Taxonomy (biology)

From New World Encyclopedia


Basic, common levels of modern classification of biological diversity. Other levels can be used, and there are proposals for higher levels above domain.

In biology, taxonomy is the science of describing, naming, and classifying living and extinct organisms, with groupings based on shared characteristics. (In a wider sense, the term taxonomy is employed relative to the classification of all things, including inanimate objects, places and events, or to the principles underlying the classification of things.) The framework for organizing the world's immense biological diversity has its foundation in the work of Swedish botanist Carl Linnaeus, who developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. The Linnaean system is a robust one that has easily been updated and adapted with the availability of more information. The current Linnaean system has been transformed into a system of modern biological classification intended to reflect the evolutionary relationships among organisms, both extant and extinct.

in biology, organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The addition of minor ranks, such as subfamily and superfamily, adds to the organizational complexity of the system. There are proposals to extend the system to include non-cellular entities (viruses), which are a major source of biological diversity, and to add such major taxonomic ranks as world and empire to accommodate both viruses and the newly uncovered diversity in unicellular eukaryotes.

An important science, taxonomy is basic to all biological disciplines, since each requires the correct names and descriptions of the organisms being studied. However, taxonomy is also dependent on the information provided by other disciplines, such as genetics, physiology, ecology, and anatomy. The term taxonomy is often used interchangeably with systematics, although the terms are variously also seen as sub-areas of the other.

Naming, describing, and classifying living organisms is a natural and integral activity of humans. Without such knowledge, it would be difficult to communicate, let alone indicate to others what plant is poisonous, what plant is edible, and so forth. The book of Genesis in the Bible references the naming of living things as one of the first activities of humanity. Some further feel that, beyond naming and describing, the human mind naturally organizes its knowledge of the world into systems, and taxonomy also satisfies a desire for humans to see their relatedness to other organisms.

In the later decades of the twentieth century, cladistics, an alternate approach to biological classification, has grown from an idea to an all-encompassing program exerting powerful influence in classification and challenging Linnaean conventions of naming.

Taxonomy, systematics, alpha and beta taxonomy: Defining terms

The term taxonomy is derived from the Greek τάξις/taxis ("arrangement" or "order" from the verb tassein, meaning “to classify”) and -νομία/nomos (“law,” "method," or “science,” such as used in “economy”). The term was introduced in 1813 by Augustin Pyramus de Candolle, in his Théorie élémentaire de la botanique (Singh 2004).

For a long time, the term taxonomy was unambiguous and used for the classification of living and once-living organisms, and the principles, rules and procedures employed in such classification. The use of the term in this sense is sometimes referred to as "biological classification" or "scientific classification," and it involves organization of taxonomic units known as "taxa" (singular "taxon")—a taxonomic group of any rank, such as sub-species, species, family, genus, and so on. Beyond classification, the discipline or science of taxonomy historically included the discovering, naming, and describing of organisms.

Over time, however, the word taxonomy has come to add a broader meaning, referring to the classification of things, or the principles underlying the classification. Almost anything may be classified according to some taxonomic scheme, such as stellar and galactic classifications, or classifications of events and places. In this article, the focus is the narrower usage of taxonomy in terms of biology and biological organisms.

Some definitions of taxonomy, in this narrower and original sense, 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 (Judd et al. 2007).
  2. A field of science (and a major component of systematics) that encompasses description, identification, nomenclature, and classification (Simpson 2010).
  3. The science of classification; in biology, the arrangement of organisms into a classification (Kirk et al. 2008).
  4. "The science of classification as applied to living organisms, including the study of means of formation of species, etc." (Wordsworth Dictionary 1988).
  5. "The analysis of an organism's characteristics for the purpose of classification" (Lawrence 2005).
  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) (Wheeler 2004).

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 (Laurin 2023). For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy (Henderson 2005):

  • 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."

