Palæos:		Glossary
Phylogeny		Glossary

Phylogeny and Systematics : Glossary

16S ribosomal RNA (or 16S rRNA) is a component of the 30S subunit of prokaryotic ribosomes. It is 1,542 nucleotides in length. Multiple sequences of 16S rRNA can exist within a single bacterium. The 16SrRNA gene is used for phylogenetic studies as it is highly conserved between different species of bacteria and archaea. Carl Woese pioneered this use of 16S rRNA. In addition to these, mitochondrial and chloroplastic rRNA are also amplified. (Wikipedia)

A.

Adams consensus: in cladistic analysis, a type of consensus method that uses the idea that a tree should be thought of as a "set of leaf subset nestings" rather than as a "set of clusters." A group nests within a larger group if the most recent common ancestor of the smaller group is a descendant of the most recent common ancestor of the larger group (from the PAUPDISPLAY Manual). This preserves all nested clades common to a set of source trees (Bininda-Emonds, 2004 - glossary) Adams consensus trees are designed to find the maximum number of components for a given set of cladograms by placing conflicting taxa at the most resolved node common to all the trees. (Forey et al 1992 pp.79-80). Only can be used for rooted trees. Usually preserves more structure than the strict methods, but may show clades in the consensus tree that do not occur in any of the trees in the set, which makes interpretation rather difficult. (from the PAUPDISPLAY Manual)

Advanced: see derived

Algorithm: In mathematics and computer science, an effective method (a procedure that reduces the solution of some class of problems to a series of rote steps that give a specific and correct answer) expressed as a finite list of well-defined instructions for calculating a function. Algorithms are used for calculation, data processing, and automated reasoning. (Wikipedia

Alpha taxonomy: is the science of finding, describing and naming species of living or fossil organisms. The term "alpha" refers to alpha taxonomy being the first and most basic step in taxonomy. This science is supported by institutions holding collections of these organisms, with relevant data, carefully curated: such institutes include natural history museums, herbaria and botanical gardens. (Wikipedia)

Ancestor: in this context, an organism, or more correctly a population, lineage, or species, that through evolution gives rise to one or more descendants that generally belong to a distinct taxon or species to itself. The identification of ancestors and descendants is a central aspect of evolutionary systematics. In contrast, cladistics denies it is ever possible to know an ancestor (unless one can actually observe evolution in a laboratory). "No matter how well we understand our group, its taxonomy, paleontology and anatomy, we can never know if one taxon is ancestral to another" (Paraphyly Watch blog - Transitional Fossils, Microbes & Patrocladistics). See also Ancestral group, common ancestor. (MAK)

Ancestral group: I decided to adapt this phrase to refer to any supra-specific taxon or evolutionary grade which gives rise to another group. Examples include pelycosaurs, thecodonts, and condylarths. Ancestral groups are central to evolutionary systematics and often included in spindle diagrams. cladistics denies the validity of ancestral groups (see paraphyly) (MAK)

Apomorphy and Synapomorphy: In cladistics, an apomorphy is a unique derived or specialized character trait found in a particular taxon, which is also possessed by a common ancestor. character.

"A trait which characterizes an ancestral species and its descendants. This is an evolutionary novelty for the group. These are evidence for the existence of a group. Put another way, attributes shared in common are taken to indicate a shared evolutionary history.

A novel evolutionary trait that is unique to a particular species and all its descendants and which can be used as a defining character for a species or group in phylogenetic terms. Hence, the possession of feathers is unique to birds and defines all members of the class Aves. An apomorphy that is restricted to a single species is termed an autapomorphy. It alone cannot provide any information about the phylogenetic relations of that species, although it can indicate the degree of divergence of a species from its nearest relatives. An example is speech, which is found solely in humans (Homo sapiens) and not in other primates. An apomorphy that is shared by two or more species or groups is termed a synapomorphy. Such traits define the strictly monophyletic groups, or clades, which are the basis of cladistic classification systems (see cladistics). Compare plesiomorphy."

A Dictionary of Biology, Oxford University Press, © Market House Books Ltd 2000

In phylogenetic nomeclature, an apomorphy-based clade is a clade the members of which are defined through their possession of that particular trait. Contrast with autapomorphy, an apomorphy found only in a single taxon and of no phylogenetic (cladistic) value.

Art: in this context I don't mean the Renaissance masters, or the French impressionists, but the role of subjective assesment and intuition in science, a heresy for the advocates of neo-pragmatism and exterme empiricism, but unavoidable if we are to understand something as subtle and complex as the history and nature of life on Earth. I very much like Mike Taylor's comments here on the "How to choose between specific and generic separation" in a Sauropod Vertebra Picture of the Week posting.

"At this point, I am reminded of when I used to be on a mailing list for wannabe writers...the best advice I saw on that list was from Jane MacDonald: My personal advice is don't overdo, or underdo, anything in your writing. Do it exactly right. That's my attitude to drawing genus boundaries. It is, frankly, an art; and there are no substitutes for taste, experience, judgement, familiarity with the group in question and all those other touchy-feely qualities that uber-cladists would love to find a way to abolish if they could. But they can't. There is no algorithm for this. I also think of an observation by computer scientist Bjarne Stroustrup, the inventor of the C++ programming language: "Design and programming are human activities; forget that and all is lost." The same is true of palaeontology. (And of, well, everything.)"

Artefact: not an ancient extraterrestrial or interdimensional device of great power, but, in the more mundane phylogenetic systematics and phylogenomic context, a false signal resulting in a distorted phylogenetic view of the group being studied. Examples include Long Branch Attraction and Heterotachy. See also Garbage in, garbage out.

Ascii Phylogenetic Tree: As here defined, an Ascii phylogeny, or more correctly an Ascii Phylogenetic Tree, is a dendrogram or tree diagram which uses ASCII-text format to draw supertrees. Ascii Phylogenetic Trees might also informly be refered to as Ascii Cladograms, but that is inaccurate because cladograms are, pragmatically speaking, not actually phylogenies but branching diagrams depicting patterns of shared similarities (O'Keefe & Sander 1999). The Ascii Phylogenetic Tree format was created by T. Mike Keesey, who used them to show dinosaur phylogentic relationships in the old Dinosauricon. Mikko Haaramo adopted this format, but refined it with the introduction of the grave ( ` ) for the corners, for his own phylogenetic archive. This useful format was then adopted on the Dinosaur Mailing List and by paleo enthusiast webmasters like Jack Conrad (The Vertebrate Phylogeny Pages), Justin S. Tweet (Thescelosaurus!), DinosØMP (The Dinosauria), and Toby White and myself (Kheper palaeo and Vertebrate Notes, and finally Palaeos com, here). The format has now become pretty standard in any paleo geek text-based phylogenetic diagram. (MAK)

Autapomorphy: a character traitunique to a particular unique to a particular taxon; Because autapomorphies do not provide information about the organism's phylogenetic relationships to other taxa, they are of no use in cladistics. However they still provide useful non-phylogenetic information about the species in question. Compare with apomorphy, plesiomorphy, homology, homoplasy.

B.

Basal: Preferred cladistic substitute for "primitive", as it is felt the latter may carry false connotations of inferiority or a lack of complexity. In cladograms, basal taxa are those terminal taxa that first diverged from the root. The term basal is only be correctly applied to clades (species or higher groups) of organisms, not to individual traits possessed by the organisms. (MAK, Wikipedia)

Basal node: the node or base of the cladogram, representing the hypothetical common ancestor of the entire clade (however if the common ancestor or something like it is known, then it is shown as a terminal taxon, see basal taxon. See graphic (MAK)

Basal taxon: general term in phylogenetic systematics for any terminal taxa that lie at the base of a cladogram, i.e. they are connected by, or else close to, the basal node, and their sister group is the sub-clade that constitutes the rest of the cladogram. Equivalent to primitive or ancestral (these terms not being used in cladistics). Included under or partially equivalent to stem group. (MAK)

Bayesian inference a method of statistical inference, used fror example in cladistics algorithms, in which some kinds of evidence or observations are used to calculate the probability that a hypothesis may be true, or else to update its previously calculated probability

Binomial nomenclature: Linnaean universal standard of biological scientific notation, according to which every species is given a distinct two-part name. The first part, think of it as like the surname, is the genus, which is capitalised, the second part the species, written completely in lower case, is like the given name. Both names are by convention written in italics (or if that is not possible, underlined, or if even that is not possible say with ascii text, then there is an underscore character before and after the name, _like this_). So in the case of Tyrannosaurus rex, Tyrannosaurus is the genus (capital "T"), and rex (small "r") the species. Finally, the name of the discoverer of the species is added (if the species has since been given a new genus the discoverer's name is placed in brackets) along with the year of publication of the scientific paper describing that particular species. Hence (etc). This usage is not mandatory in popular and semi-technical books, but is when decsribing or listing species in a technical journal or a Museum. The species name can also be abbreviated by only using the first letter of the genus and a period, after which comes the species name. the species name on its own can be written as T. rex (but never "T-rex", it's not a car!). Any student of natural histiory will be familiar with this approach. I have noticed however a tendency among paleontologists to give every new discovery a new genus as well as a new species, leading to an over-excess of monotypal genera (each genus only having one species). This was and is exacerbated by the cladistic revolution, where even species previously placed in a genus are moved to their own genus, especially if precise phylogenetic relationship is uncertain (which it almost always is in these cases) only adding to the multiplication of names (Paleo artist and author Greg Paul at one time (Predatory Dinosaurs of the World, 1988) went in the opposite direction, lumping species from even fairly distant genera together; e.g. most dromanosaurids became Velociraptor, although his more recent work Field Guid to Dinosaurs (2010) provides a nice middle of the road balance). There is also a move among proponents of phylogenetic nomenclature and the phylocode to abandon the binomial altogether, and emphasise only the phylogenetic relationships (which wouldn't necessarily be evident from the name alone). This would actually only be a small step when considering vertebrate paleontology alone in view of the above mentioned tendency (but not for example Pleistocene mammals which have a very good fossil record!), but would be a nightmare if cataloging or referencing all of the other millions of named and described species. However it is probably unlikely that the phylocode will become a majority position any time soon. (MAK)

C.

Character, Character State: any recognizable trait, feature, or property of an organism, used to reconstruct phylogenies. Characters may be morphological, behavioral, physiological, or molecular. In cladistics, the character is thought to be derived and vary from a corresponding feature in a common ancestor of the organisms being studied. (modified from PBS evolution Glossary and UCMP Understanding Evolution Glossary, also definitions from Sereno, 2007)

Character State: the mutually exclusive conditions of a character. (one of the possible alternative conditions of the character). For example, "present" and "absent" are two states of the character "hair" in mammals. Together, characters and character states compose what are termed character statements. (modified from PBS evolution Glossary and UCMP Understanding Evolution Glossary, also definitions from Sereno, 2007)

Character state change: change of the form or state of a character in the course of evolution.

