Bronze-level articleCladistics

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In biology, cladistics (from ancient Greek κλάδος, klados, "branch"; originally called phylogenetic systematics) is a taxonomical technique for arranging organisms according to how they branch in the evolutionary tree of life.[1]

A group of organisms is analysed and classified into a tree-like diagram called a cladogram, showing hypothesised lines of descent. The analysis may use morphological similarity (per earlier taxonomic methods), but most often DNA differences (molecular data) and biochemical data.

Cladistics has all but taken over from the older Linnaean taxonomy, which originated before the theories of evolution and common descent.

Cladistic techniques do not assume any particular theory of evolution, only the concept of descent with modification. As such, cladistic methods are usefully applied to non-biological systems, including historical linguistics and textual criticism.[2] Even creationism had to create its own version of cladistics, called baraminology.

Contents

[edit] History

The school of thought now known as cladistics took inspiration from the work of Willi Hennig, though he did not use the word, calling his approach phylogenetic systematics. Hennig's work systematised techniques biologists had been using for decades.

The term "clade" was introduced in 1958 by Julian Huxley, "cladistic" by Cain and Harrison in 1960 and "cladist" (for an adherent of Hennig's school) by Mayr in 1965.

[edit] Cladograms

Cladograms are tree-like relationship- diagrams.
This cladogram shows the relationship among various insect groups inferred from a dataset.

In a cladogram, all organisms lie at the leaves, and each inner node is ideally binary (two-way). The taxa on either side of a split are called sister taxa or sister groups. Each subtree (whether one item or a hundred thousand items) is called a clade. A natural group has all the organisms contained in any one clade that share a unique ancestor (one which they do not share with any other organisms on the diagram) for that clade. All of life forms a single clade.

Each clade is set off by a series of characteristics that appear in its members, but not in the other forms from which it diverged. These identifying characteristics of a clade are called synapomorphies (shared, derived characters). e.g., hardened front wings (elytra) are a synapomorphy of beetles, while circinate vernation, or the unrolling of new fronds, is a synapomorphy of ferns.

[edit] Cladistic classification

Three ways to define a clade for use in a cladistic taxonomy.
Node-based: the most recent common ancestor of A and B and all its descendants.
Stem-based: all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z.
Apomorphy-based: the most recent common ancestor of A and B possessing a certain apomorphy (derived character), and all its descendants.

A monophyletic group is a clade, comprising an ancestral form and all of its descendants, and so forming one (and only one) evolutionary group.

A paraphyletic group is similar, but excludes some of the descendants that have undergone significant changes. For instance, the traditional class Reptilia excludes birds and mammals even though they evolved from the ancestral reptile. (The current superorder Dinosauria includes birds.) Similarly, the traditional Invertebrates are paraphyletic because Vertebrates are excluded, although the latter evolved from an Invertebrate. Paraphyletic groups are not considered proper groups in phylogenetic classifications.

A group with members from separate evolutionary lines is called polyphyletic. For instance, the once-recognized Pachydermata was found to be polyphyletic because elephants and rhinoceroses arose from non-pachyderms separately. Evolutionary taxonomists consider polyphyletic groups to be errors in classification.

[edit] Cladistics v. Linnaean taxonomy

Since the 1960s, there has been a trend in biology called cladism or cladistic taxonomy that requires taxa to be clades - cladists argue that the classification system should be reformed to eliminate all non-clades. Other taxonomists insist that groups reflect phylogenies and often make use of cladistic techniques, but allow both monophyletic and paraphyletic groups as taxa.

Following Hennig, cladists argue that paraphyly is as harmful as polyphyly. The idea is that monophyletic groups can be defined objectively, in terms of common ancestors or the presence of synapomorphies. In contrast, paraphyletic and polyphyletic groups are both defined based on key characters, and the decision of which characters are of taxonomic import is inherently subjective. Many argue that they lead to "gradistic" thinking, where groups advance from "lowly" grades to "advanced" grades, which can in turn lead to teleology. In evolutionary studies, teleology is usually avoided because it implies a plan that cannot be empirically demonstrated.

