Output:
- A table with information on each excessively heterozygous locus,
including its number of observed genotypes, number of expected
genotypes, χ2 statistic, and p-values.
- A genlight object without excessively heterozygous loci.
- A vector with the names of the removed loci (i.e., excessively
heterozygous ones).
- Two plots: one ‘before’ plot with the heterozygosity of the loci
present in the input genlight, and one ‘after’ plot with the
heterozygosity of the loci present in the output genlight
(i.e., without excessively heterozygous loci).
Recommended use: We recommend caution when using this function,
because it has the potential to remove loci that reflect population
processes. For example, some loci may exhibit excessive heterozygosity
due to (i) recent admixture between previously isolated populations
(i.e., Wahlund-breaking), (ii) inbreeding avoidance, (iii) balancing
selection, such as heterozygous advantage. Therefore, the use of this
filter is best suited when there is previous understanding of the
system, and for studies assuming neutral loci.