Transformed cladistics

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Transformed cladistics, also known as pattern cladistics is an epistemological approach to the cladistic method of phylogenetic inference and classification that makes no a priori assumptions about common ancestry. It was advocated by Norman Platnick, Colin Patterson, Ronald Brady and others in the 1980s, but has few modern proponents. The book, Foundations of Systematics and Biogeography [1] by David Williams and Malte Ebach provides a thoughtful history of the origins of this point of view.

Contents

Patterns vs. processes

The traditional approach to cladistics, which traces back to Willi Hennig, [2] [3] groups together organisms based on whether or not they share derived characters or character states that are assumed to be descended from a common ancestor. Transformed cladists maintain that the assumption of common descent is uninformative and/or potentially misleading, and that therefore cladistic methods should be free from evolutionary process assumptions, and based only on parsimonious interpretation of empirical data:

"If classifications (that is, our knowledge of patterns) are ever to provide an adequate test of theories of evolutionary processes their construction must be independent of any particular theory of process." (Platnick, 1979) [4]

In other words, pattern cladists argue that the fewer evolutionary assumptions a classification presupposes, the fewer errors creep in, and greater transparency results. They draw a distinction between patterns, which are observed, and processes, which may be inferred from patterns, but which should not be presupposed. Before the emergence of cladistics as a school, Joseph Henry Woodger criticized phylogenetic systematics on the grounds that homology by way of common ancestry is "putting the cart before the horse, because descent from a common ancestor is something assumed, not observed. It belongs to theory, whereas morphological correspondence is observed.". [5] Colin Patterson later wrote similarly:

"We must remember the distinction between the cart--the explanation--and the horse--the data. And where models are introduced in phylogenetic reconstruction, we should prefer models dictated by features of the data to models derived from explanatory theories." [6]

Pattern cladists, like traditional cladists, think that classifications should be isomorphic to cladograms, recognizing groups based on nested patterns of synapomorphies, but they argue that the discovery of characters is not dependent on apriori considerations about common ancestry:

"[T]o state a cladogram is a synapomorphy scheme invites the rejoinder that a cladogram must, therefore be a phyletic concept. Not so, for by ‘synapomorphy’ we mean ‘defining character’ of an inclusive taxon." [7]

Nelson & Platnick (1981) also noted that: "all of Hennig’s groups correspond by definition to patterns of synapomorphy. Indeed, Hennig’s trees are frequently called synapomorphy schemes. The concept of ‘patterns within patterns’ seems, therefore, an empirical generalization.” Pattern cladists hence regard synapomorphies to be patterns free of processes.

Criticism

A frequent (but false) accusation against pattern cladistics is that its proponents claim that systematics should be "theory free." At some point in the 1960s and '70s pheneticists may have believed that, but pattern cladists are not pheneticists. Obviously, rejecting a priori evolutionary process theories is not the same thing as categorically rejecting "theory" in toto. Furthermore, pattern cladists do not reject post hoc evolutionary explanations for cladograms, they simply think that the evidence is independent of the explanation. [8] Nevertheless, some philosophers with a background conciliatory towards evolutionary taxonomy continue to offer criticisms in this vein:

"Pattern cladistics has remained on the fringe because of, first, its implausible assumption that there can be pure observation untainted by theory; and second, its rejection of the evolution assumption. Few systematists now think that a classification not based on evolutionary branching and history has any real signification or justification. The developing consensus is that Darwin was right – a natural classification must be genealogical." [9]

Of course, the distinction between the phenomenon and its explanation was clear to Darwin: "the grand fact in natural history of the subordination of group under group, which from its familiarity, does not always sufficiently strike us, is in my judgment fully explained." [10]

Brady [11] [12] introduced to systematics the terms explanandum for empirical patterns (the phenomenon to be explained) and explanans for process theory (the explanation), writing: "by making our explanation into the definition of the condition [data] to be explained, we express not scientific hypothesis but belief". In the above quote, Darwin's "fact" is the explanandum; his theory of descent with modification is the explanans.

In this view, whatever the characters imply as the preferred hypothesis of relationships becomes, de facto, "genealogical" when we explain it as a result of evolution. [13]

Creationist distortion

As noted, transformed cladistics does not deny common ancestry, rather it argues a logical precedence: theories regarding processes should only be formulated after patterns are discovered. Creationists have distorted this to argue that there are pattern cladists who are skeptical about whether evolution occurs.

Colin Patterson

In November, 1981, Patterson delivered a seminar to the Systematics Discussion Group in the American Museum of Natural History. [14] In the talk, Patterson asked provocatively: "Can you tell me anything about evolution, any one thing that is true?", and remarked:

"As I understand it, cladistics is theoretically neutral so far as evolution is concerned. It has nothing to say about evolution. You don’t need to know about evolution, or believe in it, to do cladistic analysis. All that cladistics demands is that groups have characters."

