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Taxonomy (biology)

From Wikipedia, the free encyclopedia

Taxonomy (from Ancient Greek τάξις (taxis), meaning 'arrangement', and -νομία (-nomia), meaning 'method') 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. The principal ranks in modern use are kingdom, phylum, class, order, family, genus and species. The Swedish botanist Carl Linnaeus is regarded as the father of taxonomy, as he developed a system known as Linnaean taxonomy 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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Transcription

This right here is a picture of Carl Linnaeus, and I'm sure I'm mispronouncing the word. He's a Swedish gentleman who lived in the 1700s, and he's known as the father of modern taxonomy. And the word taxonomy, if you just split up into its original root, it really is the science of really classifying things. But when people talk about taxonomy-- and in particular, in Carl Linnaeus' case-- they're talking about the classification of living things, so classifying organisms. And his real innovation-- before he came about, peopled realize that you had species of animals, that lions had certain properties that made them all lions, that they could interbreed and things like that, that monkey or chimpanzees would all interbreed and that would be a separate species and that polar bears were separate species and that humans were a separate species. But what he really brought to the table was he decided, well, let me not just group animals into species. Maybe I can group species into other categories. And that's where we get the genus from. You group similar species into a genus. And then he went even beyond that, because even the idea of grouping things into a genus dated back to the ancient Greeks. He said, well, why don't I group similar genuses together into orders, orders together into classes, and then classes together into kingdoms. So really what he did is he said, well, maybe I can classify-- I can create a tree. I can create a tree of life. I can create a structure so we can really see how far apart any two organisms are, and so that's why he's really the father about modern taxonomy. And he did not have many tools. All he could do was look at his powers of observations and say, OK, those kind of animals, they have fur, or they reproduce in this way. Or they lay eggs, or they don't lay eggs. Or they have spinal columns, or they don't have spinal columns. So that's the best that he could do when he did his taxonomy. But since then, there's obviously been tons of innovations in how we perceive animals, or the natural world, and our tools for studying them. So one thing that he did not know about is evolution-- this idea of common ancestry. And between our understandings of evolution and our ability to look back at the fossil record, that helps us get more precise at figuring out which animals are related to which. We can see, do they have a common ancestor more recent or further back. And what even Charles Darwin didn't have, which we now use as a tool in taxonomy, is the genetic evidence. So now we don't even have to rely on the fossil record. We could look at the DNA of two species that exist today and see how similar is that DNA. And that tells us how recently they branched apart if we were able to find it in the fossil record or how recently in the past did these two species become two different species. Now, with that said, I do want to make this clear. And this is something that I've always had a little bit-- it was fuzzy for me the first time that I was exposed to this idea of taxonomy-- is that taxonomy is as much an art as it's a science. And today, even to this day, people are debating about the best way to classify things and what do you pay attention to. And DNA has been the best tool so far in giving us a more systematic, a more analytical way, of deciding how close two animals are. But to a large degree, a lot of these categories-- deciding where to divide along kingdom, phylum, class, order, family, tribe-- these are somewhat arbitrary. These are just picked based on early taxonomists, including Carl Linnaeus, and saying, well, this looks like a grouping right over here. But they could have grouped at a broader level or a deeper level. So these things right over here are somewhat arbitrary. A more analytical way is just to see how much DNA you have in common and then use that as a measure of how far apart two animals are. Or really, I should say, two species are, because this taxonomy doesn't only apply just to animals. It applies to plants and bacteria and Archaea and all sorts of things, so it's actually a broader thing than just animals. Now, with that out of the way, what I thought would be fun-- just so that we could really get a sense of where modern taxonomy is, where the field that was essentially fathered by Carl Linnaeus, where it is now, how we-- and use that to figure out where we humans fit into the big picture. And obviously, I'm drawing just a small fraction of the universe of the organisms that we even know about right now. But at least it frames the picture in terms of something we understand-- in particular, us. In particular, humans. Now, our species, we call ourselves humans. But we're really Homo sapiens. And the sapiens is the species part, and then Homo is the genus. And what I'm doing right over here is I'm saying, well, if Homo is the genus, what other species were inside of Homo? And the reality is-- or at least as far as we know-- there are no other living species inside of Homo. We probably killed them all off. Or maybe we interbreeded with them somehow, which might have argued that maybe they weren't different species. But more likely, they were competing in the same ecosystems, and they became endangered species very quickly when they competed with our ancestors. But the most recent other species within the genus that we know about are the neanderthals, and the formal term for their species is neanderthalensis. Now, if we go further up the tree of life, further up the taxonomy-- and you'll sometimes see tribe mentioned. Sometimes you won't. And we tend to get a little bit more granular the closer we get to humans. When we go further away in the tree of life, we get a little bit less granular sometimes. But that's not always the case as well. You go a little bit further up, then you get Hominini. And I'm sure I'm mispronouncing some of this as well. But another species that's in Homonini that is not in Homo-- and I'm definitely not listing all of them, and that's why I'm showing all of these other branches over here-- is what we call the common chimpanzee. And their species name is-- their genus is Pan, and their species is troglodytes. So you would refer to them as Pan troglodytes. And that's also another convention that Carl Linnaeus came up with, is that you refer to a particular species by its genus and then its species. And you capitalize the genus, and you