A group of taxa A taxon is a group of (one or more) organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement. Defining what belongs or does not belong to such a taxonomic group is done by a taxonomist. It is not uncommon for one taxonomist to disagree with another on what exactly belongs to is said to be paraphyletic if the group contains its last In genetics, the most recent common ancestor of any set of organisms is the most recent individual from which all organisms in the group are directly descended. The term is often applied to human genealogy common ancestor In evolutionary biology, a group of organisms have common descent if they have a common ancestor. All living organisms on Earth are descended from a common ancestor or ancestral gene pool but does not contain all the descendants of that ancestor. This term is used in both phylogenetics In biology, phylogenetics is the study of evolutionary relatedness among various groups of organisms , which is discovered through molecular sequencing data and morphological data matrices. The term phylogenetics is of Greek origin from the terms phyle/phylon (φυλή/φῦλον), meaning "tribe, race," and genetikos (γενετικός[note 1] and linguistics Linguistics is the scientific study of natural language. Linguistics encompasses a number of sub-fields. An important topical division is between the study of language structure and the study of meaning (semantics and pragmatics). Grammar encompasses morphology (the formation and composition of words), syntax (the rules that determine how words.
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Phylogenetics
Relation to monophyletic groups
Groups that do include all the descendants of the most recent common ancestor are said to be monophyletic In common cladistic usage, monophyletic describes a group of organisms that form a clade, consisting of a last common ancestor and all of its descendants. The term is not synonymous with the less common term holophyly, which does not include a last common ancestor. It is contrasted with the terms paraphyly, which is a taxonomic group consisting of. A paraphyletic group is a monophyletic group from which one or more of the clades A clade[note 1] is a group consisting of an organism and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological classification. In is excluded to form a separate group (as in the paradigmatic example of reptiles and birds, shown in the picture).
A group that does not contain the most recent common ancestor of its members is said to be polyphyletic For example, the group consisting of warm-blooded animals is polyphyletic, because it contains both mammals and birds, but the most recent common ancestor of mammals and birds was cold-blooded. Warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds, so it is not a true phylogenetic grouping (Greek πολύς [polys], "many").
These terms were developed during the debates of the 1960s and 70s accompanying the rise of cladistics Cladistics is a method of classifying species of organisms into groups called clades, which consist of 1) all the descendants of an ancestral organism and 2) the ancestor itself. For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade. In the terms of biological systematics, a clade is a (a clade is a term for a monophyletic group).
Examples of paraphyletic groups
Many of the older classifications contain paraphyletic groups, especially the traditional 2–6 kingdom In biology, kingdom or regnum is a taxonomic rank, which is either the highest rank or in the more recent three-domain system, the rank below domain. Kingdoms are divided into smaller groups called phyla or divisions in botany. The complete sequence of ranks is life, domain, kingdom, phylum, class, order, family, genus, and species systems and the classic division of the vertebrates Vertebrates are members of the subphylum Vertebrata, chordates with backbones or spinal columns. About 58,000 species of vertebrates have been described. Vertebrata is the largest subphylum of chordates, and contains many familiar groups of large land animals. Vertebrates comprise cyclostomes, bony fish, sharks and rays, amphibians, reptiles,. Paraphyletic groups are often erected on the basis of (sym)plesiomorphies (ancestral similarities) instead of (syn)apomorphies In cladistics, a synapomorphy or synapomorphic character is a trait that is shared by two or more taxa and their most recent common ancestor, whose ancestor in turn does not possess the trait. A synapomorphy is thus an apomorphy visible in multiple taxa, where the trait in question originates in their last common ancestor. The word " (derived similarities). Examples of well-known paraphyletic groups includes:
