Chromista

Chromista is a eukaryotic kingdom, probably polyphyletic.[1][2] It includes all algae whose chloroplasts contain chlorophylls a and c, as well as various colorless forms that are closely related to them. As it is assumed the last common ancestor already possessed chloroplasts of red algal origin, the non-photosynthetic forms evolved from ancestors able to perform photosynthesis.[3] These chloroplasts are surrounded by four membranes, and are believed to have been acquired from some red algae.

Chromista
Scientific classification
Domain:
(unranked):
Kingdom:
Chromista

Phyla

Groups

Chromista has been defined in different ways at different times. The name Chromista was first introduced by Cavalier-Smith in 1981;[4] the earlier names Chromophyta, Chromobiota and Chromobionta correspond to roughly the same group.

It has been described as consisting of three different groups:[5]

In 2010, Thomas Cavalier-Smith indicated his desire to move Alveolata, Rhizaria and Heliozoa into Chromista.[6]

Some examples of classification of the Chromista and related groups are shown below.[7][8]

Chromophycées (Chadefaud, 1950)

The Chromophycées (Chadefaud, 1950),[9] renamed Chromophycota (Chadefaud, 1960),[10] included the current Ochrophyta (autotrophic Stramenopiles), Haptophyta (included in Chrysophyceae until Christensen, 1962), Cryptophyta, Dinophyta, Euglenophyceae and Choanoflagellida (included in Chrysophyceae until Hibberd, 1975).

Chromophyta (Christensen 1962, 1989)

The Chromophyta (Christensen 1962, 1989), defined as algae with chlorophyll c, included the current Ochrophyta (autotrophic Stramenopiles), Haptophyta, Cryptophyta, Dinophyta and Choanoflagellida. The Euglenophyceae were transferred to the Chlorophyta.

Chromophyta (Bourrelly, 1968)

The Chromophyta (Bourrelly, 1968) included the current Ochrophyta (autotrophic Stramenopiles), Haptophyta and Choanoflagellida. The Cryptophyceae and the Dinophyceae were part of Pyrrhophyta (= Dinophyta).

Chromista (Cavalier-Smith, 1981)

The Chromista (Cavalier-Smith, 1981) included the current Stramenopiles, Haptophyta and Cryptophyta.

Chromalveolata (Adl et al., 2005)

The Chromalveolata (Cavalier-Smith, 1981) included Stramenopiles, Haptophyta, Cryptophyta and Alveolata.

Chromista (Cavalier-Smith, 2010)

The Chromista (Cavalier-Smith, 2010) included SAR (Stramenopiles, Alveolata and Rhizaria) and Hacrobia (Haptista, Cryptista). A new classification of classes and phyla within Chromista was proposed by Cavalier-Smith in 2017.[11]

Phylogeny

Chromista
Hacrobia
Cryptista

Corbihelia Cavalier-Smith 2015

Cryptophyta Silva 1962

Haptista

Centroheliozoa Cushman & Jarvis 1929 sensu Durrschmidt & Patterson 1987

Haptophyta Hibberd 1976 emend. Edvardsen & Eikrem 2000

SAR supergroup
Rhizaria

Phytomyxea Engler & Prantl 1897 em. Cavalier-Smith 1993

Vampyrellidea Cavalier-Smith 2017

Filosa Leidy 1879 emend. Cavalier-Smith 2003 stat. nov.