A creationist in the audience taped segments of Patterson's talk to imply he was "agnostic" on the subject of evolution. [15] To his dismay, Patterson soon found his name quoted in creationist publications:

"I was too naive and foolish to guess what might happen: the talk was taped by a creationist who passed the tape to Luther Sunderland [...] Since, in my view, the tape was obtained unethically, I asked Sunderland to stop circulating the transcript, but of course to no effect. There is not much point in my going through the article point by point. I was putting a case for discussion, as I thought off the record, and was speaking only about systematics, a specialized field. I do not support the creationist movement in any way, and in particular I am opposed to their efforts to modify school curricula. In short the article does not fairly represent my views. But even if it did, so what? The issue should be resolved by rational discussion, and not by quoting 'authorities,' which seems to be the creationists' principal mode of argument." (Letter from Colin Patterson to Steven W. Binkley, June 17, 1982)

"Unfortunately, and unknown to me, there was a creationist in my audience with a hidden tape recorder. A transcript of my talk was produced and circulated among creationists, and the talk has since been widely, and often inaccurately, quoted in creationist literature." (Patterson, 1994)

(Note that a transcript of Patterson's talk has been published in the Linnean 18(2), and may be downloaded from the Linnean Society).

"Because creationists lack scientific research to support such theories as a young earth ... a world-wide flood ... or separate ancestry for humans and apes, their common tactic is to attack evolution by hunting out debate or dissent among evolutionary biologists. ... I learned that one should think carefully about candour in argument (in publications, lectures, or correspondence) in case one was furnishing creationist campaigners with ammunition in the form of 'quotable quotes', often taken out of context." [16]

Modern proponents

A notable contemporary pattern cladist is Andrew V. Z. Brower. [17] [18] [19]

Related Research Articles

Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms worms or fishes were used within a strict cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade', which are fruitless to precisely delineate, especially when including extinct species. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.

<span class="mw-page-title-main">Clade</span> Group of a common ancestor and all descendants

In biological phylogenetics, a clade, also known as a monophyletic group or natural group, is a grouping of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. In the taxonomical literature, sometimes the Latin form cladus is used rather than the English form. Clades are the fundamental unit of cladistics, a modern approach to taxonomy adopted by most biological fields.

In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference, methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.

<span class="mw-page-title-main">Paraphyly</span> Type of taxonomic group

Paraphyly is a taxonomic term describing a grouping that consists of the grouping's last common ancestor and some but not all of its descendant lineages. The grouping is said to be paraphyletic with respect to the excluded subgroups. In contrast, a monophyletic grouping includes a common ancestor and all of its descendants.

<span class="mw-page-title-main">Systematics</span> Branch of biology

Systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees. Phylogenies have two components: branching order and branch length. Phylogenetic trees of species and higher taxa are used to study the evolution of traits and the distribution of organisms (biogeography). Systematics, in other words, is used to understand the evolutionary history of life on Earth.

<span class="mw-page-title-main">Willi Hennig</span> German biologist and zoologist (1913–1976)

Emil Hans Willi Hennig was a German biologist and zoologist who is considered the founder of phylogenetic systematics, otherwise known as cladistics. In 1945 as a prisoner of war, Hennig began work on his theory of cladistics, which he published in German in 1950, with a substantially revised English translation published in 1966. With his works on evolution and systematics he revolutionised the view of the natural order of beings. As a taxonomist, he specialised in dipterans.

<span class="mw-page-title-main">Cladogram</span> Diagram used to show relations among groups of organisms with common origins

A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed, so many differing evolutionary trees can be consistent with the same cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. 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, either on their own or in combination with morphology.

<span class="mw-page-title-main">Homology (biology)</span> Shared ancestry between a pair of structures or genes in different taxa

In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of primates, the front flippers of whales, and the forelegs of four-legged vertebrates like dogs and crocodiles are all derived from the same ancestral tetrapod structure. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this, from Aristotle onwards, and it was explicitly analysed by Pierre Belon in 1555.

<span class="mw-page-title-main">Phylogenesis</span>

Phylogenesis is the biological process by which a taxon appears. The science that studies these processes is called phylogenetics.

Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship, progenitor-descendant relationship, and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.

<span class="mw-page-title-main">Apomorphy and synapomorphy</span> Two concepts on heritable traits

In phylogenetics, an apomorphy is a novel character or character state that has evolved from its ancestral form. A synapomorphy is an apomorphy shared by two or more taxa and is therefore hypothesized to have evolved in their most recent common ancestor. In cladistics, synapomorphy implies homology.

In phylogenetics and computational phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy. In other words, under this criterion, the shortest possible tree that explains the data is considered best. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.

In phylogenetics, long branch attraction (LBA) is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related. LBA arises when the amount of molecular or morphological change accumulated within a lineage is sufficient to cause that lineage to appear similar to another long-branched lineage, solely because they have both undergone a large amount of change, rather than because they are related by descent. Such bias is more common when the overall divergence of some taxa results in long branches within a phylogeny. Long branches are often attracted to the base of a phylogenetic tree, because the lineage included to represent an outgroup is often also long-branched. The frequency of true LBA is unclear and often debated, and some authors view it as untestable and therefore irrelevant to empirical phylogenetic inference. Although often viewed as a failing of parsimony-based methodology, LBA could in principle result from a variety of scenarios and be inferred under multiple analytical paradigms.

