32-436: See text Pipoidea are a clade of frogs, that contains the most recent common ancestor of living Pipidae and Rhinophrynidae as well as all its descendants. It is broadly equivalent to Xenoanura . The synapomorphies that define Pipoidea are the absence of mentomeckelian bones, absence of lateral alae of the parasphenoid , fusion of the frontoparietals into an azygous element , greatly enlarged otic capsules , and
64-452: A tadpole with paired spiracles and which lacks beaks and denticles. Later genetic work has supported Pipoidea as a monophyletic group. In 1993 Pipoidea was defined by Ford and Cannatella as a node-based taxon . It has variously been defined as a suborder (original definition), superfamily , or an unranked clade. There is no single, authoritative higher-level classification of frogs, and Vitt and Caldwell (2014) use name Xenoanura for
96-479: A "ladder", with supposedly more "advanced" organisms at the top. Taxonomists have increasingly worked to make the taxonomic system reflect evolution. When it comes to naming , this principle is not always compatible with the traditional rank-based nomenclature (in which only taxa associated with a rank can be named) because not enough ranks exist to name a long series of nested clades. For these and other reasons, phylogenetic nomenclature has been developed; it
128-623: A clade can be described based on two different reference points, crown age and stem age. The crown age of a clade refers to the age of the most recent common ancestor of all of the species in the clade. The stem age of a clade refers to the time that the ancestral lineage of the clade diverged from its sister clade. A clade's stem age is either the same as or older than its crown age. Ages of clades cannot be directly observed. They are inferred, either from stratigraphy of fossils , or from molecular clock estimates. Viruses , and particularly RNA viruses form clades. These are useful in tracking
160-571: A long time, archaea were seen as extremophiles that exist only in extreme habitats such as hot springs and salt lakes , but by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature. This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows
192-422: A revised taxonomy based on a concept strongly resembling clades, although the term clade itself would not be coined until 1957 by his grandson, Julian Huxley . German biologist Emil Hans Willi Hennig (1913–1976) is considered to be the founder of cladistics . He proposed a classification system that represented repeated branchings of the family tree, as opposed to the previous systems, which put organisms on
224-572: A similar clade, skipping Pipoidea altogether, as did Frost et al. (2006). The oldest record of the group is Rhadinosteus from the Late Jurassic of North America, which is more closely related to Rhinophrynidae than to Pipidae. The oldest records of Pipimorpha (which contains all pipoids more closely related to Pipidae than to Rhinophrynidae) are Aygroua anoualensis from the Tithonian or Berriasian , Neusibatrachus and Gracilibatrachus from
256-578: A small group of unusual thermophilic species sharing features of both the main phyla, but most closely related to the Thermoproteota. Other detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising Micrarchaeota and Parvarchaeota), which were discovered in 2006 and are some of the smallest organisms known. A superphylum – TACK – which includes
288-429: A suffix added should be e.g. "dracohortian". A clade is by definition monophyletic , meaning that it contains one ancestor which can be an organism, a population, or a species and all its descendants. The ancestor can be known or unknown; any and all members of a clade can be extant or extinct. The science that tries to reconstruct phylogenetic trees and thus discover clades is called phylogenetics or cladistics ,
320-499: Is also used with a similar meaning in other fields besides biology, such as historical linguistics ; see Cladistics § In disciplines other than biology . The term "clade" was coined in 1957 by the biologist Julian Huxley to refer to the result of cladogenesis , the evolutionary splitting of a parent species into two distinct species, a concept Huxley borrowed from Bernhard Rensch . Many commonly named groups – rodents and insects , for example – are clades because, in each case,
352-555: Is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. It is unknown if they are able to produce endospores . Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat, square cells of Haloquadratum walsbyi . Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for
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#1732847677614384-471: Is in turn included in the mammal, vertebrate and animal clades. The idea of a clade did not exist in pre- Darwinian Linnaean taxonomy , which was based by necessity only on internal or external morphological similarities between organisms. Many of the better known animal groups in Linnaeus's original Systema Naturae (mostly vertebrate groups) do represent clades. The phenomenon of convergent evolution
