Browsing by Author "Low, Matthew"
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- Human-mediated introgression and Varroa destructor shaped the genetic structure of honey bee populations in the AzoresPublication . Henriques, Dora; Lopes, Ana; Low, Matthew; Pinto, M. AliceThe evolutionary trajectory of island populations can be rapidly altered by human-mediated migration, a process further exacerbated when immigrants introduce invasive parasites, creating new selective pressures. Using customised SNP panels constructed with genome-wide diagnostic loci, we describe the genetic changes in honey bee populations inhabiting the Azores archipelago. As part of a breeding initiative in the 1980s, these populations were recurrently exposed to beekeeper-mediated gene flow from a highly divergent commercial line (C lineage) until the arrival of the Varroa mite to the Azores in 2000, which prompted a honey bee importation ban. Admixture analysis revealed a spatially heterogeneous introgression landscape in the Azores. Four of the five mite-free islands (Santa Maria, S & atilde;o Miguel, Terceira, and S & atilde;o Jorge) presented negligible levels of C-lineage introgression (mean Q-value: 0.004-0.091) despite repeated C-lineage importations in the past. In contrast, the three mite-infested islands (Pico, Faial, and Flores) presented high levels of introgression (mean Q-value: 0.156-0.261). The mite-free island of Graciosa harboured the most admixed population (mean Q-value: 0.392), which is consistent with efforts to eradicate the historical population and replace it with C-lineage honey bees during the implementation of the breeding program. Bayesian inference modelling indicated that the presence of a C-lineage maternal origin and Varroa were associated with increased introgression proportions (100% posterior probability), increasing the mean Q-value by 0.049 and 0.118, respectively. Our findings indicate that these anthropogenic processes altered the historically introduced gene pool and provide a foundation for developing effective conservation strategies to protect honey bees in the Azores.
- Lake Sinai virus in Azorean Honey bees: Understanding the impact of Varroa destructor on prevalence, loads, and strain distributionPublication . Lopes, Ana; Low, Matthew; Martín-Hernández, Raquel; Miranda, Joachim; Pinto, M. AliceLake Sinai virus (LSV) is a pathogen affecting honey bees worldwide. It was first discovered in 2009 in Lake Sinai, USA, and manifests as a multi-strain virus. The Azores archipelago comprises islands with and without Varroa destructor, offering a unique setting for studying viral epidemiology. Building upon insights from the heterogeneous distribution of Deformed wing virus (DWV) strains, which was modulated by varroa’s invasion, this study sought to evaluate prevalence, load, and diversity of LSV in the Azores, and explore potential changes in the viral landscape attributable to the mite’s presence. In July/August of 2014/15 and 2020, 494 colonies were sampled across the archipelago. These were screened for LSV using RT-qPCR with a primer pair that allowed detection of at least four strains (LSV-1,-2,-3, and -4). Positive samples were further examined by highthroughput sequencing (HTS). The impact of varroa on prevalence and loads was evaluated using general linear mixed models in the framework of Bayesian analysis. LSV was detected on all islands (prevalence range: 7.7%–89.9%), with varroa’s presence significantly increasing prevalence (mean increase: 19.5±9.5, Probability of increase=97.6%). HTS identified two known strains (LSV-2, LSV-3) and one novel strain (LSV-9). Phylogenetic reconstruction revealed a strong geographic structure in which LSV-2 was found dominating all varroa-infested islands (Flores, Faial, and Pico) and one varroa-free island (São Jorge). LSV-3 and LSV-9 dominated varroa-free islands, Graciosa and Terceira, and São Miguel and Santa Maria, respectively. Viral loads varied greatly among islands, from 4.77 log10 copies/bee to 8.71 log10 copies/bee. Varroa’s presence affected LSV-2 loads, with a mean increase of 2.5±0.7 log10 copies/bee (Pr=100%). Our Żndings highlight mitedriven evolutionary changes in LSV in the Azores and identify a novel strain dominating the easternmost islands, coinciding with the unique refuge of DWV-C existing in this part of the archipelago.