In 1970, Michener et al. defined "systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) in relation to one another as follows:

Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific names for organisms, (b) describes them, (c) preserves collections of them, (d) provides classifications for the organisms, keys for their identification, and data on their distributions, (e) investigates their evolutionary histories, and (f) considers their environmental adaptations. This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above.

A whole set of terms including taxonomy, systematic biology, systematics, scientific classification, biological classification, and phylogenetics have at times had overlapping meanings—sometimes the same, sometimes slightly different, but always related and intersecting (Small 1989). However, taxonomy, and in particular alpha taxonomy, is more specifically the identification, description, and naming (i.e., nomenclature) of organisms (Forte 2008), while "classification" focuses on placing organisms within hierarchical groups that show their relationships to other organisms.

In general, the term systematics includes an aspect of phylogenetic analysis (the study of evolutionary relatedness among various groups of organisms). That is, it deals not only with discovering, describing, naming, and classifying living things, but also with investigating the evolutionary relationship between taxa, especially at the higher levels. Thus, according to this perspective, systematics not only includes the traditional activities of taxonomy, but also the investigation of evolutionary relationships, variation, speciation, and so forth. However, as noted above, there remain disagreements on the technical differences between the two terms—taxonomy and systematics—and they are often used interchangeably.

"Alpha taxonomy" is a sub-discipline of taxonomy and is concerned with describing new species, and defining boundaries between species. Activities of alpha taxonomists include finding new species, preparing species descriptions, developing keys for identification, and cataloging the species. While the term alpha taxonomy is primarily used to refer to the discipline of finding, describing, and naming taxa, particularly species, in earlier literature, the term had a different meaning, referring to morphological taxonomy (Rosselló-Mora and Amann 2001). William Bertram Turrill, who introduced the term in a series of papers published in 1935 and 1937, 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 (Turrill 1938). 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 (Steyskal 1965).

"Beta taxonomy" is another sub-discipline and deals with the arrangement of species into a natural system of classification. Ernst Mayr in 1968 defined "beta taxonomy" as the classification of ranks higher than species (Mayr 1968).

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".

Universal codes and scientific nomenclature

Codes have been created to provide a universal and precise system of rules for the taxonomic classification of plants, animals, and bacteria.

  • The International Code of Zoological Nomenclature (ICZN) is a set of rules in zoology to provide the maximum universality and continuity in the naming of animals.
  • The International Code of Nomenclature for Algae, Fungi, and Plants (ICN or ICNafp) is the set of rules and recommendations dealing with the formal botanical names that are given to plants, fungi, and a few other groups of organisms, all those "traditionally treated as algae, fungi, or plants". It was formerly called the International Code of Botanical Nomenclature (ICBN); the name was changed at the International Botanical Congress in Melbourne in July 2011. The current version of the code is the Shenzhen Code adopted by the International Botanical Congress held in Shenzhen, China, in July 2017. Its intent is that each taxonomic group ("taxon", plural "taxa") within its purview has only one correct name, accepted worldwide.
  • The International Code of Nomenclature of Bacteria (ICNB) governs the scientific names for bacteria.

The following basic rules apply to all three codes (UH 2024):

  • Binomial name. Organisms are identified by their binomial name, comprised of the genus and species names (eg, brook trout's scientific name is Salvelinus fontinalis).
  • Capitalization and italicization. The genus name is always capitalized, while the species name is not. Both genus and species names are always either italicized or underlined.
  • Abbreviation. One can abbreviate genus names by their first letter, but species names cannot be abbreviated (eg. brook trout, Salvelinus fontinalis, can be written as S. fontinalis).
  • References to unknown species. Unknown species can be listed with the abbreviation sp. This sp. is not italicized. For example, Danio is a genus of small freshwater fish. Should a new species be discovered, it could be listed as Danio sp.
  • References to multiple species in a genus. To refer in general to multiple species within the same genus, one could use the genus name followed by the abbreviation spp, such as a Danio spp. to refer to a group of freshwater fish in the genus Danio. The abbreviation spp. is not italicized.