Retaria Cavalier-Smith 1999 emend. Cavalier-Smith 2017

Halvaria
Alveolata

Ciliophora Doflein 1901 stat. n. Copeland 1956

Miozoa Cavalier-Smith 1987

Heterokonta

Platysulcea Cavalier-Smith 2017

Sagenista Cavalier-Smith 1995 stat. n. 2006

Bikosea Cavalier-Smith 2013

Placidozoa Cavalier-Smith 2013

Gyrista

Bigyromonadea Cavalier-Smith 1998

Peronosporomycota Dick 1995

Hyphochytriomycota Whittaker 1969

Pirsonea Cavalier-Smith 2017

Ochrophyta Cavalier-Smith 1986

History and controversy

Molecular trees have had some difficulty resolving relationships between the different groups. All three may share a common ancestor with the alveolates (see chromalveolates), but there is evidence that suggests that the haptophytes and cryptomonads do not belong together with the heterokonts or the SAR clade, but may be associated with the Archaeplastida.[1][12] Cryptista specifically may be sister or part of Archaeplastida.[13]

See also

References

  1. ^ a b Parfrey LW, Barbero E, Lasser E, Dunthorn M, Bhattacharya D, Patterson DJ & Katz LA (December 2006). "Evaluating support for the current classification of eukaryotic diversity". PLoS Genetics. 2 (12): e220. doi:10.1371/journal.pgen.0020220. PMC 1713255. PMID 17194223.
  2. ^ Cavalier-Smith T, Allsopp MT, Chao EE (November 1994). "Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic?". Proceedings of the National Academy of Sciences of the United States of America. 91 (24): 11368–72. doi:10.1073/pnas.91.24.11368. PMC 45232. PMID 7972066.
  3. ^ Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences - NCBI
  4. ^ Cavalier-Smith T (1981). "Eukaryote kingdoms: seven or nine?". Bio Systems. 14 (3–4): 461–81. doi:10.1016/0303-2647(81)90050-2. PMID 7337818.
  5. ^ Csurös M, Rogozin IB, Koonin EV (May 2008). "Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach". Molecular Biology and Evolution. 25 (5): 903–11. doi:10.1093/molbev/msn039. PMID 18296415.
  6. ^ Cavalier-Smith T (June 2010). "Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree". Biology Letters. 6 (3): 342–5. doi:10.1098/rsbl.2009.0948. PMC 2880060. PMID 20031978.
  7. ^ de Reviers B (2006). Biologia e Filogenia das Algas. Porto Alegre: Editora Artmed. pp. 156–157.
  8. ^ Blackwell W (2009). "Chromista revisited: a dilemma of overlapping putative kingdoms, and the attempted application of the botanical code of nomenclature" (PDF). Phytologia. 91 (2): 191–225.
  9. ^ Chadefaud M (1950). "Les cellules nageuses des Algues dans l'embranchement des Chromophycées" [Seaweed swimming cells in the branch of Chromophyceae]. Comptes rendus hebdomadaires des séances de l'Académie des Sciences (in French). 231: 788–790.
  10. ^ Chadefaud M (1960). "Les végétaux non vasculaires (Cryptogamie)". In Chadefaud M, Emberger L (eds.). Traité de Botanique Systématique. Paris: Tome I.
  11. ^ Cavalier-Smith T (January 2018). "Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences". Protoplasma. 255 (1): 297–357. doi:10.1007/s00709-017-1147-3. PMID 28875267.
  12. ^ Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev SI, Jakobsen KS, Pawlowski J (August 2007). "Phylogenomics reshuffles the eukaryotic supergroups". PLOS One. 2 (8): e790. doi:10.1371/journal.pone.0000790. PMC 1949142. PMID 17726520.
  13. ^ Burki F, Kaplan M, Tikhonenkov DV, Zlatogursky V, Minh BQ, Radaykina LV, Smirnov A, Mylnikov AP, Keeling PJ (January 2016). "Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista". Proceedings. Biological Sciences. 283 (1823): 20152802. doi:10.1098/rspb.2015.2802. PMC 4795036. PMID 26817772.

External links

Cavalier-Smith's system of classification

The classification system of life introduced by British zoologist Thomas Cavalier-Smith involves systematic arrangements of all life forms on earth. Following and improving the classification systems introduced by Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy. His classification has been a major foundation in modern taxonomy, particularly with revisions and reorganisations of kingdoms and phyla.