416-515: Is responsible for many cases of misleading similarities in the morphology of groups that evolved from different lineages. With the increasing realization in the first half of the 19th century that species had changed and split through the ages, classification increasingly came to be seen as branches on the evolutionary tree of life . The publication of Darwin's theory of evolution in 1859 gave this view increasing weight. In 1876 Thomas Henry Huxley , an early advocate of evolutionary theory, proposed
448-489: Is still controversial. As an example, see the full current classification of Anas platyrhynchos (the mallard duck) with 40 clades from Eukaryota down by following this Wikispecies link and clicking on "Expand". The name of a clade is conventionally a plural, where the singular refers to each member individually. A unique exception is the reptile clade Dracohors , which was made by haplology from Latin "draco" and "cohors", i.e. "the dragon cohort "; its form with
480-663: The Early Cretaceous of Spain, with other records of the group known from Afro-Arabia and South America like modern Pipidae. The extinct pipimorph family Palaeobatrachidae , particularly the genus Palaeobatrachus were widespread and abundant in Europe during the Cenozoic , until their extinction during the Middle Pleistocene around 500,000 years ago due to being unable to cope with the increasing aridity and freezing temperatures of
512-894: The enzymes involved in transcription and translation . Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes , including archaeols . Archaea use more diverse energy sources than eukaryotes, ranging from organic compounds such as sugars, to ammonia , metal ions or even hydrogen gas . The salt-tolerant Haloarchaea use sunlight as an energy source, and other species of archaea fix carbon (autotrophy), but unlike plants and cyanobacteria , no known species of archaea does both. Archaea reproduce asexually by binary fission , fragmentation , or budding ; unlike bacteria, no known species of Archaea form endospores . The first observed archaea were extremophiles , living in extreme environments such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to
544-525: The gastrointestinal tract in humans and ruminants , where their vast numbers facilitate digestion . Methanogens are also used in biogas production and sewage treatment , and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents . For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry , morphology and metabolism . Microbiologists tried to classify microorganisms based on
576-589: The methanogens were known). They called these groups the Urkingdoms of Archaebacteria and Eubacteria, though other researchers treated them as kingdoms or subkingdoms. Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. lack of peptidoglycan in their cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed reclassifying organisms into three natural domains known as
608-681: The taxonomical literature, sometimes the Latin form cladus (plural cladi ) is used rather than the English form. Clades are the fundamental unit of cladistics , a modern approach to taxonomy adopted by most biological fields. The common ancestor may be an individual, a population , or a species ( extinct or extant ). Clades are nested, one in another, as each branch in turn splits into smaller branches. These splits reflect evolutionary history as populations diverged and evolved independently. Clades are termed monophyletic (Greek: "one clan") groups. Over
640-818: The three-domain system : the Eukarya , the Bacteria and the Archaea, in what is now known as the Woesian Revolution . The word archaea comes from the Ancient Greek ἀρχαῖα , meaning "ancient things", as the first representatives of the domain Archaea were methanogens and it was assumed that their metabolism reflected Earth's primitive atmosphere and the organisms' antiquity, but as new habitats were studied, more organisms were discovered. Extreme halophilic and hyperthermophilic microbes were also included in Archaea. For
672-1003: The Thaumarchaeota (now Nitrososphaerota ), " Aigarchaeota ", Crenarchaeota (now Thermoproteota ), and " Korarchaeota " was proposed in 2011 to be related to the origin of eukaryotes. In 2017, the newly discovered and newly named Asgard superphylum was proposed to be more closely related to the original eukaryote and a sister group to TACK. In 2013, the superphylum DPANN was proposed to group " Nanoarchaeota ", " Nanohaloarchaeota ", Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising " Micrarchaeota " and " Parvarchaeota "), and other similar archaea. This archaeal superphylum encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, DPANN may include members obligately dependent on symbiotic interactions, and may even include novel parasites. However, other phylogenetic analyses found that DPANN does not form