Most of the binomial names are Latin terms, but some are Greek, and some are derived from the names of their discovers or other personalities. A new species of pacu (a freshwater fish) was recently named Myloplus sauron, with the sauron given because a stripe on its side reminded the researchers of the eye of Sauron, referencing the dark lord Sauron in J.R.R. Tolkien's epic novel Lord of the Rings.

Classifying organisms: Taxonomic rank

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, the relative level of a group of organisms (a taxon) in an ancestral or hereditary hierarchy. A common system of biological classification (taxonomy) consists of species, genus, family, order, class, phylum, kingdom, and domain.

The major ranks: domain, kingdom, phylum, class, order, family, genus, and species, applied to the red fox, Vulpes vulpes.

A given rank subsumes less general categories under it, that is, more specific descriptions of life forms. Above it, each rank is classified within more general categories of organisms and groups of organisms related to each other through inheritance of traits or features from common ancestors. The rank of any species and the description of its genus is basic; which means that to identify a particular organism, it is usually not necessary to specify ranks other than these first two (Turland et al. 2018).

Consider a particular species, the red fox, Vulpes vulpes: the specific name or specific epithet vulpes (small v) identifies a particular species in the genus Vulpes (capital V), which comprises all the "true" foxes. Their close relatives are all in the family Canidae, which includes dogs, wolves, jackals, and all foxes; the next higher major rank, the order Carnivora, includes caniforms (bears, seals, weasels, skunks, raccoons, and all those mentioned above), and feliforms (cats, civets, hyenas, mongooses). Carnivorans are one group of the hairy, warm-blooded, nursing members of the class Mammalia, which are classified among animals with notochords in the phylum Chordata, and with them among all animals in the kingdom Animalia. Finally, at the highest rank all of these are grouped together with all other organisms possessing cell nuclei in the domain Eukarya.

Main ranks

In his landmark publications, such as the Systema Naturae, Carl Linnaeus utilized the ranks of kingdom, class, order, genus, species, and one rank below species. However, the Linnaean Natural System is a flexible one, and today there are seven main taxonomic ranks: kingdom, phylum or division, class, order, family, genus, and species. In addition, domain (proposed by Carl Woese et al. 1990) is now widely used as a fundamental rank, although it has not been canonized by any of the international taxonomic committee/nomenclature codes (van der Gulik et al. 2023), and is a synonym for dominion, introduced by Moore in 1974 (Moore 1974). More recently, van der Gulik et al. (2023) proposed to extend the Linnaean system to include the named rank of world (Latin alternative mundus) to include non-cellular entities (viruses) and empire (or imperium) to better delineate the diversity within unicellular eukaryotes. [Empire had also been proposed by Mayr (1998) and Woese (1998) as an alternative name for domain.]

Main taxonomic ranks
Latin English
regio domain
regnum kingdom
phylum phylum (in zoology) / division (in botany)
classis class
ordo order
familia family
genus genus
species species

A taxon is usually assigned a rank when it is given its formal name. The basic ranks are species and genus. When an organism is given a species name it is assigned to a genus, and the genus name is part of the species name.

Domain and Kingdom systems

At the top of the typical taxonomic classification of organisms, one can find either Domain or Kingdom.

For two centuries, from the mid-eighteenth century until the mid-twentieth century, organisms were generally considered to belong to one of two kingdoms, Plantae (plants, including bacteria) or Animalia (animals, including protozoa). Linnaeus used this division as the top rank, dividing the physical world into the vegetable, animal, and mineral kingdoms. This system of dividing living organisms into two kingdoms, as proposed by Carolus Linnaeus in the mid-eighteenth century, had obvious difficulties, including the problem of placing fungi, protists, and prokaryotes. There are single-celled organisms that fall between the two categories, such as Euglena, that can photosynthesize food from sunlight and, yet, feed by consuming organic matter.

As advances in microscopy made the classification of microorganisms possible, the number of kingdoms increased, five- and six-kingdom systems being the most common.

