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Taxonomy (biology)

From Wikipedia, the free encyclopedia

Taxonomy (from Ancient Greek: τάξις taxis, "arrangement", and -νομία -nomia, "method"[1]) is the science of defining and naming groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super group of higher rank, thus creating a taxonomic hierarchy.[2][3] The Swedish botanist Carl Linnaeus is regarded as the father of taxonomy, as he developed a system known as Linnaean classification for categorization of organisms and binomial nomenclature for naming organisms.

With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct.

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  • Taxonomy: Life's Filing System - Crash Course Biology #19
  • Learn Biology: Classification- The Taxonomic Hierarchy
  • Taxonomy and the Tree of Life
  • Classification of Life
  • Classification and Taxonomy

Transcription

Taxonomy! It's the science of classifying living things. That sounds exciting. Today we'll basically be learning the Dewey Decimel System of evolution! It's like filing! You must be on the edge of your seat. OK, shut up. When it comes down to it, this science doesn't just categorize organisms, when you look a little deeper, you realize it's telling the story of all life on earth. And it's a pretty good story. Every living thing on this planet is related to every other living thing. If you go far enough back, we all have a common ancestor. An organism that both you and I are descended from. Or something that a star fish and a blue whale are descended from. Or, even weirder, that an oak tree and a salmon are both descended from. That organism lived. It lived very long ago. But it was here. And I dig that. The trick of taxonomy, is basically figuring out where all those branches of the evolutionary tree are, and finding some convenient labels to help us understand all of these remarkable interrelationships. Let's be clear though, taxonomy isn't about describing life in all of it's ridiculous detail, it's mostly about helping humans understand it, because it's way too complicated without structure. To get that structure biologists use the taxonomic system to classify all the organisms on the Earth. It's sometimes called the Phylogenetic Tree, or the Tree of Life, and it illustrates the evolutionary relationships between all living species. There are about 2 million known species, but there could be anywhere from 5 million to 100 million species scientists really have no freaking idea. New species keep getting discovered all the time, and the more organisms we have to keep track of, the more complex the Phylogenetic Tree becomes. So, there's not always a consensus about how to classify this stuff. There's a lot of gray area in the Natural World. Actually, let me rephrase that: the Natural World is one giant Gray Area. Sometimes it's just hard to know where to put a certain group of organisms, and eventually the group gets so big, the classification system has to be messed with to make room for it. So, the system isn't perfect, but it's good enough that we've been using it for around 250 years. [Sniffing] What's that? Do you smell a Bio-lography coming on? Carl Linnaeus was a Swede born in 1707. And early in his career as a botanist he realized that the botanical nomenclature of 18th century Europe was.. well, just crap. For instance, in his day, the "formal" name of a tomato plant was Solanum caule inerme herbaceo, foliis pinnatis incisis, racemis simplicibus. Linnaeus actually said once, "I shudder at the sight of most botanical names given by modern authorities." Not only did this sloppiness bother him, he saw a whole sugarstorm blowing in: New plants were still being discovered in Europe, but that was nothing compared to the crazy stuff that was coming from the New World. Linnaeus saw that pretty soon, naming conventions were just going to collapse under all these new things to name. And THEN what? Linnaeus famously started off by naming himself. He came from a peasant family, and at the time, surnames were just for rich people, so when Carl went to college, they asked him for his surname and he just made one up: Linneaus, after the Linden trees that grew on his family's homestead. Linnaeus got a medical degree and became a professor at Uppsala University where he devoted himself to the study of nomenclature. He had his students go places and bring back specimens for him to study and categorize. The method he eventually adopted was based on morphology, or physical form and structure. This wasn't necessarily