Everything about Molecular Systematics totally explained
Molecular phylogeny, also known as
molecular systematics, is the use of the structure of
molecules to gain information on an organism's evolutionary relationships. The result of a molecular
phylogenetic analysis is expressed in a so-called
phylogenetic tree.
Techniques and applications
Every living
organism contains
DNA,
RNA, and
proteins. Closely related organisms generally 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. 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.
One application of molecular phylogeny is in
DNA barcoding, where the species of an individual organism is identified using small sections of
mitochondrial 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.
The effect on traditional
biological classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered.
Theoretical background
Early attempts at molecular systematics were also termed as
chemotaxonomy and made use of proteins,
enzymes,
carbohydrates and other molecules which were separated and characterized using techniques such as
chromatography. These have been largely replaced in recent times by
DNA sequencing which produces the exact sequences of
nucleotides or
bases in either DNA or RNA segments extracted using different techniques. These are generally considered superior for evolutionary studies since the actions of evolution are ultimately reflected in the genetic sequences. At present it's 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's 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 4
1000 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; ideally a substantial sample of individuals of the target
species or other
taxon are used however many current studies are based on single individuals. 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've 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 isn't 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's 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.
Characteristics and assumptions of molecular systematics
This example illustrates several characteristics of molecular systematics and its underlying assumptions.
- Molecular systematics is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be monophyletic.
- Molecular systematics often uses the molecular clock assumption that quantitative similarity of genotype is a sufficient measure of the recency of genetic divergence. Particularly in relation to speciation, this assumption could be wrong if either
- some relatively small genotypic modification acted to prevent interbreeding between two groups of organisms, or
- in different subgroups of the organisms being considered, genetic modification proceeded at different rates.
- In animals, it's often convenient to use mitochondrial DNA for molecular systematic analysis. However, because in mammals mitochondria are inherited only from the mother, this isn't fully satisfactory, because inheritance in the paternal line might not be detected: in the example above, Vilà et al cite more limited studies with chromosomal DNA that support their conclusions.
These characteristics and assumptions are not wholly uncontroversial among biological systematists. As a cladistic method, molecular systematics is open to the same criticisms as cladistics in general. It can also be argued that it's a mistake to replace a classification based on visible and ecologically relevant characteristics by one based on genetic details that may not even be expressed in the phenotype. However the molecular approach to systematics, and its underlying assumptions, are gaining increasing acceptance. As gene sequencing becomes easier and cheaper, molecular systematics is being applied to more and more groups, and in some cases is leading to radical revisions of accepted taxonomies.
History of molecular phylogeny
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 didn't 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.
Further Information
Get more info on 'Molecular Systematics'.
|
External Link Exchanges
Do you know how hard it is to get a link from a large encyclopaedia? Well we're different and will prove it. To get a link from us just add the following HTML to your site on a relevant page:
<a href="http://molecular_phylogeny.totallyexplained.com">Molecular phylogeny Totally Explained</a>
Then simply click through this link from your web page. Our crawlers will verify your link, extract the title of your web page and instantly add a link back to it. If you like you can remove the words Totally Explained and embed the link in article text.
As long as your link remains in place, we'll keep our link to you right here. Please play fair - our crawlers are watching. Your site must be closely related to this one's topic. Any kind of spamming, dubious practises or removing the link will result in your link from us being dropped and, potentially, your whole site being banned. |