Character optimization, character mapping: interpreting characters on a phylogenetic tree in order to reconstruct ancestral character states

Chronogram: phylogenetic tree that explicitly represents evolutionary time through its branch lengths.. (Wikipedia)

Chronospecies: One or more species which continually changes from an ancestral form along an evolutionary scale. This sequence of alterations eventually produces a population which is physically, morphologically, and/or genetically distinct from the original ancestors. Throughout this change, there is only one species in the lineage at any point in time, as opposed to cases where divergent evolution produces contemporary species with a common ancestor. Relies on an extensive fossil record, since morphological changes accumulate over time and two very different organisms could be connected by a series of intermediaries. The related term paleospecies indicates an extinct species only identified with fossil material. To avoid unnecssary multiplication of terminology (and paleontology-neontological distinctions) these terms are here synonymised. For example, changes in the Permian lepospondyl amphibian Diplocaulus over time may imply a chronospecies (= paleospecies) (MAK, Wikipedia)

Clade: term coined by Julian Huxley, in terms of evolutionary branching and ancestry, to refer to the set of all organisms descended from a particular ancestor. In cladistics, a clade is a monophyletic group of organisms that includes all the descendants of a common ancestor as well as that ancestor itself. For example, birds, dinosaurs, pterosaurs (flying reptiles), crocodiles and their extinct relatives all form the clade Archosauria. In phenotype-based Linnaean and evolutionary systematics, clades are not always suitable as units of classification, as the crown portion of a clade may be very different from its base (compare a pelycosaur reptile to a eutherian mamal for example). The phylocode attempts to formalise phylogenetic systematic taxonomy based on the use of clades. Contrast grade. (MAK)

Cladistic species concept: based on cladism, this is a definition of a species as a lineage of populations between two phylogenetic branch points (or speciation events). But because most speciation is through budding rather than cladogenesis, this definition is either problematic, or needs to be modified. Compare with biological species concept, ecological species concept, phenetic species concept, and recognition species concept. (Fossil Mall glossary, MAK)

Cladogram by Paul Olsen (original url), showing four species (human, turle, lizard and bird) and three clades, each defined buy its own synapomorphies. , according to their synapomorphies (shared unique characteristics). Most cladograms involve many hundreds of characteristics

Cladistics: Rigorous methodology first developed by Wili Hennig, which attempts to use a rigorously logical approach to reconstruct phylogeny. The results of cladistic analyses are often represented in the form of a branching diagram, called a cladogram. As with Linnaean classification, cladistics provides a nested hierarchy where an organism is assigned a series of names that more and more specifically locate and define it within the hierarchy. However, unlike Linnaean classification, phylogenetic classification only allows monophyletic clades, excludes both paraphyletic and polyphyletic groups. It also does not assign ranks (e.g. class, phylum) to the hierarchical levels. It is held by cladists that taxa (if recognized) must always correspond to clades, united by apomorphies (derived traits) which are discovered by a cladistic analysis. In contrast to evolutionary systematics, phylogenetic systematics collects character data only from the taxa being studied, and does not consider the inferred characters of ancestors, or the transformation from one species to another. More recently, cladistics uses computation and statistical procedures such as Bayesian analysis and Maximum Likelihood.

There are basically two philosophical schools of interpretation in cladistics: (a) Phylogenetic Systematics (also known as Hennegian, Numerical or Process Cladism ), and (b) Pattern or Transformed cladism (these latter two are usually synonymised, although Ebach et al 2008 refers to these as distinct), although the arguments between rival schools in the 1980s are long gone, and cladists today generally combine both interpretations.

Even so, cladistics would have remained a purely neontological approach, were it not for the pioneering efforts of vertebrate paleontologists like Jacques Gauthier (Gauthier 1986), Eugene Gaffney, Susan Evans, Michael Benton, and others, what began as an obscure alternative to phenetics and evolutionary systematics came to be the defining paradigm for understanding the evolution of life (first vertebrate, than the tree of life in general), and of great appeal to paleo geeks everywhere. And at the same time, the availability of cheap, powerful computers to run cladistic analyses means that cladistics has really taken off on the last decade, even if these new cladograms aren't excatly the same as the earlier, 1980s/90s vintage, hand-coded ones. Even so, there is something very cool about being able to construct a geneological tree of the evolution of a particular group, or all life on Earth, using empirical, repeatabl;e, scientific methodology. Even if the cladograms for the same groups differ in details (or funsdamental topology) because of differently weighted characters and differently included taxa.

I have noticed also that there seems to be no love lost between cladists and evolutionary systematists (the latter being the "old school") . So on the one hand cladistics has been criticised by many big name evolutionists, beginning with Mayr, (who coined the term cladistics for this school because he disliked it; the name was then taken onboard by pattern cladists and became an established term), and carrying through to Richard Dawkins and Thomas Cavelier-Smith. Criticisms include both excessive formalism, neo-pragmatic rejection of evolutionary realism, and refusal to consider ancestors and ancestral ("paraphyletic") groups. Evolutionary systematics in turn is attacked by cladists for excessive subjectivity, lack of easy repeatability, and attachment to paraphyletic taxa (e.g. paraphyly watch). However (again this is just my impression), the current tendency in phylogenetic systematics, at least on the popular level, seems to be towards a compromise approach, which recognises transitional and ancestral forms that strict cladism rejects.

A few random links: Phylogenetics Primer - Douglas Theobald, (recommended), Introduction to Cladistics - UCMP, also really good, Am I a pattern or transformed cladist? (mail list anecdote on phenetics and cladists); Peter Forey - Cladistics for Palaeontologists (pretty technical). (MAK) More

Cladogram: A dichotomous phylogenetic tree that branches repeatedly, suggesting a classification of organisms based on the sequence in which evolutionary branches arise; a nested diagram of synapomorphies indicating relations between groups; each point of branching represents divergence from a common ancestor. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms. The characteristics used to create a cladogram can be roughly categorized as either morphological (synapsid skull, warm blooded, notochord, unicellular, etc.) or molecular (DNA, RNA, or other genetic information). Prior to the advent of DNA sequencing, all cladistic analysis used morphological data. As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to reconstruct phylogenies. Ideally, morphological, molecular, and possibly other phylogenies should be combined into an analysis of total evidence: All have different intrinsic sources of error. For example, character convergence (homoplasy) is much more common in morphological data than in molecular sequence data, but character reversions that are unrecognizable as such are more common in the latter (see long branch attraction). Morphological homoplasies can usually be recognized as such if character states are defined with enough attention to detail. The researcher must decide which character states were present before the last common ancestor of the species group (plesiomorphies) and which were present in the last common ancestor (synapomorphies) and does so by comparison to one or more outgroups. The choice of an outgroup is a crucial step in cladistic analysis because different outgroups can produce trees with profoundly different topologies. Note that only synapomorphies are of use in characterizing clades (Wikipedia). Contrary to popular belief, cladogram nodes do not represent actual ancestral taxa. Were an actual ancestor to be included it would ideally appear (if the cladogram is correct in this regard) as the sister taxon of the sub-clade that includes all its descendants. (MAK)

There are several algorithms available to identify the "best" cladogram. Most algorithms use a metric (a mathematical function which defines a distance between elements of a set) to measure how consistent a candidate cladogram is with the data. Most cladogram algorithms use the mathematical techniques of optimization (choosing the best element from some set of available alternatives) and minimization. In general, cladogram generation algorithms must be implemented as computer programs, although some algorithms can be performed manually when the data sets are trivial (for example, just a few species and a couple of characteristics). Algorithms include least squares (minimising the sum of the squares of the errors made in solving every single equation), neighbor-joining, parsimony, maximum likelihood, and Bayesian inference. Some are useful only when the characteristic data are molecular (DNA, RNA); others only when the characteristic data are morphological, others again can be used when the characteristic data includes both molecular and morphological data. (Wikipedia.

In recent years, cladograms have tended to become bigger and more complex. Cladograms can be combined to form supertrees, cladograms of cladograms. Powerful computers make it possible to run cladistic analyses using hundreds of traits and taxa, plotted in supermatrixes. These impressive diagrams have a lot of appeal, especially as regards the goal of large scale tree of life phylogeny, although as with anything they are not without their difficulties.

From Wikipedia. Cladogram of stomiid fishes, according to Fink WL. 1985. Phylogenetic interrelationships of the stomiid fishes (Teleostei: Stomiiformes). Miscellaneous Publications of the Museum of Zoology, University of Michigan 171:1-127. The resolved cladograms of this topology have a length of 496 and consistency index of .494, without the seventy-eight generic apomorphies. With generic apormorphies included, the length is 574, the consistency index is .563. A-D show alternative resolved cladograrns for Malacosteus-Pachystomias-Aristostomias-Photostomias group. For character conventions, see Fink (1985). Diagram and text by Filip em. The letters A to Y represent nodes, the names at the right of the diagram genera.

Class: In the Linnaean classification the taxonomic rank between phylum and order, used to define major sub-group within a phylum. Classes are used in the taxonomic series of evolutionary systematics but are not used in cladistic analysis., Classes are often paraphyletic. This is shown by the spindle diagram showing the evolution of the vertebrates, where only five out of nine classes are holophyletic clades. However this is due to the fact that cladistics uses the species as its basic reference point, whereas evolutionary systematics tends to use families, orders, classes, and phyla. (MAK) more

Coalescent Theory: A method for comparison of gene sequences in populations to find the most likely common ancestor sequence. (W. R. Elsberry - talk.origins)

Common ancestor: The ancestral species that gave rise to two or more descendant lineages, and thus represents the ancestor they have in common. The idea of a common ancestor is central to evolutionary thinking from Darwin onwards. In the Modern Synthesis' Evolutionary Systematics the common ancestor is usually shown as the most suitable fossil form at the base of a lineage, where it may or (more likely given the small number of species known from those which actually lived in past ages) or may not be an actual ancestor, more often it is a sort of grand-uncle rather than grandfather). Nevertheless, some idea of a general common ancestor can be had. In an attempt to establish greater rigour and precision, Cladistic phylogeny defines the most recent common ancestor as the originator of a clade; in other words the first species or organism to possess the unique attributes of that clade. Contrary to popular opinion, cladograms do not actually show the common ancestor; in this context, see basal taxon, hypothetical common_ancestor. See also non-missing link. (MAK)

Computational phylogenetics: the application of computational algorithms, methods and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. A central element in modern cladistics. (MAK, Wikipedia)

Consensus: in cladistics, a consensus tree is the agreement between two or more trees (see diagram at right). Obviously there are many different possible soultions, as well as different methodologies. Some consensus methods include strict, majority rule, semi-strict, Nelson, and Adams consensus.