a new idea. Back then, people grouped organisms by analogous or homoplasic traits, structures that appear similar but actually come from completely independent origins. By this definition, birds would be more closely related to butterflies than to reptiles because birds and butterflies can both fly. But Linnaeus had a good mind for this stuff and turned out to have a real knack for choosing actual homologous traits for his classification system traits that stem from a common evolutionary ancestor. Linnaeus didn't know jack about evolution Darwin wouldn't come around for another 100 plus years but he just intuited that some traits were more important than others. For instance, he was struck by the fact that reproductive apparatus seemed to be a good way of classifying plants. He also caused a scandal by classifying the Class Mammalia based on the female's ability to produce milk from their nipples. Because apparently that was pretty racy stuff back then. In his lifetime Linnaeus catalogued roughly 7,700 plants and 4,400 animals, and he published his classifications in a catalog called Systema Naturae, which by the time he wrote the 12th edition, was 2,300 pages long. In the meantime, Linneaus actually adopted a personal motto: "God created, Linnaeus organized." Although taxonomy has come a long way since Linnaeus, we still use a bunch of the conventions that he invented. For instance, we still arrange things into taxa, or groups of organisms, and we still us the same Taxa as Linnaeus: kingdom, phylum, class, order, family, genus and species. We also still use Linnaeus' convention of binomial nomenclature using a unique, two-part name for every species the genus and species name, in Latin or Latin-ish. This practice actually started back in the Middle Ages when educated people were expected to know Latin. We know a lot less latin now, but we know a lot more about evolution which Linnaeus didn't. And we have technologies like genetic testing to classify relationships between organisms. And yet we still use Linnaeus's morphology-based system because genetic evidence generally agrees with classifications that are made based on structure and form. However, because there was a lot of life that Linnaeus had no idea about, we had to stick a new taxa above Linnaeus' Kingdom. We call it Domain. And it's as broad as you can get. The Domains are Bacteria, Archaea and Eukarya. The bacteria and archae are prokaryotes, meaning their genetic material goes commando with no nucleus to enclose it. While the Eukarya make up all the life forms with a nucleus and include pretty much all the life that you think of as life, and quite a lot of the life that you don't think about at all. It might seem like, since all macroscopic life only gets one domain, it's kinda silly to give prokaryotes two and for a long time, we didn't. We didn't divide them up into different domains. They hung out together in a single domain called Monera. But it later became clear that Bacteria, which live pretty much everywhere on earth, including inside of you and deep in the Earth's crust, and Archaea which are even more hardy than bacteria, have distinct evolutionary histories. Archaea being more closely related to eukaryotes and, yes, thus me and you. They have totally different cell membranes and the enzymes they use to make RNA, their RNA polymerase, is much more like ours. Under the domain Eukarya, which is by far the most interesting and even occasionally adorable domain, we have Kingdoms: Protista, Fungi, Plantae and Animalia. Now, scientists have settled on these four. For now. But these are categories that are a human creation, but there are good reasons for that human creation. The unscientific truth is that we looked at life and divided it up based on what we saw. So we were like, "Well, protists are single-celled organisms, so, they're very different from the rest of the domain. Plants get their energy from the sun and fungi look and act very different from plants and animals, and we already know what animals are, so they have to get their own kingdom." And though scientists are loathe to admit it, that system of just looking and dividing things up actually worked pretty well for us. Not perfectly, but pretty well. But there's a reason why this worked so well. Evolutionarily, there are actual categories. Each of these kingdoms is a huge branch in the tree of life. At each branch, an evolutionary change occurred that was so massively helpful that it spawned a vast diversity of descendents. Plants or Plantae are the autotrophs of the Domain