lowercase a species. So we're Homo sapiens. This is Homo neanderthalensis. This Pan troglodytes or often referred to as chimpanzees. Now, if you go up one higher level of broadness on this tree of life, you then get to the family. And we are in the family Hominidae, and I'm sure I'm mispronouncing it once again. But just to give you an example, so everything I've listed so far, everything I've talked about so far are within this family. And to show you an animal that is not in this family, you just have to look at the gorilla. And you could call it the Gorillini gorilla, or G gorilla. That's its actual species name. And this family right over here, sometimes the common term is the great apes. Now, you go one further level-- and the whole reason why I'm doing this-- and I'm not by any means being exhaustive about the other species that are in that family, but that are not in our tribe. I'm just trying to give you a picture of-- as we get further and further out, as we get further out of our tribe, our family, our order, we're getting to things where the common ancestry with human goes further and further back in time. The genetic similarities become more and more different. And even just the physical differences, if we look it at a very superficial level, become more and more and more different. So you get to even a broader category. This is where you get to the primates, and this is probably something that you might be somewhat familiar with. And the term primates is generally these animals that look like they either live in trees or a rain forest, or they're a descendant of things that live in trees. So they have these things that they can grasp things with. They're good at climbing, broadly. Not all of them are. Humans are probably the worst primates when it comes to climbing, or one of the worst. But that's the general classification. That's what we generally think of when we think of primates. And if we think of a primate that is not a great ape, you just have to think of a baboon. So this right here is a baboon. It is a primate, but it is not a great ape. It is probably a descendant-- some baboons actually don't live in trees. But all of them are probably a descendant from things that first lived in trees, and that's why their hands and their feet look the way they do. Now you get to even a broader level of classification. You get to the mammals. And once again, probably something you're used to thinking about. Mammals are air-breathing animals, and they tend to have fur or hair. They tend to provide some form of milk for their young. They have active mammary glands. There's other things we can talk about, what makes a mammal. I'm not going to go into the rigorous definition. But just to give you an example of a mammal that is not a primate, I could show you this polar bear right over here. This is a mammal that is not a primate. And I could do other things. I could show you a tiger, or I could show you a giraffe or a horse. And so by no stretch of the imagination am I being comprehensive. But let's keep getting broader. Now let's go to the class-- we're already at the class of Mammalia. Now let's go to the phylum. In phylum, we are-- humans and all mammals, we are in the phylum chordates. And chordates, we're actually in the subphylum, which I didn't write here, vertebrates, which means we have a vertebra. We have a spinal column with a spinal cord in it. Chordates are a little bit more general. Chordates is a phylum where-- kind of the arrangement of where the mouth is, where are the digestive organs, where the anus is, where the spinal column is, where are the brains, where are the eyes, where are the mouth. They're kind of all in the same place. And if you think about it, everything I've listed here kind of has the same general structure. You have a spinal column. You have a brain. You have a mouth. Then the mouth leads to some type digestive column. And at the end of it, you have an anus over there. And you have eyes in front of the brain. And so this is a general way-- and I'm not being very rigorous here, is how you describe a chordate. And to show a chordate that is not a mammal, you would just have to think of a fish or sharks. So this right over here is a non-mammal chordate This is a great white shark over here. Now, let's go even broader. As you'll see, now we're going to things that are very, very not human-like. So you go one step broader. Now we're in Animalia, the kingdom of animals. And this is the broadest category that Carl Linnaeus thought about. Well actually, he did go into trees as well. But when you think of kingdom animals and you think of things that aren't chordates, you start going into things like insects. And you start going into things like jellyfish. If you go even broader, now we're talking about the domain. You go to Eukarya. So these are all organisms that have cells. And inside those cells, they have complex structures. So if you're a Eukarya, you have cells with complex structures. If you're a Prokarya, you don't have complex structures inside your cell. But other Eukarya that are not animals include things like plants. And obviously, I'm giving no justice to this whole branch of the tree of life. It could be just as rich or richer than everything I've drawn over here. This is just a small fraction of the entire tree of life, but let's go even broader than that. So if you go even broader than that, you say, well, what's a kind of life form that isn't Eukarya, that wouldn't have these more complex cell structures, the mitochondria in the cells, the cell nucleuses? Then you just have to think about something like bacteria. And if you want to go even broader, there's things like viruses that you could even debate whether they really even are life, because they are dependent on other life forms for their actual reproduction. But they do have genetic material, like everything else. And that, to me, is kind of a mind-blowing idea. As different as a plant is-- look at a house plant that is in your house right now or the tree when you walk home or bacteria or this jellyfish. There is a commonality in that we all have DNA. And that DNA, for the most part, replicates in a very, very, very, similar way. So it's actually crazy that we actually even are related or that we even do have a common ancestor with some of these things. And then it even begs the question, well, what about things like viruses? Anyway, I'll leave you here. And I really just want to let you know that-- make sure you realize that this is a-- it's definitely worth studying, because we understand where we fit in in the universe of living things. But I also want to let you know that it is a little bit of an art on where you decide where to make these classifications or where you decide to focus on, whether you want to focus on what properties, whether it's how they reproduce or how they feed their young or can they move around or what they breathe or whatever, things like that. Anyway, I'll let you go there.