Cavalier-Smith has published extensively on the classification of protists. One of his major contributions to biology was his proposal of a new kingdom of life: the Chromista, although the usefulness of the grouping is questionable given that it is generally agreed to be an arbitrary (polyphyletic) grouping of taxa. He also proposed that all chromista and alveolata share the same common ancestor, a claim later refuted by studies of morphological and molecular evidence by other labs. He named this new group the Chromalveolates. He also proposed and named many other high-rank taxa, like Opisthokonta (1987), Rhizaria (2002), and Excavata (2002). Together with Chromalveolata, Amoebozoa (he amended their description in 1998), and Archaeplastida (which he called Plantae since 1981) the six form the basis of current taxonomy of eukaryotes. Prof. Cavalier-Smith has also published prodigiously on issues such as the origin of various cellular organelles (including the nucleus, mitochondria), genome size evolution, and endosymbiosis. Though fairly well known, many of his claims have been controversial and have not gained widespread acceptance in the scientific community to date. Most recently, he has published a paper citing the paraphyly of his bacterial kingdom, the origin of Neomura from Actinobacteria and taxonomy of prokaryotes.

According to Palaeos.com:

Prof. Cavalier-Smith of Oxford University has produced a large body of work which is well regarded. Still, he is controversial in a way that is a bit difficult to describe. The issue may be one of writing style. Cavalier-Smith has a tendency to make pronouncements where others would use declarative sentences, to use declarative sentences where others would express an opinion, and to express opinions where angels would fear to tread. In addition, he can sound arrogant, reactionary, and even perverse. On the other [hand], he has a long history of being right when everyone else was wrong. To our way of thinking, all of this is overshadowed by one incomparable virtue: the fact that he will grapple with the details. This makes for very long, very complex papers and causes all manner of dark murmuring, tearing of hair, and gnashing of teeth among those tasked with trying to explain his views of early life. See, [for example], Zrzavý (2001) [and] Patterson (1999). Nevertheless, he deals with all of the relevant facts.

Ceratium

The genus Ceratium includes species of freshwater and marine dinoflagellates. Most species of Ceratium are unicellular organisms that are characterized by their armored plates, two flagella, and horns. Species of Ceratium are found worldwide and are of concern due to their blooms.

Chlorophyll c

Chlorophyll c is a form of chlorophyll found in certain marine algae, including the photosynthetic Chromista (e.g. diatoms, brown algae) and dinoflagellates.It has a blue-greenish color and is an accessory pigment, particularly significant in its absorption of light in the 447-452 nm wavelength region, Like chlorophyll a and chlorophyll b, it helps the organism gather light and passes a quanta of excitation energy through the light harvesting antennae to the photosynthetic reaction centre. Chlorophyll c is unusual because it has a porphyrin ring structure and does not have an isoprenoid tail or a reduced ring D, features typical of the other chlorophylls commonly found in algae and plants.Chlorophyll c can be further divided into chlorophyll c1, chlorophyll c2 and chlorophyll c3, plus at least 8 other more-recently-found subtypes.

Chromalveolata

Chromalveolata was a eukaryote supergroup present in a major classification of 2005, then regarded as one of the six major groups within the eukaryotes. It was a refinement of the kingdom Chromista, first proposed by Thomas Cavalier-Smith in 1981. Chromalveolata was proposed to represent the organisms descended from a single secondary endosymbiosis involving a red alga and a bikont. The plastids in these organisms are those that contain chlorophyll c.

However, the monophyly of the Chromalveolata has been rejected. Thus, two papers published in 2008 have phylogenetic trees in which the chromalveolates are split up, and recent studies continue to support this view.

Corticata

Corticata ("one with a cortex"), in the classification of eukaryotes (living organisms with a cell nucleus), is a clade suggested by Cavalier-Smith to encompass the eukaryote supergroups of the following two groups:

Plantae, or Archaeplastida (plants, red algae, green algae, and glaucophytes)

Chromalveolata (a group including kelp, water moulds, ciliates, dinoflagellates, and other organisms)Cavalier-Smith currently includes Rhizaria as well, resulting in an equivalency to Diaphoretickes.