- Origins, diversity, and adaptive evolution of DWV in the honey bees of the Azores: the impact of the invasive mite Varroa destructorPublication . Lopes, Ana Rita; Low, Matthew; Martín-Hernández, Raquel; Pinto, M. Alice; Miranda, JoachimDeformed wing virus (DWV) is a honey bee virus, whose emergence from relative obscurity is driven by the recent host-switch, adaptation, and global dispersal of the ectoparasitic mite Varroa destructor (a highly efficient vector of DWV) to reproduction on honey bees (Apis mellifera). Our study examines how varroa affects the continuing evolution of DWV, using the Azores archipelago, where varroa is present on only three out of the eight Islands, as a natural experimental system for comparing different evolutionary conditions and trajectories. We combined qPCR of 494 honey bee colonies sampled across the archipelago with amplicon deep sequencing to reveal how the DWV genetic landscape is altered by varroa. Two of the varroa-free Islands were also free of DWV, while a further two Islands were intriguingly dominated by the rare DWV-C major variant. The other four Islands, including the three varroa-infested Islands, were dominated by the common DWV-A and DWV-B variants. The varroa-infested Islands had, as expected, an elevated DWV prevalence relative to the uninfested Islands, but not elevated DWV loads, due the relatively high prevalence and loads of DWV-C on the varroa-free Islands. This establishes the Azores as a stable refuge for DWV-C and provides the most convincing evidence to date that at least some major strains of DWV may be capable of not just surviving, but actually thriving in honey bees in the absence of varroa-mediated transmission. We did not detect any change in DWV genetic diversity associated with island varroa status but did find a positive association of DWV diversity with virus load, irrespective of island varroa status.
- Varroa destructor shapes the unique viral landscapes of the honey bee populations of the Azores archipelagoPublication . Lopes, Ana Rita; Low, Matthew; Martín-Hernández, Raquel; Miranda, Joachim; Pinto, M. AliceThe worldwide dispersal of the ectoparasitic mite Varroa destructor from its Asian origins has fundamentally transformed the relationship of the honey bee (Apis mellifera) with several of its viruses, via changes in transmission and/or host immunosuppression. The extent to which honey bee-virus relationships change after Varroa invasion is poorly understood for most viruses, in part because there are few places in the world with several geographically close but completely isolated honey bee populations that either have, or have not, been exposed long-term to Varroa, allowing for separate ecological, epidemiological, and adaptive relationships to develop between honey bees and their viruses, in relation to the mite's presence or absence. The Azores is one such place, as it contains islands with and without the mite. Here, we combined qPCR with meta-amplicon deep sequencing to uncover the relationship between Varroa presence, and the prevalence, load, diversity, and phylogeographic structure of eight honey bee viruses screened across the archipelago. Four viruses were not detected on any island (ABPV-Acute bee paralysis virus, KBV-Kashmir bee virus, IAPV-Israeli acute bee paralysis virus, BeeMLV-Bee macula-like virus); one (SBV-Sacbrood virus) was detected only on mite-infested islands; one (CBPV-Chronic bee paralysis virus) occurred on some islands, and two (BQCV-Black queen cell virus, LSV-Lake Sinai virus,) were present on every single island. This multi-virus screening builds upon a parallel survey of Deformed wing virus (DWV) strains that uncovered a remarkably heterogeneous viral landscape featuring Varroa-infested islands dominated by DWV-A and -B, Varroa-free islands na & iuml;ve to DWV, and a refuge of the rare DWV-C dominating the easternmost Varroa-free islands. While all four detected viruses investigated here were affected by Varroa for one or two parameters (usually prevalence and/or the Richness component of ASV diversity), the strongest effect was observed for the multi-strain LSV. Varroa unambiguously led to elevated prevalence, load, and diversity (Richness and Shannon Index) of LSV, with these results largely shaped by LSV-2, a major LSV strain. Unprecedented insights into the mite-virus relationship were further gained from implementing a phylogeographic approach. In addition to enabling the identification of a novel LSV strain that dominated the unique viral landscape of the easternmost islands, this approach, in combination with the recovered diversity patterns, strongly suggests that Varroa is driving the evolutionary change of LSV in the Azores. This study greatly advances the current understanding of the effect of Varroa on the epidemiology and adaptive evolution of these less-studied viruses, whose relationship with Varroa has thus far been poorly defined.