Molecular phylogenetics

History of molecular phylogenetics

The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl, Emanuel Margoliash, Linus Pauling, and Walter M. Fitch.^[1] 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). Work with protein electrophoresis began around 1956. Although the results were not quantitative and did not initially improve on morphological classification, they provided tantalizing hints that long-held notions of the classifications of birds, for example, needed substantial revision. In the period of 1974–1986, DNA-DNA hybridization was the dominant technique.^[2]

Techniques and applications

Every living Sanger sequencing in 1977 it became possible to isolate and identify these molecular structures.^[3][4]

The most common approach is the comparison of mitochondrial DNA or chloroplast DNA. Another application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever-more-popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on evidence known as genetic fingerprinting.

A comprehensive step-by-step protocol on constructing 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^[5]

Theoretical background

Early attempts at molecular systematics were also termed as haplotype. In principle, since there are four base types, with 1000 base pairs, we could have 4¹⁰⁰⁰ distinct haplotypes. However, for organisms within a particular species or in a group of related species, it has been found empirically that only a minority of sites show any variation at all and most of the variations that are found are correlated, so that the number of distinct haplotypes that are found is relatively small.

In a molecular systematic analysis, the haplotypes are determined for a defined area of genetic material; a substantial sample of individuals of the target species or other taxon is used, however many current studies are based on single individuals. Haplotypes of individuals of closely related, but different, taxa are also determined. Finally, haplotypes from a smaller number of individuals from a definitely different taxon are determined: These are referred to as an out group. The base sequences for the haplotypes are then compared. In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: This is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example the insertion of a section of nucleic acid in one haplotype that is not present in another). The difference between organisms is usually re-expressed as a percentage divergence, by dividing the number of substitutions by the number of base pairs analysed: the hope is that this measure will be independent of the location and length of the section of DNA that is sequenced.

An older and superseded approach was to determine the divergences between the genotypes of individuals by DNA-DNA hybridisation. The advantage claimed for using hybridisation rather than gene sequencing was that it was based on the entire genotype, rather than on particular sections of DNA. Modern sequence comparison techniques overcome this objection by the use of multiple 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, or not. Any group of haplotypes that are all more similar to one another than any of them is to any other haplotype may be said to constitute a clade. Statistical techniques such as bootstrapping and jackknifing help in providing reliability estimates for the positions of haplotypes within the evolutionary trees.

Limitations of molecular systematics

Molecular systematics is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be monophyletic.

The recent discovery of extensive horizontal gene transfer among organisms provides a significant complication to molecular systematics, indicating that different genes within the same organism can have different phylogenies.

In addition, molecular phylogenies are sensitive to the assumptions and models that go into making them. They face problems like long-branch attraction, saturation, and taxon sampling problems: This means that strikingly different results can be obtained by applying different models to the same dataset.^[6]

See also

• Computational phylogenetics
• Microbial phylogenetics
• Molecular evolution
• PhyloCode
• Phylogenetic nomenclature

Notes and references

Further reading

• Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates Incorporated. ISBN 0-87893-177-5.
• Hillis, D. M. & Moritz, C. 1996. Molecular systematics. 2nd ed. Sinauer Associates Incorporated. ISBN 0-87893-282-8.
• Page, R. D. M. & Holmes, E. C. 1998. Molecular evolution: a phylogenetic approach. Blackwell Science, Oxford. ISBN 0-86542-889-1.
• Soltis, P.S., Soltis, D.E., and Doyle, J.J. (1992) Molecular systematics of plants. Chapman & Hall, New York. ISBN 0-41202-231-1.
• Soltis, P.S., Soltis, D.E., and Doyle, J.J. (1998) Molecular Systematics of Plants II: DNA Sequencing. Kluwer Academic Publishers Boston, Dordrecht, London. ISBN 0-41211-131-4.
• San Mauro, D.; Agorreta, A. (2010). "Molecular systematics: a synthesis of the common methods and the state of knowledge". Cellular & Molecular Biology Letters 15 (2): 311–341.  

External links

• NCBI – Systematics and Molecular Phylogenetics
• The promise of a DNA taxonomy (Mark L. Blaxter)
• from Encyclopedia Britannica.