A phylogenetic tree is a tree which shows the relations of relationships between entities supposed to have a common ancestor. Each node of the tree represents the common ancestor of its descendants. The tree can be enraciné or not, according to whether one managed to identify the ancestor common to all the sheets.

The phylogenetic trees do not consider the horizontal transfers, and a new model develops in Phylogénie, that of graph or phylogenetic Réseau which makes it possible to take them into account, as well as the recombinations.

There exist several techniques of construction of the phylogenetic trees, more or less fast and more or less reliable.

Definition and methods of construction

Methods

One can seek to optimize several criteria in the tree: the distance, parsimony, or probability.

For the methods of distance, it is first of all a question of choosing the criterion of distance between the future sheets of the tree. For example, if these sheets are sequences of DNA, one can choose as outdistances between two of them the number of Nucléotide S which differ. To determine this value, one is brought to carry out a alignment of it. Then one can use the method UPGMA or that of the Neighbor Joining to deduce the tree from it.

The methods of parsimony consist in finding the tree which minimizes the number of changes, délétions, or insertions specific to pass from one sequence to the other. It is a very slow method if one generates all the possible trees to calculate parsimony of it.

Lastly, the methods of probability are more probabilists. While being based on the rate of substitution for each basic element (nucleotide for sequences of DNA) during time, one estimates the probability of the position and length of the branches of the tree.

Root

If one obtained a tree not enraciné by one of the methods above, one can try to find of it the root by the method of the outgroup or the median point. That of the outgroup consists in adding to the sequences treated, before the calculation of the tree, very distant: the node-root will be the father of this sequence. That of the median point consists to assign to each node of the tree a sequence corresponding to the consensus of its sons, and to choose as root the node to which the sequence is closest to the sequence consensus of all the sheets.

The phylogenetic tree of the alive one

It is a particular case of phylogenetic tree: that of the alive species.

Precautions and remarks

In debate

Debates exist between the systematicians to determine the most relevant criteria of classification. This classification, whose essential summary in French is the book phylogenetic Classification of alive the , is likely to be still largely modified in the years to come, according to any probability. The attempt at development of current knowledge as regards classification installation by Guillaume Lecointre and Herve Guyader is not to consider, as they say it themselves, like a final document.

The tree which results from it in their work finds with the article which carries the title from there.

A ramification to be followed

The tree annexed to the present article, limited to the alive cellular (without the Virus, therefore), comprises more developed ramification, and was updated. The names of let us tax, except exception, are carried there in Latin, in accordance with international scientific conventions (and with the convention of naming of let us tax higher than the kind, in this Wikipédia). It comprises the fossil groups, which increase its size sometimes considerably, including in width. Also, for a better legibility, the “thick” branches more were developed below the general tree.

Classes, orders and families disappeared

“─o” indicates a “node” (when it did not receive a scientific name, it is simply not named here) or a final “branch” (when it did not receive a scientific name yet, it bears in italic the name of a kind). “─? ” means an uncertainty on the site of the clade in the tree, uncertainty of the contributors, or the systematicians themselves. Moreover, all “node” carrying more than two “branches” means already an uncertainty of the cladistic analysis.

It will be noted that with each “node”, the order in which one indicates the various branches does not have importance other than graphic: if has and B are brothers, then B and has too! A “node” not carrying that only one branch does not have a direction: when the names of traditional classification are very different, one generally indicated the two principal names on the same line. One generally preferred the name of the order to that of the family when they were equivalent.

Contingencies

Names of let us tax, previously paraphyletic (not comprising all the descendants of the same ancestor), saw their meaning being restricted or being increased, and still appear in the tree; do other names of tax paraphyletic or polyphyletic purely and simply disappeared from phylogenetic classification (subject to new analyzes), and are not more in this tree, the such Procaryote S, the Protiste S, the Protozoaire S, the Actinopode S, the Héliozoaire S, the Algue S, the Ptéridophyte S, the Gymnosperme S, the Dicotylédone S, the Invertébré S, the Spongiaires or Porifères, the Sclérosponges, the Cœlentéré S (?), the Poisson S, the Agnathe S, the Ostracoderme S, the Holostéen S, the Reptile S, the Ongulés, the Ciconiiformes, the Ptérobranches, the Pseudocœlomates, the Uniramés, the Maxillopodes, the Turbellarié S, the Polychètes, etc, and perhaps also the Bacteria, Eubactéries, Choanozoaires, Protostomiens, Platyhelminthes, others still…

Some “small” let us tax (generally of the “subfamilies” or “families” of traditional classification), though paraphyletic, still appear in the tree as such; it would have been necessary, if not, “to go down” on the level from the kinds, even of the species! Elsewhere, in fact whole pieces maintain here by defect a classification more traditional, called to be modified by new analyzes or new publications…

Errors can in addition be made, and this tree remains in perpetual update; it is not advised to trust there. If you made modifications, take care to refer to you to the last classification (?) into force at the systematicians. Some external bonds indicates the topicality of it on Internet.

Tree of the alive one

The tree which has its place at this place, and to which the remarks apply above, is very “heavy” to download. If your connection allows it, will consult it on the page:

  • Phylogenetic tree of alive the .

See too

Internal bonds

One will consult also the trees, very reduced compared to the general tree, published in the articles:

Trees by taxon

One will find, with the article Eukaryota (phylogenetic classification), the base of the phylogenetic tree of alive for this branch, with the starting points towards the following articles. In this series of articles, each taxon of higher level is presented with one or more summarized trees, and the corresponding part of the Phylogenetic tree of alive the, as well as possible alternative assumptions, and a bibliography.

External bonds

Method

  • To use a phylogenetic classification out of school framework

  • methods of rebuilding of the phylogenetic trees on the site infobiogen (closed Web site)
  • a handbook of phylogeny in French

The tree of the alive one

(Thank you with them, which “inspired” the tree rebuilds here.)

Articles:

  • Thomas Rider-Smith: “Revised six-kingdom system off life has”, in Biological reviews 73 (1998)
  • Jan Zrzavy: “The interrelationships off metazoan parasitic… ”, 2001
  • Thomas Rider-Smith: “The phagotrophic origin off eukaryotes and phylogenetic classification off Protozoa”, 2002
  • Kenneth Mr. Halanych: “The New View off Animal Phylogeny”, 2004
  • Sina Mr. Adl '' and Al '': “The New Higher Level Classification off Eukaryotes”, 2005

Internet sites:

  • Tree off Life Web Project
  • NCBI Taxonomy
  • Museum of paleontology of the University of California, Berkeley
  • Mikko' S Phylogeny Files
  • Palaeos and Palaeos.org
  • Systema naturae 2000
  • the tree of the life of the University of Montpellier
  • Molecular phylogeny off amoeboid protists, Université of Geneva
  • Micro*scope
  • Protsville
  • Angiosperm Phylogeny Website
  • Man and Mollusc

Random links:Ålesund | Luquet | Bingu wa Mutharika | Desert of Agriates | Baccalaureat sciences and technologies of agronomy and the alive one