Graphic: A Consensus Cladogram, from How We Look at the Relationships of Taxa

Consistency index (CI): In cladistics, the measure of the parsimony fit of a character to a tree, or of the average fit of all characters to a tree. Varies from 1.0 (perfect fit) to a value asymptotically approaching zero (poorest fit). It is inflated by autapomorphies which can only take the value 1.0; thus a totally uninformative data set (consisting only of autapomorphies) could return a CI equal to 1.0. Compare retention index. (Michael D. Crisp - Introductory glossary of cladistic terms). The per-character consistency index (ci) is defined as m/s, where m is the minimum possible number of character changes (steps) on any tree, and s is the actual number of steps on the current tree. This index hence varies from one (no homoplasy) and down towards zero (a lot of homoplasy). The ensemble consistency index CI is a similar index summed over all characters. (Øyvind Hammer - PAST - Paleontological Statistics Software)

Crown group: in cladistics, a group consisting of living representatives, their ancestors back to the most recent common ancestor of that group, and all of that ancestor's descendants. The name was given by Willi Hennig as a way of classifying living organisms relative to extinct ones. Though formulated in the 1970s, it was not commonly used until its reintroduction in the 2000s. The usual definition of a crown group is the smallest monophyletic group, or "clade", to contain the last common ancestor of all extant members, and all of that ancestor's descendants. Extinct side branches on the family tree will still be part of a crown group. For example, if we consider the crown-birds (i.e all extant birds and the rest of the family tree down to their last common ancestor), extinct side branches like the dodo or great auk are still descended from the last common ancestor of all living birds, so falls within the bird crown group. Therefore, this is a purely relative and arbitrary category, as it depends on a particular period in geological or even historical time, and hence is always changing. More precisely, the period of time cladists use as a standard in this context is uniformly the present, which shows a neontological and ultimately even an anthropocentric bias, why should the present moment be any superior from an evolutionary, deep time perspective, other than that is when the scientist doing the systematics is around? But to be truely objective, a theory should not have to depend on human prespectives. Regarding the problems of basing crown groups on extant taxa see also Extinct or Extant. An alternative definition does not require all members of a crown group to be extant, only to have resulted from a "major cladogenesis event". The problem is how this is to be defined. These definitions and problems stem from the neontological origins of cladistic methodology. Note, the crown group is shown in pink in the following diagram. See also Stem Group, Pan Group (Modified from Wikipedia)

From Wikipedia. The stem and crown group concept. The two pink groups represent a pair of crown groups, the last common node of which is the basal node. Terminology is from Craske, A. J. and Jefferies, R. P. S. (1989) A new mitrate from the late Ordovician of Norway, and a new approach to subdividing a plesion. Palaeontology 32, 69–99 and Budd, G. E. (2001) Tardigrades as "stem-group" arthropods: the evidence from the Cambrian fauna. Zoologischer Anzeiger 240, 265-279. Diagram and text by Graham Budd. The diagram shown here is revised from the original to clarify that the stem group does not include the basal node (ancestor) of the crown group. text and revision by Peter Coxhead. For explanation of terminology see Wikipedia - Crown Group page.

D.

Daughter group: see Sister group

Dendrogram: Any branching diagram or tree, such as a cladogram. (Michael D. Crisp - Introductory glossary of cladistic terms). Mayr & Bock 2002 use the rather different definition of an evolutionary systematics tree, when they contrast the "Hennigian cladogram" with the "Darwinian dendrogram". The wikipedia page gives another definition again: "a tree diagram frequently used to illustrate the arrangement of the clusters produced by hierarchical clustering. Dendrograms are often used in computational biology to illustrate the clustering of genes or samples." (Wikipedia). (MAK)

Derived: same as apomorphy; a derived character / trait is inferred to be a modified version of a more primitive condition of that character and therefore inferred to have arisen later in the evolution of the clade

Descendent: in this context, a population, lineage, or species, that arises through evolution from an ancestor (an earlier species or taxon). Where a number of descendants share the same ancestor (cladogenesis), the ancestor is called a common ancestor. (MAK)

Distance: phylogenetic or evolutionary divergence. Distances are usually expressed pair-wise among terminal taxa, and can be calculated based on a specified evolutionary model; the model specifies the probabilities of character-state changes through evolutionary time. Distances are popular for building phylogenetic trees from molecular sequence data Compare with maximum likelihood, parsimony. (Michael D. Crisp - Introductory glossary of cladistic terms)

E.

Elvis taxon: a taxon which has been misidentified as having re-emerged in the fossil record after a period of presumed extinction, but is not actually a descendant of the original taxon, instead having developed a similar morphology through convergent evolution. This implies the extinction of the original taxon is real, and the two taxa are polyphyletic. The term was coined by D. H. Erwin and M. L. Droser in a 1993 paper to distinguish descendant from non-descendant taxa: "Rather than continue the biblical tradition favored by Jablonski [for Lazarus taxa], we prefer a more topical approach and suggest that such taxa should be known as Elvis taxa, in recognition of the many Elvis impersonators who have appeared since the death of The King." Lobothyris subgregaria, a brachiopod from the early Jurassic period, is one example of such a taxon. By contrast, a Lazarus taxon is one which actually is a descendant of the original taxon, and highlights missing fossil records, which may be filled later. A Zombie taxon is a taxon sample that was mobile in the time between its original death and its subsequent discovery in a site of younger classification, like, for example, a trilobite that gets eroded out of its Cambrian-aged limestone matrix, and reworked into Miocene-aged siltstone. (Wikipedia)

Evolutionary classification see Evolutionary systematics

Evolutionary clock see Molecular clock

Evolution of the Horse diagram from Bruce MacFadden, 1985. "Patterns of Phylogeny and Rates of Evolution in Fossil Horses: Hipparions from the Miocene and Pliocene of North America" Paleobiology, Vol. 11, No. 3. (Summer, 1985), pp. 245-257, retrieved from "Laelaps" blog (Brian Switek), The Branching Bush of Horse Evolution

Evolutionary systematics, Evolutionary taxonomy, Evolutionary classification, or Darwinian classification: same as synthetic systematics; a way to determine natural relationships of organisms by studying a group in detail and comparing degree of similarity. Evolutionary systematics does not have an explicit methodology, but rather relies on the expertise of authorities very familiar with the group in question. This type of taxonomy tends to consider supra-specific taxa rather than single species, so that groups of species give rise to new groups. The concept found its current form in the modern evolutionary synthesis of the early 1940s and stems specially from the work of George Gaylord Simpson and Ernst Mayr. In this school of thought, classification reflects both phylogenetic relatedness as well as morphological disparity (overall similarity). The origin of a major new trait or apomorphy (e.g., flowers in angiosperms, endothermy and lactation in mammals) results in the formation of a new "natural group" of the same Linnaean rank as the "natural" group from which it arose (in these examples gymnosperms and reptiles respectively).

Evolutionary systematics remained the standard paradigm in paleontology and evolution until the 1980s, when it was supplanted by phenetics which in turn was replaced, as was evolutionary systematics, by phylogenetic systematics.

Both Evolutionary systematics and Phylogenetic systematics (Cladistics) use evolution trees, but differ radically in how the tree is drawn. Where each taxon must consist of a single hypothetical ancestor and all its descendants, phylogeny in evolutionary taxonomy allows for groups to be excluded from their parent taxa (e.g. dinosaurs are not considered to include birds, but to have given rise to them). It assumes that ancestor-descendant relationships can be inferred from nodes on phylogenetic trees and considers paraphyletic groups to be natural and discoverable, and at times designated as ancestors (Mayr 1942). Also includes the default "It doesn't really matter" school of classification (Felsenstein 2003).

Evolutionary systematics often use spindle diagrams that map taxonomic diversity (usually mapped on the horizontal axis) against geological time (mapped vertically, in keeping with the geologists' tendency to equate time with geological strata and hence verticality). The classic example of this, frequently reproduced in old textbooks, is the famous evolution of the horse; see right for a recent version. Evolutionary systematics also makes possible the organising of organisms into groups (taxa) and hierarchies of such groups (classification systems), in contrast to cladistic, which instead identifies clades and produces cladograms; so both systems can be correct by their own standards.

Evolutionary systematics has been criticised for being based on imprecise, subjective, and complicated sets of rules that only scientists with experience working with their organisms were able to use. This resulting phylogenies became impossible to reproduce other than by the specialists themselves. This practice of systematics was more of an art than a quantitative science, and led to a call for more repeatable and objective methods. Whether this is still the case is upto the reader to decide. In any case, despite the predominance of cladistics and molecular phylogeny (although this started out as a distinct field, the two converging through the use of computers to create elaborate dendrgrams), a number of scientists, such as Richard Dawkins, Tom Cavalier-Smith and the authors of Res Botanica, support evolutionary taxonomy. Contemporary evolutionary systematists are included in Ebach et al 2008's typology of phylogenetic schools, under the rather amorphous category "gradists"

Compare to phenetics/numerical taxonomy and phylogenetic systematics/cladistics

(MAK, Wikipedia, Grant, 2003, IAB blog, quoting Ebach et al 2008, UCMP Virtual Paleobotanical Laboratory) more

Extant Phylogenetic Bracket; Phylogenetic bracketing: In 1999, Larry Witmer described how unknown character states for fossil taxa are reconstructed with respect to extant taxa called the extant phylogenetic bracket (EPB). This is the bracket formed on either side of the taxon with the missing information by extant taxa in which the character state is known. Using it, we can make three types of inference, listed in order of decreasing confidence. Consider the distribution of a soft-tissue character - the four-chambered heart - among three fossil reptiles:

• Type I Inference: Tyrannosaurus is bracketed by birds and crocodilians, both of which have the derived character. With no contrary positive evidence, the simplest assumption is that Tyrannosaurus had it also.
• Type II Inference: The basal archosauriform Euparkeria is bracketed by crocodilians and squamates. Crocs have the derived character, squamates don't. Thus, we are much less secure than above in inferring it in Euparkeria , but presence of some sort of hard tissue correlate of that trait might increase our confidence.
• Type III Inference: The basal diapsid Petrolacosaurus is bracketed by squamates and turtles, neither of which have the derived character. Our confidence in its presence in the extinct form is very low. We would need strong positive fossil evidence to argue for its presence.

Text and diagram by John Merck

F.

Family: In the Linnaean classification the taxonomic rank between order and genus (or order and tribe, tribe being a mostly botanical rank between family and genus), used to define group of related organisms. Used in evolutionary systematics but not cladistics. (MAK) more

Five Kingdoms: evolutionary classification of life developed by Robert Whittaker and Lynn Margulis, according to which organisms are divided into five kingdoms: Monera, Protist, Plants, Fungi, and Animals. more

G.

