a logical value indicating whether the diagonal of the distance matrix should be printed by print.dist
upper
a logical value indicating whether the upper triangle of the distance matrix should be printed by print.dist
Details
Let A a table containing allelic frequencies with t populations (rows) and m alleles (columns).
Let ν the number of loci. The locus j gets m(j) alleles.
m=∑_{j=1}^{ν} m(j)
For the row i and the modality k of the variable j, notice the value a_{ij}^k (1 ≤q i ≤q t, 1 ≤q j ≤q ν,
1 ≤q k ≤q m(j)) the value of the initial table.
a_{ij}^+=∑_{k=1}^{m(j)}a_{ij}^k and p_{ij}^k=frac{a_{ij}^k}{a_{ij}^+}
Let P the table of general term p_{ij}^k p_{ij}^+=∑_{k=1}^{m(j)}p_{ij}^k=1, p_{i+}^+=∑_{j=1}^{ν}p_{ij}^+=ν, p_{++}^+=∑_{j=1}^{ν}p_{i+}^+=tν
The option method computes the distance matrices between populations using the frequencies p_{ij}^k.
Distance 1:
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.
Distance 2:
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).
Distance 3:
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.
Distance 4:
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.