Going further, some cladists argue that ranks for groups above species are too subjective to present any meaningful information, and so argue that they should be abandoned. Thus they have moved away from Linnaean taxonomy towards a simple hierarchy of clades. The validity of this argument hinges crucially on how often in evolution gradualist near-equilibria are punctuated. A quasi-stable state will result in phylogenies which may be all but unmappable onto the Linnaean hierarchy, whereas a punctuation event that balances a taxon out of its ecological equilibrium is likely to lead to a split between clades that occurs in comparatively short time and thus lends itself readily for classification according to the Linnaean system.

Other evolutionary systematists argue that all taxa are inherently subjective, even when they reflect evolutionary relationships, since living things form an essentially continuous tree. Any dividing line is artificial, and creates both a monophyletic section above and a paraphyletic section below. Paraphyletic taxa are necessary for classifying earlier sections of the tree – for instance, the early vertebrates that would someday evolve into the family Hominidae cannot be placed in any other monophyletic family. They also argue that paraphyletic taxa provide information about significant changes in organisms' morphology, ecology, or life history – in short, that both taxa and clades are valuable but distinct notions, with separate purposes. Many use the term monophyly in its older sense, where it includes paraphyly, and use the alternate term holophyly to describe clades (monophyly in Hennig's sense). As an unscientific rule of thumb, if a distinct lineage that renders the containing clade paraphyletic has undergone marked adaptive radiation and collected many synapomorphies - especially ones that are radical and/or unprecedented -, the paraphyly is usually not considered a sufficient argument to prevent recognition of the lineage as distinct under the Linnaean system (but it is by definition sufficient in phylogenetic nomenclature). For example, as touched upon briefly above, the Sauropsida ("reptiles") and the Aves (birds) are both ranked as a Linnaean class, although the latter are a highly derived offshoot of some forms of the former which themselves were already quite advanced.

A formal code of phylogenetic nomenclature, the PhyloCode, is currently under development for cladistic taxonomy. It is intended for use by both those who would like to abandon Linnaean taxonomy and those who would like to use taxa and clades side by side. In several instances (see for example Hesperornithes) it has been employed to clarify uncertainties in Linnaean systematics so that in combination they yield a taxonomy that is unambiguously placing the group in the evolutionary tree in a way that is consistent with current knowledge.

[edit] A cautionary view of cladistics and phylogenetics

Efforts in combining modern methods of cladistics, phylogenetics, and DNA analysis with classical views of taxonomy have recently appeared. Certain authors have found that phylogenetic analysis is acceptable scientifically as long as paraphyly at least for certain groups is allowable. Such a stance is promoted in papers by Tod F. Stuessy and others. A particularly strict form of evolutionary systematics has been presented by Richard H. Zander in a number of papers, but summarized in his "Framework for Post-Phylogenetic Systematics".[3] Simplified explanations are also available.[4] [5] [6] [7]

Besseyan cactus evolutionary tree of the moss genus Didymodon showing both shared and serial descent. Support values are given with Bayes factors using deciban analysis of taxon transformation.
Briefly, Zander's pluralistic systematics is thus: A method that cannot falsify a hypothesis is as unscientific as a hypothesis that cannot be falsified. Cladistics generates only trees of shared ancestry, not serial ancestry. Taxa evolving seriatim cannot be dealt with by analyzing shared ancestry with cladistic methods. Hypotheses such as adaptive radiation from a single ancestral taxon cannot be falsified with cladistics. Cladistics offers a way to cluster by trait transformations but no evolutionary tree can be entirely dichotomous. Phylogenetics posits shared ancestral taxa as causal agents for dichotomies yet there is no evidence for the existence of such taxa. Molecular systematics uses DNA sequence data for tracking evolutionary changes, thus paraphyly and sometimes phylogenetic polyphyly signal ancestor-descendant transformations at the taxon level,[8] but otherwise molecular phylogenetics makes no provision for extinct paraphyly. Additional transformational analysis is needed to infer serial descent. The Besseyan cactus or commagram is the best evolutionary tree for showing both shared and serial ancestry.