"Garbage in, garbage out": self-explanatory phrase borrowed from computer programming. If the characters used in phylogenomics (and cladistic analysis in general) are unreliable, even the most accurate tree reconstruction method can fail. Therefore, methods focusing on the most reliable characters have been developed in order to reduce the impact of inconsistency. (Delsuc et al 2005)

Genealogy: (from Greek genea, "generation"; and logos, "knowledge") the study of families and the tracing of their lineages and history. Genealogists use oral traditions, historical records, genetic analysis, and other records to obtain information about a family and to demonstrate kinship and pedigrees of its members. The results are often displayed in charts or written as narratives. In evolutionary thought, such as cladistics, the term can be used as a poetic synsonym for phylogeny. (from Wikipedia)

Genetic Algorithms: Computational systems based upon an implementation of natural selection as an algorithm for classification or optimization. (W. R. Elsberry - talk.origins)

Genus: In the Linnaean classification the taxonomic rank between family or tribe and species, and used to define group of closely related organisms that differ in only very minor ways. In the Linnaean system of binomial nomenclature, the genus is written in italics, with a capital letter, in front of the species name, or on its own. e.g. with Tyrannosaurus rex, the name Tyrannosaurus is the genus, and T. rex (no hyphen!) is the species. Used in evolutionary systematics; in cladistic classification every genus is only allowed two species (because of excessive formalism regarding cladogensis), and Linnaean genera are always oversplit and new names created, resulting in much taxonomic confusion (for example in paleontology the established dinosaur genus Iguanodon has been split into about a dozen different monospecific genera (link). See also the discussion at Sauropod Vertebra Picture of the Week. It may be that the phylocode will discard binomial nomenclature altogether (although there is obvious resistance to this) . (MAK) more

Ghost lineage: in cladistics, a phylogenetic lineage that is inferred to exist, for example by matching a cladogram against geological time, but is not known from the fossil record.

When we know that two taxa are sister taxa (descendants of the same recent common ancestor), we in essence know that they originated at the same point in geologic time - the time of their last common ancestor and the speciation event that gave rise to them. Say we know one of these taxa from 100 million year old rocks, and the other from 90 million year old rocks. Even without seeing a fossil, we know that the second group must have representatives dating back at least to 100 million years, simply from its sister-taxon relationship with the other. A lineage like this, whose existence can be inferred from the cladogram, but which is not known from actual fossils is called a ghost lineage. The examination of ghost lineages should allow biostratigraphers to refine their models of the stratigraphic ages of organisms.

- John Merck

Links: UCMP, evowiki, Dave Hone's Archosaur Musings (MAK)

Grade, Evolutionary: a paraphyletic group showing similarities in morphology, ecology or life history; a horizontal taxon consisting of transitional forms between two other taxa. (MAK). In alpha taxonomy, a grade refers to a taxon united by a level of morphological and/or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit (Wikipedia)

Gradist: see evolutionary systematics

Great chain of being: term coined by historian of ideas Arthur O. Lovejoy for the historical idea that all beings constitute a continuous series of forms an unbroken gradation from the Absolute (later, God) down through intermediate spiritual and material stages to formless matter. The premise was developed by Greek philosophers such as Plato (transcendent ideas), Aristotle (scala naturae), and Plotinus. In the Middle Ages it was the basis for both scholastic theology (ranking all of creation from dirt through to humans to angels) and feudal social stratification; it formed a centeral element in the Elizabethan understanding of the world still evident in Shakespeare's plays. It continued through 17th, 18th and 19th century Europe and North America, in an understanding of the universe as the highest good, complete and full (Lovejoy refers to this belief as "the Principle of Plenitude") in which every species of being has its perfect place and no species can ever become extinct (to do so would result in a gap in God's creation), and understanding this marmonious linear order of nature as a product of God's benign creative activity was a meaningful pursuit. From the end of the 18th century, with the "temporalization of the great chain of being" the meme persisted in evolutionary form (now as ascent rather than descent) through 19th century German Idealism and Naturphilosophie. Despite the rise of Darwinian evolution and a branching tree of life, the idea of a single line of ascent continued through mid 19th to early 20th century ideas of sociological evolution and social darwinism, and early to mid 20th century psychology. It even continues in some contemporary approaches such as Integral Theory. (MAK)

H.

Holophyletic, Holophyly: Ashlock 1971 coined the term to resolve the ambiguity between the Haeckelian (evolutionary systematic) and Hennigian (phylogenetic systematic, cladistics) definitions of monophyly, and that usage is followed here. Refers specifically to the definition that a group contains the common ancestor, all organisms descended from the common ancestor, and no other organisms. The term has not gained widespread acceptance in the scientific community, probably because monophyletic is so widely used and has the same meaning. (MAK, Wikipedia

Horizontal classification: as described by Simpson, a taxon based on overall similarity between its members at a particular time. All members share a common ancestry and are therefore monophyletic at that time slice, however, only the memebers extant at that particular time are considered. An evolutionary grade. Evolutionary systematics includes the interplay of both horizontal andvertical classification, whereas cladistics only considers vertical (MAK) More

Hypothetical common ancestor: it is necessary to distinguish between cladistics and evolutionary systematics, as the two tend to confused in a sort of mishmash in the popular imagination and on some wikipedia diagrams. In contrast to the evolution trees (spindle diagrams and so on) that evolutionary taxomists use, cladograms are not intended to portray actual phylogeny. i.e. a cladogram does not have a time axis, and it does not portray ancestors, but only branching patterns, that is, sister relationships between terminal taxa and other nodes. This means that the internal nodes that lie at the base of each nested clade do not represent an actual species which can be described in terms of traits and characters, but rather a hypothetical and abstract representation of the common ancestor of that particular clade. (MAK)

I.

International Code of Zoological Nomenclature: widely accepted convention in zoology that rules the formal scientific naming of organisms treated as animals. The rules principally regulate:

1. how names are correctly established in the frame of binominal nomenclature,
2. which name has to be used in case of conflicts among various names,
3. how names are to be cited in the scientific literature.

The rules and recommendations have one fundamental aim: to provide the maximum universality and continuity in the scientific naming of animals. The code is published by the International Commission on Zoological Nomenclature (ICZN), an organization dedicated to "achieving stability and sense in the scientific naming of animals". The rules in the Code determine what names are valid for any taxon in the family group, genus group, and species group. It has additional (but more limited) provisions on names in higher ranks. Several cladists have argued that the Linnaean based ICZN code needs to be replaced by a new cladistically-based system, the phylocode (Wikipedia)

Intuition: in this context, arriving at a scientific (or any creative) hypothesis through a leap of insight. For example, Einstein discovered Special Relativity by imagining what it would be like to ride on a photon. From another perspective, gut-feelings, hunches, creativity, and more. See also art. In systematics, advocates of Phenetics and Cladistics argue on pragmatic grounds that evolutionary systematics should be rejected because it is too "intuitive", and not sufficently verifiable. However their use of quantative empirical data without intuition meant they were not able to distinguish homology from homoplasy. Hence all science will always include some intuition and subjectivity. (MAK)

J.

Junior synonym: giving a new name to a species, supra-specific taxon, or clade which already has a scientific name. As a standard, the first applied name is the one that is used in biological and paleontological systematics. Junior synonyms are redundant and hence usually rejected in scientific nomenclature; the exception being when the more recent name is so well known that to change it would cause confusion. For example, the first named fossil which can be attributed to Tyrannosaurus rex consists of two partial vertebrae found by Edward Drinker Cope in 1892 and named Manospondylus gigas. It was only later realised that they belong to the same animal. In this case, the newer name, Tyrannosaurus rex (named by Henry Fairfield Osborn in 1905) was retained, and the older one Manospondylus gigas, rejected. (MAK, Wikipedia)

K.

Kingdom: In the Linnaean classification the highest taxonomic rank. Traditionally only included plants and animals; Whittaker-Margulis classification scheme adds three more kingdoms, and other researchers such as Thomas Cavalier-Smith have added additional kingdoms.

L.

Lazarus taxon: a taxon that disappears from one or more periods of the fossil record, only to appear again later. An example is Lazarussuchus, an Oligocene member of a clade of freshwater reptiles (Choristodera) thought to have gone extinct at the end of the Mesozoic. As Lazarussuchus is thought to be outside the clade including other choristoderans, it may indicate a ghost lineage going back to the Late Triassic, a span of over 170 million years. There are also examples of "Burgess Shale type fauna", best known from the Early and Middle Cambrian periods, but which, since 2006, have been found in rocks from the Ordovician, Silurian and Early Devonian periods, in other words up to 100 million years after the Burgess Shale (Kühl et al 2009; Siveteretal07). The term "Lazarus taxon" refers to the account in the Gospel of John, in which Jesus raised Lazarus from the dead. Lazarus taxa are observational artifacts that appear to occur either because of (local) extinction, later resupplied, or as a sampling artifact. If the extinction is conclusively found to be total (global or worldwide) and the supplanting species is not a lookalike (an Elvis species), the observational artifact is overcome. The fossil record is inherently imperfect (only a very small fraction of organisms become fossilized) and contains gaps not necessarily caused by extinction, particularly when the number of individuals in a taxon becomes very low. If these gaps are filled by new fossil discoveries, a taxon will no longer be classified as a Lazarus taxon. A subtle difference is sometimes made between a "living fossil" and a "Lazarus taxon". A Lazarus taxon is a taxon (either one species or a group of species) that suddenly reappears, either in the fossil record or in nature, while a living fossil is a species that (seemingly) hasn't changed during its very long lifetime. Sometimes however, the two are confused or conflated, as with the Coleocanth, which is also called a "living fossil" because it was thought o be extenct for tens of millions of years, but then discovered alive. (modified from Wikipedia)

Length: The length, or number of steps, is the total number of character state changes necessary to explain the relationship of the taxa in a tree. According to the principle of parsimony, the fewer number of character state changes required, the more likely the tree. A tree with a lower length has less homoplasies and so fits the data betterthan a tree with a higher length. The tree with the lowest length assumes fewer homoplasies and hence is more parsimonious, and so represents the hypothesis of taxa relationship that is selected. Lipscom 1998

Linnaean classification: hierarchical taxonomy developed by the 18th century Swedish botanist Carl von Linné, (Linneaus). It was the first systematic classification of life on Earth, in which every species is given it's own binomial designation. So for example anatomically modern human beings are Homo sapiens, genus (the "family name") Homo and species (the specific name) sapiens. In contrast, neanderthal man is Homo neanderthalensis. Linnaean classification provides a nested hierarchy of levels, each with its own specific characteristics. In this way any organism or species is grouped more and more specifically within the hierarchy. The Linnaean system was originally static, being based on creationism. In the 19th century, applied to the evolution of life and the modern synthesis it became evolutionary systematics, and was used to consteruct phylogenetic trees. Still foundational to modern biology, Linnaean classification is in the process of being superseded by phylogeny-based cladistic systematics. Unfortunately, this latter, with its indefinite series of nested clades, lacks the categorical simplicity and ease of use of the old Linnaean system. Some attempts have been made to integrate the two, but the incompatable methodologies mean these have not been very successful. more

Diagram from Gribaldo & Philippe 2002. "The classical view of the universal tree of life, topology inspired from Stetter 1996, mainly based on rRNA comparison. Branches that could be affected by long branch attraction artifacts (e.g., the placement of the root in the bacterial branch or the early emergence of hyperthermophilic taxa amongst bacteria) are given as thick lines."

