Tree of life (biology)

The tree of life is a metaphor which expresses the idea that all life is related by common descent.
Charles Darwin was the first to use this metaphor in modern biology. It had been used many times before for other purposes.
The "evolutionary tree" shows the relationships among various biological groups. It includes data from DNA, RNA and protein analysis.
Tree of life work is a product of traditional comparative anatomy, and modern molecular evolution and molecular clock research. Below is a simplified version of present-day understanding. 
Precursors.
Lamarck.
Jean-Baptiste Lamarck (1744–1829) produced the first branching tree of animals in his "Philosophie Zoologique" (1809). It was an upside-down tree starting with worms and ending with mammals. However, Lamarck did not believe in common descent of all life. Instead, he believed that life consists of separate parallel lines advancing from simple to complex.
Hitchcock.
The American geologist Edward Hitchcock (1763–1864) published in 1840 the first tree of life based on paleontology in his "Elementary Geology". On the vertical axis are paleontological periods. Hitchcock made a separate tree for plants (left) and animals (right). The plant and animal trees are not connected at the bottom of the chart. Furthermore, each tree starts with multiple origins. However, they were not "evolutionary" trees, because Hitchcock believed that a deity was the agent of change.
Vestiges.
The first edition of Robert Chambers' "Vestiges of the Natural History of Creation" was published anonymously in 1844. It contained a tree-like diagram in the chapter 'Hypothesis of the development of the vegetable and animal kingdoms'. It shows a model of embryological development where fish (F), reptiles (R), and birds (B) represent branches from a path leading to mammals (M).
In the text this branching tree idea is tentatively applied to the history of life on earth: "there may be branching".p191
Darwin's tree of life.
Charles Darwin (1809–1882) was the first to produce an evolutionary tree of life. He was very cautious about the possibility of reconstructing the history of life. In "On the Origin of Species" (1859) Chapter IV he presented an abstract diagram of a theoretical tree of life for species of an unnamed large genus (see figure).
In Darwin's own words: "Thus, the small differences distinguishing varieties of the same species, will steadily tend to increase till they come to equal the greater differences between species of the same genus, or even of distinct genera."
This is a branching pattern with no names given to species, unlike the more linear tree Ernst Haeckel made years later.
In his summary to the section as revised in the 6th edition of 1872, Darwin explains his views on the Tree of Life:
The tree of life today.
The model of a tree is still considered valid for eukaryotic life forms. Research into the earliest branches of the eukaryote tree suggests a tree with either four supergroups, or two supergroups. There does not yet appear to be a consensus; in a review article, Roger and Simpson conclude that "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution".
Biologists now recognize that the prokaryotes, the bacteria and archaea have the ability to transfer genetic information between unrelated organisms through horizontal gene transfer (HGT). Recombination, gene loss, duplication, and gene creation are a few of the processes by which genes can be transferred within and between bacterial and archaeal species, causing variation that is not due to vertical transfer.
There is emerging evidence of HGT occurring within the prokaryotes at the single and multicell level and the view is now emerging that the tree of life gives an incomplete picture of life's evolution. It was a useful tool in understanding the basic processes of evolution but cannot explain the full complexity of the situation.