Genetics: Estimation of genetic differentiation measures

In SpadeR: Species-Richness Prediction and Diversity Estimation with R

Description

Genetics: Estimation allelic differentiation among subpopulations based on multiple-subpopulation genetics data. The richness-based indices include the classic Jaccard and Sorensen dissimilarity indices; the abundance-based indices include the conventional Gst measure, Horn, Morisita-Horn and regional species-differentiation indices.

Only Type (1) abundance data (datatype="abundance") is supported; input data for each sub-population include sample frequencies in an empirical sample of individuals. When there are multiple subpopulations, input data consist of an allele-by-subpopulation frequency matrix.

Usage

Genetics(X, q = 2, nboot = 200)

Arguments

X	a matrix, or a data.frame of allele frequencies.
q	a specified order to use to compute pairwise dissimilarity measures. If q = 0, this function computes the estimated pairwise Jaccard and Sorensen dissimilarity indices. If q = 1, this function computes the estimated pairwise equal-weighted and size-weighted Horn indices; If q = 2, this function computes the estimated pairwise Morisita-Horn and regional species-diffrentiation indices.
nboot	an integer specifying the number of bootstrap replications.

Value

a list of ten objects:

$info for summarizing data information.

$Empirical_richness for showing the observed values of the richness-based dis-similarity indices including the classic Jaccard and Sorensen indices.

$Empirical_relative for showing the observed values of the equal-weighted dis-similarity indices for comparing allele relative abundances including Gst, Horn, Morisita-Horn and regional differentiation measures.

$Empirical_WtRelative for showing the observed value of the dis-similarity index for comparing size-weighted allele relative abundances, i.e., Horn size-weighted measure based on Shannon-entropy under equal-effort sampling.

The corresponding three objects for showing the estimated dis-similarity indies are:
$estimated_richness, $estimated_relative and $estimated_WtRelative.

$pairwise and $dissimilarity.matrix for showing respectively the pairwise dis-similarity estimates (with related statistics) and the dissimilarity matrix for various measures depending on the diversity order q specified in the function argument.

$q for showing which diversity order q to compute pairwise dissimilarity.

References

Chao, A., and Chiu, C. H. (2016). Bridging the variance and diversity decomposition approaches to beta diversity via similarity and differentiation measures. Methods in Ecology and Evolution, 7, 919-928.

Chao, A., Jost, L., Hsieh, T. C., Ma, K. H., Sherwin, W. B. and Rollins, L. A. (2015). Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model. Plos One, 10:e0125471.

Jost, L. (2008). G_{ST} and its relatives do not measure differentiation. Molecular Ecology, 17, 4015-4026.

Examples

## Not run: 
# Type (1) abundance data 
data(GeneticsDataAbu)
Genetics(GeneticsDataAbu,q=2,nboot=200)

## End(Not run)

Example output

(1) BASIC DATA INFORMATION:

    The loaded set includes abundance (or frequency) data from 4 subpopulations
    and a total of 25 distinct alleles are found.

    Sample size in each subpopulation                           n1   = 70 
                                                                n2   = 96 
                                                                n3   = 98 
                                                                n4   = 92 

    Number of observed alleles in one subpopulation             D1   = 20 
                                                                D2   = 16 
                                                                D3   = 16 
                                                                D4   = 13 

    Number of observed shared alleles in two subpopulations     D12  = 13 
                                                                D13  = 12
                                                                D14  = 10
                                                                D23  = 14
                                                                D24  = 12
                                                                D34  = 11

    Number of bootstrap replications for s.e. estimate                 200 

(2) EMPIRICAL DIS-SIMILARITY INDICES: 

                                         Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based dis-similarity

        1-C04 (q=0, Sorensen)             0.1795       0.0243       0.1319       0.2271 
        1-U04 (q=0, Jaccard)              0.4667       0.0415       0.3854       0.5480 

    (b) Measures for comparing alleles relative abundances

        1-C14=1-U14 (q=1, Horn)           0.2044       0.0242       0.1569       0.2519 

        1-C24 (q=2, Morisita-Horn)        0.3259       0.0461       0.2355       0.4163 
        1-U24 (q=2, Regional diff.)       0.1078       0.0233       0.0621       0.1536 

        Gst                               0.0303       0.0060       0.0186       0.0419 

    (c) Measures for comparing size-weighted alleles relative abundances

        Horn size-weighted(q=1)           0.1933       0.0221       0.1499       0.2366 

(3) ESTIMATED DIS-SIMILARITY INDICES: 

                                         Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based dis-similarity

        1-C04 (q=0, Sorensen)             0.1524       0.0677       0.0197       0.2851 
        1-U04 (q=0, Jaccard)              0.4183       0.1190       0.1850       0.6516 

    (b) Measures for comparing alleles relative abundances

        1-C14=1-U14 (q=1, Horn)           0.2013       0.0278       0.1468       0.2558 

        1-C24 (q=2, Morisita-Horn)        0.2585       0.0524       0.1557       0.3612 
        1-U24 (q=2, Regional diff.)       0.0802       0.0237       0.0337       0.1266 

        Gst                               0.0218       0.0060       0.0100       0.0335 

    (c) Measures for comparing size-weighted alleles relative abundances

        Horn size-weighted (q=1)          0.1903       0.0243       0.1427       0.2379 

(4) ESTIMATED PAIRWISE DIS-SIMILARITY:

    -----------------------Measure 1-C22------------------------

    Estimator      Estimate        s.e.        95% Confidence Interval

    1-C22(1,2)     0.338           0.088          ( 0.165 , 0.512 )
    1-C22(1,3)     0.290           0.101          ( 0.093 , 0.488 )
    1-C22(1,4)     0.602           0.087          ( 0.431 , 0.774 )
    1-C22(2,3)     0.015           0.067          ( 0.000 , 0.146 )
    1-C22(2,4)     0.188           0.091          ( 0.009 , 0.368 )
    1-C22(3,4)     0.137           0.088          ( 0.000 , 0.309 )

    Average pairwise dis-similarity = 0.262 

    Pairwise dis-similarity matrix: 

    1-C22(i,j)1       2       3       4       
       1      0   0.338   0.290   0.602   
       2              0   0.015   0.188   
       3                      0   0.137   
       4                              0   

    -----------------------Measure 1-U22------------------------

    Estimator      Estimate        s.e.        95% Confidence Interval

    1-U22(1,2)     0.204           0.072         ( 0.063 , 0.344 )
    1-U22(1,3)     0.170           0.079         ( 0.016 , 0.324 )
    1-U22(1,4)     0.431           0.097         ( 0.240 , 0.622 )
    1-U22(2,3)     0.007           0.038         ( 0.000 , 0.082 )
    1-U22(2,4)     0.104           0.061         ( 0.000 , 0.224 )
    1-U22(3,4)     0.074           0.056         ( 0.000 , 0.184 )

    Average pairwise dis-similarity = 0.165 

    Pairwise dis-similarity matrix: 

    1-U22(i,j)1       2       3       4       
       1      0   0.204   0.170   0.431   
       2              0   0.007   0.104   
       3                      0   0.074   
       4                              0   

    NOTE: Any estimate greater than 1 is replaced by 1; any estimate less than 0 is replaced by 0.

SpadeR documentation built on May 2, 2019, 3:59 p.m.