Long branch attraction (LBA): A phenomenon in molecular phylogenetic analyses, especxially those employing maximum parsimony. Unrelated species or lineages sharing rapid evolutionary rates are artefactually grouped together and hence considered closely related, regardless of their true evolutionary relationships. For example, in DNA sequence-based analyses, the problem arises when sequences from two (or more) lineages evolve rapidly. For example, rRNA evolutionary rates may vary by a factor of 100 among planktonic foraminifers. As there are only four possible nucleotides, when DNA substitution rates are high, the probability that two lineages will evolve the same nucleotide at the same site increases. When this happens, parsimony erroneously interprets this homoplasy as a synapomorphy (i.e., evolving once in the common ancestor of the two lineages). In phylogenies rooted by a distant outgroup, unrelated fast evolving ingroups will emerge independently as the deepest offshoots, being attracted by the long branch of the outgroup. LBA artifact currently represents a major concern to phylogeneticists, as it is believed to affect the position of virtually every deep-branching lineage. As a result, many organismal relationships in the universal tree, shown as bold lines in the diagram on the right, should be regarded as suspect (note: this particular topology has since been corrected by more recent revisions) This problem can be minimized through improved models of sequence evolution and by using methods that correct for multiple substitutions at the same site, through increased or modified taxonomic sampling and by breaking up long branches adding taxa related to those with the long branches or by using alternative slower evolving traits. (Wikipedia, Gribaldo & Philippe 2002, Delsuc et al 2005)

LUCA (Last Universal Common Ancestor). Also Universal Common Ancestor. The postulated most recent common ancestor of every living thing on Earth; the root of the tree of life. According to Carl Woese, horizontal gene transfer between the three domains early in the history of life makes the idea of a single common ancestor meaningless. more

M.

Majority rule consensus: in cladistic analysis, a consensus method that preserves all relationships appearing in 50% of the source trees. This method allows a group to appear in the consensus even if some of the trees in the set contradict it, as long as a majority of the trees (generally half or more) support the grouping. In fully resolved majority rule consensus, these can appear in the consensus solution so long as they do not contradict relationships that occur more frequently. When comparing only two trees, this method is equivalent to the strict consensus method. (Bininda-Emonds, 2004 - glossary, from the PAUPDISPLAY Manual)

Maximum likelihood: In cladistics, one of several criteria that may be optimised in building phylogenetic trees from molecular sequence data. The optimal tree is the one that maximises the statistical likelihood that the specified evolutionary model produced the observed character-state data; the models specify the probabilities of character-state changes through evolutionary time. Compare with distance, parsimony. (Michael D. Crisp - Introductory glossary of cladistic terms)

Molecular clock: the premise that the rate at which mutational changes accumulate is constant over time. The difference between the form of a molecules in two species is then assumed to be proportional to the time since the species diverged from a common ancestor, and molecules can be used to date the tree of life. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism (Adaptationism), with natural selection as the only important cause of evolutionary change. (Wikipedia, etc). Although subject to certain caveats and continuing debate, the notion of the molecular clock has proven to be an important and useful tool in many contexts Searls, 2003 glossary The tendency now is to calibrate the molecular clock by the fossil record (Donoghue & Benton 2007). Earlier problems associated wityh this method for example, the evolution of animal phyla during the Precambrian (early in the Proterozoic (ref), for which there is absolutely no fossil evidence) have since been largely rectified. Even so, it is difficult to believe that the molecular clock rate does not vary greatly at particuylar times, for example accelerating during periods of rapid evolutionary radiation (the Cambrian explosion in this example). In other instances evolution may be more constant, and molecular clocks more reliable. The choice of molecule used may also be significant (ref) (MAK)

Molecular phylogeny, Molecular systematics: Use of molecular data as characters for phylogenetic analyses. That is, the use of the structure of molecules to gain information on an organism's evolutionary relationships. Includes methods based on overall similarity (Phenetics), like electrophoresis, immuno-distance and DNA-DNA-hybridisation, as well as methods that are based on parsimony, like restriction-site-analysis and sequencing (DNA, RNA, and/or protein sequencing). Generally speaking, the more closely related two organisms are, the more similar their gene sequences will be. By statistically comparing the similarities and differences in the sequence between the same gene from various organisms, we can deduce the pattern of how those organisms are related, and shown in a phylogram. Shown on the right is a highly resolved Tree Of Life, based on completely sequenced genomes. Despite the similarities (both involve dichotomous branched trees), these are not cladograms. Over the last decade or so, molecular phylogeny has supplanted cladistic morphological phylogeny as the primary way of understanding the evolution of life on Earth, giving rise to phylogenetics, the synthesis of molecular phylogeny and phylogenetic systematics, leading to the total evidence approach and supermatrix trees. (MAK) More. Criticism.

Monophyletic, Monophyletic group, Monophyly: A confusing term defined differently in evolutionary systematics and cladistics Originally coined by Haeckel to refer to a group of organisms that is descended from its most recent known or inferred common ancestor (Haeckel, 1866). This usage was also retained by Simpson, Mayr (Mayr & Ashlock, 1991), etc. A monophyletic group in this traditional sense of the word may include all or only a part of the descendants of the common ancestor, and the ancestor may be a taxon of various ranks (Grant, 2003). Hennig (1966) restricts "Monophyly" to the only those groups in which no descendent is a part of any other group. Here monophyletic refers to a group containing all the inferred descendants of a common ancestor, i.e. Ashlock's holophyletic group. This is called a clade, and is the only valid taxon recognised. Ashlock 1968, 1971 1974 uses "Monophyly" to include both Holophyly & Paraphyly, and suggests replacing Hennig's redefinition of monophetic with the neologism holophyletic. This suggestion has not widely caught on. Although Hennig's terminology has been criticised by Mayr (Mayr & Bock 2002) and Cavalier-Smith (Cavalier-Smith 2010) among others, it remains the most popularily accepted and indeed currently standard usage in the the scientific community, and for that reason is retained here. (MAK)

Morphology-based phylogeny: Infrequently used term (and mostly by molecular phylogenists) to refer to, yes, you guessed it, phylogeny based on morphology rather than molocules.

N.

Neighbor-joining: a bottom-up clustering method for the creation of phenetic trees (phenograms), created by Naruya Saitou and Masatoshi Nei. Usually used for trees based on DNA or protein sequence data, the algorithm requires knowledge of the distance between each pair of taxa (e.g., species or sequences) in the tree. (Wikipedia

From Wikipedia. This genetic distance map made in 2002 is an estimate of 18 world human groups by a neighbour-joining method based on 23 kinds of genetic information. Public domain diagram by Jason Spatola.

Numerical cladism: see Phylogenetic systematics

Numerical taxonomy: same as phenetics; a method of generating phylogenies that is based on large numbers of quantifiable (measurable) characters which groups organisms with respect to overall similarity (UCMP)

Node: any point in a cladogram where branches diverge or end. In cladistics, Nodes of phylogenetic trees represent taxonomic units. Internal nodes (or branches) refer to hypothetical ancestors whereas terminal nodes (or leaves).External nodes, which are at the end of a each branch represent terminal taxa, generally extant species but where paleontological data is considered they can also include fossil species. Internal nodes are where a single ancestral lineage breaks into two or more descendant lineages. In rooted trees, internal nodes represent hypothetical common ancestors. (Modified from Douglas Theobald's Phylogenetics Primer and UCMP Understanding Evolution Glossary)

O.

Order: In the Linnaean classification the taxonomic rank between class and family, used to define middle-level sub-group. Orders are used in evolutionary systematics but not cladistics. (MAK) more

Overall similarity method by which organisms that share the most similarities are grouped together; characters are not distinguished as to whether they are primitive or derived or whether they are evolutionary meaningful; also see numerical taxonomy (phenetics); contrast with phylogenetic systematics (UCMP)

Outgroup: in cladistics, a taxon that is not part of the clade under consideration, but is including in the analysis in order to provide a baseline. In cladograms, outgroups are shown branching off at the base of the tree. (MAK)

P.

Pan-group, Total group: A crown group and its stem group considered together. The Pan-Aves thus contain the living birds and all (fossil) organisms more closely related to birds than to crocodiles (their closest living relatives). Pan-Mammalia are all mammals and their fossil ancestors down to the phylogenetic split from the remaining amniotes (the Sauropsida). Pan-Mammalia is thus an alternative name for the clade Synapsida. With teh exception of a few taxa, such as turtles, the pan-group approach has not caught on because it results in unnecessary junior synonyms. (Wikipedia)

Paraphyly, Paraphyletic group: neologism coined by Hennig (Hennig 1966) to refer to groups that have a common ancestry but that do not include all descendents (Horandl & Stuessy 2010, p.1642). They constitute one of the two types of monophyletic groups sensu Haeckel ; e.g. protist, reptile (see that entry for diagram), thecodont, condylarth; i.e. an ancestral taxon or evolutionary grade. Constitute "a group of organisms that has descended from a common ancestor but that does not include all descendants from this ancestor. A paraphyletic group of species was holophyletic before a younger derivative species (or derivatives) arose from that group" (Horandl & Stuessy 2010, p.1643). Cladists consider paraphyletic groups invalid (see also following diagram), whereas evolutionary systematics regard them as perfectly acceptable. The reasom for the latter being "there is no paraphyly in a Darwinian classification because the ancestral group stays essentially unchanged, and likewise, because the newly evolved side-branch is considered to have no effect on the nature of the branch from which it arose. Paraphyly is a consequence of the cladistic method of making holophyletic branches the units of their ordering system rather than taxa." Mayr & Bock 2002 p.181-2). Choice of methodology can therefore have profound consequences. "Application or nonapplication of the paraphyly rule can make a large difference in a system. The system can have one arrangement of groups in a taxonomic classification and a different arrangement in its cladistic version because of the paraphyly rule alone." (Grant, 2003 p.1268) In contrast some sites like Paraphyly watch provide a strong cladist critique (MAK) more

Parsimony: Also known as Occam's Razor (after the medieval theologian William of Ockham (c. 1285–1349), who rejected the idea of universals) is the principle that recommends when choosing between two competing hypotheses, that the simplest explanation of the evidence or observation is to be preferred, when the hypotheses are equal in other respects. A central premise in cladistics, where computer algorithms routinely generate huge numbers of cladistic trees. When reconstructing the phylogenetic relationships of a group of species or taxa, the principle of parsimony implies that we should prefer the the branching pattern or phylogeny that requires the fewest number of evolutionary changes (see above diagram). Unfortunately, the picture becomes more complex when homoplasy is taken into account. (MAK)

Use of parsomony in cladistics. It is considered more likely that trait B evolved only once (right hand cladogram) rather than twice (left-hand cladogram). Diagram adapted from here

Pattern cladism, Transformed cladism: Dissenting Cladistic school, distinguished from phylogenetic or process cladism. Ssometimes known as Cladists with a capital C (Williams and Ebach 2006). Transformed cladism is usually included here as well, although following Ebach et al 2008 they are given a separate entry. Founded by Gareth Nelson and Nelson Platnick ("New York Cladists") (Glossary of Phylogenetic Systematics - Günter Bechly although the latter is also associated with transformed cladism Ebach et al 2008.

