see text
48-435: Excavata is an extensive and diverse but paraphyletic group of unicellular Eukaryota . The group was first suggested by Simpson and Patterson in 1999 and the name latinized and assigned a rank by Thomas Cavalier-Smith in 2002. It contains a variety of free-living and symbiotic protists, and includes some important parasites of humans such as Giardia and Trichomonas . Excavates were formerly considered to be included in
96-622: A PKD domain S-layer . They also share the three-way ES39 expansion in LSU rRNA with eukaryotes. Gene clusters or operons encoding ribosomal proteins are often less conserved in their organization in the Asgard group than in other Archaea, suggesting that the order of ribosomal protein coding genes may follow the phylogeny. Asgard archaea are generally obligate anaerobes , though Kariarchaeota, Gerdarchaeota and Hodarchaeota may be facultative aerobes . They have
144-415: A Wood–Ljungdahl pathway and perform glycolysis . Members can be autotrophs , heterotrophs , or phototrophs using heliorhodopsin . One member, Candidatus Prometheoarchaeum syntrophicum , is syntrophic with a sulfur-reducing proteobacteria and a methanogenic archaea. The RuBisCO they have is not carbon-fixing, but likely used for nucleoside salvaging. Asgard are widely distributed around
192-481: A monophyletic group. Phylogenetic analyses often do not place malawimonads on the same branch as the other Excavata. Excavates were thought to include multiple groups: Euglenozoa and Heterolobosea (Percolozoa) or Eozoa (as named by Cavalier-Smith) appear to be particularly close relatives, and are united by the presence of discoid cristae within the mitochondria (Superphylum Discicristata ). A close relationship has been shown between Discicristata and Jakobida ,
240-692: A ubiquitin modifier system, and N-glycosylation pathway homologs. Asgard archaeons have a regulated actin cytoskeleton , and the profilins and gelsolins they use can interact with eukaryotic actins. In addition, Asgard archaea tubulin from hydrothermal-living Odinarchaeota ( OdinTubulin ) was identified as a genuine tubulin. OdinTubulin forms protomers and protofilaments most similar to eukaryotic microtubules, yet assembles into ring systems more similar to FtsZ , indicating that OdinTubulin may represent an evolution intermediate between FtsZ and microtubule -forming tubulins. They also seem to form vesicles under cryogenic electron microscopy . Some may have
288-479: A "single common ancestor" organism. Paraphyly is common in speciation , whereby a mother species (a paraspecies ) gives rise to a daughter species without itself becoming extinct. Research indicates as many as 20 percent of all animal species and between 20 and 50 percent of plant species are paraphyletic. Accounting for these facts, some taxonomists argue that paraphyly is a trait of nature that should be acknowledged at higher taxonomic levels. Cladists advocate
336-592: A cell nucleus, a plesiomorphy ) from its excluded descendants. Also, some systematists recognize paraphyletic groups as being involved in evolutionary transitions, the development of the first tetrapods from their ancestors for example. Any name given to these hypothetical ancestors to distinguish them from tetrapods—"fish", for example—necessarily picks out a paraphyletic group, because the descendant tetrapods are not included. Other systematists consider reification of paraphyletic groups to obscure inferred patterns of evolutionary history. The term " evolutionary grade "
384-419: A group of dinosaurs (part of Diapsida ), both of which are "reptiles". Osteichthyes , bony fish, are paraphyletic when circumscribed to include only Actinopterygii (ray-finned fish) and Sarcopterygii (lungfish, etc.), and to exclude tetrapods ; more recently, Osteichthyes is treated as a clade, including the tetrapods. The " wasps " are paraphyletic, consisting of the narrow-waisted Apocrita without
432-439: A kind of lizard). Put another way, viviparity is a synapomorphy for Theria within mammals, and an autapomorphy for Eulamprus tympanum (or perhaps a synapomorphy, if other Eulamprus species are also viviparous). Groupings based on independently-developed traits such as these examples of viviparity represent examples of polyphyly , not paraphyly. The following list recapitulates a number of paraphyletic groups proposed in