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#1732847677614704-455: The culturable and well-investigated species of archaea are members of two main phyla , the " Euryarchaeota " and the Thermoproteota (formerly Crenarchaeota). Other groups have been tentatively created, such as the peculiar species Nanoarchaeum equitans — discovered in 2003 and assigned its own phylum, the " Nanoarchaeota ". A new phylum " Korarchaeota " has also been proposed, containing
736-502: The detection and identification of organisms that have not been cultured in the laboratory. The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors. These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships among organisms ( molecular phylogenetics ). Most of
768-412: The discovery of archaea in almost every habitat , including soil, oceans, and marshlands . Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life . They are part of the microbiota of all organisms. In the human microbiome , they are important in the gut , mouth, and on
800-734: The domain Archaea includes eukaryotes, the term "archaea" ( sg. : archaeon / ɑːr ˈ k iː ɒ n / ar- KEE -on , from the Greek "αρχαίον", which means ancient) in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria , receiving the name archaebacteria ( / ˌ ɑːr k i b æ k ˈ t ɪər i ə / , in the Archaebacteria kingdom ), but this term has fallen out of use. Archaeal cells have unique properties separating them from Bacteria and Eukaryota . Archaea are further divided into multiple recognized phyla . Classification
832-546: The group consists of a common ancestor with all its descendant branches. Rodents, for example, are a branch of mammals that split off after the end of the period when the clade Dinosauria stopped being the dominant terrestrial vertebrates 66 million years ago. The original population and all its descendants are a clade. The rodent clade corresponds to the order Rodentia, and insects to the class Insecta. These clades include smaller clades, such as chipmunk or ant , each of which consists of even smaller clades. The clade "rodent"
864-411: The ice ages. Taxonomy after A. M. Aranciaga Rolando et al. 2019 Clade In biological phylogenetics , a clade (from Ancient Greek κλάδος (kládos) 'branch'), also known as a monophyletic group or natural group , is a grouping of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree . In
896-590: The last few decades, the cladistic approach has revolutionized biological classification and revealed surprising evolutionary relationships among organisms. Increasingly, taxonomists try to avoid naming taxa that are not clades; that is, taxa that are not monophyletic . Some of the relationships between organisms that the molecular biology arm of cladistics has revealed include that fungi are closer relatives to animals than they are to plants, archaea are now considered different from bacteria , and multicellular organisms may have evolved from archaea. The term "clade"
928-518: The latter term coined by Ernst Mayr (1965), derived from "clade". The results of phylogenetic/cladistic analyses are tree-shaped diagrams called cladograms ; they, and all their branches, are phylogenetic hypotheses. Three methods of defining clades are featured in phylogenetic nomenclature : node-, stem-, and apomorphy-based (see Phylogenetic nomenclature§Phylogenetic definitions of clade names for detailed definitions). The relationship between clades can be described in several ways: The age of
960-454: The skin. Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling ; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example. No clear examples of archaeal pathogens or parasites are known. Instead they are often mutualists or commensals , such as the methanogens (methane-producing strains) that inhabit
992-612: The spread of viral infections . HIV , for example, has clades called subtypes, which vary in geographical prevalence. HIV subtype (clade) B, for example is predominant in Europe, the Americas and Japan, whereas subtype A is more common in east Africa. Archaea Archaea ( / ɑːr ˈ k iː ə / ar- KEE -ə ) is a domain of organisms . Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic , as eukaryotes are now known to have evolved from archaea. Even though
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1024-488: The structures of their cell walls , their shapes, and the substances they consume. In 1965, Emile Zuckerkandl and Linus Pauling instead proposed using the sequences of the genes in different prokaryotes to work out how they are related to each other. This phylogenetic approach is the main method used today. Archaea were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox , based on their ribosomal RNA (rRNA) genes. (At that time only
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