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Molecular phylogenetics

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Molecular phylogenetics /məˈlɛkjʊlər flɵɪˈnɛtɪks/ is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.

History of molecular phylogeneticsEdit

Further information: History of molecular evolution


Techniques and applications Edit

Every living organism contains DNA, RNA, and proteins. In general, closely related organisms have a high degree of agreement in the molecular structure of these substances, while the molecules of organisms distantly related usually show a pattern of dissimilarity. Conserved sequences, such as mitochondrial DNA, are expected to accumulate mutations over time, and assuming a constant rate of mutation provides a molecular clock for dating divergence. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. Not until recent decades, however, has it been possible to isolate and identify these molecular structures.


Theoretical backgroundEdit


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 systematicsEdit


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.[3]

See alsoEdit


  1. Edna Suárez-Díaz & Victor H. Anaya-Muñoz (2008) History, objectivity, and the construction of molecular phylogenies. Stud. Hist. Phil. Biol. & Biomed. Sci. 39:451–468
  2. Ahlquist, Jon E., 1999: Charles G. Sibley: A commentary on 30 years of collaboration. The Auk, vol. 116, no. 3 (July 1999). A PDF or DjVu version of this article can be downloaded from the issue's table of contents page.
  3. DOI:10.1371/journal.pbio.1000602

Further readingEdit

  • 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.

External linksEdit

Topics in phylogenetics
Relevant fields: phylogenetics | computational phylogenetics | molecular phylogeny | cladistics
Current topics: PhyloCode | DNA barcoding
List of evolutionary biology topics

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