480-420: A mitochondrial organelle in greatly modified form (e.g. a hydrogenosome or mitosome ). Among those with mitochondria, the mitochondrial cristae may be tubular, discoidal , or in some cases, laminar. Most excavates have two, four, or more flagella . Many have a conspicuous ventral feeding groove with a characteristic ultrastructure , supported by microtubules —the "excavated" appearance of this groove giving
528-549: A more inclusive clade, it often makes sense to study the paraphyletic group that remains without considering the larger clade. For example, the Neogene evolution of the Artiodactyla (even-toed ungulates, like deer, cows, pigs and hippopotamuses - Cervidae , Bovidae , Suidae and Hippopotamidae , the families that contain these various artiodactyls, are all monophyletic groups) has taken place in environments so different from that of
SECTION 10
#1732854706184576-484: A narrow longitudinal groove down one side of the cell. The ancyromonad groove is not used for "suspension feeding", unlike in "typical excavates" (e.g. malawimonads, jakobids, Trimastix , Carpediemonas , Kiperferlia , etc). Ancyromonads instead capture prokaryotes attached to surfaces. The phylogenetic placement of ancyromonads is poorly understood (in 2020), however some phylogenetic analyses place them as close relatives of malawimonads. The conventional explanation for
624-424: A phylogenetic species concept that does not consider species to exhibit the properties of monophyly or paraphyly, concepts under that perspective which apply only to groups of species. They consider Zander's extension of the "paraphyletic species" argument to higher taxa to represent a category error When the appearance of significant traits has led a subclade on an evolutionary path very divergent from that of
672-741: A phylogenetic tree with the metamonad Parabasalia as basal Eukaryotes. Discoba and the rest of the Eukaryota appear to have emerged as sister taxon to the Preaxostyla, incorporating a single alphaproteobacterium as mitochondria by endosymbiosis. Thus the Fornicata are more closely related to e.g. animals than to Parabasalia. The rest of the Eukaryotes emerged within the Excavata as sister of the Discoba; as they are within
720-511: A possible link between the simple prokaryotic microorganisms and the complex eukaryotic microorganisms occurring approximately two billion years ago. The phylogenetic relationships of the Asgard archaea have been studied by several teams in the 21st century. Varying results have been obtained, for instance using 53 marker proteins from the Genome Taxonomy Database . In 2023, Eme, Tamarit, Caceres and colleagues reported that
768-439: Is a monophyletic group from which one or more subsidiary clades (monophyletic groups) are excluded to form a separate group. Philosopher of science Marc Ereshefsky has argued that paraphyletic taxa are the result of anagenesis in the excluded group or groups. A cladistic approach normally does not grant paraphyletic assemblages the status of "groups", nor does it reify them with explanations, as in cladistics they are not seen as
816-433: Is allowed as a synonym of Magnoliopsida. Phylogenetic analysis indicates that the monocots are a development from a dicot ancestor. Excluding monocots from the dicots makes the latter a paraphyletic group. Among animals, several familiar groups are not, in fact, clades. The order Artiodactyla ( even-toed ungulates ) as traditionally defined is paraphyletic because it excludes Cetaceans (whales, dolphins, etc.). Under
864-442: Is paraphyletic with respect to birds . Reptilia contains the last common ancestor of reptiles and all descendants of that ancestor except for birds. Other commonly recognized paraphyletic groups include fish , monkeys , and lizards . The term paraphyly , or paraphyletic , derives from the two Ancient Greek words παρά ( pará ), meaning "beside, near", and φῦλον ( phûlon ), meaning "genus, species", and refers to
912-482: Is sometimes used for paraphyletic groups. Moreover, the concepts of monophyly , paraphyly, and polyphyly have been used in deducing key genes for barcoding of diverse group of species. Current phylogenetic hypotheses of tetrapod relationships imply that viviparity , the production of offspring without the external laying of a fertilized egg, developed independently in the lineages that led to humans ( Homo sapiens ) and southern water skinks ( Eulampus tympanum ,
960-503: The Cetacea (whales, dolphins, and porpoises) that the Artiodactyla are often studied in isolation even though the cetaceans are a descendant group. The prokaryote group is another example; it is paraphyletic because it is composed of two Domains (Eubacteria and Archaea) and excludes (the eukaryotes ). It is very useful because it has a clearly defined and significant distinction (absence of