Eukarya. Autotrophs meaning that they can feed themselves, through photosynthesis of course. Their cellulose-based cell walls and chloroplasts giving them a distinct difference from all other multi-cellular life. There are two other sorts of -trophs. The heterotrophs, which get their energy by eating other organisms. And Chemotrophs, which are weird and crazy and only show up in bacteria and achaea, and they get their energy from chemicals. Now the kingdom Protista is weird because it contains both autotrophs and heterotrophs. Some protists can photosynthesize, while others eat living things. Protists are basically a bunch of weird, eukaryotic single-celled organisms that may or may not be evolutionarily related to each other scientists are still trying to figure it out. Some are plant-like, like algae, some are more animal-like, like amoebas, and some are fungus-like, like slime molds. Protists are one of those gray areas I was telling you about. So don't be surprised if, by the time you're teaching this to your biology students, there are more than four kingdoms in Eukarya. Fungi, which are, you know—the funguses. They include mushrooms, smuts, puffballs, truffles, molds, and yeasts and they're pretty cool because they have cell walls like plants, but instead of being made of cellulose, they're made of another carbohydrate called chitin, which is also what the beak of a giant squid is made out of, or the exoskeleton of a beetle. Because fungi are heterotrophs like animals, they have these sort of digestive enzymes that break down their food and get reabsorbed. But they can't move, they don't require a stomach for digestion they just grow on top of whatever it is they're digesting and digest it right where it is. Which is super convenient! And finally, we have Kingdom Animalia. Which is the lovely kingdom that we find ourselves and 100% of adorable organisms in. Animals are multicellular, always. We're heterotrophic, so we spend a lot of our time hunting down food because we can't make it ourselves. Almost all of us can move, at least during some stage of our life cycle. And most of us develop either two or three germ layers during embryonic development, wait for it... ...unless you're a sponge. So like I said, we use this taxonomic system to describe the common ancestry and evolutionary history of an organism. Looking at the phylogenetic tree, you can tell that humans are more closely related to mice than we are to fish, and more closely related to fish than we are to fruit flies. So how about we pick an organism and follow it all the way through the taxa, from kingdom to species, just to see how it works. I know! Let's pick this kitty. Because I know she'd like it. Right, cat? So, kitties have cells that have nuclei and membrane surrounded organelles. And they're multicellular and heterotrophic and have three germ layers of cells when they're embryos, so they're in the kingdom Animalia. And they have a spinal cord running down their backs, protected by vertebrae, and disks in between them. And they have a tail that doesn't have a butthole at the end of it like a worm, which I'm really glad about. And that puts her in the phylum Chordata. Kitty clearly does not like this, so I'm going to put her down now. And the kitty lactates and gives birth to young like a cow, instead of laying eggs like a chicken, and they have fur and three special tiny bones in their ears that only mammals have, so they're in the class Mammalia. So, she is more closely related to a cow than a chicken. Good to know! And like a bunch of other placental mammals that eat meat like weasels (the mustelids), and dogs, (the canines), kitties are in the order Carnivora. And they're in the cat family, Felidae, whose members have lithe bodies and roundish heads and, except for cheetahs, retractable claws. And they're littler than tigers and panthers, which puts them in the genus Felis. And then, at the level of the species, the descriptions get pretty dang detailed, so let's just say that, you know what a cat is right? So the species name is catus. And look at that: Felis catus! Aw. Kitty. I could have that whole thing cross-stitched onto a pillow for you to sleep on! And it would be cute! Thank you for watching our taxider- I mean, our taxonomy episode of Crash Course Biology. We hope that you learned something. Thanks to everybody who helped put this episode together. If you have any questions for us, please leave them on Facebook or Twitter or in the comments below. And we will get to them. Hopefully very quickly. I will see you next time!

