rgenotypes.arich: Estimates allelic richness from population data sets with...

In UWMAlberto-Lab/StandArich2: Standardizes n to estimate allelic richness and plots

Estimates allelic richness from population data sets with varying number of resampled genotypes

Description

Permutes the data from n=1 to n=N (N sample size for each pop) for each population and for each n a number of times set by number of replicates. For each replicate the number of alleles for each locus in the permuted sample is returned as well as the mean and st dev across all loci. Then a tables with mean allelic richness across replicates for each n for each population is returned, as well as the st dev across replicates for each n for each population summarizes the

Usage

rgenotypes.arich((Popdata, n.replicates,loc.labels)

Arguments

Popdata	A data table with all populations on top of each other. Lines correspond to individual genotypes. The first column has the population codes, the 2nd column the individual codes. The following columns have the allele codes, in integers, using three or two digits (but be consistent!). Missing data is represented by the value 999.There is no header in this file
n.replicates	The number of replicates used for each n resampling step
loc.labels	A character vector with the names of loci used in the order found in Popdata

Details

In order to estimate population allelic richness that it comparable among populations, the mean number of alleles per locus is estimated for population data sets with varying number of resampled genotypes (g), for all possible n values from n=1 to n=N, N being the total number of genotypes observed in each population.

Standardization of N to an equal n for all populations is necessary to obtain comparable estimates across populations. The multiple random reduction (Leberg 2002b) employed here gives similar estimates to the rarefraction method (Petit et al. 1998)

With StandArich.2 this functions removes the need to use stand.Arich function after using rgenotypes.arich. All results are now returned in a list

Value

The function returns a list with three elements R, A and A.sd. R is a table containing information for all permutations, showing number of alleles observed at each n per loci, the mean number of alleles observed across loci (i.e., allelic richness per permutation), and the standard deviation of the number of alleles observed across loci. A is a table with the mean allelic richness across all permutations for each level of n for each population. Population data is organized by rows and different n values by columns. Finally, A.sd is a table with the standard deviation across all permutations for each level of n for each population. The table format is identical to A, population by rows and n by columns. To get the allelic richness for a particular value of n for all populations, often the smallest sample size across all populations, just extract the column with corresponding n index from A.

Author(s)

Filipe Alberto, Department of Biological Sciences, University of Wisconsin-Milwaukee [e-mail]

References

Alberto F, Arnaud-Haond S, Duarte CM, Serrao EA (in press) Genetic diversity of a clonal angiosperm near its range limit: the case of Cymodocea nodosain the Canary Islands. Marine Ecology Progress Series

Leberg PL (2002) Estimating allelic richness: Effects of sample size and bottlenecks. Mol Ecol 11: 2445-2449

Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conservation Biology, 12: 844-855

See Also

plot.allele.freq, allele.genotype.plot

Examples

data(Exdata)
rgenotypes.arich(Exdata,g=10,loc.labels=paste("L",1:8,sep="."))
{manip}

UWMAlberto-Lab/StandArich2 documentation built on March 28, 2023, 1:10 a.m.