Calculate Genetic Distance for a genind or genclone object.

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Description

These functions are modified from the function dist.genpop to be applicable for distances between individuals.

Usage

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nei.dist(x, warning = TRUE)

edwards.dist(x)

rogers.dist(x)

reynolds.dist(x)

provesti.dist(x)

prevosti.dist(x)

Arguments

x

a genind, genclone, or matrix object.

warning

If TRUE, a warning will be printed if any infinite values are detected and replaced. If FALSE, these values will be replaced without warning. See Details below.

Details

It is important to be careful with the interpretation of these distances as they were originally intended for calculation of between-population distance. As Nei's distance is the negative log of 0:1, this means that it is very possible to obtain distances of infinity. When this happens, infinite values are corrected to be 10 * max(D) where D is the distance matrix without infinite values.

Value

an object of class dist with the same number of observations as the number of individuals in your data.

Note

Prevosti's distance is identical to diss.dist, except that diss.dist is optimized for a larger number of individuals (n > 125) at the cost of required memory. Both prevosti.dist and provesti.dist are the same function, provesti.dist is a spelling error and exists for backwards compatibility.

These distances were adapted from the adegenet function dist.genpop to work with genind objects.

Author(s)

Zhian N. Kamvar (poppr adaptation) Thibaut Jombart (adegenet adaptation) Daniel Chessel (ade4)

References

Nei, M. (1972) Genetic distances between populations. American Naturalist, 106, 283-292.

Nei M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 23, 341-369.

Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.

Edwards, A.W.F. (1971) Distance between populations on the basis of gene frequencies. Biometrics, 27, 873-881.

Cavalli-Sforza L.L. and Edwards A.W.F. (1967) Phylogenetic analysis: models and estimation procedures. Evolution, 32, 550-570.

Hartl, D.L. and Clark, A.G. (1989) Principles of population genetics. Sinauer Associates, Sunderland, Massachussetts (p. 303).

Reynolds, J. B., B. S. Weir, and C. C. Cockerham. (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics, 105, 767-779.

Rogers, J.S. (1972) Measures of genetic similarity and genetic distances. Studies in Genetics, Univ. Texas Publ., 7213, 145-153.

Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.

Prevosti A. (1974) La distancia genetica entre poblaciones. Miscellanea Alcobe, 68, 109-118.

Prevosti A., Oca\~na J. and Alonso G. (1975) Distances between populations of Drosophila subobscura, based on chromosome arrangements frequencies. Theoretical and Applied Genetics, 45, 231-241.

For more information on dissimilarity indexes:

Gower J. and Legendre P. (1986) Metric and Euclidean properties of dissimilarity coefficients. Journal of Classification, 3, 5-48

Legendre P. and Legendre L. (1998) Numerical Ecology, Elsevier Science B.V. 20, pp274-288.

See Also

aboot diss.dist poppr.amova

Examples

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data(nancycats)
(nan9   <- popsub(nancycats, 9))
(neinan <- nei.dist(nan9))
(ednan  <- edwards.dist(nan9))
(rodnan <- rogers.dist(nan9))
(reynan <- reynolds.dist(nan9))
(pronan <- prevosti.dist(nan9))

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