Computational protocol: Genetic structure of the gentle Africanized honey bee population (gAHB) in Puerto Rico

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Protocol publication

[…] The number of alleles, allele frequencies, and observed (Ho) and expected (He) heterozygosity of each microsatellite locus were estimated using GENEPOP 4.0 []. GENEPOP 4.0 was also used to test for linkage disequilibrium and HWE. A regression analysis was used to relate the allelic frequency of European population from Puerto Rico with the reference European population. The reference European population was taken from [,]. Our results were compared with Texas results from [] that were divided in two groups: first (1991-1996) and second (1997-2001) group, representing early and later stages of Africanization. Estimates of population structure and gene flow were assessed using F-statistics, also with GENEPOP 4.0. Unbiased gene diversity (Hd), and allelic richness (Rs) per locus and population sample were computed using FSTAT version 2.9.3 package []. In FSTAT, the sample size for allelic richness estimation is fixed as the smallest number of individuals typed for a locus in a sample, which in this study was 72 (Locus ED1). Population structure was also analyzed using a Bayesian model-based clustering method provided in STRUCTURE 2.3.3 [,]. This program infers structure of populations using allele frequencies of unlinked markers (microsatellites). The parameter set was programmed for independent alleles and individuals to have a mixed ancestry. The program was asked to place individuals from all populations into one and two groups, and in three runs the analyses consisted of 10000, 100000, and 1000000 burn-in replicates, and run lengths of 10000, 100000, and 1000000 replicates. The best estimate of K or the number of populations was determined by looking at the values of log Pr(X/K) and the value of α [,]. In structure analysis we did not use Culebra samples, because the low sample number dissuaded us from doing the comparison. Single and multiloci Fst values were estimated using the weighed analysis of variance method by [] to measure genetic differentiation with the GENETIX 4.02 program []. We analyzed distant locations that appeared to be genealogically close on an unrooted neighbor joining tree based on genetic distance, constructed using the Phylip 3.57 program []. […]

Pipeline specifications

Software tools Genepop, PHYLIP
Application Population genetic analysis
Organisms Apis mellifera