As with phenetics, character rooting and synapomorphies are not used, although monophyletic groups are acknolwedged. Essentially a reaction to Mayr's evolutionary systematics, Pattern Cladism constructs cladograms the pattern of their characters alone, without any recourse to evolution, through separation of "pattern and process". Unlike phenetics, pattern cladism distinguishes between synapomorphy, homoplasy and symplesiomorphy. But like phenetics, pattern and transformed cladists strove to be as "objective" and non-evolutionary as possible. and rejected the possibility of phylogeny as verifiable fact in favour of a sort of Neo-Kantean pragmatism. For this reason they deny that cladograms actually portray actual phylogenies, instead following the "postmodernist" position of considering evolutionary accounts "Just so" stories. In other words, in contrast to phylogenetic systematics which argues that cladograms actually reflect the evolutionary relationships of species, Pattern Cladism asserted that a cladogram was merely a summary of shared characters, that could at best test a historical reconstruction (The philosophy of classification Pattern cladism and the myth of theory dependence of observation - John Wilkins) But although Pattern cladists purport to classify biological taxa in a way that is theory neutral, but the idea of a theory-neutral science is philosophically problematic (Pearson 2010). Criticised by Richard Dawkins' The Blind Watchmaker, (quotes and comments here, and defense of pattern and transform cladism). Ebach et al 2008 relate Transformed cladism to the works of Colin Patterson (1982) and Platnick (1979) and say that in contrast to pattern cladists who are Non-Hennigian, Transformed cladists are Hennigian and root their trees according to either outgroups, ontogeny or concepts such as set theory.... They opt for a definition of monophyly that does not include the most recent ancestor. They do not reject totally transformation, but they do use a concept of character rooting that is inherent within set theory". It seems however that these differences are mostly minor and the two being more usually synonymised. (MAK, IAB blog)

Phenetic species concept: A definition of a species as a set of organisms that are phenotypically similar to one another. Compare with biological species concept, cladistic species concept, ecological species concept, and recognition species concept. (Fossil Mall glossary) See other species definitions

Phenetics, Phenetic systematics: School of numerical taxonomy developed in the late 1950s by bacteriologist Peter H. Sneath, entomologist Charles D. Michener, and quantitative geneticist Robert R. Sokal, that classifies organisms on the basis of overall morphological or genetic similarity. This mainly involves observable similarities and differences irrespective of whether or not the organisms are related. It involves grouping types together in clusters; types with many close relatives would be in a cluster. The development of Phenetics, which was intended to replace evolutionary systematics, was inspired through the quantitative successes and advances in genetics (e.g. discovery of DNA by Watson & Crick (1953)), chemistry and physics, on the other hand as a reaction to positivism and incorporation of a strictly pragmatic approach, which denies that we can know the thing in itself (hence the rejection of phylogeny and evolution). The availability of computers (at this time still big hulking things) also facilitated and encouraged quantitative data comparisons. This approach classifies organisms on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It stressed the use of many unweighted characters assessed by overall similarity, purging all intuition and subjectivity and striving to be theory neutral, objective, and quantitative, with observation, description and ordering performed as precisely, objectively and repeatably as possible. Hence all evolutionary and phylogenetic interpretations are rejected as too difficult and subjective. It was considered that phylogenetic reconstruction was nearly impossible to know with any degree of certainty, and therefore, if classification were to be scientific, this futile quest should be abandoned. (Stuessy 2009, UCMP)

In the end Phenetics was unsuccessful and eventually abandoned for a number of reasons, including numerous difficulties encountered owing to convergence (homoplasy, as individual characters assumed to be homologous were not carefully analysed), mosaic evolution, and a shortage of diagnostic characters (Mayr & Ashlock 1991, pp. 195–205). For this reason, phenetics was superseded by cladism. 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. (Wikipedia) Also, with the rise of molecular systematics, distance methods, which are basically phenetic methods, have become popular . These are vulnerable to the same problems especially that of homoplasy (Mayr & Bock 2002 p.180).

Phenetic pattern analysis uses numerical methods for taxonomic classification; very similar to Phenetics and generally synonymised.

Phenogram: A branching diagram (tree) showing the phenetic similarity among terminal taxa. Compare cladogram, dendrogram, phylogram. (Michael D. Crisp - Introductory glossary of cladistic terms)

Phenotype: The set of measurable or detectable physical or behavioral features of an individual. The phenotype represents the expression of the genotype of the individual as modified by environmental conditions during the individual's ontogeny. (W. R. Elsberry - talk.origins)

PhyloCode: abbreviation for the International Code of Phylogenetic Nomenclature, a developing draft for a formal set of rules governing phylogenetic nomenclature. Its current version is specifically designed to regulate the naming of clades, leaving the governance of species names up to the rank-based codes. Unlike Linnaean-based nomenclatural codes the PhyloCode does not require the use of ranks, although it does optionally allow their use. Rather than define taxa using a rank (such as genus, family, etc.) and a type specimen or type subtaxon, the content of taxa are delimited using a definition that is based on phylogeny (i.e., ancestry and descent) and uses specifiers (e.g., species, specimens, apomorphies) to indicate actual organisms. The formula of the definition indicates an ancestor. The defined taxon, then, is that ancestor and all of its descendants. Thus, the content of a phylogenetically-defined taxon relies on a phylogenetic hypothesis. In the phylocode, clades may be node-based, stem-based, or apomorphy-based (see diagram at right).

The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and Gauthier, which was foreshadowed by earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree. The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2011, whether the code will be implemented and if so, how widely it will be followed. (Wikipedia)

Phylogenetic bracketing: see Extant Phylogenetic Bracket.

Phylogenetic classification, Phylogenetic nomenclature, Phylogenetic taxonomy: classification and taxonomy based on cladistic (Phylogenetic systematic) principles ("vertical" ancestry, not "horizontal" similarity), proposed as a rank-free alternative to the Linnean system of classification, redefining taxa previously named under evolutionary systematics (e.g. Synapsida), and accepting only monophyletic clades. The goal is to make classification synonymous with phylogeny; i.e. to get rid of similarity altogether. Phylogenetic nomenclature has led to a number of controversial proposals, such as the abandonment of Linnaean binomial nomenclature, the rejection Linnean ranks, and the migration of established names to crown clades (Benton 2007, p.651); e.g. tetrapoda (this last reflecting an emphasis on neontology over paleontology that is still found in cladistics). Despite the logical and theoretical appeal of this approach, there are still problems in applying it in practice (Carlson, 2001, p.1113). See also PhyloCode (MAK)

Phylogenetic systematics: Also known as Hennigian systematics, Numerical cladism, Phylogenetic cladism, and Process cladism, or sometimes just cladistics or phylogeny. Derives from Hennig's work and that of others such as James S. Farris, Walter Fitchand, and Herb Wagner. States that only shared derived characters can provide information about phylogeny . Those taxa that share a greater number of shared features are considered more closely related than those that don't. However, the shared (called characteristics have to be advanced (derived) rather than on primitive. The relationship between them is shown in a branching hierarchical tree called a cladogram. The cladogram is based on the principle that the fewest number of changes to map all the changes of character states is the most likely one; called the principle of parsimony. Only monophyletic (= holophyletic Mayr & Ashlock) groups are recognised. Unlike pattern cladism , which only aims at the calculation of most parsimonious cladograms from large data-sets, phylogenetic systematics also seeks to reconstruct phylogenetic schemes, in which all branching points are convincingly supported by characters. Because there are a number of possible trees, optimization (transformation series) (sensu Farris 1983) and discarding non-monophyletic groups from classification. In the 1980s and 90s phylogenetic systematics has become the dominant paradigm used in biological systematics, supplanting the previous Linnaean-based evolutionary taxonomy in all fields except botany. Together with molecular phylogeny forms the current Phylogenetic paradigm. (MAK, referencing W. R. Elsberry talk.origins via W.J. Hudson; IAB blog, quoting Ebach et al 2008, Lipscom 1998, Günter Bechly, UCMP Understanding Evolution Glossary, and Wikipedia) more

Phylogenetic tree: See Tree

Phylogenetics: (from the Greek phylon, "tribe", and genetikos "relative to birth"). The synthesis of phylogenetic systematics and molecular phylogeny, phylogenetics is the study of evolutionary relatedness among groups of organisms (e.g. species, populations), which is discovered through molecular sequencing data and morphological data matrices. Wikipedia. See also Daniel F. Simola - Molecular Evolution and Phylogeny (pdf) for synoptic overview. More recently, phylogenetics has begun to incorporate other fields such as evo-devo as well (Telford & Budd 2003) which implies this is all leading to a new evolutionary synthesis (replacing the 20th modern synthesis).

Phylogenomics: the intersection between the fields of evolution and genomics. The use of phylogenetic principles to interpret genome data, and better understanding of gene function. One branch of phylogenomics involves the use of these data to reconstruct the evolutionary history of organisms. Another, "Pharmacophylogenomics" is the use of phylogenomics in aid of drug discovery, through improved target selection and validation (Delsuc et al 2005, Searls, 2003, Wikipedia

Phylogeny: term coined by Haeckel (Haeckel 1866): the study of the family history of life, the evolutionary relationships among groups of organisms, often illustrated with a branching diagram called a tree. There are several different forms:

• Haeckelian/evolutionary systematics: phylogeny maps the inferred lines of descent of a group of organisms, in order to reconstruct the common ancestors of that group, map the amount of divergence among the descendants of the common ancestor, and explore the evolutionary history of a group of organisms (Mayr & Bock 2002 p.192).
• Hennigian cladistics or Phylogenetic systematics (Hennig (1950, 1966)) is the analysis of and relationship between monophyly taxa (clades), using shared unique characteristics (synapomorphies).
• Molecular phylogeny is the use of molecular data (derived for example from DNA, RNA, and/or protein sequencing) for phylogenetic analyses. Generally speaking, the more closely related two organisms are, the more similar their gene sequences will be. By comparing the similarities and differences we can deduce the pattern of how those organisms are related.

