4.3.3.4. Genetic diversity measures and reconstruction of queen genotypes

The drone genotypes are obtained either directly, by genotyping drones caught in a DCA, or indirectly, by inferring their genotype from the worker offspring of a single queen.

  1. Construct tables with the genotypes of all drones for each sample set (see Tables 13 and 14).
    Note: Queen genotypes inferred from worker genotypes are given in parenthesis. Drone genotypes inferred from workers and queens are highlighted in bold.
  2. When using unlinked markers, rearrange the tables by grouping all individuals sharing allelic combinations in three or more loci to facilitate the identification and counting of their colonies of origin. The more loci the individuals share, the higher the probability they share a mother queen (see section 4.3.3.5. on non-detection errors below). When using linked markers (Shaibi et al., 2008), first group all individuals sharing the same allelic combination at all loci within each linkage group. The haplotypes found in each linkage group are equivalent to individual alleles.
  3. Exclude individuals that showed two or less successfully amplified loci, or that could not be assigned to a specific haplotype in at least one linkage group (because of low polymorphism or misamplifications at some loci).
  4. Introduce the alleles/haplotypes into a sibship reconstruction software (e.g. COLONY, Wang, 2004) to reconstruct the genotype of individual drone-producing queens.

 

Table 13. Genotypes obtained from genotyping drones.

Drone ID

Locus 1

Locus 2

Locus 3

1

a

c

a

2

a

b

b

3

b

a

c


Table 14.
Genotypes inferred from genotyping workers of a single queen.

Worker ID

Locus 1

(b/b)

Locus 2

(a/b)

Locus 3

(c/c)

1

a/b

c/a

a/c

2

a/b

b/a

b/c

3

b/b

a/b

c/c

 

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