Meta-analysis of genetic diversity and intercolony relatedness among reproductives in commercial honey bee populations
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ABSTRACT:
SUBMITTER: Tarpy D
PROVIDER: S-EPMC10926410 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:The genetic diversity of the USA honey bee (Apis mellifera L.) populations was examined through a molecular approach using two mitochondrial DNA (mtDNA) markers. A total of 1,063 samples were analyzed for the mtDNA intergenic region located between the cytochrome c oxidase I and II (COI-COII) and 401 samples were investigated for the NADH dehydrogenase 2 (ND2) coding gene. The samples represented 45 states, the District of Colombia and two territories of the USA. Nationwide, three maternal evolutionary lineages were identified: the North Mediterranean lineage C (93.79%), the West Mediterranean lineage M (3.2%) and the African lineage A (3.01%). A total of 27 haplotypes were identified, 13 of them (95.11%) were already reported and 14 others (4.87%) were found to be novel haplotypes exclusive to the USA. The number of haplotypes per state/territory ranged between two and eight and the haplotype diversity H ranged between 0.236-0.763, with a nationwide haplotype diversity of 0.597. Furthermore, the honey bee populations of the USA were shown to rely heavily (76.64%) on two single haplotypes (C1 = 38.76%, C2j = 37.62%) of the same lineage characterizing A. m. ligustica and A. m. carnica subspecies, respectively. Molecular-variance parsimony in COI-COII and ND2 confirmed this finding and underlined the central and ancestral position of C2d within the C lineage. Moreover, major haplotypes of A. m. mellifera (M3a, M7b, M7c) were recorded in six states (AL, AR, HI, MO, NM and WA). Four classic African haplotypes (A1e, A1v, A4, A4p) were also identified in nine states and Puerto Rico, with higher frequencies in southern states like LA, FL and TX. This data suggests the need to evaluate if a restricted mtDNA haplotype diversity in the US honey bee populations could have negative impacts on the beekeeping sustainability of this country.
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Project description:Plant pollination by the western honey bee Apis mellifera is an irreplaceable agroecological and economic cornerstone currently under threat. Recent colony loss has been consistently linked to the increased prevalence of deformed wing virus (DWV), an Iflavirus transmitted from the ecoparasitic mite Varros destructor. While DWV has been detected in the honey bee brain and causally linked to behavioral impairment, the molecular impact of infection on brain gene expression is largely unknown. Recently, we discovered that two published and two new brain transcriptomic studies conducted in our lab contained DWV contamination in over 99% of sequenced honey bee samples. This unanticipated finding sharply contrasted with the experimental paradigms of these four studies, as no physical or behavioral signs of DWV were detected in any of the 335 individual honey bees sampled. We took this opportunity to perform a meta-analysis and test the hypothesis that DWV influences brain gene expression, a relationship which could be linked to the massive depopulation events observed around the world. Results from our study support commonalities in the molecular consequences of DWV in the honey bee brain and implicate specific genes and biological processes associated with infection. Next, we used single-cell RNA-Sequencing to implicate glia as active responders to viral infection. Finally, we performed viral gene expression analysis on a subset of samples and found DWV type A as well as a previously unreported A-B recombinant in the brain. We present this meta-analysis as a first step toward addressing a potential missing link between viral infection and behavior in honey bees.
2020-02-04 | GSE130785 | GEO
Project description:This dataset represents RNA-Seq data that was later found to have widespread contamination with Deformed Wing virus (DWV). It has been incorporated in a meta-analysis of DWV's impact on brain gene expression
2020-02-04 | GSE130702 | GEO
Project description:This dataset represents RNA-Seq data that was later found to have widespread contamination with Deformed Wing virus (DWV). It has been incorporated in a meta-analysis of DWV's impact on brain gene expression
2020-02-04 | GSE130700 | GEO
Project description:The diversity and local differentiation of honey bees are subjects of broad general interest. In particular, the classification of Ethiopian honey bees has been a subject of debate for decades. Here, we conducted an integrated analysis based on classical morphometrics and a putative nuclear marker (denoted r7-frag) for elevational adaptation to classify and characterize these honey bees. Therefore, 660 worker bees were collected out of 66 colonies from highland, midland and lowland agro-ecological zones (AEZs) and were analyzed in reference to populations from neighboring countries. Multivariate morphometric analyses show that our Ethiopian samples are separate from Apis mellifera scutellata, A. m. jemenitica, A. m. litorea and A. m. monticola, but are closely related to A. m. simensis reference. Linear discriminant analysis showed differentiation according to AEZs in the form of highland, midland and lowland ecotypes. Moreover, size was positively correlated with elevation. Similarly, our Ethiopian samples were differentiated from A. m. monticola and A. m. scutellata based on r7-frag. There was a low tendency towards genetic differentiation between the Ethiopian samples, likely impacted by increased gene flow. However, the differentiation slightly increased with increasing elevational differences, demonstrated by the highland bees that showed higher differentiation from the lowland bees (FST = 0.024) compared to the midland bees (FST = 0.015). An allelic length polymorphism was detected (denoted as d) within r7-frag, showing a patterned distribution strongly associated with AEZ (X2 = 11.84, p < 0.01) and found predominantly in highland and midland bees of some pocket areas. In conclusion, the Ethiopian honey bees represented in this study are characterized by high gene flow that suppresses differentiation.
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Project description:BackgroundThe Algerian honey bee population is composed of two described subspecies A. m. intermissa and A. m. sahariensis, of which little is known regarding population genomics, both in terms of genetic differentiation and of possible contamination by exogenous stock. Moreover, the phenotypic differences between the two subspecies are expected to translate into genetic differences and possible adaptation to heat and drought in A. m. sahariensis. To shed light on the structure of this population and to integrate these two subspecies in the growing dataset of available haploid drone sequences, we performed whole-genome sequencing of 151 haploid drones.ResultsIntegrated analysis of our drone sequences with a similar dataset of European reference populations did not detect any significant admixture in the Algerian honey bees. Interestingly, most of the genetic variation was not found between the A. m. intermissa and A. m. sahariensis subspecies; instead, two main genetic clusters were found along an East-West axis. We found that the correlation between genetic and geographic distances was higher in the Western cluster and that close-family relationships were mostly detected in the Eastern cluster, sometimes at long distances. In addition, we selected a panel of 96 ancestry-informative markers to decide whether a sampled bee is Algerian or not, and tested this panel in simulated cases of admixture.ConclusionsThe differences between the two main genetic clusters suggest differential breeding management between eastern and western Algeria, with greater exchange of genetic material over long distances in the east. The lack of detected admixture events suggests that, unlike what is seen in many places worldwide, imports of queens from foreign countries do not seem to have occurred on a large scale in Algeria, a finding that is relevant for conservation purposes. In addition, the proposed panel of 96 markers was found effective to distinguish Algerian from European honey bees. Therefore, we conclude that applying this approach to other taxa is promising, in particular when genetic differentiation is difficult to capture.
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