1008-569: The ICN ) abandoned consideration of bacterial nomenclature in 1975; currently, prokaryotic nomenclature is regulated under the ICNB with a starting date of 1 January 1980 (in contrast to a 1753 start date under the ICBN/ICN). Among plants, dicotyledons (in the traditional sense) are paraphyletic because the group excludes monocotyledons . "Dicotyledon" has not been used as a botanic classification for decades, but
SECTION 20
#17328547061841056-520: The Lokiarchaeota phylum based on phylogenetic analyses using a set of highly conserved protein-coding genes. The group was named for the shape-shifting Norse god Loki , in an allusion to the hydrothermal vent complex from which the first genome sample originated. The Loki of mythology has been described as "a staggeringly complex, confusing, and ambivalent figure who has been the catalyst of countless unresolved scholarly controversies", analogous to
1104-743: The White Oak River estuary in the United States contained Odinarchaeota and Heimdallarchaeota; following the Norse deity naming convention, these groups were named for Odin and Heimdall respectively. Researchers therefore named the superphylum containing these microbes " Asgard ", after the home of the gods in Norse mythology. Two Lokiarchaeota specimens have been cultured, enabling a detailed insight into their morphology. Asgard members encode many eukaryotic signature proteins, including novel GTPases , membrane-remodelling proteins like ESCRT and SNF7 ,
1152-638: The ants and bees . The sawflies ( Symphyta ) are similarly paraphyletic, forming all of the Hymenoptera except for the Apocrita, a clade deep within the sawfly tree. Crustaceans are not a clade because the Hexapoda (insects) are excluded. The modern clade that spans all of them is the Tetraconata . One of the goals of modern taxonomy over the past fifty years has been to eliminate paraphyletic "groups", such as
1200-565: The three-domain system . In the summer of 2010, sediments were analysed from a gravity core taken in the rift valley on the Knipovich ridge in the Arctic Ocean, near the Loki's Castle hydrothermal vent site. Specific sediment horizons previously shown to contain high abundances of novel archaeal lineages were subjected to metagenomic analysis . In 2015, an Uppsala University -led team proposed
1248-448: The tree model of historical linguistics . Paraphyletic groups are identified by a combination of synapomorphies and symplesiomorphies . If many subgroups are missing from the named group, it is said to be polyparaphyletic. The term received currency during the debates of the 1960s and 1970s accompanying the rise of cladistics , having been coined by zoologist Willi Hennig to apply to well-known taxa like Reptilia ( reptiles ), which
1296-895: The Eukaryota are deep within Asgard, as sister of Hodarchaeales within the Heimdallarchaeota. TACK Jordarchaeia Odinarchaeia Baldrarchaeia Lokiarchaeales Helarchaeales Thorarcheaia Hermodarcheaia Sifarchaeia Wukongarchaeia Njordarchaeales Gerdarchaeales Heimdallarchaeaceae Kariarchaeaceae Hodarchaeales [REDACTED] [REDACTED] [REDACTED] Thermoproteota ( TACK ) " Thorarchaeia " (MBG-B) " Njordarchaeia " " Odinarchaeia " "Freyrarchaeaceae" "Jordarchaeaceae" " Baldrarchaeia " " Hermodarchaeia " "Helarchaeales" "Sigynarchaeaceae" Promethearchaeaceae ["Lokiarchaeaceae"] "Sifarchaeales" "Borrarchaeales" " Wukongarchaeia " "Hodarchaeales" "Gerdarchaeales" (JABLTI01) "Kariarchaeales" "Heimdallarchaeales" In
1344-495: The actual products of evolutionary events. A group whose identifying features evolved convergently in two or more lineages is polyphyletic (Greek πολύς [ polys ], "many"). More broadly, any taxon that is not paraphyletic or monophyletic can be called polyphyletic. Empirically, the distinction between polyphyletic groups and paraphyletic groups is rather arbitrary, since the character states of common ancestors are inferences, not observations. These terms were developed during
1392-458: The composition of the excavates is given below, indicating that the group is paraphyletic. Except for some Euglenozoa , all are non- photosynthetic . Most excavates are unicellular, heterotrophic flagellates. Only some Euglenozoa are photosynthetic. In some (particularly anaerobic intestinal parasites), the mitochondria have been greatly reduced. Some excavates lack "classical" mitochondria , and are called "amitochondriate", although most retain