In 1969, American ecologist Robert H. Whittaker proposed a system with five kingdoms: Monera (prokaryotes—bacteria and blue-green algae), Protista (unicellular, multicellular, and colonial protists), Fungi, Plantae, and Animalia. This system was widely used for three decades but is largely abandoned today (van der Gulik 2023).

Domains are a relatively new grouping. First proposed in 1977, and elaborated on by Woese et al. in 1990, Carl Woese's three-domain system was not generally accepted until later. Also called a "Superregnum" or "Superkingdom," one of the reasons this top-level grouping was advanced was because research revealed the unique nature of anaerobic bacteria (called Archaeobacteria, or simply Archaea). These "living fossils" are genetically and metabolically very different from oxygen-breathing organisms. 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), with the Eukaryota for all organisms whose cells contain a nucleus (Cracraft and Donaghue 2004). Thus, in the three-domain system, the three groupings are: Archaea; Bacteria; and Eukaryota, emphasizing the separation of prokaryotes into two groups, the Bacteria (originally labeled Eubacteria) and the Archaea (originally labeled Archaebacteria).

In some classifications, authorities keep the kingdom as the higher-level classification, rather than domain, but recognize a sixth kingdom, the Archaebacteria or Archaea.

In summary, today there are several competing top classifications of life. Among these are:

Linnaeus
1735
2 kingdoms
Haeckel
1866
3 kingdoms
Chatton
1937
2 empires
Copeland
1956
4 kingdoms
Whittaker
1969
5 kingdoms
Woese et al.
1977
6 kingdoms
Woese et al.
1990
3 domains
(not treated) Protista Prokaryota Monera Monera Eubacteria Bacteria
Archaebacteria Archaea
Eukaryota Protista Protista Protista Eukarya
Vegetabilia Plantae Fungi Fungi
Plantae Plantae Plantae
Animalia Animalia Animalia Animalia Animalia

Ranks in zoology

The International Code of Zoological Nomenclature defines rank as: "The level, for nomenclatural purposes, of a taxon in a taxonomic hierarchy (e.g. all families are for nomenclatural purposes at the same rank, which lies between superfamily and subfamily)." There are definitions of the following taxonomic ranks in this code: superfamily, family, subfamily, tribe, subtribe, genus, subgenus, species, subspecies (ICZN 1999).

The International Code of Zoological Nomenclature divides names into "family-group names", "genus-group names" and "species-group names." The Code explicitly mentions the following ranks for these categories (ICZN 1999):

  • Family-groups
    • Superfamily (-oidea)
    • Family (-idae)
    • Subfamily (-inae)
    • Tribe (-ini)
    • Subtribe (-ina)
  • Genus-groups
  • Species-groups

At higher ranks (family and above) a lower level may be denoted by adding the prefix "infra", meaning lower, to the rank. For example, infraorder (below suborder) or infrafamily (below subfamily).

Ranks in botany

Botanical ranks categorize organisms based on their relationships. They start with Kingdom, then move to Division (or Phylum), Class, Order, Family, Genus, and Species. Each rank reflects shared characteristics and evolutionary history. Understanding these ranks aids in taxonomy and studying biodiversity. The International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code)—referenced here as ICN and cited as Turland et al. 2018—governs the naming.

Ranks in ICN (Turland et al. 2018).
Rank Type Suffix
kingdom (regnum) primary N/A
subregnum further N/A
division (divisio)
phylum (phylum)
primary ‑phyta
-mycota (fungi)
subdivisio or subphylum further ‑phytina
-mycotina (fungi)
class (classis) primary ‑opsida (plant)
‑phyceae (algae)
-mycetes (fungi)
subclassis further ‑idae (plant)
‑phycidae (algae)
-mycetidae (fungi)
order (ordo) primary -ales
subordo further -ineae
family (familia) primary -aceae
subfamilia further ‑oideae
tribe (tribus) secondary -eae
subtribus further ‑inae
genus (genus) primary N/A
subgenus further N/A
section (sectio) secondary N/A
subsectio further N/A
series (series) secondary N/A
subseries further N/A
species (species) primary N/A
subspecies further N/A
variety (varietas) secondary N/A
subvarietas further N/A
form (forma) secondary N/A
subforma further N/A

There are definitions of the following taxonomic categories in the International Code of Nomenclature for Cultivated Plants: cultivar group, cultivar, grex.