Contents

Definition

The exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception, naming, and classification of groups of organisms.[4] As points of reference, recent definitions of taxonomy are presented below:

  1. Theory and practice of grouping individuals into species, arranging species into larger groups, and giving those groups names, thus producing a classification[2]
  2. A field of science (and major component of systematics) that encompasses description, identification, nomenclature, and classification[3]
  3. The science of classification, in biology the arrangement of organisms into a classification[5]
  4. "The science of classification as applied to living organisms, including study of means of formation of species, etc."[6]
  5. "The analysis of an organism's characteristics for the purpose of classification"[7]
  6. "[Systematics] studies phylogeny to provide a pattern that can be translated into the classification and names of the more inclusive field of taxonomy" (listed as a desirable but unusual definition)[8]

The varied definitions either place taxonomy as a sub-area of systematics (definition 2), invert that relationship (definition 6), or appear to consider the two terms synonymous. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy (definitions 1 and 2), or a part of systematics outside taxonomy.[9] For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy:[7]

  • Systematics: "The study of the identification, taxonomy and nomenclature of organisms, including the classification of living things with regard to their natural relationships and the study of variation and the evolution of taxa".

A whole set of terms including taxonomy, systematic biology, systematics, biosystematics, scientific classification, biological classification, and phylogenetics have at times had overlapping meanings – sometimes the same, sometimes slightly different, but always related and intersecting.[4][10] The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique.[11]

Alpha and beta taxonomy

The term "alpha taxonomy" is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species.[12] In earlier literature, the term had a different meaning, referring to morphological taxonomy, and the products of research through the end of the 19th century.[13]

William Bertram Turrill introduced the term "alpha taxonomy" in a series of papers published in 1935 and 1937 in which he discussed the philosophy and possible future directions of the discipline of taxonomy.[14]

… there is an increasing desire amongst taxonomists to consider their problems from wider view-points, to investigate the possibilities of closer co-operation with their cytological, ecological and genetical colleagues and to acknowledge that some revision or expansion, perhaps of a drastic nature, of their aims and methods may be desirable … Turrill (1935) has suggested that while accepting the older invaluable taxonomy, based on structure, and conveniently designated "alpha", it is possible to glimpse a far-distant taxonomy built up on as wide a basis of morphological and physiological facts as possible, and one in which "place is found for all observational and experimental data relating, even if indirectly, to the constitution, subdivision, origin and behaviour of species and other taxonomic groups". Ideals can, it may be said, never be completely realized. They have, however, a great value of acting as permanent stimulants, and if we have some, even vague, ideal of an "omega" taxonomy we may progress a little way down the Greek alphabet. Some of us please ourselves by thinking we are now groping in a "beta" taxonomy.[14]

Turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy (pages 365–366).

Later authors have used the term in a different sense, to mean the delimitation of species (not subspecies or taxa of other ranks), using whatever investigative techniques are available, and including sophisticated computational or laboratory techniques.[15][12] Thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species.[16]

An understanding of the biological meaning of variation and of the evolutionary origin of groups of related species is even more important for the second stage of taxonomic activity, the sorting of species into groups of relatives ("taxa") and their arrangement in a hierarchy of higher categories. This activity is what the term classification denotes; it is also referred to as beta taxonomy.

Microtaxonomy and macrotaxonomy

How species should be defined in a particular group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy.[17][18][12] By extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species.[12]

History

While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, a truly scientific attempt to classify organisms did not occur until the 18th century. Earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in this scientific thinking. Early taxonomy was based on arbitrary criteria, the so-called "artificial systems", including Linnaeus's system of sexual classification. Later came systems based on a more complete consideration of the characteristics of taxa, referred to as "natural systems", such as those of de Jussieu (1789), de Candolle (1813) and Bentham and Hooker (1862–1863). These were pre-evolutionary in thinking. The publication of Charles Darwin's On the Origin of Species (1859) led to new ways of thinking about classification based on evolutionary relationships. This was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler (1883) and Engler (1886–1892). The advent of molecular genetics and statistical methodology allowed the creation of the modern era of "phylogenetic systems" based on cladistics, rather than morphology alone.[19][20][21]

Pre-Linnaean

Early taxonomists

Naming and classifying our surroundings has probably been taking place as long as mankind has been able to communicate. It would always have been important to know the names of poisonous and edible plants and animals in order to communicate this information to other members of the family or group.[citation needed]