Other approaches are possible too, for example developmental. In this way, phylogeny is used to understand the evolutionary history of life on Earth. (MAK)

Phylogeography: research field that investigates the principles and processes that govern the geographic distributions of genealogical lineages, especially those within and among closely related species. (Phylogeography)

Phylogram: A phylogenetic tree usually distinguished from a cladogram in that the branch lengths are proportional to the amount of inferred evolutionary change (Michael D. Crisp - Introductory glossary of cladistic terms, Wikipedia)

Phylum: In the Linnaean classification the taxonomic rank between kingdom and class, and hence one of the highest levels of taxonomic classification, used to define major groups of organisms; e.g. molluscs, arthropods, echinoderms, chordates. Phyla can be thought of as groupings of animals based on a shared general body plan. What this means is that despite the seemingly different external appearances of organisms, they can be classified into phyla based on their internal and developmental organizations. Despite their obvious differences, spiders and barnacles both belong to the phylum Arthropoda; but earthworms and tapeworms, although similar in shape, belong to different phyla. Although Linnaean rankings are not used in cladistic analysis, the majority of phyla are still accepted as they constitute monophyletic clades. (There are a few exceptions; e.g. growing consensus on the basis of molecular phylogeny is that Porifera (sponges) constitute an evolutionary grade. The rank of Phylum was not in Linneaus' original classification system, but was coined later by Haeckel. (MAK, Wikipedia)

Plesiomorphy, Plesiomorphic trait: in cladistic analysis, an ancestral or primitivecharacter state present before the last common ancestor of the species group evolved, and hence not unique to the clade in question. Also called a primitive trait

"Features shared more widely than in a group of interest. These are primitive for the group in question and cannot provide evidence for the group. An evolutionary trait that is homologous within a particular group of organisms but is not unique to members of that group (compare apomorphy) and therefore cannot be used as a diagnostic or defining character for the group. For example, vertebrae are found in zebras, cheetahs, and orang-utans, but the common ancestor in which this trait first evolved is so distant that the trait is shared by many other animals. Therefore, possession of vertebrae sheds no light on the phylogenetic relations of these three species."

A Dictionary of Biology, Oxford University Press, © Market House Books Ltd 2000

Polarity: in phylogenetic cladistics this refers to the ordering of a particular character state, determined either independently of tree construction (direct method) or more usually from a rooted tree (indirect method) (Michael D. Crisp - Introductory glossary of cladistic terms) To quote Telford & Budd 2003 p.487: "In order for an analysis to be useful in an evolutionary sense, it needs to be rooted, in other words we need to know the polarity of change of the characters that interest us. If we consider two taxa in isolation (say a lizard and a mouse) that differ in a certain character (e.g. hairless or hairy) how do we know which of the two has the primitive character state and which the derived? ...(T)o determine the direction in which the evolution of this character has proceeded...knowledge of the state of the character in a species that is an outgroup (is needed)...in this case, a frog would be appropriate. As the frog is hairless, parsimony suggests that hairlessness is the primitive character and we can infer from this that hair has evolved in the lineage leading to mice after this lineage had diverged from reptiles." Polarity is one of the ways in which phylogenetic systematics is distinguished from non-phylogenetic ordering systems such as phenetics and pattern cladistics.

Polyphyly, Polyphyletic group: A group that does not share a common ancestor, but is defined on the basis of independently aquired or convergent (non-homologous) character states. Examples for polyphyletic groups would be the old taxon Pachydermata which includes the thick-skinned hippos, rhinos and elephants, or the taxon Haemothermia (endorsed at one time by Lovtrup and Gardiner) for a grouping of haemothermic birds and mammals. Polyphyletic groups are considered invalid by both evolutionary and phylogenetic systematics. (MAK, Glossary of Phylogenetic Systematics - Günter Bechly

Polytomy: in a cladistic phylogeny, a node where more than two lineages descend from a single ancestral lineage. This indicates either that we don't know how the descendent lineages are related or the descendent lineages speciated simultaneously. Where a branching pattern cannot be resolved, the branches in question can be collapsed to show the absence of a hypothesis for the relationships among the lineages that they represent. (UCMP Understanding Evolution Glossary; Keeling & Palmer 2008 p.607 ).

Primitive trait
same as plesiomorphy; acharacter that is present in the common ancestor of a clade; a primitive trait is inferred to be the original character state of that character within the clade under consideration; compare to derived trait (UCMP)

Process cladism see Phylogenetic Systematics.

Q.

R.

Retention index (RI): Similar to the consistency index, but defined so that the highest possible value for any character is 1.0 and the lowest is 0.0; removes bias due to autapomorphies. (Michael D. Crisp - Introductory glossary of cladistic terms). The per-character retention index (ri) is defined as (g-s)/(g-m), where where m is the minimum possible number of character changes (steps) on any tree, s the actual number of steps on the current tree, and g is the maximal number of steps for the character on any cladogram (Farris 1989). The retention index measures the amount of synapomorphy on the tree, and varies from 0 to 1. (Øyvind Hammer - PAST - Paleontological Statistics Software)

Reversal: in cladistics, the loss of a character trait, or more technically, the evolutionary reversion from an apomorphic to a plesiomorphic character state. For example whales in returning to the sea lost their legs and thus reverted to the character state of fish-like ancestors. Compare with homoplasy.

Root: in cladistics, the common ancestor of all taxa represented in a cladogram. The root is often determined using an outgroup taxon to determine the evolution in the taxa of interest (Delsuc et al 2005). See also base node

Rooted tree: A cladogram with a hypothetical ancestor, which equates to the root. When outgroups are used, this is the node that connects the outgroups to the ingroup, and which thus specifies the direction of evolutionary change among the character-states. Contrast with unrooted tree. (Michael D. Crisp - Introductory glossary of cladistic terms)

S.

Scala Naturae "Natural ladder", is a sort of proto-taxonomy first developed by Aristotle, according to which the natural world can be arranged in a single linear series from inanimate matter through plants, invertebrates, higher vertebrates, and finally man. Along with Plato's Principle of Plenitude it led to the idea of the Great chain of being. Scala Naturae and Great Chain of Being remained central ideas in natural philosophy until the mid 19th century.

Semistrict consensus: also called "combinable component" consensus. If a particular grouping in one tree is not contradicted by the other trees, it will be retained in the consensus. When there is a conflict in grouping, semistrict consensus behaves like strict consensus. (from the PAUPDISPLAY Manual)

Sequencing: any of several methods and technologies that are used for determining the order of proteins in a cell, or nucleotide bases (adenine, guanine, cytosine, and thymine) in a molecule of RNA or DNA. An essential element in modern biological systematics (molecular phylogeny). The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of the human genome (the Human Genome Project). Related projects, often by scientific collaboration across continents, have generated the complete sequences of many animal, plant, and microbial genomes. (Wikipedia)

Similarity: the degree to which two or more species resemble or don't resemble each other is one of the two factors that could be considered in any biological classification and taxonomy, the other being phylogeny. Similarity could be the result of common descent and divergence (homology) or convergence (homoplasy). Pre-Darwinian natural philosophy considered only similarity (being unaware of phylogeny), evolutionary systematics gave equal weight to both, phenetics and pattern cladistics rejected phylogeny as impractical and thus revert to similarity only, whilst Hennigian cladistics and phylogenetic nomenclature goes to the other extreme and rejects similarity altogether, emphasising only phylogeny. (MAK)

Sister group: Cladistic term for any of the descendant branches from a node on a cladogram. In a phylogeny, the descendants of an ancestor are called daughters, while the siblings after a speciation event are called sisters (so a descendant is a daughter relative to its ancestor and is a sister relative to its other sibling). Note that if either of the daughters undergoes further speciation then the sister to a particular terminal taxon may actually be a group of terminal taxa. (Michael D. Crisp - Introductory glossary of cladistic terms)

Species:  Highly controversial term given a variety of definitions by biologists. Currently, the Biological Species Concept (BSC) is widely popular: Groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups (Mayr, 1963, Animal Species and Evolution). More (W. R. Elsberry talk.origins via W.J. Hudson) See alsocladistic species concept, ecological species concept, phenetic species concept, and recognition species concept. (Fossil Mall glossary) See other species definitions

The spindle diagram shown on the right is typical of mid 20th century phylogenies. This particular diagram which I found through google image search is from an online Creationist book ( original url). The taxa correspond to orders, subclasses, or classes, in the Linnaean ranking. The caption reads: Fig. 20. Family tree of the vertebrates. On the left is a geological time scale. Phylogenetic origins of various groups of vertebrates. A) Urodela, B) Lepospondylii, C) Apoda, D) Anura, E) Labyrinthodontia, F) Apisidospondylii, G) Chelonia, H) Anapsida, I) Cotylosauria, J) Eurapsida, K) Diapsida, L) Eosuchia, M) Squamata, N) Rhyncocephalia, O) Ornithischia, P)Thecodontia, Q) Synapsida, R) Parapsida, S) Pelycosauria, T) Pterosauria, U) Crocodilia, V) Aves, W) Saurischia, X) Prototheria, Y) Metatheria, Z) Pantotheria, AA) Therapsida, BB) Eutheria, CC) Ichthyosauria. The width of the spindle shows taxonomic diversity, numeric abundance (the abundance of fossils of the group in strata of the particular geologic period), or both; the distinction here being often poorly defined. In an effort to introduce precision, spindle width may be drawn according to the number of genera or families known from a particular time period (see above diagram), but even determin8ing what qualifies as a genus or family can be arbitrary (see splitters versus lumpers). Contrast this diagram with cladistic dendrograms and cladograms which show relationships between individual species, without referencing time, transformation, or lineage (however lineages should ideally emerge as clades or paraphyletic groupings). (MAK)

Spindle diagram: An evolution tree that maps lineage diversity or abundance mapped against geologic time. Spindle diagrams are employed in evolutionary taxonomy, but not phylogenetic systematics. They frequently emphasise ancestral or paraphyletic groups, transitional forms, and transformation of one lineage into another. Note the way the various more recent spindles emerge from earlier lineages.