Examples of classifications

The usual classifications of five representative species follow: the fruit fly so familiar in genetics laboratories (Drosophila melanogaster); humans (Homo sapiens); the peas used by Gregor Mendel in his discovery of genetics (Pisum sativum); the fly agaric mushroom Amanita muscaria; and the bacterium Escherichia coli. The eight major ranks are given in bold; a selection of minor ranks is given as well.

Rank Fruit fly Human Pea Fly Agaric E. coli
Domain Eukarya Eukarya Eukarya Eukarya Bacteria
Kingdom Animalia Animalia Plantae Fungi Monera
Phylum or Division Arthropoda Chordata Magnoliophyta Basidiomycota Eubacteria
Subphylum or subdivision Hexapoda Vertebrata Magnoliophytina Hymenomycotina
Class Insecta Mammalia Magnoliopsida Homobasidiomycetae Proteobacteria
Subclass Pterygota Placentalia Magnoliidae Hymenomycetes
Order Diptera Primates Fabales Agaricales Enterobacteriales
Suborder Brachycera Haplorrhini Fabineae Agaricineae
Family Drosophilidae Hominidae Fabaceae Amanitaceae Enterobacteriaceae
Subfamily Drosophilinae Homininae Faboideae Amanitoideae
Genus Drosophila Homo Pisum Amanita Escherichia
Species D. melanogaster H. sapiens P. sativum A. muscaria E. coli

Notes:

  • Botanists and mycologists use systematic naming conventions for taxa higher than genus by combining the Latin stem of the type genus for that taxon with a standard ending characteristic of the particular rank. (See below for a list of standard endings.) For example, the rose family Rosaceae is named after the stem "Ros-" of the type genus Rosa plus the standard ending "-aceae" for a family.
  • Zoologists use similar conventions for higher taxa, but only up to the rank of superfamily.
  • Higher taxa and especially intermediate taxa are prone to revision as new information about relationships is discovered. For example, the traditional classification of primates (class Mammalia—subclass Theria—infraclass Eutheria—order Primates) is challenged by new classifications such as McKenna and Bell (class Mammalia—subclass Theriformes— infraclass Holotheria—order Primates). These differences arise because there are only a small number of ranks available and a large number of proposed branching points in the fossil record.
  • Within species, further units may be recognized. Animals may be classified into subspecies (for example, Homo sapiens sapiens, modern humans). Plants may be classified into subspecies (for example, Pisum sativum subsp. sativum, the garden pea) or varieties (for example, Pisum sativum var. macrocarpon, snow pea), with cultivated plants getting a cultivar name (for example, Pisum sativum var. macrocarpon "Snowbird"). Bacteria may be classified by strains (for example Escherichia coli O157:H7, a strain that can cause food poisoning).

Group suffixes

Taxa above the genus level are often given names derived from the Latin (or Latinized) stem of the type genus, plus a standard suffix. The suffixes used to form these names depend on the kingdom, and sometimes the phylum and class, as set out in the table below.

Rank Plants Algae Fungi Animals
Division/Phylum -phyta -mycota
Subdivision/Subphylum -phytina -mycotina
Class -opsida -phyceae -mycetes
Subclass -idae -phycidae -mycetidae
Superorder -anae
Order -ales
Suborder -ineae
Infraorder -aria
Superfamily -acea -oidea
Family -aceae -idae
Subfamily -oideae -inae
Tribe -eae -ini
Subtribe -inae -ina

Notes

  • The stem of a word may not be straightforward to deduce from the nominative form as it appears in the name of the genus. For example, Latin "homo" (human) has stem "homin-", thus Hominidae, not "Homidae".
  • For animals, there are standard suffixes for taxa only up to the rank of superfamily (ICZN article 27.2).

