that reproduce via the growth of embryos that pass through at least a blastula stage of development after some form of sexual congress.[14]

    • Animals first appeared in marine environments about 700 million years ago, with the first hard-shelled animals appearing about 580 million years ago, and the first amphibious tetrapods emerging onto land about 360 million years ago.

    • Motility and heterotrophy are intimately associated with each other in the evolutionary development of animals.


  5. Kingdom Plantae ("plant," "shoot," "twig," "sprout")
    • Multicellular, eukaryotic autotrophs whose anatomies utilize cellulose in their cell walls and are generally non-motile, except for seed and spore dispersal.

    • The first true land plants appeared about 470 million years ago.

    • Almost all plants contain some combination of chlorophylls a and b which, together, produce a green color.


For reasons stated above, many organisms, chiefly those in protista and the algaes, are difficult, if not impossible, to place precisely in any one of the aforementioned kingdoms, and their grouping varies depending on the classification scheme and the agreed-upon conventions and definitions.

Notes

  1. Whether these organisms constitute true "life" forms, rather than extremely complex, non-living, chemical substances, is a matter of debate.
  2. A notable, possible exception is the clade of nucleocytoplasmic large DNA viruses, where genomic studies indicate a simpler, common ancestor, thus indicating an evolution toward greater complexity.
  3. Since T. Cavalier-Smith's landmark paper on phylogeny, The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa, 52 Int. J. Syst. Evol. Microbiol. (part 2) 297–354 (Mar. 2002), the trend among taxonomists has been toward a more generally dichotomous set of groupings. The theory justifying a generally dichotomous "tree of life" hypothesizes that the evolution of all organisms would tend to descend in pairs of groups from a common ancestor, rather than many groups always ranking in a similar fashion throughout the tree. The proponents of this system hypothesize that the event of a single mutation causing three or more groups to descend from a common ancestor simultaneously is extremely unlikely from a thermodynamic, chemical standpoint. Therefore, the evolution of organisms would generally favor a dichotomous descent, instead of expecting nature to somehow (and unexplainably) organize herself so that all groups of organisms would fit into the same set of hierarchies in every case and regardless of their own particular evolutionary histories. For this reason, and except where morphological differences are conventionally useful, this outline generally follows the Two Empire system.
  4. C. Woese, G. Fox, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, 74 Proc. Natl. Acad. Sci. USA (issue 11) 5088–90 (1977); C. Woese, O. Kandler, M. Wheelis, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, 87 Proc. Natl. Acad. Sci. USA (issue 12) 4576–9 (1990).
  5. The "Six Kingdom" system was the system proposed by Cavalier-Smith in 1998. T. Cavalier-Smith, A revised six-kingdom system of life, 73 Biological Reviews (issue 3) 203–66 (1998). Since then, Cavalier-Smith has tended toward the Two Empire system described above. See T. Cavalier-Smith, The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa, 52 Int. J. Syst. Evol. Microbiol. (part 2) 297–354 (Mar. 2002). In the "Five Kingdom" system, hypothesized by Margulis and Schwartz, the Kingdom Protista would be eliminated and that grouping's organisms distributed among the five remaining kingdoms based on cellular, morphological similarities. See L Margulis, K.V. Schwartz, Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, pub. W.H. Freeman & Company, ISBN 0-613-92338-3 (1997). In the older and now deprecated "Four Kingdom" system, the protists are redistributed as in the Five Kingdom system and the kingdom of Chromalveolata is subsumed under the Plant Kingdom. In the even older (and now entirely defunct) "Three Kingdom" system (which is distinct from the "Three Domain" system previously described in this outline), the Kingdoms are those of Eukaryota (including the archaebacteria), Plantae, and Animalia, with the protists divided up as before, and with chromalveolata and fungi both subsumed under Plantae, all on a purely morphologic basis. This last system is entirely defunct because fungi are now clearly determined, on a purely genetic basis, to be more closely related to animals than plants and should not be considered "plant-like." See K. Shalchian-Tabrizi, M.A. Minge, M. Espelund, R. Orr, T. Ruden, K.S. Jakobsen, T. Cavalier-Smith, Multigene phylogeny of choanozoa and the origin of animals, 3 PLoS ONE (5) e2098. Proponents of the Two Empire system (Bacteria and Neomura) claim their system is truly monophyletic on all levels, whereas all of the other Kingdom systems described on this page are polyphyletic, at least at the top level.
  6. As opposed to the "non-living" organisms of Acytota.
  7. J.W. Schopf, A.B. Kudryavtsev, A.D. Czaja, A.B. Tripathi, Evidence of Archean life: Stromatolites and microfossils, 158 Precambrian Research 141-155 (2007); J.W. Schopf, Fossil evidence of Archaean life, 361 Philos. Trans. R. Soc. Lond. B. Biol. Sci. (1470) 869-85 (2006).
  8. The water vapor had mostly condensed out of the atmosphere at this time, becoming the oceans in which the first life evolved.
  9. Y. Ohtomo, T. Kakegawa, A. Ishida, T Nagase, M.T. Rosing, Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks, Nature Geoscience (2013); N. Noffke, D. Christian, D. Wacey, R.M. Hazen, Microbially Induced Sedimentary Structures Recording an Ancient Ecosystem in the ca. 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia, Astrobiology (2013).
  10. D.T. Flannery, R.M. Walter, Archean tufted microbial mats and the Great Oxidation Event: new insights into an ancient problem, 59 Australian Journal of Earth Sciences (issue 1) 1–11 (2012)
  11. This hypothesis is also supported by numerous gene sequence trees. See C. Woese, G. Fox, Phylogenetic structure of the prokaryotic domain: The primary kingdoms, 74 Proc. Natl. Acad. Sci. U.S.A. (issue 11) 5088–90 (Nov. 1977); C.R. Woese, O. Kandler, M.L. Wheelis ML, Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya, 87 Proc. Natl. Acad. Sci. U.S.A. (issue 12) 4576–9 (Jun. 1990); T.M. Schmidt, The maturing of microbial ecology, 9 Int. Microbiol. (issue 3) 217–23 (2006).
  12. J.A. Lake, Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences, 331 Nature (issue 6152) 184-186.
  13. According to most phylogenists, with the notable exception of Cavalier-Smith in 1998, the general consensus is to deprecate the term "protist" as not taxonomically valid and subsume the various "protists" under classifications that are more generally dichotomous. The theory justifying a generally dichotomous "tree of life" hypothesizes that the evolution of all organisms would tend to descend in pairs of groups from a common ancestor, rather than many groups always ranking in a similar fashion throughout the tree. The proponents of this system hypothesize that the event of a single mutation causing three or more groups to descend from a common ancestor simultaneously is extremely unlikely from a thermodynamic, chemical standpoint. Therefore, the evolution of organisms would generally favor a dichotomous descent, instead of expecting nature to somehow (and unexplainably) organize herself so that all groups of organisms would fit into the same set of hierarchies in every case and regardless of their own particular evolutionary histories. For this reason, and except where morphological differences are conventionally useful, this outline generally follows the Two Empire system, the term Protist is used in this outline only for classifying unicellular eukaryotes of uncertain placement.
  14. Although some species can also reproduce asexually.
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