Molecular phylogeny
149544
212348176
2008-05-14T13:46:00Z
Eugene van der Pijll
22016
/* Techniques and applications */
'''Molecular phylogeny''', also known as '''molecular systematics''', is the use of the structure of [[molecule]]s to gain information on an organism's evolutionary relationships. The result of a molecular [[phylogenetics|phylogenetic]] analysis is expressed in a so-called [[phylogenetic tree]].
== Techniques and applications ==
Every living [[organism]] contains [[DNA]], [[RNA]], and [[protein]]s. 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, [[enzyme]]s, [[carbohydrate]]s 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 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 pair]]s. 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<sup>1000</sup> 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 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.
An older and superseded approach was to determine the divergences between the [[genotype]]s 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 (statistics)|bootstrapping]] and [[Resampling (statistics)#Jackknife|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 [[Cladistics|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 is often convenient to use mitochondrial DNA for molecular systematic analysis. However, because in [[mammal]]s [[mitochondrion|mitochondria]] are inherited only from the mother, this is not 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 is 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==
{{see|History of molecular evolution}}
Molecular systematics was pioneered by [[Charles Sibley|Charles G. Sibley]] ([[bird]]s), [[Herbert C. Dessauer]] ([[herpetology]]), and [[Morris Goodman]] ([[primate]]s), followed by [[Allan Wilson|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 [[bird]]s, for example, needed substantial revision. In the period of 1974–1986, [[DNA-DNA hybridization]] was the dominant technique.<ref>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 [http://elibrary.unm.edu/sora/Auk/v116n03/index.php table of contents page].</ref>
==Further reading==
*[[Joe Felsenstein|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.
==References==
{{reflist}}
==See also==
*[[molecular evolution]]
*[[computational phylogenetics]]
*[[PhyloCode]]
==External links==
* [http://www.ncbi.nlm.nih.gov/About/primer/phylo.html NCBI - Systematics and Molecular Phylogenetics]
{{phylo}}
[[Category:Phylogenetics]]
[[Category:Molecular evolution]]
[[ja:分子系統学]]
[[uk:Молекулярна філогенетика]]