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.
The same relationship, expressed as a cladogram typical for cladistics

A pattern of groups nested within groups was specified by Linnaeus' classifications of plants and animals, and these patterns began to be represented as dendrograms (diagrams representing by trees) of the animal and plant kingdoms toward the end of the 18th century, well before Charles Darwin's On the Origin of Species was published. The pattern of the "Natural System" did not entail a generating process, such as evolution, but may have implied it, inspiring early transmutationist thinkers. Among early works exploring the idea of a transmutation of species were Zoonomia in 1796 by Erasmus Darwin (Charles Darwin's grandfather), and Jean-Baptiste Lamarck's Philosophie zoologique of 1809. The idea was popularized in the Anglophone world by the speculative but widely read '[Vestiges of the Natural History of Creation, published anonymously by Robert Chambers in 1844 (Secord 2000).

With Darwin's theory, a general acceptance quickly appeared that a classification should reflect the Darwinian principle of common descent. Tree of life (science)|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 (Black 2010). 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 (Huxley 1877). 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 (Rudwick 1985). 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 (Paterlini 2007).

The cladistic method has emerged since the 1960s. In 1958, Julian Huxley used the term clade. Later, in 1960, Cain and Harrison introduced the term cladistic. The salient feature is arranging taxa in a hierarchical evolutionary tree, with the desideratum that all named taxa are monophyletic. A taxon is called monophyletic if it includes all the descendants of an ancestral form (Taylor 2003). Groups that have descendant groups removed from them are termed paraphyletic, while groups representing more than one branch from the tree of life are called polyphyletic (Taylor 2003). Monophyletic groups are recognized and diagnosed on the basis of synapomorphies, shared derived character states (Brower and Schuh 2021).

Cladistics

Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms worms or fishes were used within a strict cladistic framework, these terms would include humans.

As a hypothesis, a clade can be rejected only if some groupings were explicitly excluded. It may then be found that the excluded group did actually descend from the last common ancestor of the group, and thus emerged within the group. ("Evolved from" is misleading, because in cladistics all descendants stay in the ancestral group). To keep only valid clades, upon finding that the group is paraphyletic this way, either such excluded groups should be granted to the clade, or the group should be abolished (Hickman 2014).

Branches down to the divergence to the next significant (e.g. extant) sister are considered stem-groupings of the clade, but in principle each level stands on its own, to be assigned a unique name. For a fully bifurcated tree, adding a group to a tree also adds an additional (named) clade, and a new level on that branch. Specifically, also extinct groups are always put on a side-branch, not distinguishing whether an actual ancestor of other groupings was found.

Cladistics has become a commonly used method to classify organisms (UCMP 2005). To a certain extent, cladistic classifications are compatible with traditional Linnaean taxonomy and the codes of zoological and botanical nomenclature (Schuh 2003). But cladistics findings also are posing a difficulty for taxonomy, where the rank and (genus-)naming of established groupings may turn out to be inconsistent. An alternative system of nomenclature, the International Code of Phylogenetic Nomenclature or PhyloCode has been proposed, which regulates the formal naming of clades (Queiroz and de Cantino 2020, Laurin 2023). Linnaean ranks are optional and have no formal standing under the PhyloCode, which is intended to coexist with the current, rank-based codes (Queiroz and de Cantino 2020). While popularity of phylogenetic nomenclature has grown steadily in the last few decades (Laurin 2023), it remains to be seen whether a majority of systematists will eventually adopt the PhyloCode or continue using the current systems of nomenclature that have been employed—and modified, but arguably not as much as some systematists wish (Dubois 2007; Dubois et al. 2019)—for over 250 years.