Cladistic analysis groups taxa by shared traits but incorporates a dichotomous branching model borrowed from phenetics. It is essentially a simplified dichotomous natural key, although reversals are tolerated. The problem, of course, is that evolution is not necessarily dichotomous. An ancestral taxon generating two or more descendants requires a longer, less parsimonious tree. This is why a tree based solely on shared traits is not called an evolutionary tree but merely a cladistic tree. This tree reflects to a large extent evolutionary relationships through trait transformations but ignores relationships made by species-level transformation of extant taxa.

Phylogenetics (as opposed to cladistics) attempts to inject a serial element by postulating ad hoc, undemonstrable shared ancestors at each node of a cladistic tree. There are in number, for a fully dichotomous cladogram, one less invisible shared ancestor than the number of terminal taxa. We get, then, in effect a dichotomous natural key with an invisible shared ancestor generating each couplet. This cannot imply a process-based explanation[9] without justification of the dichotomy, and supposition of the shared ancestors as causes. The cladistic form of analysis of evolutionary relationships cannot falsify any genuine evolutionary scenario incorporating serial transformation, according to Zander.

In evolutionary systematics, A → B means A is the inferred immediate ancestor of B. The taxonomic level of A and B signals the degree of resolution. Thus higher taxa can give rise in diagrams to higher taxa with the assumption that one higher taxon derived from another is ultimately associated some natural process such as mutation of an individual or isolation and drift of a population. When an ancestral taxon is unknown, such as A ← ? → B, then the unknown immediate shared ancestor is predicted as possibly found in the future, at the same taxonomic level as A and B, and commonly unspecialized relative to A and B.

In cladistics (A, B) means A and B are sister groups, which theoretically could be due to:

1. A is ancestral taxon of taxon B or vice versa, or

2. A and B share an immediate ancestral taxon, or

3. A is far away from B in the same clade but intermediate branches are extinct and there is no immediate shared ancestral taxon for both A and B, or

4. A is polyphyletic with B but all associated branches are extinct, e.g. (A, C)(B, D) and C and D are extinct.

Thus, A and B are unrelated in the immediate sense (i.e., of course all taxa are related in some way but the sister group is misleading about monophyly). Most sister groups that are of rather different taxa are probably polyphyletic, and further collections should support this annoying but logical prediction.

The term “sister-group” does not refer to any single intrinsic evolutionary process in nature but only to a particular grouping in a cladistic analysis, which may be caused or affected by a number of different natural processes, including extinction. A shared ancestor in cladistics is not a specific theoretical prediction of how a new discovery might fit into an evolutionary tree, but is instead a structural part of the cladistic method, and must remain unnamed. If cladistic prediction, on the other hand, means that a new taxon is expected to fit into a clade, then there is little evolutionary information about that taxon in such a prediction.

The method of cladistics investigates evolution using only sister group relationships, i.e., shared descent. Serial descent, as in one taxon giving rise to another, is ignored as an analytic tool. But in many groups, there may be clear indication that one extant taxon has been derived from another, or even several taxa from one progenitor taxon. Thus, a cladogram is the worst possible model for evolution since all nodes are required to be a theoretical (unnamed and unknowable place holder) taxon different from any of the terminal taxa. That is, no taxon is allowed to be derived from one of the other taxa, otherwise that portion of the tree would be constrained rather than analytic. The best possible model is one that maximizes the number of inferable extant progenitor-descendant transformations. Given the suppression of true serial descent modeling in both cladistics and phylogenetics, it is no wonder that creationism uses a cladistic-like technique (baraminology) for biblically based studies. Commonly, evolutionists are now presenting cladograms in their textbooks and research papers, at least tacitly accepting the methodological imposition of unknown and unnamable shared ancestors in place of clearly inferable, nameable progenitors. This should be disconcerting.