Stem group: The concept of stem groups was introduced in phylogenetic systematics to cover evolutionary "aunts" and "cousins" of living groups. A crown group is a group of closely-related living animals plus their last common ancestor plus all its descendants. A stem group is a set of offshoots from the lineage at a point earlier than the last common ancestor of the crown group; it is a relative concept, for example tardigrades are living animals which form a crown group in their own right, but Budd (1996) regarded them also as being a stem group relative to the arthropods. Stem group shown in yellow in this diagram. (Wikipedia)

How do we identify ghost lineages and measure their prevalence in a cladogram. All other things being equal, we expect the terminal taxa that branch off of a cladogram first to appear first in the fossil record. When this is true, the cladogram is said to be stratigraphically congruent. Often, cladograms are not stratigraphically congruent. This happens when there are long ghost lineages. - diagram and caption by John Merck

Stratigraphic congruence The degree to which the terminal taxa that branch off of a cladogram match the order with which they first appear in the fossil record. A simple measure of stratigraphic congruence is the Stratigraphic Congruence Index (SCI) of Huelsenbeck (1994) is defined as the proportion of stratigraphically consistent nodes on the cladogram, and varies from 0 to 1. A node is stratigraphically consistent when the oldest first occurrence above the node is the same age or younger than the first occurrence of its sister taxon (node). (Øyvind Hammer - PAST - Paleontological Statistics Software)

Strict consensus: this is the most conservative consensus method used in in cladistic analysis, which only recognises clades that appear in all of the trees. It's advantage is that it only includes data that is totally unambiguous. The disadvantage is that it is thrown off by the slightest difference. For example, two trees may be identical except for the placement of a single sequence, yet their strict consensus tree might be completely unresolved. The resulting is a "star" phylogeny, a broad polytomy with onlty radiating lines, and very little or no resolution or phylogenetic structure. This is shown by the blue cladogram on the right, which is placed next to a more conventional, brabnching phylogeny. (from the PAUPDISPLAY Manual, Forey et al 1992 p.78)

Subspecies: A grouping of organisms less inclusive than a species. The term is usually applied to groups within a species that have distinct forms and live in a restricted area. (UCMP Understanding Evolution Glossary)

Supermatrix: One of the new developments in cladistics that have become possible through cheap and powerful computing, supermatrixes involve simultaneous analysis of all available character data. Rather than separate analyses of data sets and subsequent integration of the resulting trees (supertree), all character data is considered simultaneously to enable incorporation of diverse kinds of data, including characters from fossils, morphology, and molecular phylogeny. (de Queiroz & Gatesy 2007) (MAK)

Supertree: In cladistics, a "supertree" refers to the synthesis of a number of distinct cladograms, combining morphological, molecular, and other data from the different individual phylogenies. Supertrees result from combining many smaller, overlapping phylogenetic trees into a single, more comprehensive tree. They are distinguished from classic consensus techniques in that the source trees need only have overlapping rather than identical taxon sets. Because supertree construction uses other tree topologies rather than the primary data underlying those trees, they can be constructed using all available phylogenetic hypotheses, even those based on incompatible data types, or lacking data entirely. Supertree have produced phylogenies of a number of large taxonomic groups. However supertree strength is also its weakness, and this approach has been harshly criticised by systematists precisely because it only considers the topology of the source trees, effectively discarding primary data. A supertree or quasi-supertree approach is also standard with Ascii phylogenetic trees. Supertree construction is probably as old as the field of systematics itself, and remains our only way of visualizing the Tree of Life as a whole. References: Pisani et al 2002 who give the example of a dinosaur supertree (see diagram, right), Bininda-Emonds, 2004. (MAK)

Supra-specific taxon: a taxon above the species level: anything from subgenus and genus upwards (family, order, etc). Useful for understanding biotic diversity through time and large scale patterns of evolution. Recognised by evolutionary systematics, but not by cladistics. See also rank. (MAK)

Symplesiomorphy A shared plesiomorphic character trait, which is shared between two or more taxa, but which is also shared with other taxa which have an earlier last common ancestor with the taxa under consideration. An example is pharyngeal gill breathing in bony and cartilaginous fishes. The former are more closely related to Tetrapoda (terrestrial vertebrates, which evolved out of a clade of bony fishes) that breathe via their skin or lungs, rather than to the sharks, rays, etc. Their kind of gill respiration is shared by the "fishes" because it was present in their common ancestor and lost in the other living vertebrates. Contrast with apomorphy/synapomorphy. (Wikipedia)

Synapomorphy: an apomorphy shared by (syn-) several taxa, where the trait in question originates in their last common ancestor. Being shared by multiple taxa, synapomorphies can be used to diagnose (describe) a clade (a monophyletic group). Compare with homology. True synapomorphies usually are a given set of terminal groups, shared by two or more terminal taxa, but this is not essential to the concept. Thus, if some descendants of a last common ancestor possess a synapomorphic trait, in the case of reversals it is not strictly necessary that all of its descendants must possess the same trait. Contrast with plesiomorphy and homoplasy, which are shared primitive and shared convergent characteristics also of no phylogenetic value. (based on Wikipedia, Michael D. Crisp - Introductory glossary of cladistic terms)

Systematics, Systematic biology: as defined here, the study of the diversification of life on the planet Earth, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees. Here there are two main paradigms, evolutionary systematics (now rarely used, except for a few eccentrics such as myself) and phylogenetic systematics. Evolutionary systematics interprets Linnaean classification in terms of the modern evolutionary synthesis and provides evolutionary taxonomies above the species level. It maps lineages against a geological time to give a spindle diagram showing diversity or abundance. Cladistic phylogenies (cladograms) are based at the species level and emphasise greater verifiability. They have two components, branching order (showing group relationships) and (in the case of phylograms) branch length (showing amount of evolution). Almost all systematics nowadays is cladistically-derived. Phylogenetic trees of species and higher taxa are used to study the evolution of traits (e.g., anatomical or molecular characteristics) and the distribution of organisms (biogeography).

Systematic biology, taxonomy, and scientific classification are often confused and used interchangeably. However, taxonomy is more specifically the identification, description, and naming (i.e. nomenclature) of organisms, classification focuses on placing organisms within hierarchical groups that show their relationships to other organisms, and systematics alone deals specifically with relationships through time, and can be synonymous with phylogenetics, broadly dealing with the inferred evolutionary hierarchy of organisms. (MAK, Wikipedia)

Systematic paleontology: organising or classifying fossil organisms (paleontology) accordding to the principles of systematic biology (Systematics) (MAK)

T.

Taxon: (plural: taxa) a group of organisms, considered to be a unit, and which generally has been formally named with a scientific (Latin or Greek) proper name and a rank. Defining what belongs or does not belong to such a taxonomic group is done by a taxonomist with the science of taxonomy. It is not uncommon for one taxonomist to disagree with another on what exactly belongs to a taxon, or on what exact criteria should be used for inclusion. Traditionally, a taxon is given a formal or scientific name, which is governed by one of the Nomenclature Codes, which sets out rules to determine which scientific name is correct for that particular grouping. Generally, a good taxon as one that reflects presumptive evolutionary (phylogenetic) relationships, being derived from a common ancestor . Whether or not clades are acceptable as taxons is a matter of dispute; although evolutionary systematists (Mayr & Bock 2002 p.182) deny that they are, whereas cladists have proposed phylogenetic nomenclature and a new phylocode which requires taxa to be monophyletic and rejects Linnaean supra-specific ranks (MAK, Wikipedia)

Taxonomy: the practice and science of classification. Taxonomy uses taxonomic units, known as taxa (singular taxon). In addition, the word is also used as a count noun: a taxonomy, or taxonomic scheme, is a particular classification ("the taxonomy of ..."), arranged in a hierarchical structure. See also Alpha taxonomy , cladistics, Linnaean classification, Systematics (Wikipedia). In biological taxonomy there are, according to Ereshefsky (2000, p. 7) "no fewer than four general schools of taxonomy: evolutionary taxonomy, pheneticism, process cladism, and pattern cladism". Each of those schools have their own view on how to get from the characteristics of an individual organism to a species, and also the meaning of the term species varies between schools of taxonomy. (cited from Birger Hjørland)

Tetrapod: four-legged, land-living vertebrate, or any secondarily limbless (e.g. snakes) or aquatic (e.g. whales) descendants of such. Cladistic terminology disagrees over whether "tetrapod" should be used to include all four-legged animals (stem-based definition) or only those that include the common ancestor of all living tetrapods and its descendants (crown-based definition). More

Terminal, Terminal taxon: Not the end of the evolutionary line, but in phylogenetic systematics formalism, one of the units whose collective phylogeny is reconstructed; shown diagramatically as the undivided tips of a cladistic tree. Terminals may be higher taxa, species, populations, individuals, fossils or even genes. There should be some rational basis for accepting the integrity of each terminal (for the purpose of the analysis), e.g. a monophyletic or diagnosable unit. Despite the claims by some authors, terminals do not need to be monophyletic; in fact, many species-level terminals are unavoidably paraphyletic. However, higher taxa used as terminals should be monophyletic. (Michael D. Crisp - Introductory glossary of cladistic terms)

Three-domain system: biological classification introduced by Carl Woese that rejects the old prokaryote-eukaryote distinction and divides cellular life forms into archaea, bacteria, and eukarya domains (usually interpreted as a taxonomic grade above kingdom). Woese argued that, on the basis of differences in 16S rRNA genes, the three groups each arose separately from an ancestor with poorly developed genetic machinery, called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. He conjectured an era in which there was a considerable amount of lateral transfer of genes between organisms. Species formed when organisms stopped treating genes from other organisms with equal importance to their own genes. Lateral transfer during this period was responsible for the fast early evolution of complex biological structures. (MAK, corrected from Wikipedia also Wikipedia). Refs Woese et al 1990

Topology: in this context, the particular shape or arrangement of the branches of a cladogram

Total evidence: the philosophical principle that the best hypothesis is the one derived from all the available data. In phylogenetic systematics, this principle has come to be equated with the supermatrix approach (Bininda-Emonds, 2004 - glossary)

Total group: see Pan-group

Transformed cladism: see Pattern cladism

Tree: also Phylogenetic tree: a branching tree-like, diagramatic representation of the evolutionary relationships and patterns of branching in the history of the organisms being considered. One type of phylogenetic tree, called a cladogram, is central to cladistics (especially phylogenetic systematics). Dendrogram is sometimes used to refer to a more informal diagram. (MAK)

U.

Unrooted tree: A cladogram for which the ancestor (the root) has not been hypothesized, and which thus does not specify the direction of evolutionary change among the character-states. An unrooted tree can be rooted on any of its branches, and so there are many rooted trees that can be derived from a single unrooted tree. Contrast with rooted tree. (Michael D. Crisp - Introductory glossary of cladistic terms)

V.

Vertical classification: as described by Simpson, a taxon based on ancestor and descendant (phylogenetic) relationship between its members, a clade. Evolutionary systematics considers both horizontal and vertical classification in taxonomy, whereas cladistics (phylogenetic systematics) is based on vertical classification only. (MAK) More

W.

Wastebasket taxon: a taxon that includes all species or groups that cannot be easily or conveniently placed elesewhere. e.g. for a while all large theropod dinosaurs that could not be included under the Ceratosauridae, Allosauridae or Tyrannosauridae were named "Megalosaurus".

Weighting: in cladistics, the empirically controversial (because non-quantifiable) yet necessary task of determining the phylogenetic significance of a particular character trait. For example, if there are three species of animals, one with brown fur, another with black fur, and one with brown scales, the presence or absense of fur is more important than the external colour, and hence would be given greater weight in phylogenetic analysis. Weighting is unavoidable if one is to address the problem of homoplasy vs homology. (MAK)

X.

Y.

Z.

Zombie taxon, Zombie effect: Before the zombie craze took over geek/nerd culture (perhaps as a counterpole to the excessively feminine/romantic "supernatural romance" vampire story) the technical term fora fiossil of this sort was term "reworked". Refers to a fossil such as a dinosaur tooth that was washed out of sediments and re-deposited in rocks and/or sediments millions of years younger. This basic mistake in the interpretation of the age of the fossil leads to its title. The discovered fossil was at some point mobile (or "walking") while the original animal or plant had long been dead. (MAK, Wikipedia)

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