Genetic distance measurement

The recombination frequency provides a measure of the genetic distance between any pair of linked loci. Genetic distances are often expressed in centiMorgans (cM). One centiMorgan is equal to a 1% recombination frequency between two loci (for example, two loci that are 10 cM apart would have a recombination frequency of 10%). Physically, 1 cM is approximately equal to 1 million base pairs of DNA (1 Mb). This relationship is only approximate, however, because crossover frequencies vary somewhat throughout the genome (e.g., crossovers are less common near centromeres and more common near telomeres). 

These authors tested 120 allele frequencies in 42 human populations. They calculated from these measurements genetic distances between the populations and estimated the times of their separation. They summarized their data, and thus constructed nine population clusters (Fig. 1). The greatest differences were between African and all non-African populations, in support of the theory that all present human beings derived from a wave of emigrants who left Africa approximately 100,000 years ago. 

Centimorgan A measure of genetic distance that tells how far apart physically two genes are, based on the frequency of recombination or crossover between the two gene loci. A frequency of 1% recombination in meiosis is 1 centimorgan and equals about 1 million base pairs. See Southern, E.M., Rrospects for a... 

The simplest method for developing a genetic distance matrix is the average distance method or UPGMA (58). This method is used not only to construct a phenogram, but it can also be used to construct a phylogenetic tree. In UPGMA, a measure of evolutionary distance is computed for all pairs of... 

Figure 4 Dendrogram of UPGMA cluster analysis of representative isolates from different hosts of the six European Epichloe spp E. clarkii is sexually compatible with the E. typhina mating population, but is characterized by a distinct morphology. The distance measure is based on Nei s genetic identity using allozyme variation at 12 loci. (Modified from Leuchtmann and Schardl, 1998.)...

Rogers JS (1972) Measures of genetic similarity and genetic distance. Studies in genetics VII. Univ Texas Publ 7213 145-153... 

F-statistics, by means of the Fjj index, allow the measure of genetic differences among populations that is, the extent to which the studied populations, taken as a whole, move away from panmixia (also known as Hardy-Weinberg equilibrium, HWE) and differ from each other. Fjj is therefore a measure of genetic distance between populations. This index is calculated as Hj - where Hj is the expected heterozygosity under HWE when aU individuals from all... 

Linkage map A map of the relative positions of genetic loci on a chromosome, constructed from data how often the loci are inherited together. The distance is measured in centimorgans (see also centimorgan) (cM). 

The correlation of the landscape measures the fitness similarity between a sequence and its d-mutant neighbors, where d is the number of mutations. As a sequence accumulates mutations, the fitness is increasingly altered. On smooth landscapes, the rate of fitness change is slow and therefore the landscape is correlated. Conversely, on rugged landscapes, the rate is more rapid and the landscape is uncorrelated. Studies of the relationship between fitness and distance have been used to quantitate the correlation among population ensembles on the RNA landscape (Fontana and Shuster, 1987), recombination dynamics (Born-holdt, 1998), and the success of genetic algorithms (Manderick et al., 1991 Jones and Forrest, 1995). 

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