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The idea of a tree of life arose from ancient notions of a ladder-like progression from lower into higher forms of life (such as in the Great Chain of Being).Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged.The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins.
The term polyphyly, or polyphyletic, derives from the two Ancient Greek words πολύς (polús) 'many, a lot of', and φῦλον (phûlon) 'genus, species', [8] [9] and refers to the fact that a polyphyletic group includes organisms (e.g., genera, species) arising from multiple ancestral sources.
The results are a phylogenetic tree—a diagram setting the hypothetical relationships between organisms and their evolutionary history. [4] The tips of a phylogenetic tree can be living taxa or fossils, which represent the present time or "end" of an evolutionary lineage, respectively. A phylogenetic diagram can be rooted or unrooted.
Molecular evolution is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree. [6]
[15] Darwin's tree is not a tree of life, but rather a small portion created to show the principle of evolution. Because it shows relationships (phylogeny) and time (generations), it is a timetree. In contrast, Ernst Haeckel illustrated a phylogenetic tree (branching only) in 1866, not scaled to time, and of real species and higher taxa. In his ...
The science that tries to reconstruct phylogenetic trees and thus discover clades is called phylogenetics or cladistics, the latter term coined by Ernst Mayr (1965), derived from "clade". The results of phylogenetic/cladistic analyses are tree-shaped diagrams called cladograms; they, and all their branches, are phylogenetic hypotheses. [12]
[6] HGT is thus a potential confounding factor in inferring phylogenetic trees from the sequence of one gene. For example, if two distantly related bacteria have exchanged a gene, a phylogenetic tree including those species will show them to be closely related even though most other genes have diverged substantially. For this reason it is ...