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Phylogenetic inertia or phylogenetic constraint refers to the limitations on the future evolutionary pathways that have been imposed by previous adaptations. [ 1 ] Charles Darwin first recognized this phenomenon, though the term was later coined by Huber in 1939. [ 2 ]
The principle of phylogenetic reconciliation was introduced in 1979 [14] to account for differences between genes and species-level phylogenies. In a parsimonious setting, two evolutionary events, gene duplication and gene loss were invoked to explain the discrepancies between a gene tree and a species tree.
Biological constraints are factors which make populations resistant to evolutionary change. One proposed definition of constraint is "A property of a trait that, although possibly adaptive in the environment in which it originally evolved, acts to place limits on the production of new phenotypic variants."
Edward Hitchcock's fold-out paleontological chart in his 1840 Elementary Geology. Although tree-like diagrams have long been used to organise knowledge, and although branching diagrams known as claves ("keys") were omnipresent in eighteenth-century natural history, it appears that the earliest tree diagram of natural order was the 1801 "Arbre botanique" (Botanical Tree) of the French ...
Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species .
Computational phylogenetics, phylogeny inference, or phylogenetic inference focuses on computational and optimization algorithms, heuristics, and approaches involved in phylogenetic analyses. The goal is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of genes , species , or taxa .
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It has been called a "universal phylogenetic tree in rooted form". [1] This tree and its rooting became the subject of debate. [49] [b] In the meantime, numerous modifications of this tree, mainly concerning the role and importance of horizontal gene transfer for its rooting and early ramifications have been suggested (e.g. [53] [48]).