How do I read a phylogenetic tree

A phylogenetic tree is a tree that represents the evolutionary relationships between different species or other entities believed to have a common ancestor. A phylogenetic tree is thus a form of the cladogram. In a phylogenetic tree, each node with ancestors represents the closest common relatives of these ancestors. The edge length usually corresponds to the estimated time in which the species separated or the number of mutations that occurred during this development. Each node in a phylogenetic tree is called a taxonomic unit where internal nodes are often referred to as hypothetical taxonomic units denotes when the corresponding species or units cannot be observed.

Data sources and interpretation

Phylogenetic trees are now mostly built on the basis of sequenced genes of the examined species. A sequence alignment of the same gene (or possibly the same genes) of these species is calculated and the similarities and differences appearing in the alignment are used to build the tree. Species with similar sequences are probably closer together in the tree than those with very different sequences. However, since the complexity of the computation of such trees increases exponentially with the number of sequences, heuristics are used to generate the trees. The standard methods of molecular phylogenetic tree construction methods include maximum likelihood, neighbor joining, maximum parsimony and Bayesian analysis methods.

The aim of creating phylogenetic trees is to explain evolution in as much detail as possible. However, we now know that genes did not develop evenly. For example, some genes that are found in humans today only have common ancestors with the chimpanzee, others are found in all mammals, etc.

This is why the phylogenetic analysis of different genes of the same species can result in different phylogenetic trees, which are all correct in themselves. In order to determine the points of origin and branches in the evolution of the individual species, different gene regions must therefore be examined. Furthermore, results from classical phylogeny and morphological features should be used for interpretation.

Rooted and unrooted trees

A more rooted phylogenetic tree is a directed tree with a single node that corresponds to the (mostly computationally determined) closest common ancestor of all units in the tree.

A more unrooted Tree, on the other hand, does not have an excellent closest common ancestor, but is only intended to represent the closeness or distance of the individual species. You can read more about rooted and unrooted trees in the article Tree (graph theory).

Differences between gene and species trees

Different forms of gene / species development: Usually the first case is assumed: Speciation goes hand in hand with the splitting of gene development. A reconstruction of the species tree is made more difficult by the three other cases:

  1. the gene is only taken over by one of the new species (gene loss)
  2. the gene is duplicated, which leads to ambiguous possibilities for comparison in a subsequent speciation (not shown)
  3. horizontal gene transfer takes place between two different species, which are thereby mistakenly moved together during tree reconstruction

See inter alia: [1] and [2], homologous genes, orthologous genes, paralogue genes, as well as the paragraph criticism.


  • By definition it can be phylogenetic TreesHybridization and lateral gene transfer, which are also important methods of gene transfer, do not represent. This is why some researchers argue that you can't get one tree Rather, it should build a phylogenetic network (which in the sense of graph theory differs from a tree in that it allows "cross-connections" between otherwise not directly related species).
  • Trees that do not contain extinct species must be interpreted with caution (see also the comment above on interpretation).


  • Knoop, Volker; Müller, Kai: Genes and Family Trees - A Guide to Molecular Phylogenetics. Spectrum Academic Publishing House / Heidelberg 2006, ISBN 3-8274-1642-6
  • Arndt von Haeseler, Dorit Liebers: Molecular evolution, Fischer 2003, ISBN 3596153654
  • Wiesemüller, B., Rothe, H., Henke, W. Phylogenetic systematics. Springer / Berlin 2003, ISBN 978-3-540-43643-0

See also

Categories: Taxonomy | Bioinformatics | evolution