The phylogenetic tree

The phylogenetic tree is a diagram that shows the evolutionary interrelations between a
set of homologous characters in various biological species or other entities (homology is the
relationship of two characters that have descended from a common ancestor). The character can
be a protein sequence, a gene sequence, a structural trait, a behavioural feature, etc.

The ancestor is the tree trunk, the descendents are placed at the ends of the branches. The
distance between groups indicates the degree of relationship, that is, closely related groups are
located on branches close to one another. The branch length in some trees may be interpreted as
time periods or as amounts of change a certain characteristic has suffered.

Although Charles Darwin was not the first one to imagine such a representation (the
concept arose in ancient times and the first “tree of life” was published by the French botanist
Augustin Augier in 1801), he was the one to sketch an evolutionary “tree of life” and to
popularise the notion. In his book, The origin of species, Darwin explains his views on the
matter:

“The affinities of all the beings of the same class have sometimes been represented by a great
tree. I believe this simile largely speaks the truth. The green and budding twigs may represent
existing species; and those produced during former years may represent the long succession of
extinct species. At each period of growth all the growing twigs have tried to branch out on all
sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species
and groups of species have at all times overmastered other species in the great battle for life.”

There are several types of phylogenetic trees:

 rooted phylogenetic trees: a unique node corresponds to the most recent common
ancestor of the entities represented by the “leaves”;
 unrooted phylogenetic trees: it shows the relations between “leaves”, without identifying
the ancestor;
 a dendrogram is a broad term for the graphical representation of a phylogenetic tree
(dendro, from Greek dendron, which means tree);
 a cladogram is a phylogenetic tree whose branches do not represent time periods or
amounts of change; the diagram is only a branching pattern that focuses on the historical
sequence of the acquisition of novel characters;
 a chronogram is a phylogenetic tree that explicitly represents evolutionary time through
its branch lengths.
 Although a phylogenetic tree provides a significant insight into evolution and the degree of
kinship between species, it is important to remember that it does have limitations. For example,
trees based on genic data may not take into account several factors: DNA degradation over time,
DNA expression mutations, lateral gene transfers and recombination. Also, the builder must
make sure that the characters he will illustrate are homologous and not only similar, for
similarity can also point to homoplasy (similarity in species of different ancestry that is the result
of convergent evolution).