Evolutionary taxonomy

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Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship (shared descent), progenitor-descendant relationship (serial descent), 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. [1] The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.

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Evolutionary taxonomy differs from strict pre-Darwinian Linnaean taxonomy (producing orderly lists only) in that it builds evolutionary trees. While in phylogenetic nomenclature each taxon must consist of a single ancestral node and all its descendants, 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), thus permitting paraphyletic taxa. [2] [3]

Origin of evolutionary taxonomy

Jean-Baptiste Lamarck's 1815 diagram showing branching in the course of invertebrate evolution Lamarck 1815 diagram of animal evolution.png
Jean-Baptiste Lamarck's 1815 diagram showing branching in the course of invertebrate evolution

Evolutionary taxonomy arose as a result of the influence of the theory of evolution on Linnaean taxonomy. The idea of translating Linnaean taxonomy into a sort of dendrogram of the Animal and Plant kingdoms was formulated toward the end of the 18th century, well before Charles Darwin's book On the Origin of Species was published. [4] The first to suggest that organisms had common descent was Pierre-Louis Moreau de Maupertuis in his 1751 Essai de Cosmologie, [5] [6] Transmutation of species entered wider scientific circles with Erasmus Darwin's 1796 Zoönomia and Jean-Baptiste Lamarck's 1809 Philosophie Zoologique . [7] The idea was popularised in the English-speaking world by the speculative but widely read Vestiges of the Natural History of Creation , published anonymously by Robert Chambers in 1844. [8]

Following the appearance of On the Origin of Species, Tree of Life representations became popular in scientific works. In On the Origin of Species, the ancestor remained largely a hypothetical species; Darwin was primarily occupied with showing the principle, carefully refraining from speculating on relationships between living or fossil organisms and using theoretical examples only. [7] In contrast, Chambers had proposed specific hypotheses, the evolution of placental mammals from marsupials, for example. [9]

Following Darwin's publication, Thomas Henry Huxley used the fossils of Archaeopteryx and Hesperornis to argue that the birds are descendants of the dinosaurs. [10] Thus, a group of extant animals could be tied to a fossil group. The resulting description, that of dinosaurs "giving rise to" or being "the ancestors of" birds, exhibits the essential hallmark of evolutionary taxonomic thinking.

The past three decades have seen a dramatic increase in the use of DNA sequences for reconstructing phylogeny and a parallel shift in emphasis from evolutionary taxonomy towards Hennig's 'phylogenetic systematics'. [7]

Today, with the advent of modern genomics, scientists in every branch of biology make use of molecular phylogeny to guide their research. One common method is multiple sequence alignment.[ citation needed ]

Thomas Cavalier-Smith, [7] G. G. Simpson and Ernst Mayr [11] are some representative evolutionary taxonomists.

New methods in modern evolutionary systematics

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 [12] 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". [13]

Briefly, Zander's pluralistic systematics is based on the incompleteness of each of the theories: 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, but otherwise molecular phylogenetics makes no provision for extinct paraphyly. Additional transformational analysis is needed to infer serial descent.

Cladogram of the moss genus Didymodon showing taxon transformations. Colors denote dissilient groups. Cladogram of Didymodon with taxon transformations.png
Cladogram of the moss genus Didymodon showing taxon transformations. Colors denote dissilient groups.

The Besseyan cactus or commagram is the best evolutionary tree for showing both shared and serial ancestry. First, a cladogram or natural key is generated. Generalized ancestral taxa are identified and specialized descendant taxa are noted as coming off the lineage with a line of one color representing the progenitor through time. A Besseyan cactus or commagram is then devised that represents both shared and serial ancestry. Progenitor taxa may have one or more descendant taxa. Support measures in terms of Bayes factors may be given, following Zander's method of transformational analysis using decibans.

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. A cladogram node summarizes all traits distal to it, not of any one taxon, and continuity in a cladogram is from node to node, not taxon to taxon. This is not a model of evolution, but is a variant of hierarchical cluster analysis (trait changes and non-ultrametric branches. 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.

A Besseyan cactus evolutionary tree of the moss genus Didymodon with generalized taxa in color and specialized descendants in white. Support measures are given in terms of Bayes factors, using deciban analysis of taxon transformation. Only two progenitors are considered unknown shared ancestors. DidymCactus.png
A Besseyan cactus evolutionary tree of the moss genus Didymodon with generalized taxa in color and specialized descendants in white. Support measures are given in terms of Bayes factors, using deciban analysis of taxon transformation. Only two progenitors are considered unknown shared ancestors.