Van der Gulik et al. (2023) state the the strong evidence that eukaryotes arose from a merger of an Asgard archaeon and a alpha-proteobacterium represents a unique "and in our minds, insurmountable challenge to strictly cladistic taxonomy."

Phenetics

A comparison of phylogenetic and phenetic (character-based) concepts

In phenetics, also known as taximetrics, or numerical taxonomy, organisms are classified based on overall similarity, regardless of their phylogeny or evolutionary relationships (Jain). It results in a measure of hypergeometric "distance" between taxa. Phenetic methods have become relatively rare in modern times, largely superseded by cladistic analyses, as phenetic methods do not distinguish shared ancestral (or plesiomorphic) traits from shared derived (or apomorphic) traits. However, certain phenetic methods, such as neighbor joining, have persisted, as rapid estimators of relationships when more advanced methods (such as Bayesian inference) are too computationally expensive (McDonald 2008).

Historical developments

Classification of organisms is a natural activity of humans and may be the oldest science, as humans needed to classify plants as edible or poisonous, snakes and other animals as dangerous or harmless, and so forth.

While some descriptions of taxonomic history date taxonomy to ancient civilizations, a truly scientific attempt to classify organisms did not occur until the 18th century, with the possible exception of Aristotle, whose works hint at a taxonomy (Voultsiadou and Vafidis 2007; Voutsiadou et al. 2017). 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 for plants (Linnaeus's 1735 classification of animals was entitled "Systema Naturae" ("the System of Nature"), implying that he, at least, believed that it was more than an "artificial system").

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 classifications described empirical patterns and were pre-evolutionary in thinking.

The publication of Charles Darwin's On the Origin of Species (1859) led to a new explanation for classifications, 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 cladistic methodology in the 1970s led to classifications based on the sole criterion of monophyly, supported by the presence of synapomorphies. Since then, the evidentiary basis has been expanded with data from molecular genetics that for the most part complements traditional morphology (Datta 1988).

Pre-Linnaean

Early taxonomists

Naming and classifying human surroundings likely began with the onset of language. Distinguishing poisonous plants from edible plants is integral to the survival of human communities. Medicinal plant illustrations show up in Egyptian wall paintings from around 1500 B.C.E., indicating that the uses of different species were understood and that a basic taxonomy was in place (Manktelow 2010).

Ancient times

Description of rare animals (写生珍禽图), by Song dynasty painter Huang Quan (903–965)

Organisms were first classified by Aristotle (Greece, 384–322 B.C.E.) during his stay on the Island of Lesbos (Mayr 1982; Cain 2024). 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. He divided all living things into two groups: plants and animals. 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 sharks and cetaceans, are commonly used (Leroi 2014; von Lieven and Humar 2008; Laurin and Humar 2022). His student Theophrastus (Greece, 370–285 B.C.E.) carried on this tradition, mentioning some 500 plants and their uses in his Historia Plantarum. Several plant genera can be traced back to Theophrastus, such as Cornus, Crocus, and Narcissus.

Medieval

Taxonomy in the Middle Ages was largely based on the Aristotelian system, with additions concerning the philosophical and existential order of creatures. The Aristotelian system did not classify plants or fungi, due to the lack of microscopes at the time (Cain 2024), as his ideas were based on arranging the complete world in a single continuum, as per the scala naturae (the Natural Ladder).Advances were made by scholars such as Procopius, Timotheus of Gaza, Demetrios Pepagomenos, and Thomas Aquinas.

Renaissance and early modern

During the Renaissance and the Age of Enlightenment, categorizing organisms became more prevalent, 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" (Britannica 2024). His magnum opus De Plantis libri XVI came out in 1583, and has been described as the "first textbook of botany" (Britannica 2024); it described more than 1500 plant species (Cesalpino and Marescotti 1583; Britannica 2024). Two large plant families that he first recognized are in use: the Asteraceae and Brassicaceae (Jaime 2010).