In phylogenetics, a primitive character, trait, or feature of a lineage or taxon is one that is inherited from the common ancestor of a clade and has undergone little change since. Conversely, a trait that appears within the clade group is called advanced or derived. A clade is a group of organisms that consists of a common ancestor and all its lineal descendants.

<span class="mw-page-title-main">Plesiomorphy and symplesiomorphy</span> Ancestral character or trait state shared by two or more taxa

In phylogenetics, a plesiomorphy and symplesiomorphy are synonyms for an ancestral character shared by all members of a clade, which does not distinguish the clade from other clades.

<span class="mw-page-title-main">Autapomorphy</span> Distinctive feature, known as a derived trait, that is unique to a given taxon

In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon. It can therefore be considered an apomorphy in relation to a single taxon. The word autapomorphy, introduced in 1950 by German entomologist Willi Hennig, is derived from the Greek words αὐτός, autos "self"; ἀπό, apo "away from"; and μορφή, morphḗ = "shape".

Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional method, by which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is regulated currently by the International Code of Phylogenetic Nomenclature (PhyloCode).

Colin Patterson FRS (1933–1998), was a British palaeontologist at the Natural History Museum in London from 1962 to his official retirement in 1993 who specialised in fossil fish and systematics, advocating the transformed cladistics school.

<span class="mw-page-title-main">Character evolution</span>

Character evolution is the process by which a character or trait evolves along the branches of an evolutionary tree. Character evolution usually refers to single changes within a lineage that make this lineage unique from others. These changes are called character state changes and they are often used in the study of evolution to provide a record of common ancestry. Character state changes can be phenotypic changes, nucleotide substitutions, or amino acid substitutions. These small changes in a species can be identifying features of when exactly a new lineage diverged from an old one.

There are two main approaches currently used to analyze archaeological remains from an evolutionary perspective: evolutionary archaeology and behavioral ecology. The former assumes that cultural change observed in the archaeological record can be best explained by the direct action of natural selection and other Darwinian processes on heritable variation in artifacts and behavior. The latter assumes that cultural and behavioral change results from phenotypic adaptations to varying social and ecological environments. 

References

  1. ↑ Williams, D. M. and M. C. Ebach. 2008. Foundations of Systematics and Biogeography. Springer Science+Business Media, New York.
  2. ↑ Hennig, W. 1950. Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag, Berlin.
  3. ↑ Hennig, W. 1966. Phylogenetic systematics. University of Illinois Press, Urbana, IL.
  4. ↑ Platnick, N. I. (1979). "Philosophy and the transformation of cladistics". Systematic Zoology. 28: 537–546.
  5. ↑ Woodger, S. (1945). “On Biological Transformations”. In: Essays on Growth and Form. Le Gros Clark, W. E., Medawar, P. B (eds.). Oxford: Clarendon Press.
  6. ↑ Patterson, C. (1994). "Null or minimal models". In: Models In Phylogeny Reconstruction. Scotland, R. W., Siebert, D. J. (eds.). Systematics Association Special Volume; 173-192.
  7. ↑ Nelson, G. J., Platnick, N. I. (1981). Systematics and biogeography: cladistics and vicariance (Vol. 214). New York: Columbia University Press.
  8. ↑ Brady, R. H. (1985). "On the independence of systematics". Cladistics. 1: 113-126.
  9. ↑ Ruse, M. (2008). The Oxford Handbook of Philosophy of Biology. Oxford University Press. 171-172.
  10. ↑ Darwin, C. 1859. On the Origin of Species. John Murray, London, p. 413.
  11. ↑ Brady, R. H. (1982). "Theoretical Issues and 'Pattern Cladistics'". Systematic Zoology. 3. 286-291.
  12. ↑ Brady, R. H. (1985). "On the independence of systematics". Cladistics. 1: 113-126.
  13. ↑ Brower, A. V. Z. 2002. Cladistics, phylogeny, evidence and explanation - a reply to Lee. Zool. Scripta 31:221-223.
  14. ↑ Patterson, C. 2002. Systematics and creationism. The Linnean 18:13-37.
  15. ↑ Colin Patterson: Evolution, Reports of the National Center for Science Education
  16. ↑ Bartelt, Karen (May–June 2000). "Review: Evolution". Reports of the National Center for Science Education (Book review). 20 (3): 38–39. ISSN   2158-818X . Retrieved 2015-05-21. Bartelt quoting from Patterson, Evolution (1999), p. 122
  17. ↑ Brower, A. V. Z. (2000). Evolution is not a necessary assumption of cladistics. Cladistics 16: 143-154 .
  18. ↑ Brower, A. V. Z. (2018). Fifty shades of cladism. Biology and Philosophy 33: 8 (DOI: 10.1007/s10539-018-9622-6)
  19. ↑ Brower, A. V. Z. (2019). Background knowledge: the assumptions of pattern cladistics. Cladistics 35: 717-731 (DOI: 10.1111/cla.12379).

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