Phylogenetics 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 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. [14]

Zander has detailed methods for generating support measures for molecular serial descent [15] and for morphological serial descent using Bayes factors and sequential Bayes analysis through Turing deciban or Shannon informational bit addition. [16] [17] [18] [19]

The Tree of Life

Evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are often used in evolutionary taxonomy. Spindle diagram.jpg
Evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are often used in evolutionary taxonomy.

As more and more fossil groups were found and recognized in the late 19th and early 20th century, palaeontologists worked to understand the history of animals through the ages by linking together known groups. [20] The Tree of life was slowly being mapped out, with fossil groups taking up their position in the tree as understanding increased.[ citation needed ]

These groups still retained their formal Linnaean taxonomic ranks. Some of them are paraphyletic in that, although every organism in the group is linked to a common ancestor by an unbroken chain of intermediate ancestors within the group, some other descendants of that ancestor lie outside the group. The evolution and distribution of the various taxa through time is commonly shown as a spindle diagram (often called a Romerogram after the American palaeontologist Alfred Romer) where various spindles branch off from each other, with each spindle representing a taxon. The width of the spindles are meant to imply the abundance (often number of families) plotted against time. [21]

Vertebrate palaeontology had mapped out the evolutionary sequence of vertebrates as currently understood fairly well by the closing of the 19th century, followed by a reasonable understanding of the evolutionary sequence of the plant kingdom by the early 20th century. The tying together of the various trees into a grand Tree of Life only really became possible with advancements in microbiology and biochemistry in the period between the World Wars.[ citation needed ]

Terminological difference

The two approaches, evolutionary taxonomy and the phylogenetic systematics derived from Willi Hennig, differ in the use of the word "monophyletic". For evolutionary systematicists, "monophyletic" means only that a group is derived from a single common ancestor. In phylogenetic nomenclature, there is an added caveat that the ancestral species and all descendants should be included in the group. [2] The term "holophyletic" has been proposed for the latter meaning. As an example, amphibians are monophyletic under evolutionary taxonomy, since they have arisen from fishes only once. Under phylogenetic taxonomy, amphibians do not constitute a monophyletic group in that the amniotes (reptiles, birds and mammals) have evolved from an amphibian ancestor and yet are not considered amphibians. Such paraphyletic groups are rejected in phylogenetic nomenclature, but are considered a signal of serial descent by evolutionary taxonomists. [22]

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.

<span class="mw-page-title-main">Monophyly</span> Property of a group of including all taxa descendant from a common ancestral species

In biological cladistics for the classification of organisms, monophyly is the condition of a taxonomic grouping being a clade – that is, a grouping of taxa which meets these criteria:

  1. the grouping contains its own most recent common ancestor, i.e. excludes non-descendants of that common ancestor
  2. the grouping contains all the descendants of that common ancestor, without exception

In biology, phylogenetics is the study of the evolutionary history of life using genetics, which known as phylogenetic inference. It establishes the relationship between organisms with the empirical data and observed heritable traits of DNA sequences, protein amino acid sequences, and morphology. The results are a phylogenetic tree—a diagram setting the hypothetical relationships between organisms and their evolutionary history.

In biology, phenetics, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually with respect to morphology or other observable traits, regardless of their phylogeny or evolutionary relation. It is related closely to numerical taxonomy which is concerned with the use of numerical methods for taxonomic classification. Many people contributed to the development of phenetics, but the most influential were Peter Sneath and Robert R. Sokal. Their books are still primary references for this sub-discipline, although now out of print.

<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.

In biology, taxonomy is the scientific study of naming, defining (circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum, class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.

<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.

A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.

<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.

<span class="mw-page-title-main">Outgroup (cladistics)</span>

In cladistics or phylogenetics, an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny.

<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.

<span class="mw-page-title-main">Pseudoextinction</span> Phenomenon where a species is perpetuated by a daughter species

Pseudoextinction of a species occurs when all members of the species are extinct, but members of a daughter species remain alive. The term pseudoextinction refers to the evolution of a species into a new form, with the resultant disappearance of the ancestral form. Pseudoextinction results in the relationship between ancestor and descendant still existing even though the ancestor species no longer exists.

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 sister group or sister taxon, also called an adelphotaxon, comprises the closest relative(s) of another given unit in an evolutionary tree.

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">Evolutionary grade</span> Non-monophyletic grouping of organisms united by morphological or physiological characteristics

A grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.

<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).

