Molecular systematics: Encyclopedia II - Molecular systematics - Theoretical background

Molecular systematics - Theoretical background

Molecular systematics has been made possible by the availability of techniques for DNA sequencing, which allow the determination of the exact sequence of nucleotides or bases in either DNA or RNA, not necessarily restricted to genes. At present it is still a long and expensive process to sequence the entire DNA of an organism (its genome), and this has been done for only a few species. However it is quite feasible to determine the sequence of a defined area of a particular chromosome. Typical molecular systematic analyses require the sequencing of around 1000 base pairs. At any location within such a sequence, the bases found in a given position may vary between organisms. The particular sequence found in a given organism is referred to as its 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 turns out as a matter of empirical fact that

• only a minority of sites show any variation at all
• 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; preferably this is from a substantial sample of individuals of the target species or other taxon. But in reality it does happen that conclusions are published on the taxonomic disposition of an entire family (with hundreds of species) based on a single individual. Haplotypes of individuals of closely related, but supposedly 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). Usually the difference between organisms is 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.

A different approach is to determine the divergences between the genotypes of individuals by DNA-DNA hybridisation instead of by determining and comparing gene sequences. The advantage of using hybridisation rather than gene sequencing is that is based on the entire genotype, rather than a particular section of DNA. Its disadvantage is that precise haplotypes are not determined.

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 significance tests are available to examine whether it is possible to reject the hypothesis that a particular of haplotypes lie in a single clade.

Adapted from the Wikipedia article "Theoretical background", under the G.N U Free Docmentation License. Please also see http://en.wikipedia.org/wiki