Population Structure and Diversity in European Honey Bees (Apis mellifera L.)—An Empirical Comparison of Pool and Individual Whole-Genome Sequencing

Abstract

Background: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). Methods: We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. Results: Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. Conclusions: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.

Genetic Drift Shapes the Evolution of a Highly Dynamic Metapopulation

“…1 and table 1, supplementary table S1, Supplementary Material online) in order to sequence the pooled genotypes, called pool-seq. Pool-seq is a powerful and cost-efficient way to estimate the genome-wide allele frequencies of populations, as it provides allele frequency estimates of SNPs that are mostly comparable to individualbased sequencing at less cost and with less time (Chen et al 2022;Dorant et al 2019;Gautier et al 2013;Kurland et al 2019). We collected random subpopulation samples by sieving with hand-held plankton nets through the ponds, aiming for 50 animals per pond and excluding ponds with very small populations at the time of sampling to avoid disrupting natural dynamics.…”

Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid drones

“…Previous analyses on worldwide data sets were published, either by whole genome sequencing of workers (Chen et al, 2022 ; Dogantzis et al, 2021 ; Wallberg et al, 2014 ) or by sequencing the mitochondrial DNA (Tihelka et al, 2020 ). These were intended to understand worldwide populations, the geographical origins and migration routes of Apis mellifera , a topic still under debate.…”

Genetic drift shapes the evolution of a highly dynamic metapopulation

“…Our aim was to collect D. magna from all occupied ponds (subpopulations) in the core sampling area in late May/early June of 2014 (Figure 1, Table 1 and S1) in order to sequence the pooled genotypes, called pool-seq. Pool-seq is a powerful and cost-efficient way to estimate the genome-wide allele frequencies of populations, as it provides allele frequency estimates of SNPs that are mostly comparable to individual-based sequencing at less cost and with less time (Chen et al, 2022; Dorant et al, 2019; Gautier et al, 2013; Kurland et al, 2019). We collected random subpopulation samples by sieving with hand-held plankton nets through the ponds, aiming for 50 animals per pond and excluding ponds with very small populations at the time of sampling to avoid disrupting natural dynamics.…”