Critically endangered

A critically endangered (CR) species is one that has been categorized by the International Union for Conservation of Nature (IUCN) as facing an extremely high risk of extinction in the wild.As of 2014, there are 2,464 animal and 2,104 plant species with this assessment.As the IUCN Red List does not consider a species extinct until extensive, targeted surveys have been conducted, species that are possibly extinct are still listed as critically endangered. IUCN maintains a list of "possibly extinct" CR(PE) and "possibly extinct in the wild" CR(PEW) species, modelled on categories used by BirdLife International to categorize these taxa.

Cryptista

Cryptista is a clade of algae-like eukaryotes. It is sometimes placed along with Haptista in the group Hacrobia, within the kingdom Chromista.

However, in 2016, a broad phylogenomic study found that cryptists fall within the group Archaeplastida, while haptophytes are closely related to the SAR supergroup.

Excavata

Excavata is a major supergroup of unicellular organisms belonging to the domain Eukaryota. Introduced by Thomas Cavalier-Smith in 2002 as a new phylogenetic category, it contains a variety of free-living and symbiotic forms, and also includes some important parasites of humans, including Giardia and Trichomonas. Excavates were formerly considered to be included in the now obsolete Protista kingdom. They are classified based on their flagellar structures, and they are considered to be the most basal Flagellate lineage. Except for Euglenozoa, they are all non-photosynthetic.

Heterokont

The heterokonts or stramenopiles (formally, Heterokonta or Stramenopiles) are a major line of eukaryotes. Most are algae, ranging from the giant multicellular kelp to the unicellular diatoms, which are a primary component of plankton. Other notable members of the Stramenopiles include the (generally) parasitic oomycetes, including Phytophthora of Irish potato famine infamy and Pythium which causes seed rot and damping off.

The name "heterokont" refers to the type of motile life cycle stage, in which the flagellated cells possess two differently shaped flagella (see zoospore).

Interim Register of Marine and Nonmarine Genera

The Interim Register of Marine and Nonmarine Genera (IRMNG) is a taxonomic database containing the scientific names of the genus, species, and higher ranks of many plants, animals and other kingdoms, both living and extinct, within a standardized taxonomic hierarchy, with associated machine-readable information on habitat (e.g. marine/nonmarine) and extant/fossil status for the majority of entries. The database aspires to provide complete coverage of both accepted and unaccepted genus names across all kingdoms, with a subset only of species names included as a lower priority. In its March 2019 release, IRMNG contained 490,095 genus names, of which 236,514 were listed as "accepted", 120,194 "unaccepted", 7,391 of "other" status i.e. interim unpublished, nomen dubium, nomen nudum, taxon inquirendum or temporary name, and 125,996 as "uncertain" (unassessed for taxonomic status at this time). The data originate from a range of (frequently domain-specific) print, online and database sources, and are reorganised into a common data structure to support a variety of online queries, generation of individual taxon pages, and bulk data supply to other biodiversity informatics projects. IRMNG content can be queried and displayed freely via the web, and download files of the data down to the taxonomic rank of genus as at specific dates are available in the Darwin Core Archive (DwC-A) format.

