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The idea of a tree of life arose from ancient notions of a ladder-like progression from lower into higher forms of life (such as in the Great Chain of Being).Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).
Distance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch lengths).
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, [ 1 ] [ 2 ] [ 3 ] and some authors view it as untestable and therefore irrelevant to empirical phylogenetic inference. [ 4 ]
Furthermore, the correctness of the output tree topology is guaranteed as long as the distance matrix is 'nearly additive', specifically if each entry in the distance matrix differs from the true distance by less than half of the shortest branch length in the tree. [7]
The incongruence length difference test (ILD) is a measurement of how the combination of different datasets (e.g. morphological and molecular, plastid and nuclear genes) contributes to a longer tree. It is measured by first calculating the total tree length of each partition and summing them.
Typically, a branch length of a phylogenetic tree is expressed as the expected number of substitutions per site; if the evolutionary model indicates that each site within an ancestral sequence will typically experience x substitutions by the time it evolves to a particular descendant's sequence then the ancestor and descendant are considered to ...
Tree: The full input Newick Format for a single tree Subtree: an internal node (and its descendants) or a leaf node Leaf: a node with no descendants Internal: a node and its one or more descendants BranchSet: a set of one or more Branches Branch: a tree edge and its descendant subtree. Name: the name of a node Length: the length of a tree edge.
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 ...