Phylogenetics compares support values for different branch orders on this worst of all possible evolutionary models. Constraint trees based on known progenitor-descendant relationships must always have 100 percent bootstrap or Bayesian posterior probability support. The problem is not whether a given clade has better support than another clade including the same taxa on a fully resolved cladogram, but whether one constraint tree of nodes named as terminal taxa is better than a different constraint tree of the same taxa. Constrained clades are determined as such by data not in a standard phylogenetic data set. Evaluation of transformations of one taxon into another (macroevolution) requires, for example, morphological trait analysis of taxic transformations using Bayes factors and decibans. After such analysis, that molecular cladograms match morphological groups is then expected and incongruencies are good information about possible mistakes and alternative evolutionary classifications. Simply matching taxa to phylogenetic clades, and trimming or splitting when they do not fit, does not add information because the tree is the worst possible tree and mistakes are added, not eliminated.

Cladistics cannot determine monophyly because no nodes in their trees of descent are named or nameable. Only shared descent is an acceptable measure of evolutionary relationship in cladistics. Serial-descent blindness is a common disease among present-day systematists. In the country of the blind, the guy with a cladogram is king. What blinds systematists? Money. An examination of grants awarded by the US National Science Foundation for 2014 reveals that there are 575 grants now (Jan. 2015) funded and active that are associated with phylogenetic research, totaling more than US$260 million. These grants usually last three years, thus a quarter of a billion dollars has been spent on phylogenetic analysis or research involving phylogenetic analysis in some important way in the years 2012 through 2014. Although there are programs for “traditional taxonomy” in NSF, it is clear that present and potential success in systematics is measured by phylogenetics research.

Phylogenetic systematics makes changes in classifications based solely on perceived shared ancestry. This yields a taxonomic chaos of splitting, lumping, and generation of trivial new cryptic taxa at the family, genus and species level. Changes made in classifications have been considered of little consequence because classifications are easily modified if wrong. But in the context of the need for scientific guidance during a world extinction event, wrong though potentially corrigible classifications, even if ephemeral, can greatly affect conservation planning, triage, political decisions, and scientific evaluations of biodiversity. It may be that phylogenetics as now practiced will eventually be recognized as the biggest scam in the biological sciences since the Lysenko affair.

[edit] How to do cladistics

Simple cladistics.png

A cladistic analysis is applied to a certain set of information. The information is organised by characters, which have character states. e.g., if one species has red feathers and another has blue feathers, then we have the character "colour of feathers" which has character states "red feathers" and "blue feathers".

The researcher decides 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) by considering one or more outgroups - an organism considered not to be part of the group in question, but to be closely related to the group. (This makes the choice of an outgroup an important task, since this choice can profoundly change the topology of a tree.) Only synapomorphies are of use in determining clades.

Possible cladograms are then drawn up and evaluated. Ideally, clades have many "agreeing" synapomorphies, with a sufficient number of true synapomorphies to overwhelm homoplasies caused by convergent evolution - characters that resemble each other because of environmental conditions or function, not because of common ancestry. A character "presence of wings" is an example - though the wings of birds and insects serve the same function, each evolved independently, as can be seen by their anatomy. If a bird and a winged insect were scored for the character "presence of wings", a homoplasy would be introduced into the dataset and confound the analysis, possibly resulting in an erroneous picture of evolution. Homoplasies can often be avoided by defining characters more precisely and increasing their number, e.g., using "wings supported by bony endoskeleton" and "wings supported by chitinous exoskeleton" as characters.

When analyzing "supertrees" (datasets incorporating as many taxa of a suspected clade as possible), it may be unavoidable to introduce character definitions that are unprecise, as otherwise the characters might not apply at all to a large number of taxa. The "wings" example would be hardly useful if attempting a phylogeny of all Metazoa as most of these don't have wings at all. Cautious choice and definition of characters thus is another important element in cladistic analyses. With a faulty outgroup and/or character set, no method of evaluation is likely to produce a phylogeny representing the evolutionary reality.

Many cladograms are possible for any given set of taxa, but one is chosen based on the principle of parsimony: the most compact arrangement, that is, with the fewest character state changes (synapomorphies), is the hypothesis of relationship accept here (see Occam's razor for a discussion of the principle of parsimony and possible complications). Though at one time this analysis was done by hand, computers are now used to evaluate much larger data sets. Sophisticated software packages such PAUP allow the statistical evaluation of the confidence we can put in the veracity of the nodes of a cladogram.

Note that the nodes of cladograms do not represent divergences of evolutionary lineages per se, but divergences of character states between evolutionary lineages. DNA sequence characters can only diverge after gene flow between (sub)populations has been reduced below some threshold, whereas comprehensive morphological alterations, usually being epistatic (the product of interactions of several genes), usually occur only after lineages have already evolved separately for quite some time - biological subspecies can usually be distinguished genetically but often not by internal anatomy.

As DNA sequencing has become cheaper and easier, molecular systematics has become more popular. As well as a parsimony criterion, you can also use non-Hennigian methods such as maximum likelihood and Bayesian inference, which incorporate explicit models of sequence evolution. Another powerful method is the use of genomic retrotransposon markers, which are thought to be less prone to the problem of reversion that plagues sequence data. They are also generally assumed to have a low incidence of homoplasies because it was once thought that their integration into the genome was entirely random, although it now appears that this is sometimes not the case.

Ideally, morphological, molecular and possibly other (behavioral etc.) phylogenies should be combined into an analysis of total evidence: none of the methods is "superior", but 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 state reversions that cannot be noticed as being such are more common in the DNA. Morphological homoplasies can usually be recognized as such if character states are defined with enough attention to detail.

[edit] Definitions

A character state that is present in both the outgroups and in the ancestors is called a plesiomorphy (meaning "close form", also called an ancestral state). A character state that occurs only in later descendants is called an apomorphy (meaning "separate form", also called a "derived" state) for that group. The adjectives plesiomorphic and apomorphic are used instead of "primitive" and "advanced" to avoid placing value-judgments on the evolution of the character states, since both may be advantageous in different circumstances. It is not uncommon to refer informally to a collective set of plesiomorphies as a ground plan for the clade or clades they refer to.

A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade. Usually a basal group is very species-poor as compared to a more derived group. It is not a requirement that a basal group be present. For example, when considering birds and mammals together, neither is basal to the other: both have many derived characters.

A clade or species located within another clade is nested within that clade.


[edit] External links

[edit] Footnotes

  1. Luria et al. (1981).
  2. Example of cladistics used in textual criticism
  3. Zander, R. H. 2013. A Framework for Post-Phylogenetic Systematics. Zetetic Publications, St. Louis. CreateSpace Independent Publishing Platform, Amazon.
  4. Zander, R. H. 2014. Classical determination of monophyly, exemplified with Didymodon s. lat. (Bryophyta). Part 1 of 3, synopsis and simplified concepts. Phytoneuron 2014-78: 1–7.
  5. Zander, R. H. 2014. Classical determination of monophyly, exemplified with Didymodon s. lat. (Bryophyta). Part 2 of 3, concepts. Phytoneuron 2014-79: 1–23.
  6. Zander, R. H. 2014. Classical determination of monophyly exemplified with Didymodon s. lat. (Bryophyta). Part 3 of 3, analysis. Phytoneuron 2014-80: 1–19.
  7. Zander, R. H. 2014. Response to a particularly nasty review in the journal Cladistics. Phytoneuron 2014-110: 1–4.
  8. Zander, R. H. 2014. Support measures for caulistic macroevolutionary transformations in evolutionary trees. Annals of the Missouri Botanical Garden 100: 100–107.
  9. Zander, R. H. 2010 (2011). Structuralism in phylogenetic systematics. Biological Theory 5: 383–394.
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