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.[1] 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[4]
  4. "The science of classification as applied to living organisms, including study of means of formation of species, etc."[5]
  5. "The analysis of an organism's characteristics for the purpose of classification"[6]
  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)[7]

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.[8] For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy:[6]

  • 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.[1][9] The broadest meaning of "taxonomy" is used here. The term itself was introduced in 1813 by de Candolle, in his Théorie élémentaire de la botanique.[10]

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.[11] 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.[12]

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.[13]

… 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.[13]

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 (pp. 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.[14][11] Thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species.[15]

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.[16][17][11] By extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species.[11]

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.[18][19][20]

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.[21] 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]

Bhagavata Purana

In Canto 3, chapter 10 of Bhagavata Purana 6 types of trees are recognised, by name:[22]

  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.[23][24][25] 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.[26] He divided all living things into two groups: plants and animals.[24] 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.[27] 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.[24]

Medieval

Taxonomy in the Middle Ages was largely based on the Aristotelian system,[26] 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,[26] again deriving ultimately from Aristotle. Aristotelian system did not classify plants or fungi, due to the lack of microscope at the time,[25] as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder).[24] This, as well, was taken into consideration in the Great chain of being.[24] 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.[24]

Renaissance and Early Modern

During the Renaissance, the Age of Reason, and the Enlightenment, categorizing organisms became more prevalent,[24] 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".[28] His magnum opus De Plantis came out in 1583, and described more than 1500 plant species.[29][30] Two large plant families that he first recognized are still in use today: the Asteraceae and Brassicaceae.[31] Then in the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works.[25] Arguably his greatest accomplishment was Methodus Plantarum Nova (1682),[32] 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).[33] 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.[21]

The Linnaean era

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

The Swedish botanist Carl Linnaeus (1707–1778)[26] ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735,[34] Species Plantarum in 1753,[35] and Systema Naturae 10th Edition,[36] he revolutionized modern taxonomy. His works implemented a standardized binomial naming system for animal and plant species,[37] 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.[37] Thus the Linnaean system was born, and is still used in essentially the same way today as it was in the 18th century.[37] Currently, plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively).[38] Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar[39]). Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean.[21]

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.[25] 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.[11] 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.[40]

With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent.[41] 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.[42] 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.[43][44] 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.[45] 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.[41] In 1958, Julian Huxley used the term clade.[11] Later, in 1960, Cain and Harrison introduced the term cladistic.[11] The salient feature is arranging taxa in a hierarchical evolutionary tree, ignoring ranks.[41] A taxon is called monophyletic, if it includes all the descendants of an ancestral form.[46][47] Groups that have descendant groups removed from them (e.g. dinosaurs, with birds as offspring group) are termed paraphyletic,[46] while groups representing more than one branch from the tree of life are called polyphyletic.[46][47] The International Code of Phylogenetic Nomenclature or PhyloCode is intended to regulate the formal naming of clades.[48][49] Linnaean ranks will be optional under the PhyloCode, which is intended to coexist with the current, rank-based codes.[49]

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.[50] 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.[51] 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),[50] with the Eukaryota for all organisms whose cells contain a nucleus.[52] A small number of scientists include a sixth kingdom, Archaea, but do not accept the domain method.[50]

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.[53] 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.[54]

Linnaeus
1735[55]
Haeckel
1866[56]
Chatton
1925[57]
Copeland
1938[58]
Whittaker
1969[59]
Woese et al.
1990[60]
Cavalier-Smith
1998[53]
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,[61] which covers eukaryotes only with an emphasis on protists, and Ruggiero et al., 2015,[62] covering both eukaryotes and prokaryotes to the rank of Order, although both exclude fossil representatives.[62]

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.[63] 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.[64][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.[8] In zoology, the nomenclature for the more commonly used ranks (superfamily to subspecies), is regulated by the International Code of Zoological Nomenclature (ICZN Code).[65] 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).[66]

The initial description of a taxon involves five main requirements:[67]

  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.[68]

Author citation

An "authority" may be placed after a scientific name.[69] The authority is the name of the scientist or scientists who first validly published the name.[69] 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".[70] 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).[71] The system for assigning authorities differs slightly between botany and zoology.[8] 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.[72]

Phenetics

In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships.[11] 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.[73] 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.[74]

Databases

Modern taxonomy uses database technologies to search and catalogue classifications and their documentation.[75] While there is no commonly used database, there are comprehensive databases such as the Catalogue of Life, which attempts to list every documented species.[76] 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.[77]

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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