- In the flowering plants The flowering plants , also known as Angiospermae or Magnoliophyta, are the most diverse group of land plants. Together with gymnosperms, they are the only extant groups of seed-producing plants, but they can be distinguished from the gymnosperms by a series of synapomorphies (derived characteristics). These characteristics include flowers,, Dicotyledons Dicotyledons, also known as dicots, is a name for a group of flowering plants whose seed typically has two embryonic leaves or cotyledons. There are around 199,350 species within this group. Flowering plants that are not dicotyledons are monocotyledons, typically having one embryonic leaf, in the traditional sense, because they exclude Monocotyledons Monocotyledons, also known as monocots, are one of two major groups of flowering plants that are traditionally recognized, the other being dicotyledons, or dicots. Monocot seedlings typically have one cotyledon (seed-leaf), in contrast to the two cotyledons typical of dicots. Monocots have been recognized at various taxonomic ranks, and under. The former name has not been used as an ICBN The International Code of Botanical Nomenclature is the set of rules and recommendations dealing with the formal botanical names that are given to plants. Its intent is that each taxonomic group ("taxon", plural "taxa") of plants has only one correct name that is accepted worldwide. The value of a scientific name is that it is classification for decades, but is allowed as a synonym of Magnoliopsida.[note 2] The former angiosperms (Magnoliophyta), or flowering plants, comprised both. Phylogenetic analysis, however, indicates that the monocots are a development from a dicot ancestor. Excluding them from the dicots makes the latter a paraphyletic group.[2]
- The order Artiodactyla The even-toed ungulates is a paraphyletic taxonomic group that contains many hoofed animals such as pigs, peccaries, hippopotamuses, camels, chevrotains , deer, giraffes, pronghorn, antelopes, sheep, goats, and cattle, but excludes whales even though they share a common ancestor. They are ungulates whose weight is borne about equally by the third (Even-toed ungulates), because it excludes Cetaceans The order Cetacea (pronounced /sɨˈteɪʃə/, L. cetus, whale, from Greek) includes the marine mammals commonly known as whales, dolphins, and porpoises. Cetus is Latin and is used in biological names to mean "whale"; its original meaning, "large sea animal", was more general. It comes from Ancient Greek κῆτος (kētos), (whales, dolphins, etc). In the ICZN Code, the two taxa are orders of equal rank. Molecular studies, however, have shown that the Cetacea descend from the Artiodactyl ancestors, although the precise phylogeny within the order remains uncertain. Without the Cetacean descendants the Artiodactyls must be paraphyletic.[3]
- The class Reptilia Reptiles are animals in the class Reptilia characterized by breathing air, a "cold-blooded" (poikilothermic) metabolism, laying tough-shelled amniotic eggs (or retaining the same membrane system in species with live birth), and skin with scales or scutes. They are tetrapods (either having four limbs or being descended from four-limbed as traditionally defined, because it excludes birds (class Aves Birds are winged, bipedal, endothermic (warm-blooded), egg-laying, vertebrate animals. There are around 10,000 living species, making them the most varied of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from the 5 cm (2 in) Bee Hummingbird to the 2.75 m (9 ft) Ostrich). In the ICZN Code, the two taxa are classes of equal rank. Phylogenetic analysis, however, indicates that the birds are descended from the Diapsida Diapsids are a group of reptiles that developed two holes (temporal fenestra) in each side of their skulls, about 300 million years ago during the late Carboniferous period. Living diapsids are extremely diverse, and include all crocodiles, lizards, snakes, and tuatara. Under modern classification systems, even birds are considered diapsids, since, which were reptiles (see the illustration above). Reptiles would be monophyletic if they were defined to include Aves.[1]
- The Prokaryotes The prokaryotes are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles. The word prokaryote comes from the Greek πρό- (pro-) & (single-celled life forms without cell nuclei), because the Archaea The Archaea (/ɑrˈkiːə/ ar-KEE-ə) are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon (sometimes spelled "archeon"). They have no cell nucleus or any other organelles within their cells. In the past they were viewed as an unusual group of bacteria and named archaebacteria descend from a common ancestor with the Eukaryotes A eukaryote is an organism whose cells contain complex structures enclosed within membranes. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. The presence of a nucleus gives eukaryotes their name, which comes from the. The Prokayote/Eukaryote distinction was proposed by Edouard Chatton in 1937[4] and was generally accepted after being adopted by Roger Stanier and C.B. van Niel in 1962. It was never adopted by any code because by that time the inappropriateness of the ICBN The International Code of Botanical Nomenclature is the set of rules and recommendations dealing with the formal botanical names that are given to plants. Its intent is that each taxonomic group ("taxon", plural "taxa") of plants has only one correct name that is accepted worldwide. The value of a scientific name is that it is code and the ICZN Code for classifying life forms that are neither plant nor animal was also generally recognized and the ICNB code did not appear until 1975. It did recognize Prokaryotic taxa beginning in 1980.