Phylogenetic tree

A phylogenetic tree is a tree that represents the evolutionary relationships between different species or other units of which it is believed that they have a common ancestor. This is a phylogenetic tree is a form of Kladogramms. In a phylogenetic tree, each node represents the closest common ancestor with relatives of this ancestor. The edge length usually corresponds to the estimated time in which the species have separated, or the number of mutations during this development. Each node in a phylogenetic tree is referred to as taxonomic unit, said internal nodes is often referred to as hypothetical taxonomic units, when the relevant species or units can not be observed.

Data sources and interpretation

Phylogenetic trees are now mostly built on the basis of sequenced genes of the species tested. Here, we calculate a sequence alignment of the same gene (or possibly the same genes ) of these species, and used that appear on the alignment similarities and differences in order to build the tree. Species whose sequences are similar, lie in the tree then probably closer to each other than those with very different sequences. Since the computational complexity of such trees, however, increases exponentially with the number of the sequences, using heuristics in order to generate the trees. To the standard methods of molecular phylogenetic tree construction methods include maximum-likelihood, Neighbor joining, maximum parsimony analysis and Bayesian methods.

The aim of the creation of phylogenetic trees is to reconstruct the evolution as detailed as possible and to describe. However, we now know that the genes have not developed equally. Some genes that are today present in humans, for example, have only a common ancestor with the chimpanzees, others are found in all mammals, etc.

Therefore, different phylogenetic trees occur, but all are correct for themselves in the phylogenetic analysis of different genes of the same species. To determine the origin and branching points in the evolution of the various species, so different gene regions need to be investigated. Furthermore, results from the classical phylogeny and morphological features for interpretation should be consulted.

To get these problems under control, a large number of genes are simultaneously examined recently; Irregularities in development rate offset each other so.

Optimally, the lineage relationships can be developed, if known by all species considered the entire genome and its genes are determined. After assignment of all each other orthologous genes are those left over that differ between the species. Phylogenetic trees based on such considerations of orthology, are considered the most reliable and are available for all sequenced species available - in particular the so- created family trees of bacteria and archaea have been providing a detailed overview of their pedigree relationships.

Important fundamental work for the construction of phylogenetic trees were developed in the late 1960s by Walter M. Fitch.

Rooted trees and ungewurzelte

A Rooted phylogenetic tree is a directed tree with a specific single edge, in which the position of the closest common ancestor of all units is assumed in the tree. (This ancestor itself would correspond to an additional node. )

A ungewurzelter tree, however, does not have an excellent next common ancestor, but is merely the relationship near or distant the individual species present. Usually ungewurzelte trees are introduced only as processing step. Since the actual evolution has expired directed time, a tree ungewurzelter provide only an imperfect model of reality.

In order to root a constructed tree, different methods are applicable. The by far most important is the use of outer groups. An outgroup is a taxon with parsed, which is closely related to the study group, but known and clearly stands outside the family circle. The sequence analyzed with the outside group will nearly always rooting. The method fails if the sequence of the outgroup is very different from the sequences analyzed, for example, because it is related to distance. In this case, the comparison with their sequence corresponds more or less to the casual with a. Other possible Verwurzelungsverfahren that are based on assumed rates of change (molecular clock ) or the assumption of irreversible change patterns are therefore particularly at very basal branches, for which no closely related outgroup is available, important.

For more information and to rooted trees ungewurzelten is in the article Tree ( graph theory) read.

Differences between gene and species trees

Various forms of gene / species development: Usually it is assumed that the first case: speciation is accompanied by the splitting of the Genentwicklung. A reconstruction of the tree species is complicated by the other three cases:

→ See also: homology ( genetics).

Methods

Sequence analyzes

Conventional methods of bioinformatics to phylogenetic sequence analysis are parsimony, in which the least number of "explanations", in this case, sequence similarities, to clarify the lineage relationships. In the neighbor-joining all sequences in an alignment with all are compared, which are most similar to each other than related perceived and treated in the next round of the joinings as a common type, until a complete tree is created. Is most frequently used at present, the maximum likelihood model, which is based on statistical assumptions about the evolution of sequences.

Orthology investigations

Many known genomes and are characterized in the individual genes, as is already the case in particular in bacteria, genes orthologous between individuals can be labeled. All that is not ortholog, comes from a insertion or deletion of a gene, depending on the time sequence is accepted. Thus, only those events have to be analyzed to determine the lineage relationships.

Criticism

• By definition may phylogenetic trees hybridization and lateral gene transfer, which are also important methods of gene transfer that do not represent. Therefore, some researchers argue that one should not build a tree, but rather a phylogenetic network (which in the sense of graph theory from a tree differs in that it allows " cross-links " between otherwise not directly related species ).

• Trees that do not include extinct species, must be interpreted with caution (see above note on interpretation).

History of the tree metaphor

The term tree is derived from earlier ideas of life as a progression from " lower " to " higher", more complex forms, each attributed to development level was indicated by the level of placement in an "evolutionary tree ". The model for the graphical representation of such a tree often served a real tree.

A change in the family tree metaphor to a "regular flow " was proposed by Richard Dawkins: One could interpret the cladogram as bifurcation flow system, which among other things, the advantage was that this metaphor might suggest no higher development.