In the 17th century John Ray (England, 1627–1705) wrote many important taxonomic works (Cain 2024). Arguably his greatest accomplishment was Methodus Plantarum Nova (1682), 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). 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 (Manktelow 2010).

Linnaean era

Title page of Systema Naturae, Leiden, 1735

The Swedish botanist Carl Linnaeus (1707–1778) ushered in a new era of taxonomy. With his major works Systema Naturae 1st Edition in 1735, Species Plantarum in 1753, and Systema Naturae 10th Edition, he revolutionized modern taxonomy. Van der Gulik et al. (2023) state "the publication of Systema Naturae by Carl Linnaeus in 1735 . . . had an enormous impact on the development of biology as a scientific discipline, reminiscent of the impact on the physical sciences of the advent of Philosophiæ Naturalis Principia Mathematica by Isaac Newton in 1687."

Linnaeus is well known for his introduction of the method still used to formulate the scientific name of every species. Before Linnaeus, long, many-worded names had been used, but as these names gave a description of the species, they were not fixed. By consistently using a two-word Latin name—the genus name followed by the specific epithet—Linnaeus separated nomenclature from taxonomy. This convention for naming species is referred to as binomial nomenclature. His implementation of a standardized binomial naming system for animal and plant species proved to be an elegant solution to a chaotic and disorganized taxonomic literature.

Linnaeus 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.

Plant and animal taxonomists regard Linnaeus' work as the "starting point" for valid names (at 1753 and 1758 respectively) (Donk 1957). Van der Gulik et al. (2023) reiterate this point: "two of his works, the first edition of the Species Plantarum (Linnaeus, 1753) for plants and the 10th edition of the Systema Naturae (Linnaeus,, 1758) are accepted as part of the starting points of nomenclature." Names published before these dates are referred to as "pre-Linnaean", and not considered valid (with the exception of spiders published in Svenska Spindlar. Even taxonomic names published by Linnaeus himself before these dates are considered pre-Linnaean (Manktelow 2010). Hull (1988) notes that Linnaeus consciously based his system of nomenclature and classification on what he knew of Aristotle.

The digital era of taxonomy

Modern taxonomy is heavily influenced by technology such as DNA sequencing, bioinformatics, databases, and imaging.

Classification after Linnaeus

Some major developments in the system of taxonomy since Linnaeus were the development of different ranks for organisms and codes for nomenclature (see Domain and Kingdom systems, and Universal Codes above), and the inclusion of Darwinian concepts in taxonomy.

According to Hull (1988), "in its heyday, biological systematics was the queen of the sciences, rivaling physics." Lindroth (1983) referenced it as the "most lovable of the sciences." But at the time of Darwin, taxonomy was not held in such high regard as it was earlier. It gained new prominence with the publication of Darwin's The Origin of Species, and particularly since the Modern Synthesis. Since then, although there have been, and continue to be, debates in the scientific community over the usefulness of phylogeny in biological classification, it is generally accepted by taxonomists today that classification of organisms should reflect or represent phylogeny, via the Darwinian principle of common descent.

A vertical orientation yields a cladogram reminiscent of a tree.

Taxonomy remains a dynamic science, with developing trends, diversity of opinions, and clashing doctrines. Two of these competing groups that formed in the 1950s and 1960s were the pheneticists and cladists.

Begun in the 1950s, the pheneticists prioritized quantitative or numerical analysis and the recognition of similar characteristics among organisms over the alternative of speculating about process and making classifications based on evolutionary descent or phylogeny.

Cladistic taxonomy or cladism groups organisms by evolutionary relationships, and arranges taxa in an evolutionary tree. Most modern systems of biological classification are based on cladistic analysis. Cladistics is the most prominent of several taxonomic systems, which also include approaches that tend to rely on key characters (such as the traditional approach of evolutionary systematics, as advocated by G. G. Simpson and E. Mayr). Willi Hennig (1913-1976) is widely regarded as the founder of cladistics.

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