[5] Chatton's system became known as the two-empire system The two-empire system was the top-level biological classification system in general use before the establishment of the three-domain system. It classified cellular life into Prokaryota and Eukaryota. When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system but the latter was replaced by Carl Woese Carl Richard Woese is an American microbiologist and physicist. Woese is famous for defining the Archaea (a new domain or kingdom of life) in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. He was also the originator of the RNA world hypothesis in 1967, although not by that's three-domain system The three-domain system is a biological classification introduced by Carl Woese in 1990 that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria and Archaebacteria (now Archaea). Woese argued that, on the basis of published in 1990. The former Prokaryotes became the Bacteria The bacteria ( [bækˈtɪəriə] ; singular: bacterium)[α] are a large group of single-celled, prokaryote microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic hot springs, radioactive waste, and the Archaea The Archaea (/ɑrˈkiːə/ ar-KEE-ə) are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon (sometimes spelled "archeon"). They have no cell nucleus or any other organelles within their cells. In the past they were viewed as an unusual group of bacteria and named archaebacteria, while the third domain remained the Eukaryotes A eukaryote is an organism whose cells contain complex structures enclosed within membranes. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried. The presence of a nucleus gives eukaryotes their name, which comes from the. Subsequent phylogenetic analysis led to a conclusion that the Archaea and the Eukaryotes share a common ancestor.[6]
- Agnatha Agnatha is a class or superclass of jawless fish in the phylum Chordata, subphylum Vertebrata. The group excludes all vertebrates with jaws, known as gnathostomes, jawless fish, because of its two significant animal groups, hagfish Hagfish are marine craniates of the class Agnatha or Myxini, also known as Hyperotreti. Some researchers regard Myxini as not belonging to the subphylum Vertebrata. That is, they are the only living animals that have a skull but not a vertebral column and lampreys A lamprey is a parasitic marine/aquatic animal with a toothed, funnel-like sucking mouth. Translated directly, their name means stone lickers (lambere: to lick, and petra: stone). While lampreys are well known for those species which bore into the flesh of other fish to suck their blood, these species make up the minority. In zoology, lampreys are, the lampreys descend from the the stem of the Gnathostomes. In 1806 Duméril united the hagfish with the lampreys under Cyclostomi, which Cope in 1889 made into Agnatha, as opposed to Gnathostome, the jawed fish. These two taxa became classes or superclasses in the ICZN Code. In the late 20th century phylogenetic analysis using dozens of characters (features) indicated the lampreys came from gnathostome ancestors, but the original agnatha/gnathostome ancestor did not have a jaw. The removal of the lampreys from the Agnatha downgraded the latter to a paraphyletic group.[7]
- Osteichthyes Osteichthyes , also called bony fish, are a taxonomic group of fish that have bony, as opposed to cartiligeous, skeletons. The vast majority of fish are osteichthyes, which is an extremely diverse and abundant group consisting of over 29,000 species. It is the largest class of vertebrates in existence today. Osteichthyes is divided into the ray-, bony fish, are paraphyletic because they include Actinopterygii The ray-finned fishes are so called because they possess lepidotrichia or "fin rays", their fins being webs of skin supported by bony or horny spines , as opposed to the fleshy, lobed fins that characterize the class Sarcopterygii which also, however, possess lepidotrichia. These actinopterygian fin rays attach directly to the proximal (ray-finned fish) and Sarcopterygii Sarcopterygii -- sometimes considered synonymous with Crossopterygii ("fringe-finned fishes", from Greek κροσσός, krossos, fringe) is a clade (traditionally a class or subclass) of fleshy-finned or lobe-finned fishes, the living descendants of which are the coelacanths, lungfishes and all tetrapods (lungfish, etc). However, tetrapods Tetrapods are vertebrate animals having four feet, legs or leglike appendages. Amphibians, reptiles, dinosaurs, birds, and mammals are all tetrapods, and even the limbless snakes are tetrapods by descent. The earliest tetrapods radiated from the Sarcopterygii, or lobe-finned fish are descendants of the nearest common ancestor of Actinopterygii and Sarcopterygii, and tetrapods are not in Osteichthyes, hence Osteichthyes is paraphyletic.[8]
- Porifera Sponges are animals of the phylum Porifera (pronounced /pɒˈrɪfərə/). Their bodies consist of jelly-like mesohyl sandwiched between two thin layers of cells. While all animals have unspecialized cells that can transform into specialized cells, sponges are unique in having some specialized cells that can transform into other types, often - Now divided into Siliceous Sponges and Calcareous sponges, which together are not monophyletic.[citation needed]
- Invertebrates An invertebrate is an animal without a backbone. The group includes 95% of all animal species — all animals except those in the chordate subphylum Vertebrata are defined as all animals other than vertebrates Vertebrates are members of the subphylum Vertebrata, chordates with backbones or spinal columns. About 58,000 species of vertebrates have been described. Vertebrata is the largest subphylum of chordates, and contains many familiar groups of large land animals. Vertebrates comprise cyclostomes, bony fish, sharks and rays, amphibians, reptiles,, although vertebrates are derived from this larger group.