Medicinal plant illustrations show up in Egyptian wall paintings from c. 1500 BC.[22] The paintings clearly show that these societies valued and communicated the uses of different species, and therefore had a basic taxonomy in place.[citation needed]

Srimadbhagavata Purana

In Canto 3, chapter 10 of Srimadbhagavata purana 6 types of trees are recognised and they are:[23]

  1. Vanaspatis – large trees that grow fruits without flowering.
  2. Drumas – large trees that bloom and give fruits.
  3. Osadhis – trees that die soon after they give fruits.
  4. Latas – creepers and tiny plants.
  5. Viruts – plants that grow as bushes.
  6. Tvaksaras – plants hollow inside with strong barks like bamboos.

Ancient times

Organisms were first classified by Aristotle (Greece, 384–322 BC), during his stay on the Island of Lesbos.[24][25][26] He classified beings by their parts, or in modern terms attributes, such as having live birth, having four legs, laying eggs, having blood, or being warm-bodied.[27] He divided all living things into two groups: plants and animals.[25] Some of his groups of animals, such as Anhaima (animals without blood, translated as invertebrates) and Enhaima (animals with blood, roughly the vertebrates), as well as groups like the selachians and cetaceans, are still commonly used today.[28] His student Theophrastus (Greece, 370–285 BC) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum. Again, several plant groups currently still recognized can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus.[25]

Medieval

Taxonomy in the Middle Ages was largely based on the Aristotelian system,[27] with additions concerning the philosophical and existential order of creatures. This included concepts such as the Great chain of being in the Western scholastic tradition,[27] again deriving ultimately from Aristotle. Aristotelian system did not classify plants or fungi, due to the lack of microscope at the time,[26] as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder).[25] This, as well, was taken into consideration in the Great chain of being.[25] Advances were made by scholars such as Procopius, Timotheos of Gaza, Demetrios Pepagomenos, and Thomas Aquinas. Medieval thinkers used abstract philosophical and logical categorizations more suited to abstract philosophy than to pragmatic taxonomy.[25]

Renaissance and Early Modern

During the Renaissance, the Age of Reason, and the Enlightenment, categorizing organisms became more prevalent,[25] and taxonomic works became ambitious enough to replace the ancient texts. This is sometimes credited to the development of sophisticated optical lenses, which allowed the morphology of organisms to be studied in much greater detail. One of the earliest authors to take advantage of this leap in technology was the Italian physician Andrea Cesalpino (1519–1603), who has been called "the first taxonomist".[29] His magnum opus De Plantis came out in 1583, and described more than 1500 plant species.[30][31] Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae.[32] Then in the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works.[26] Arguably his greatest accomplishment was Methodus Plantarum Nova (1682),[33] in which he published details of over 18,000 plant species. At the time, his classifications were perhaps the most complex yet produced by any taxonomist, as he based his taxa on many combined characters. The next major taxonomic works were produced by Joseph Pitton de Tournefort (France, 1656–1708).[34] His work from 1700, Institutiones Rei Herbariae, included more than 9000 species in 698 genera, which directly influenced Linnaeus, as it was the text he used as a young student.[22]

The Linnaean era

 Title page of Systema Naturae, Leiden, 1735
Title page of Systema Naturae, Leiden, 1735

The Swedish botanist Carl Linnaeus (1707–1778)[27] ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735,[35] Species Plantarum in 1753,[36] and Systema Naturae 10th Edition,[37] he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species,[38] which proved to be an elegant solution to a chaotic and disorganized taxonomic literature. He not only introduced the standard of class, order, genus, and species, but also made it possible to identify plants and animals from his book, by using the smaller parts of the flower.[38] Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century.[38] Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively).[39] Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar[40]). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.[22]

Modern system of classification

 Evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical for Evolutionary taxonomy
Evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical for Evolutionary taxonomy
 The same relationship, expressed as a cladogram typical for cladistics
The same relationship, expressed as a cladogram typical for cladistics