<span class="mw-page-title-main">Outline of evolution</span> Overview of and topical guide to change in the heritable characteristics of organisms

The following outline is provided as an overview of and topical guide to evolution:

References

  1. ↑ Mayr, Ernst & Bock, W.J. (2002), "Classifications and other ordering systems" (PDF), J. Zool. Syst. Evol. Research, 40 (4): 169–94, doi:10.1046/j.1439-0469.2002.00211.x
  2. 1 2 Grant, V. (2003), "Incongruence between cladistic and taxonomic systems", American Journal of Botany, 90 (9): 1263–70, doi:10.3732/ajb.90.9.1263, PMID   21659226
  3. ↑ Aubert, D (2015). "A formal analysis of phylogenetic terminology: Towards a reconsideration of the current paradigm in systematics". Phytoneuron. 2015–66: 1–54.
  4. ↑ Archibald, J. David (2009). "Edward Hitchcock's Pre-Darwinian (1840) 'Tree of Life'" (PDF). Journal of the History of Biology. 42 (3): 561–592. CiteSeerX   10.1.1.688.7842 . doi:10.1007/s10739-008-9163-y. PMID   20027787. S2CID   16634677.
  5. ↑ J. S. Bromley, The new Cambridge modern history: The rise of Great Britain and Russia, 1688-1715/25, CUP Archive, 1970, ISBN   978-0-521-07524-4, pgs. 62-63.
  6. ↑ Geoffrey Russell Richards Treasure, The making of modern Europe, 1648-1780, Taylor & Francis, 1985, ISBN   978-0-416-72370-0, pg. 142
  7. 1 2 3 4 Cavalier-Smith, Thomas (2010). "Deep phylogeny, ancestral groups and the four ages of life" (PDF). Philosophical Transactions of the Royal Society B . 365 (1537): 111–132. doi:10.1098/rstb.2009.0161. PMC   2842702 . PMID   20008390.
  8. ↑ Secord, James A. (2000), Victorian Sensation: The Extraordinary Publication, Reception, and Secret Authorship of Vestiges of the Natural History of Creation, Chicago: University of Chicago Press, ISBN   978-0-226-74410-0, archived from the original on 16 May 2008, retrieved 17 January 2011
  9. ↑ Chambers, Robert (1844). Vestiges of the Natural History of Creation. London: John Churchill. p. 122. Retrieved 10 May 2013.
  10. ↑ Huxley, T.H. (1876): Lectures on Evolution. New York Tribune. Extra. no 36. In Collected Essays IV: pp 46-138 original text w/ figures
  11. ↑ Mahner, Martin; Bunge, Mario. Foundations of Biophilosophy. Springer, p. 251.
  12. ↑ Stuessy, Tod F. (2010). "Paraphyly and the origin and classification of angiosperms". Taxon. 59 (3): 689–693. doi:10.1002/tax.593001.
  13. ↑ Zander, Richard (2013). Framework for Post-Phylogenetic Systematics. St. Louis: Zetetic Publications, Amazon CreateSpace.
  14. ↑ Zander, Richard (2014). "Response to a particularly nasty review in the journal Cladistics". Phytoneuron. 2014 (110): 1–4.
  15. ↑ Zander, Richard (2014). "Support measures for caulistic macroevolutionary transformations in evolutionary trees". Annals of the Missouri Botanical Garden. 100 (1–2): 100–107. doi:10.3417/2012090. S2CID   86754093.
  16. ↑ Zander, Richard (2014). "Classical determination of monophyly exemplified with Didymodon s. lat. (Bryophyta). Part 1 of 3, synopsis and simplified concepts" (PDF). Phytoneuron. 2014 (78): 1–7. Retrieved 4 January 2015.
  17. ↑ Zander, Richard (2014). "Classical determination of monophyly, exemplified with Didymodon s. lat. (Bryophyta). Part 2 of 3, concepts" (PDF). Phytoneuron. 2014 (79): 1–23. Retrieved 4 January 2015.
  18. ↑ Zander, Richard (2014). "Classical determination of monophyly exemplified with Didymodon s. lat. (Bryophyta). Part 3 of 3, analysis" (PDF). Phytoneuron. 2014 (80): 1–19. Retrieved 4 January 2015.
  19. ↑ Zander R. H. 2018. Macroevolutionary Systematics of Streptotrichaceae of the Bryophyta and Application to Ecosystem Thermodynamic Stability. Edition 2. Zetetic Publications,  CreateSpace Independent Publishing, Amazon, St. Louis.
  20. ↑ Rudwick, M. J. S. (1985), The Meaning of Fossils: Episodes in the History of Palaeontology, University of Chicago Press, p. 24, ISBN   978-0-226-73103-2
  21. ↑ White, T.; Kazlev, M. A. "Phylogeny and Systematics : Glossary - Romerogram". palaeos.com. Retrieved 21 January 2013.
  22. ↑ Zander, R. H. (2008). "Evolutionary inferences from non-monophyly on molecular trees". Taxon. 57 (4): 1182–1188. doi:10.1002/tax.574011.
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