- Recently Crustaceans Crustaceans form a very large group of arthropods, usually treated as a subphylum, which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill and barnacles. The 50,000 described species range in size from Stygotantulus stocki at 0.1 mm (0.004 in), to the Japanese spider crab with a leg span of up to 14 ft (4.3 m) and a mass has been defined as paraphyletic group by molecular phylogenetic study, so Hexapods The subphylum Hexapoda constitutes the largest (in terms of number of species) grouping of arthropods and includes the insects as well as three much smaller groups of wingless arthropods: Collembola, Protura, and Diplura (all of these were once considered insects). The Collembola (or springtails) are very abundant in terrestrial environments would be evolved from a subfamily of this group.[citation needed]
Cladistics generally discourages paraphyletic groups
In most cladistics Cladistics is a method of classifying species of organisms into groups called clades, which consist of 1) all the descendants of an ancestral organism and 2) the ancestor itself. For example, birds, dinosaurs, crocodiles, and all descendants of their most recent common ancestor form a clade. In the terms of biological systematics, a clade is a-based schools of taxonomy Taxonomy is the practice and science of classification. The word finds its roots in the Greek τάξις, taxis and νόμος, nomos (meaning 'law' or 'science'). Taxonomy uses taxonomic units, known as taxa (singular taxon), the existence of paraphyletic groups (as well as polyphyletic For example, the group consisting of warm-blooded animals is polyphyletic, because it contains both mammals and birds, but the most recent common ancestor of mammals and birds was cold-blooded. Warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds, so it is not a true phylogenetic grouping groups) in a classification is discouraged. Monophyletic In common cladistic usage, monophyletic describes a group of organisms that form a clade, consisting of a last common ancestor and all of its descendants. The term is not synonymous with the less common term holophyly, which does not include a last common ancestor. It is contrasted with the terms paraphyly, which is a taxonomic group consisting of groups (that is, clades A clade[note 1] is a group consisting of an organism and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological classification. In) are considered by these schools of thought to be the most important grouping of organisms, for the following reasons:
- Clades are simple to define: a typical clade definition is "All descendants of the nearest common ancestor of species X and Y". On the other hand, polyphyletic and paraphyletic groups are always defined in terms of clades, for example "reptiles are the Sauropsid clade, minus the Aves Birds are winged, bipedal, endothermic (warm-blooded), egg-laying, vertebrate animals. There are around 10,000 living species, making them the most varied of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from the 5 cm (2 in) Bee Hummingbird to the 2.75 m (9 ft) Ostrich clade". Or "Warm-blooded animals are the Aves Birds are winged, bipedal, endothermic (warm-blooded), egg-laying, vertebrate animals. There are around 10,000 living species, making them the most varied of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from the 5 cm (2 in) Bee Hummingbird to the 2.75 m (9 ft) Ostrich clade plus the Mammals clade". Because polyphyletic and paraphyletic groups are defined in terms of clades, they are considered less important than clades.
- For a given evolutionary tree of, say, N nodes, there are exactly N clades (one per node). However, the number of paraphyletic groups and polyphyletic groups is exponentially larger than that, on the order of 2N. Yet only a small fraction of the paraphyletic groups are given names or discussed.
- Paraphyletic groups often have their origin in traditional taxonomy, based on similar morphological characteristics. The original perception may have been that the group was entirely descended from a single ancestor. If such a group is later discovered (for instance, due to convergent evolution) to be paraphyletic, rather than monophyletic, then such a group loses its original significance.
Uses for paraphyletic groups
Others argue that paraphyletic groups are necessary for a comprehensive classification including extinct groups, since each species, genus, and so forth necessarily originates from part of another.
For instance, the Prokaryote group is paraphyletic because it excludes many of its descendent organisms (the Eukaryotes), yet the Prokaryote group is very useful because it has a clearly-defined and significant distinction (no cell nucleus) from its excluded descendants. So, even though Prokaryotes are not a clade, the term is still useful.
