Three-taxon analysis

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Three-taxon analysis (or TTS, three-item analysis, 3ia) is a cladistic based method of phylogenetic reconstruction. Introduced by Nelson and Platnick (1991) [1] to reconstruct organisms' phylogeny, this method can also be applied to biogeographic areas. It attempts to reconstruct complex phylogenetic trees by breaking the problem down into simpler chunks. Rather than try to resolve the relationships of all X taxa at once, it considers taxa 3 at a time. It is relatively easy to generate three-taxon statements (3is); that is, statements of the form "A and B are more closely related to one another than to C". [2] Once each group of three taxa has been considered, the method constructs a tree that is consistent with as many three-item statements as possible. [2] Computer program that implement three-taxon analysis is LisBeth [3] (for systematic and biogeographic studies). LisBeth have been freely released. [4] A recent simulation-based study found that Three-taxon analysis yields good power and an error rate intermediate between parsimony with ordered states and parsimony with unordered states. [5]

Three-taxon analysis (3ia). Modified from Figure 1 from this paper:Grand A, Corvez A, Duque Velez LM, Laurin M. 2013.
Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements. Biol J Linn Soc. 110(4): 914-930. Grand et al. Fig. 1 col.tif
Three-taxon analysis (3ia). Modified from Figure 1 from this paper:Grand A, Corvez A, Duque Velez LM, Laurin M. 2013.
Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three-item statements. Biol J Linn Soc. 110(4): 914–930.

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Cladistics A method of biological systematics in evolutionary biology

Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. Hypothesized relationships are typically based on shared derived characteristics (synapomorphies) that can be traced to the most recent common ancestor and are not present in more distant groups and ancestors. A key feature of a clade is that a common ancestor and all its descendants are part of the clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if within a strict cladistic framework the terms animals, bilateria/worms, fishes/vertebrata, or monkeys/anthropoidea were used, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade'. Radiation results in the generation of new subclades by bifurcation, but in practice sexual hybridization may blur very closely related groupings.

Phylogenetics Study of evolutionary relationships between organisms

In biology, phylogenetics is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits. The result of these analyses is a phylogeny —a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, and represent the 'end', or the present, in an evolutionary lineage. A phylogenetic tree can be rooted or unrooted. A rooted tree indicates the common ancestor, or ancestral lineage, of the tree. An unrooted tree makes no assumption about the ancestral line, and does not show the origin or "root" of the gene or organism in question. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.

Cladogram A 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; nevertheless, many evolutionary trees can be inferred from a single 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.

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.

Outgroup (cladistics)

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.

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A sister group or sister taxon is a phylogenetic term denoting the closest relative(s) of another given unit in an evolutionary tree.

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<i>Rubeostratilia</i> genus of amphibians (fossil)

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References

  1. Nelson, G.; Platnick, N. I. (1991). "Three-Taxon Statements: A More Precise Use of Parsimony?". Cladistics. 7 (4): 351. doi:10.1111/j.1096-0031.1991.tb00044.x.
  2. 1 2 Zaragueta-Bagils, R.; Bourdon, E. (2007). "Three-item analysis: Hierarchical representation and treatment of missing and inapplicable data". Comptes Rendus Palevol. 6 (6–7): 527. doi:10.1016/j.crpv.2007.09.013.
  3. Bagils, R. Z. E.; Ung, V.; Grand, A. S.; Vignes-Lebbe, R. G.; Cao, N. L.; Ducasse, J. (2012). "LisBeth: New cladistics for phylogenetics and biogeography". Comptes Rendus Palevol. 11 (8): 563. doi:10.1016/j.crpv.2012.07.002.
  4. "LisBeth package".
  5. Grand, Anaïs; Corvez, Adèle; Duque Velez, Lina Maria; Laurin, Michel (2013). "Phylogenetic inference using discrete characters: Performance of ordered and unordered parsimony and of three-item statements". Biological Journal of the Linnean Society. 110 (4): 914–930. doi: 10.1111/bij.12159 .