Whereas Linnaeus classified for ease of identification, the idea of the Linnaean taxonomy as translating into a sort of dendrogram of the Animal- and Plant Kingdoms was formulated toward the end of the 18th century, well before On the Origin of Species was published.[26] Among early works exploring the idea of a transmutation of species were Erasmus Darwin's 1796 Zoönomia and Jean-Baptiste Lamarck's Philosophie Zoologique of 1809.[12] The idea was popularised in the Anglophone world by the speculative but widely read Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844.[41]

With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent.[42] Tree of Life representations became popular in scientific works, with known fossil groups incorporated. One of the first modern groups tied to fossil ancestors was birds.[43] Using the then newly discovered fossils of Archaeopteryx and Hesperornis, Thomas Henry Huxley pronounced that they had evolved from dinosaurs, a group formally named by Richard Owen in 1842.[44][45] The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, is the essential hallmark of evolutionary taxonomic thinking. As more and more fossil groups were found and recognized in the late 19th and early 20th centuries, palaeontologists worked to understand the history of animals through the ages by linking together known groups.[46] With the modern evolutionary synthesis of the early 1940s, an essentially modern understanding of the evolution of the major groups was in place. As evolutionary taxonomy is based on Linnaean taxonomic ranks, the two terms are largely interchangeable in modern use.[citation needed]

The cladistic method (or cladism) has emerged since the 1960s.[42] In 1958, Julian Huxley used the term clade.[12] Later, in 1960, Cain and Harrison introduced the term cladistic.[12] The salient feature is arranging taxa in a hierarchical evolutionary tree, ignoring ranks.[42] A taxon is called monophyletic, if it includes all the descendants of an ancestral form.[47][48] Groups that have descendant groups removed from them (e.g. dinosaurs, with birds as offspring group) are termed paraphyletic,[47] while groups representing more than one branch from the tree of life are called polyphyletic.[47][48] The International Code of Phylogenetic Nomenclature or PhyloCode is intended to regulate the formal naming of clades.[49][50] Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes.[50]

Kingdoms and domains

 The basic scheme of modern classification. Many other levels can be used; the highest level, domain, is both new and disputed.
The basic scheme of modern classification. Many other levels can be used; the highest level, domain, is both new and disputed.

Well before Linnaeus, plants and animals were considered separate Kingdoms.[51] Linnaeus used this as the top rank, dividing the physical world into the plant, animal and mineral kingdoms. As advances in microscopy made classification of microorganisms possible, the number of kingdoms increased, five and six-kingdom systems being the most common.

Domains are a relatively new grouping. First proposed in 1977, Carl Woese's three-domain system was not generally accepted until later.[52] One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera),[51] with the Eukaryota for all organisms whose cells contain a nucleus.[53] A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.[51]

Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade that groups together the Archaea and Eucarya, would have evolved from Bacteria, more precisely from Actinobacteria. His 2004 classification treated the archaeobacteria as part of a subkingdom of the Kingdom Bacteria, i.e. he rejected the three-domain system entirely.[54] Stefan Luketa in 2012 proposed a five "dominion" system, adding Prionobiota (acellular and without nucleic acid) and Virusobiota (acellular but with nucleic acid) to the traditional three domains.[55]

Linnaeus
1735[56]
Haeckel
1866[57]
Chatton
1925[58]
Copeland
1938[59]
Whittaker
1969[60]
Woese et al.
1990[61]
Cavalier-Smith
1998[54]
2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 3 domains 6 kingdoms
(not treated) Protista Prokaryota Monera Monera Bacteria Bacteria
Archaea
Eukaryota Protoctista Protista Eucarya Protozoa
Chromista
Vegetabilia Plantae Plantae Plantae Plantae
Fungi Fungi
Animalia Animalia Animalia Animalia Animalia