It has been suggested that paraphyletic groups be clearly marked to distinguish them from clades, for instance with asterisks: Reptilia*. The term evolutionary grade is sometimes used for such groups.[9]
Linguistics
Main article: Tree modelThe 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 as the term refers to the nine branches of the Austronesian family that are not Malayo-Polynesian and restricted to the island of Taiwan.[10]
Notes
- ^ A paraphyletic group is defined in terms of a clade; that is, the group is the same as the equivalent clade, except that it lacks one or more of the clade's full complement. The concept of the last common ancestor is the same, but it has been expanded to be node-based, branch-based and apomorphy-based. Those terms are defined under Phylogenetic nomenclature.
- ^ The history of flowering plant classification can be found under History of the classification of flowering plants.
References
- ^ a b Laurin, Michel; Gauthier, Jacques A. (1996). "Amniota". Tree of Life Web Project. http://tolweb.org/amniota. Retrieved 25 January 2010.
- ^ Simpson 2006, pp. 139–140. "It is now thought that the possession of two cotyledons is an ancestral feature for the taxa of the flowering plants and not an apomorphy for any group within. The 'dicots' ... are paraphyletic ...."
- ^ O'Leary, Maureen A. (2001). "The Phylogenetic Position of Cetaceans: Further Combined Data Analyses, Comparisons with the Stratigraphic Record and a Discussion of Character Optimization". American Zoologist 41 (3): 487–506. doi:10.1093/icb/41.3.487. http://icb.oxfordjournals.org/cgi/content/full/41/3/487.
- ^ Sapp, Jan (June 2005). "The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology". Microbiology and Molecular Biology Reviews 69 (2): 292–305. doi:10.1128/MMBR.69.2.292-305.2005. PMID 15944457. PMC 1197417. http://mmbr.asm.org/cgi/content/full/69/2/292?ijkey=9c01f67410bfc780c9d62495284c6efd50dc4f46#THE_TALE_OF_EDOUARD_CHATTON.
- ^ Stackebrabdt, E.; Tindell, B.; Ludwig, W.; Goodfellow, M. (1999). "Prokaryotic Diversity and Systematics". in Lengeler, Joseph W.; Drews, Gerhart; Schlegel, Hans Günter. Biology of the prokaryotes. Stuttgart: Georg Thieme Verlag. p. 679
- ^ Berg, Linda (2008). Introductory Botany: Plants, People, and the Environment (2nd ed.). Belmont CA: Thomson Corporation. p. 360. ISBN 0030754534.
- ^ Janvier, Philippe (2002) [1996]. Early Vertebrates. Oxford Monographs in Geology. Oxford: Oxford University Press. p. 44. ISBN 0198540477.
- ^ A Tree of Life
- ^ Dawkins, Richard (2004). "Mammal-like Reptiles". The Ancestor's Tale, A Pilgrimage to the Dawn of Life. Boston: Houghton Mifflin Company. ISBN 0-618-00583-8.
- ^ Greenhill, Simon J. and Russell D. Gray. (2009.) "Austronesian Language and Phylogenies: Myths and Misconceptions About Bayesian Computational Methods," in Austronesian Historical Linguistics and Culture History: a Festschrift for Robert Blust, edited by Alexander Adelaar and Andrew Pawley. Canberra : Pacific Linguistics, Research School of Pacific and Asian Studies, The Australian National University.
Bibliography
- Simpson, Michael George (2006). Plant systematics. Burlington; San Diego; London: Elsevier Academic Press. ISBN 0126444609.
- Colin Tudge (2000). The Variety of Life. Oxford University Press. ISBN 0198604262.
External links
- Funk, D. J.; Omland, K. E. (2003). "Species-level paraphyly and polyphyly: Frequency, cause and consequences, with insights from animal mitochondrial DNA". Annual Review of Ecology, Evolution and Systematics 34: 397–423. doi:10.1146/annurev.ecolsys.34.011802.132421. http://www.umbc.edu/biosci/Faculty/OmlandLabWebpage/NewPages/papers/FunkOmlandARev.pdf.
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ancestor of birds Without birds included reptiles is a paraphyletic group Groups are polyphyletic when they include multiple taxa but not the common ancestors Determining Phylogenetic Relationships Phylogenetic relationships are established by analyzing homologous traits Homologous traits are traits which are similar in two taxa
menvall
Wed, 18 Feb 2009 23:51:34 GM
obviously missing that also . paraphyletic. groups can be separated from the rest by a single cut (eg the clade representing humans and the clade representing chimps, excluding their ancestor). such . paraphyletic. groups are thus also ...