The data include homonyms (with their authorities), including both available (validly published) and selected unavailable names.IRMNG was initiated in 2006 by the Ocean Biogeographic Information System (OBIS) Australia at CSIRO Marine and Atmospheric Research, and subsequently has been hosted by the Flanders Marine Institute (VLIZ) from 2016 onwards. VLIZ also hosts the World Register of Marine Species (WoRMS), using a common infrastructure.Content from IRMNG is used by several global Biodiversity Informatics projects including Open Tree of Life, the Global Biodiversity Information Facility (GBIF), and the Encyclopedia of Life (EOL), in addition to others including the Atlas of Living Australia and the Global Names Architecture (GNA)'s Global Names Resolver. From 2018 onwards, IRMNG data are also being used to populate the taxonomic hierarchy and provide generic names for a range of taxa in the areas of protists (kingdoms Protozoa and Chromista) and plant algae (Charophyta, Chlorophyta, Glaucophyta and Rhodophyta) in the Catalogue of Life. IRMNG identifiers have also been associated with numerous Wikipedia taxon pages, based on content harvested from IRMNG and stored in Wikidata.IRMNG was initiated and designed by Tony Rees. For his work on this and other projects, GBIF awarded him the 2014 Ebbe Nielsen Prize. The citation said, in part:

IRMNG in particular has been a tool of enormous importance to GBIF and others in supplying much of the detail for a global taxonomic classification of all life and as high-value taxon trait data in a form which can readily be reused in data validation and to enhance species pages.

IRMNG is currently (2019) managed and curated by Rees, with assistance from the VLIZ team.

Kingdom (biology)

In biology, kingdom (Latin: regnum, plural regna) is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

Traditionally, some textbooks from the United States used a system of six kingdoms (Animalia, Plantae, Fungi, Protista, Archaea/Archaebacteria, and Bacteria/Eubacteria) while textbooks in countries like Great Britain, India, Greece, Australia, Latin America and other countries used five kingdoms (Animalia, Plantae, Fungi, Protista and Monera).

Some recent classifications based on modern cladistics have explicitly abandoned the term "kingdom", noting that the traditional kingdoms are not monophyletic, i.e., do not consist of all the descendants of a common ancestor.

List of Chromista by conservation status

As of July 2016, the International Union for Conservation of Nature (IUCN) has evaluated the conservation status of 15 species within Chromista.

The IUCN has not evaluated any protist species other than those in Chromista. No Chromista subspecies or subpopulations have been evaluated. No evaluated Chromista species are confirmed to be extinct, but four are tagged as possibly extinct.

As of 2005 the New Zealand Threat Classification System has evaluated 38 species of macroalgae as Threatened and 23 as Data Deficient. Some of these species are only of concern nationally.

Lists of IUCN Red List critically endangered species

Version 2014.2 of the IUCN Red List of Threatened Species identified 4574 Critically Endangered species, subspecies and varieties, stocks and subpopulations.

For IUCN lists of critically endangered species by kingdom, see:

Animals (kingdom Animalia) — IUCN Red List Critically Endangered species (Animalia)

Amphibians — List of critically endangered amphibians

Birds — List of critically endangered birds

Fish — List of critically endangered fishes

Invertebrates — List of critically endangered invertebrates

Arthropods — List of critically endangered arthropods

Insects — List of critically endangered insects

Molluscs List of critically endangered molluscs

Mammals — List of critically endangered mammals

Reptiles — List of critically endangered reptiles

Fungi (kingdom Fungi) — List of fungi by conservation status

Plants (kingdom Plantae) — List of critically endangered plants

Protists (kingdom Protista) — List of Chromista by conservation status

Lists of IUCN Red List data deficient species

On 29 January 2010, the IUCN Red List of Threatened Species identified 6,702 (5,913 Animalia (1 Annelida, 1,328 Arthropoda, 3,814 Chordata, 149 Cnidaria, 617 Mollusca, 3 Nemertina, 1 Onychophora), 780 Plantae, 9 Protista) data deficient species.

