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Encyclopedia > Molecular systematics

Molecular systematics is a phrase used to indicate a branch of the traditional field of systematics that utilizes molecular biology techniques. The evolutionary relationships of organisms are studied using their DNA, RNA and protein sequences to establish their systematic positions. They make use of cladistic and phylogenetic methods. These techniques help in objectively determining the importance of characters or markers and in evaluating evolutionary hypotheses. Image File history File links Please see the file description page for further information. ... Molecular phylogeny is the use of the structure of molecules to gain information on an organisms evolutionary relationships. ... In biology, systematics is the study of the diversity of organism characteristics, and especially how they relate evolutionarily. ... Molecular biology is the study of biology at a molecular level. ... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the biological development of a cellular form of life or a virus. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... Greek clados = branch) or phylogenetic systematics is a branch of biology that determines the evolutionary relationships of living things based on derived similarities. ... A phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually of a species. ...


Related fields include bioinformatics, molecular genetics and molecular evolution. From the mid 1990s molecular systematics has introduced major revisions in many groups of organisms. Map of the human X chromosome (from the NCBI website). ... Molecular genetics is the field of biology which studies the structure and function of genes at a molecular level. ... Molecular evolution is the process of the genetic material in populations of organisms changing over time. ... See also 1990s, the band Germans dancing on the Berlin Wall in late 1989, the symbol of the cold war divide falls down as the world unites in the 1990s. ...


Theoretical background

Early attempts at molecular systematics where 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 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 DNA sequencing is the process of determining the nucleotide order of a given DNA fragment, called the DNA sequence. ... A nucleotide is an organic molecule consisting of a heterocyclic nucleobase (a purine or a pyrimidine), a pentose sugar (deoxyribose in DNA or ribose in RNA), and a phosphate or polyphosphate group. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... Figure 1: Chromosome. ... A haplotype, a contraction of the phrase haploid genotype, is the genetic constitution of an individual chromosome. ...

  • 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; 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. A taxon (plural taxa), or taxonomic unit, is a grouping of organisms (named or unnamed). ...


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. The genotype is the specific genetic makeup (the specific genome) of an individual, in the form of DNA. Together with the environmental variation that influences the individual, it codes for the phenotype of that individual. ... DNA-DNA hybridization is a method in genetics to measure the degree of genetic similarity between DNA 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. In the mathematical discipline of linear algebra, a triangular matrix is a special kind of square matrix where the entries below or above the main diagonal are zero. ... Data clustering is a common technique for data analysis, which is used in many fields, including machine learning, data mining, pattern recognition, image analysis and bioinformatics. ... A dendrogram is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm (see cluster analysis). ... A clade is a term belonging to the discipline of cladistics. ... For Wikipedia statistics, see m:Statistics Statistics is the science and practice of developing human knowledge through the use of empirical data expressed in quantitative form. ... Look up bootstrapping in Wiktionary, the free dictionary. ... Jackknifing means the accidental folding of an articulated vehicle (i. ...


Characteristics and assumptions of molecular systematics

This example illustrates several characteristics of molecular systematics and its underlying assumptions.

  1. Molecular systematics is an essentially cladistic approach: it assumes that classification must correspond to phylogenetic descent, and that all valid taxa must be at least paraphyletic and preferably monophyletic.
  2. 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
    1. some relatively small genotypic modification acted to prevent interbreeding between two groups of organisms, or
    2. in different subgroups of the organisms being considered, genetic modification proceeded at different rates.
  3. In animals, it is often convenient to use mitochondrial DNA for molecular systematic analysis. However, because in mammals 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, VilĂ  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. Paraphyletic - Wikipedia /**/ @import /skins-1. ... In phylogenetics, a group is monophyletic (Greek: of one stem) if all organisms in that group are known to have developed from a common ancestral form, and all descendants of that form are included in the group. ... The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in genetics, which researchers use to date when two species diverged. ... Charles Darwins first sketch of an evolutionary tree from his First Notebook on Transmutation of Species (1837) Speciation is the theory of the evolutionary process by which new biological species are believed by some to arise. ... Orders Multituberculata (extinct) Palaeoryctoides (extinct) Triconodonta (extinct) Subclass Australosphenida Ausktribosphenida Monotremata Subclass Eutheria (excludes extinct ancestors) Afrosoricida Anagaloidea (extinct) Arctostylopida (extinct) Artiodactyla Carnivora Cetacea Chiroptera Cimolesta (extinct) Cingulata Creodonta (extinct) Condylarthra (extinct) Dermoptera Desmostylia (extinct) Dinocerata (extinct) Embrithopoda (extinct) Hyracoidea Insectivora Lagomorpha Leptictida (extinct) Litopterna (extinct) Macroscelidea Mesonychia (extinct) Notoungulata... Electron micrograph of a mitochondrion showing its mitochondrial matrix and membranes In cell biology, a mitochondrion (plural mitochondria) (from Greek μιτος or mitos, thread + κουδριον or khondrion, granule) is a membrane-enclosed organelle, found in most eukaryotic cells. ...


See also


  Results from FactBites:
 
Molecular systematics - Wikipedia, the free encyclopedia (892 words)
Molecular systematics is a phrase used to indicate a branch of the traditional field of systematics that utilizes molecular biology techniques.
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.
Molecular systematics often uses the molecular clock assumption that quantitative similarity of genotype is a sufficient measure of the recency of genetic divergence.
Phylogenetics Factsheet (5910 words)
Systematics reaches beyond taxonomy to elucidate new methods and theories that can be used to classify species based on similarity of traits and possible mechanisms of evolution, a change in the gene pool of a population over time.
Molecular Clock Hypothesis: states that nucleotide substitutions, or amino acid substitutions if proteins are being compared, occur at a constant rate, that is, the degree of difference between two sequences can be used to assign a date to the time at which their ancestral sequence diverged.
Furthermore, molecular clocks require calibration with fossils to determine timing of origin of clades, and thus their accuracy is crucially dependent on the fossil record, or lack thereof, for the groups under study.
  More results at FactBites »

 
 

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