Relatedness measurement

If DNA from two different species are mixed, denatured, and allowed to cool slowly so that reannealing can occur, artificial hybrid duplexes may form, provided the DNA from one species is similar in nucleotide sequence to the DNA of the other. The degree of hybridization is a measure of the sequence similarity or relatedness between the two species. Depending on the conditions of the experiment, about 25% of the DNA from a human forms hybrids with mouse DNA, implying that some of the nucleotide sequences (genes) in humans are very similar to those in mice. Mixed RNA DNA hybrids can be created in vitro if single-stranded DNA is allowed to anneal with RNA copies of itself, such as those formed when genes are transcribed into mRNA molecules. 

Proteins serving the same function in different species may have different primary structures. The extent of the differences is a measure of their relatedness on the evolutionary tree of life. 

The definition of a species, whether of higher plants, animals, or microorganisms, has as its basis the principle of genetic isolation. Simply put, members of a species are considered interfertile, whereas genetically separate species are not.3 When measurements of DNA reassociation are used to define species, the extent of DNA relatedness expected between members of a species must first be determined. The discussion at the conclusion of this chapter addresses this issue and offers guidelines for predicting genetic relatedness from the extent of DNA complementarity. 

Methods for measuring DNA relatedness fall into two general categories (1) the free-solution technique, in which all of the reactants are solubilized, and (2) filter membrane technique, in which the DNA of one strain is immobilized on nitrocellulose or other filter materials and DNA... 

It is sometimes necessary to remove rapidly renaturing sequences from DNA samples before measuring the extent of relatedness, and this can be done on HA columns as described by Price et al.6 Self-annealing of the radiolabeled probe DNA can be minimized if the ratio of target to probe is kept to at least 1000 1. It may also be useful to determine the amount of self-annealing to be certain that this does not bias the calculated relatedness. Finally, a simplified version of the HA procedure was described by Lachance24 in which HA-containing minicolumns maintained under controlled temperatures are used to separate the duplexed DNAs. 

Fig. 1. Correlation of fertility with extent of nuclear DNA complementarity among heterothallic yeasts showing low to intermediate DNA relatedness. Mating responses parallel measurable DNA reassociation. These and other data suggest that strains showing 70% or greater DNA relatedness will, in most cases, represent members of the same biological species.10 37 P., Pichia /., Issatchenkia F., Filobasidiella.

AquaporinS arc on the small side, consist of about 260 amino acids, and have a molecular weight of about 30 kDa. They weave six times in or out of the plasma membrane (Preston eta ., 1994 Rainaff af., 1995 Deen al., 1994). The aquaporins are related to each other, and constitute a family of proteins. This means that if one were to line up all the polypeptides, one on top of the other, one would find that about half of all amino acids occur at identical positions, when viewing their order from the N terminus to the C terminus. The technical term for measuring relatedness in any protein is sequence homology,... 

A modified Tanimoto coeffident was also proposed to measure the degree of relatedness of the shapes of two structures [Hahn, 1997]. 

Warwick, R.M. Clarke, K.R. (2001). Practical Measures of Marine Biodiversity Based on Relatedness of Species. Oceanography and Marine Biology, An Annual Review, Vol. 39, pp. 207-231. 

Cross-reactivity. The ability of an antibody or a T cell specific for one antigen to react with a second antigen a measure of relatedness between two antigenic substances and/or polyspecificity of the antibody molecule (e.g. some rheumatoid factors) or of the T cell receptor. 

Such competition assays can be used to determine the similarity of antigens in the same system competing for a single antiserum. The slopes of the competition lines can be compared to obtain a measure of antigenic relatedness. 

Lansman RA, Shade RO, Shapira JF, Avise JC (1981) The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. III. techniques and potential applications. J Mol Evol 17 214-226... 

Hydroxyapatite (HA, calcium phosphate hydroxide) can be used to separate double-stranded (ds) from single-stranded (ss) DNA, and hence to measure the extent of DNA DNA hybridization. This is an important criterion in the taxonomy of bacteria, in particular, as it is often critical for the definition of species and genera. The DNA from a reference strain is radioactively labelled and hybridized in phosphate buffer solution with an excess of unlabelled DNA from each of the strains to be compared with it. Hybridization goes essentially to completion. No membrane-bound DNA is involved. HA in phosphate buffer of suitable molarity is used to sq>arate the hybrid dsDNA from ssDNA, and both column and batch procedures have been used for this purpose. The percentage relatedness between the reference strain and each of the other strains is obtained by expressing the radioactivity associated with dsDNA as a percentage of the total radioactivity in solution. 

MEE Multilocus enzyme electrophoresis (MEE) can be used to estimate genetic relatedness among strains or species by measuring the relative mobility of cellular enzymes under nondenaturing conditions. The allelic profiles or MEE types may be used to compare... 

The relationships among samples are revealed by their projections (scores) on the latent variables. This information is displayed in bivariate scoreplots. Similar samples group together in the score plots. The orthonormality between latent variable Wa vectors means that the distance between samples represents a quantitative measure of relatedness. Standardized scores can be used. In most instances, however, scores weighted in accordance with the size (proportional to ta ) of the latent variables are preferred. These are the scores used in Equation 6.1. Score plots are very useful for visual detection of atypical samples, that is, outliers. 

---