Lists of data deficient speciesAnimals

Amphibians — List of data deficient amphibians

Birds — List of data deficient birds

Fish — List of data deficient fishes

Invertebrates — List of data deficient invertebrates

Arthropods — List of data deficient arthropods

Insects — List of data deficient insects

Molluscs List of data deficient molluscs

Mammals — List of data deficient mammals

Reptiles — List of data deficient reptiles

Plants — IUCN Red List data deficient species (Plantae)

Chromista / Protista — List of Chromista by conservation status (9 data deficient species)

Fungi — List of fungi by conservation status (1 data deficient species)

Ochrophyta

Ochrophyta is a group of mostly photosynthetic heterokonts.The classification of the group is still being worked out. Some authors (e.g., Cavalier-Smith) divide it into two subphyla, Phaeista Cavalier-Smith 1995 (comprising Hypogyristea and Chrysista in some classifications, or Limnista and Marista in others) and Khakista Cavalier-Smith, 2000 (comprising Bolidomonas and diatoms). Others prefer not to use the subphyla, listing only lower taxa (e.g., Reviers, 2002, Guiry & Guiry, 2014).

Pirsoniales

Pirsoniales is a non photosynthetic lineage of Heterokonts.

Protozoa

Protozoa (also protozoan, plural protozoans) is an informal term for single-celled eukaryotes, either free-living or parasitic, which feed on organic matter such as other microorganisms or organic tissues and debris. Historically, the protozoa were regarded as "one-celled animals", because they often possess animal-like behaviors, such as motility and predation, and lack a cell wall, as found in plants and many algae. Although the traditional practice of grouping protozoa with animals is no longer considered valid, the term continues to be used in a loose way to identify single-celled organisms that can move independently and feed by heterotrophy.

In some systems of biological classification, Protozoa is a high-level taxonomic group. When first introduced in 1818, Protozoa was erected as a taxonomic class, but in later classification schemes it was elevated to a variety of higher ranks, including phylum, subkingdom and kingdom. In a series of classifications proposed by Thomas Cavalier-Smith and his collaborators since 1981, Protozoa has been ranked as a kingdom. The seven-kingdom scheme presented by Ruggiero et al. in 2015, places eight phyla under Kingdom Protozoa: Euglenozoa, Amoebozoa, Metamonada, Choanozoa sensu Cavalier-Smith, Loukozoa, Percolozoa, Microsporidia and Sulcozoa. Notably, this kingdom excludes several major groups of organisms traditionally placed among the protozoa, including the ciliates, dinoflagellates, foraminifera, and the parasitic apicomplexans, all of which are classified under Kingdom Chromista. Kingdom Protozoa, as defined in this scheme, does not form a natural group or clade, but a paraphyletic group or evolutionary grade, within which the members of Fungi, Animalia and Chromista are thought to have evolved.

SAR supergroup

SAR or Harosa (informally the SAR supergroup) is a clade that includes stramenopiles (heterokonts), alveolates, and Rhizaria. The first letter of each group provides the "SAR" in the name (alternatively spelled "RAS").The term "Harosa" (at the subkingdom level) has also been used for this grouping by Cavalier-Smith (2010). Adl et al. (2012) formalized the SAR supergroup as the node-based taxon Sar. They defined it as:

Sar: the least inclusive clade containing Bigelowiella natans Moestrup & Sengco 2001 (Rhizaria), Tetrahymena thermophila Nanney & McCoy 1976 (Alveolata), and Thalassiosira pseudonana Cleve 1873 (Stramenopiles). This is a node-based definition in which all of the specifiers are extant.

Members of the SAR supergroup were once included under the separate supergroups Chromalveolata (Chromista and Alveolata) and Rhizaria, until phylogenetic studies confirmed that stramenopiles and alveolates diverged with Rhizaria. This apparently excluded haptophytes and cryptomonads, leading Okamoto et al. (2009) to propose the clade Hacrobia to accommodate them.

Thomas Cavalier-Smith

Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (born 21 October 1942), is a Professor of Evolutionary Biology in the Department of Zoology, at the University of Oxford. His research has led to discovery of a number of unicellular organisms (protists) and definition of taxonomic positions, such as introduction of the kingdom Chromista, and other groups including Chromalveolata, Opisthokonta, Rhizaria, and Excavata. He is well known for his system of classification of all organisms.

Diaphoretickes
Discoba
Loukozoa
Podiata
Hemimastigophora
Incertae sedis

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