Recent comprehensive classifications

Partial classifications exist for many individual groups of organisms and are revised and replaced as new information becomes available, however comprehensive treatments of most or all life are rarer; two recent examples are that of Adl et al., 2012,[62] which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015,[63] covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives.[citation needed]

Application

Biological taxonomy is a sub-discipline of biology, and is generally practiced by biologists known as "taxonomists", though enthusiastic naturalists are also frequently involved in the publication of new taxa. The work carried out by taxonomists is crucial for the understanding of biology in general. Two fields of applied biology in which taxonomic work is of fundamental importance are the studies of biodiversity and conservation.[64] Without a working classification of the organisms in any given area, estimating the amount of diversity present is unrealistic, making informed conservation decisions impossible.[citation needed]

Classifying organisms

Biological classification is a critical component of the taxonomic process. As a result, it informs the user as to what the relatives of the taxon are hypothesized to be. Biological classification uses taxonomic ranks, including among others (in order from most inclusive to least inclusive): Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.[65][Note 1]

Taxonomic descriptions

 Type specimen for Nepenthes smilesii, a tropical pitcher plant.
Type specimen for Nepenthes smilesii, a tropical pitcher plant.

The "definition" of a taxon is encapsulated by its description or its diagnosis or by both combined. There are no set rules governing the definition of taxa, but the naming and publication of new taxa is governed by sets of rules.[9] In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code).[66] In the fields of botany, phycology, and mycology, the naming of taxa is governed by the International Code of Nomenclature for algae, fungi, and plants (ICN).[67]

The initial description of a taxon involves five main requirements:[68]

  1. The taxon must be given a name based on the 26 letters in the Latin alphabet (a binomial for new species, or uninomial for other ranks).
  2. The name must be unique (i.e. not a homonym).
  3. The description must be based on at least one name-bearing type specimen.
  4. It should include statements about appropriate attributes either to describe (define) the taxon, or to differentiate it from other taxa (the diagnosis, ICZN Code, Article 13.1.1, ICN, Article 38). Both codes deliberately separate defining the content of a taxon (its circumscription) from defining its name.
  5. These first four requirements must be published in a work that is obtainable in numerous identical copies, as a permanent scientific record.

However, often much more information is included, like the geographic range of the taxon, ecological notes, chemistry, behavior, etc. How researchers arrive at their taxa varies: depending on the available data, and resources, methods vary from simple quantitative or qualitative comparisons of striking features, to elaborate computer analyses of large amounts of DNA sequence data.[69]

Author citation

An "authority" may be placed after a scientific name.[70] The authority is the name of the scientist or scientists who first validly published the name.[70] For example, in 1758 Linnaeus gave the Asian elephant the scientific name Elephas maximus, so the name is sometimes written as "Elephas maximus Linnaeus, 1758".[71] The names of authors are frequently abbreviated: the abbreviation L., for Linnaeus, is commonly used. In botany, there is, in fact, a regulated list of standard abbreviations (see list of botanists by author abbreviation).[72] The system for assigning authorities differs slightly between botany and zoology.[9] However, it is standard that if a species' name or placement has been changed since the original description, the original authority's name is placed in parentheses.[73]

Phenetics

In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships.[12] It results in a measure of evolutionary "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by cladistic analyses, as phenetic methods do not distinguish plesiomorphic[clarification needed] from apomorphic traits.[74] However, certain phenetic methods, such as neighbor joining, have found their way into cladistics, as a reasonable approximation of phylogeny when more advanced methods (such as Bayesian inference) are too computationally expensive.[75]

Databases

Modern taxonomy uses database technologies to search and catalogue classifications and their documentation.[76] While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life, which attempts to list every documented species.[77] The catalogue listed 1.64 million species for all kingdoms as of April 2016, claiming coverage of more than three quarters of the estimated species known to modern science.[78]

See also

Notes

  1. ^ This ranking system can be remembered by the mnemonic "Do Kings Play Chess On Fine Glass Sets?"

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Bibliography

External links

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