1440-490: The debates of the 1960s and 1970s accompanying the rise of cladistics . Paraphyletic groupings are considered problematic by many taxonomists, as it is not possible to talk precisely about their phylogenetic relationships, their characteristic traits and literal extinction. Related terms are stem group , chronospecies , budding cladogenesis, anagenesis, or 'grade' groupings. Paraphyletic groups are often relics from outdated hypotheses of phylogenic relationships from before
1488-456: The depicted scenario, the Eukaryota are deep in the tree of Asgard. A favored scenario is syntrophy, where one organism depends on the feeding of the other. An α-proteobacterium was incorporated to become the mitochondrion . In culture, extant Asgard archaea form various syntrophic dependencies. Gregory Fournier and Anthony Poole have proposed that Asgard is part of "the Eukaryote tree", forming
Excavata - Misplaced Pages Continue
1536-471: The descendants of a unique common ancestor. By comparison, the term polyphyly , or polyphyletic , uses the Ancient Greek prefix πολύς ( polús ), meaning "many, a lot of", and refers to the fact that a polyphyletic group includes organisms arising from multiple ancestral sources. Groups that include all the descendants of a common ancestor are said to be monophyletic . A paraphyletic group
1584-450: The examples given here, from formal classifications. Species have a special status in systematics as being an observable feature of nature itself and as the basic unit of classification. Some articulations of the phylogenetic species concept require species to be monophyletic, but paraphyletic species are common in nature, to the extent that they do not have a single common ancestor. Indeed, for sexually reproducing taxa, no species has
1632-492: The island of Taiwan . Heimdallarchaeia see text Asgard or Asgardarchaeota is a proposed superphylum belonging to the domain Archaea that contain eukaryotic signature proteins. It appears that the eukaryotes , the domain that contains the animals , plants , and fungi , emerged within the Asgard , in a branch containing the Heimdallarchaeota. This supports the two-domain system of classification over
1680-741: The latter having tubular cristae like most other protists, and hence were united under the taxon name Discoba , which was proposed for this supposedly monophyletic group. Metamonads are unusual in not having classical mitochondria—instead they have hydrogenosomes , mitosomes or uncharacterised organelles. The oxymonad Monocercomonoides is reported to have completely lost homologous organelles. There are competing explanations. The malawimonads have been proposed to be members of Excavata owing to their typical excavate morphology, and phylogenetic affinity to other excavate groups in some molecular phylogenies. However, their position among eukaryotes remains elusive. Ancyromonads are small free-living cells with
1728-605: The literature, and provides the corresponding monophyletic taxa. The concept of paraphyly has also been applied to historical linguistics , where the methods of cladistics have found some utility in comparing languages. For instance, the Formosan languages form a paraphyletic group of the Austronesian languages because they consist of the nine branches of the Austronesian family that are not Malayo-Polynesian and are restricted to
1776-444: The now obsolete Protista kingdom. They were distinguished from other lineages based on electron-microscopic information about how the cells are arranged (they have a distinctive ultrastructural identity ). They are considered to be a basal flagellate lineage. On the basis of phylogenomic analyses, the group was shown to contain three widely separated eukaryote groups, the discobids, metamonads, and malawimonads. A current view of
1824-493: The organisms their name. However, various groups that lack these traits are considered to be derived excavates based on genetic evidence (primarily phylogenetic trees of molecular sequences). The Acrasidae slime molds are the only excavates to exhibit limited multicellularity. Like other cellular slime molds , they live most of their life as single cells, but will sometimes assemble into larger clusters. Excavate relationships were always uncertain, suggesting that they are not
