Molecular phylogenetics
[6] The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl, Emanuel Margoliash, Linus Pauling, and Walter M.
[7] Applications of molecular systematics were pioneered by Charles G. Sibley (birds), Herbert C. Dessauer (herpetology), and Morris Goodman (primates), followed by Allan C. Wilson, Robert K. Selander, and John C. Avise (who studied various groups).
[8] Early attempts at molecular systematics were also termed chemotaxonomy and made use of proteins, enzymes, carbohydrates, and other molecules that were separated and characterized using techniques such as chromatography.
In general, these are considered superior for evolutionary studies, since the actions of evolution are ultimately reflected in the genetic sequences.
Once the divergences between all pairs of samples have been determined, the resulting triangular matrix of differences is submitted to some form of statistical cluster analysis, and the resulting dendrogram is examined in order to see whether the samples cluster in the way that would be expected from current ideas about the taxonomy of the group.
Statistical techniques such as bootstrapping and jackknifing help in providing reliability estimates for the positions of haplotypes within the evolutionary trees.
Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms.
One method, including a comprehensive step-by-step protocol on constructing a phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test (testing best-fitting substitution models), and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol.
The following step consists of performing a multiple sequence alignment, which is the fundamental basis of constructing a phylogenetic tree.
The normalized Hamming distance and the Jukes-Cantor correction formulas provide the degree of divergence and the probability that a nucleotide changes to another, respectively.
Bootstrapping is an approach that is commonly used to measure the robustness of topology in a phylogenetic tree, which demonstrates the percentage each clade is supported after numerous replicates.
The flow chart displayed on the right visually demonstrates the order of the five stages of Pevsner's molecular phylogenetic analysis technique that have been described.
[13] Molecular systematics is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be monophyletic.
Firstly, sequences must be aligned; then, issues such as long-branch attraction, saturation, and taxon sampling problems must be addressed.
[14][15] The tree-building method also brings with it specific assumptions about tree topology, evolution speeds, and sampling.
