Newfoundland Study
DNA sequenced from pooled samples was analysed to (1) identify metagenomic signatures and (2) to characterise allele frequencies in the context of several honey bee lineages.
Metagenomic analysis was performed on sequencing reads that did not align to the honey bee genome (Amel_HAv3.1) using the HoloBee-MoP database with kraken2, and the results formatted with Krona. Below are links for each sample analysed:
Variant allele frequencies for each sample were derived for AmelHap variants using the GATK Mutect2 variant caller. Ancestry estimates were derived for each sample by referencing the variant allele frequencies across a range of reference populations which C and M lineages from AmelHap, and C, M, and O lineages from SmartBees data.
The resulting ancestry estimates, based on the there being 4 genetic backgrounds, are presented in the bar chart beneath the genetic distance matrix opposite. The y axis indicates the stacked proportion of each ancestry, which was broadly consistent with the exception of BB763 which is predominantly of Italian (ligustica) background.
The genetic distance matrix above the bar chart indicates how genetically distant pairwise samples are based on Nei's D, where the darker the cell the more genetically distant the samples. The dendrograms adjacent to the rows and columns are based on the matrix values and broadly illustrate two clusters: (1) comprising disimilar samples (BB760, BB763, BB764) and another (2) comprising samples that are broadly similar.