1872-437: The origin of the Eukaryotes is that a heimdallarchaeian or another Archaea acquired an alphaproteobacterium as an endosymbiont , and that this became the mitochondrion , the organelle providing oxidative respiration to the eukaryotic cell. Caesar al Jewari and Sandra Baldauf argue instead that the Eukaryotes possibly started with an endosymbiosis event of a Deltaproteobacterium or Gammaproteobacterium , accounting for
1920-568: The otherwise unexplained presence of anaerobic bacterial enzymes in Metamonada. The sister of the Preaxostyla within Metamonada represents the rest of the Eukaryotes which acquired an Alphaproteobacterium. In their scenario, the hydrogenosome and mitosome , both conventionally considered "mitochondrion-derived organelles", would predate the mitochondrion, and instead be derived from the earlier symbiotic bacterium. In 2023, using molecular phylogenetic analysis of 186 taxa, Al Jewari and Baldauf proposed
1968-675: The ranks of the ICZN Code , the two taxa are separate orders. Molecular studies, however, have shown that the Cetacea descend from artiodactyl ancestors, although the precise phylogeny within the order remains uncertain. Without the Cetaceans the Artiodactyls are paraphyletic. The class Reptilia is paraphyletic because it excludes birds (class Aves ). Under a traditional classification, these two taxa are separate classes. However birds are sister taxon to
Excavata - Misplaced Pages Continue
2016-563: The rise of cladistics. The prokaryotes (single-celled life forms without cell nuclei) are a paraphyletic grouping, because they exclude the eukaryotes , a descendant group. Bacteria and Archaea are prokaryotes, but archaea and eukaryotes share a common ancestor that is not ancestral to the bacteria. The prokaryote/eukaryote distinction was proposed by Edouard Chatton in 1937 and was generally accepted after being adopted by Roger Stanier and C.B. van Niel in 1962. The botanical code (the ICBN, now
2064-566: The role of Lokiarchaeota in the debates about the origin of eukaryotes. In 2016, a University of Texas -led team discovered Thorarchaeota from samples taken from the White Oak River in North Carolina, named in reference to Thor , another Norse god. Samples from Loki's Castle, Yellowstone National Park , Aarhus Bay , an aquifer near the Colorado River , New Zealand's Radiata Pool , hydrothermal vents near Taketomi Island , Japan, and
2112-526: The root of a tree is often difficult to pinpoint. Metakaryota Paraphyletic Paraphyly is a taxonomic term describing a grouping that consists of the grouping's last common ancestor and some but not all of its descendant lineages. The grouping is said to be paraphyletic with respect to the excluded subgroups. In contrast, a monophyletic grouping (a clade ) includes a common ancestor and all of its descendants. The terms are commonly used in phylogenetics (a subfield of biology ) and in
2160-423: The same clade but are not cladistically considered part of the Excavata yet, the Excavata are in this analysis highly paraphyletic. Hodarchaeales Parabasalia Fornicata Preaxostyla Jakobida Heterolobosea Euglenozoa and allies Amorphea (inc. animals, fungi) SAR Archaeplastida (inc. plants) The Anaeramoeba are associated with Parabasalia, but could turn out to be more basal as
2208-405: The situation in which one or several monophyletic subgroups of organisms (e.g., genera, species) are left apart from all other descendants of a unique common ancestor. Conversely, the term monophyly , or monophyletic , builds on the Ancient Greek prefix μόνος ( mónos ), meaning "alone, only, unique", and refers to the fact that a monophyletic group includes organisms consisting of all
2256-504: The world, both geographically and by habitat. Many of the known clades are restricted to sediments, whereas Lokiarchaeota, Thorarchaeota and another clade occupy many different habitats. Salinity and depth are important ecological drivers for most Asgard archaea. Other habitats include the bodies of animals, the rhizosphere of plants, non-saline sediments and soils, the sea surface, and freshwater. In addition, Asgard are associated with several other microorganisms. The phylum Heimdallarchaeota
2304-502: Was found in 2017 to have N-terminal core histone tails , a feature previously thought to be exclusively eukaryotic. Two other archaeal phyla, both outside of Asgard, were found to also have tails in 2018. In January 2020, scientists found Candidatus Prometheoarchaeum syntrophicum , a member of the Lokiarcheota, engaging in cross-feeding with two bacterial species. Drawing an analogy to symbiogenesis , they consider this relationship
#183816