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A cladogram (from Greek clados "branch" and gramma "character") 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 ...
A simple cladogram showing the evolutionary relationships between four species: A, B, C, and D. Here, Species A is the outgroup, and Species B, C, and D form the ingroup. In cladistics or phylogenetics, an outgroup [1] 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 ...
In general, pairwise distance data are an underestimate of the path-distance between taxa on a phylogram. Pairwise distances effectively "cut corners" in a manner analogous to geographic distance: the distance between two cities may be 100 miles "as the crow flies," but a traveler may actually be obligated to travel 120 miles because of the ...
Phylogenetic diversity is a measure of biodiversity which incorporates phylogenetic difference between species. It is defined and calculated as "the sum of the lengths of all those branches that are members of the corresponding minimum spanning path ", [ 1 ] in which 'branch' is a segment of a cladogram , and the minimum spanning path is the ...
MrBayes is a free software tool that performs Bayesian inference of phylogeny. It was originally written by John P. Huelsenbeck and Frederik Ronquist in 2001. [28] As Bayesian methods increased in popularity, MrBayes became one of the software of choice for many molecular phylogeneticists.
The requirement for a rank is a major difference between traditional and phylogenetic nomenclature. It has several consequences: it limits the number of nested levels at which names can be applied; it causes the endings of names to change if a group has its rank changed, even if it has precisely the same members (i.e. the same circumscription ...
The difference between the statement "B is part of A" (phylogenetic approach) and "B has evolved from A" (evolutionary approach) is, however, one of semantics rather than of phylogeny. Both express the same phylogeny, but the former emphasizes the phylogenetic continuum while the latter emphasizes a distinct shift in anatomy or ecology in B ...
Neighbor joining takes a distance matrix, which specifies the distance between each pair of taxa, as input. The algorithm starts with a completely unresolved tree, whose topology corresponds to that of a star network, and iterates over the following steps, until the tree is completely resolved, and all branch lengths are known: