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OPTION 5 - Basic Information

(adapted from the original Genepop 4.0 documentation written by Francois Rousset)

This option 5 provides information such as allele frequencies, genotype frequencies, Fis estimates for each allele following Weir and Cockerham (1984), global estimate of Fis according to Weir and Cockerham (1984) and Robertson and Hill (1984), and gene diversities. Previous versions of Genepop showed relatively little interest for gene diversities ('heterozygosities') per se. However, these computations turn out to be sometimes useful.

Suboption 2 allows one to compute multilocus heterozygosities per individual, which may be useful e.g. in studies of inbreeding depression. They will appear in the last table of the output file if your entered each individual as a 'sample', (separated by a 'Pop') in the input file. Suboption 3 will likewise return multilocus averages of the squared difference between the size of the two alleles of an individual.

Sub-option 1 - Allele and genotype frequencies

This option provides basic information on the data set.
For each locus in each sample, several variables are calculated:

• allele frequencies.
• observed and expected genotype proportions.
• Fis estimates for each allele following Weir and Cockerham (1984).
• global estimate of Fis according to Weir and Cockerham (1984) (or W&C) and Robertson and Hill (1984) (or R&H).
• observed and 'expected' number of homozygotes and heterozygotes. 'Expected' here means the expected numbers, conditional on observed allelic counts, under HW equilibrium; the difference from naive products of observed allele frequencies is sometimes called Levene's correction, after Levene (1949).
• the genotypic matrix.

A table of allele frequencies for each locus and for each sample is also computed.

Sub-option 2 - Identity-based gene diversities and F_IS

This option computes diversity within individuals ('1-Qintra'), and among individuals within samples ('1-Qinter') per locus per sample, and averaged over samples or over loci. Corresponding Fis estimates are also computed. This option takes the observed frequencies of identical pairs of genes as estimates ( ) of corresponding probabilities of identity ( ) and then simply computes diversities as : gene diversity within individuals (1-Qintra), and among individuals within samples (1-Qinter), per locus per sample, and averaged over samples or over loci. One-locus F_IS estimates are also computed in a way consistent with Weir & Cockerham (1984). No estimate is given when no information is available (e.g. no estimate of diversity between individuals within a sample when only one individual has been genotyped).

For haploid data, only the gene diversity among individuals is computed. Multilocus estimates ignore haploid loci, or on the contrary ignore diploid loci if the setting EstimationPloidy=Haploid is used. Single-locus estimates are computed for both haploid and diploid loci irrespective of this setting.

Sub-option 3 - Allele size-based gene diversities and r_IS

Option 5.3 is analogous to option 5.2. This option computes measures of diversity based on allele size, namely mean squared allele size differences within individuals ('MSDintra'), and among individuals within samples ('MSDinter'), per locus per sample, and averaged over samples or over loci. Corresponding r_IS estimates (the FIS analog, see the appendix) are also computed. This option assumes that allele size corresponds to the allele entries in the data file. See Option 6, suboptions 3 and 4, for details.

For haploid data, only the mean squared dierence MSDinter among individuals is computed. Multilocus estimates ignore haploid loci, or on the contrary ignore diploid loci if the setting EstimationPloidy=Haploid is used. Single-locus estimates are computed for both haploid and diploid loci irrespective of this setting.

For all suboptions, results are returned via your web browser which you can then save to you local machine. You may also choose to have them emailed to you.