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- First detection of Nosema ceranae in honey bees (Apis mellifera L.) of the Macaronesian archipelago of MadeiraPublication . Lopes, Ana; Martín-Hernández, Raquel; Higes, Mariano; Segura, Sara K.; Henriques, Dora; Pinto, M. AliceThe Microsporidia Nosema ceranae is an invasive pathogen affecting honey bee health, particularly in warm climates. In this study, N. ceranae was detected for the first time in honey bees (Apis mellifera L.) of the Madeira archipelago, indicating that this pathogen is now spreading across the entire Macaronesia. Nosema apis was not detected, and the high prevalence (67.7%) of N. ceranae indicates its dominance over N. apis.
- Projeto BEEHAPPY: sanidade da abelha melífera (Apis mellifera L.) dos Açores: comparação dos padrões epidemiológicos num laboratório natural únicoPublication . Pinto, M. Alice; Henriques, Dora; Rodrigues, Pedro João; Miranda, Joachim; Martín-Hernández, Raquel; Amaral, Joana S.O BEEHAPPY é um projeto financiado pela Fundação para a Ciência e a Tecnologia (FCT), é coordenado pelo CIMO e envolve uma equipa de 16 especialistas multidisciplinares provenientes de várias instituições nacionais (CIMO-Centro de Investigação de Montanha, REQUIMTE-Rede de Química e Tecnologia, CEDRI -Centro de Investigação em Digitalização e Robótica Inteligente) e estrangeiras (SLU-Swedish University of Agricultural Sciences, CIAPA-IRIAF- Centro de Investigación Apícola y Agroambiental- Instituto Regional de Investigación y Desarrollo Agralimentario y Forestal, INIA-Peru- Instituto Nacional de Innovación Agraria). O BEEHAPPY centra-se nas populações de abelha dos Açores e tem como principais objectivos (i) o estudo da interação entre a abelha e as suas principais doenças (viroses e Nosemose) e (ii) o desenvolvimento de ferramentas com vista a identificar as populações de abelha (ferramenta informática) e avaliar a autenticidade do mel dos Açores (ferramenta molecular), o qual apresenta um grande potencial comercial. Para se atingirem tais objetivos, irão ser executadas 10 tarefas dedicadas à abelha (Tarefas 1, 4, 5, 6, 7, 8, 9), patogénios (Tarefas 1, 2, 3) e mel (Tarefa 10; Figura 1).
- Viral genetic landscape in the honey bee populations of the Azores archipelagoPublication . Lopes, Ana Rita; Miranda, Joachim; Martín-Hernández, Raquel; Pinto, M. AliceHoney bee decline can be attributed to many stressors, including pathogens and parasites, such as varroa and its vectored viruses. The global honey bee trade poses an important risk of pathogen dissemination. The arrival of varroa in the Azores because of (illegal) queen importations is clear evidence of that. Varroa was Ƥrst detected on Pico in 2000, on Flores in 2001, and on Faial in 2008. The other six islands of the archipelago remain mite-free. Therefore, the Azores provide an interesting setting to study the impact of varroa in the viral landscapes, adding to previous studies. In July/August of 2014/2015 we sampled 402 colonies distributed across 8 islands. These were screened for DWV, BQCV and LSV by RT-qPCR and the positive samples were further examined by high-throughput sequencing (HTS) to uncover whether varroa has altered the viral genetic composition. Of the 8 islands, São Jorge and Terceira had no DWV-positive colonies and Pico and Flores showed the highest DWV prevalence. BQCV and LVS were detected on all the islands. The HST data indicated that DWV-A, -B, and -C variants were all present in the Azores, although with varying prevalences (DWV-A: 56%; DWV-C: 31.2%; DWV-B: 12.2%). The phylogenetic tree revealed a geographic pattern, in which most of the DWV variants from São Miguel and Santa Maria formed a clade with the DWV-C reference, whereas Pico, Faial, Flores, and Graciosa clustered with the DWV-A reference. Interestingly, the DWV-A sequences from Pico were more closely related with those from Faial than with those from Flores. If the DWV-A variant was introduced with varroa, then the illegal queen imports on Pico and Flores had independent origins, whereas the DWV-A variants on Faial might have originated from Pico. DWV-A and B have acquired a world-wide distribution in the wake of varroa, while variants DWV-C and DWV-D have become extremely rare, one plausible scenario is that DWV-C was one of the original genotypes in the Azores predating varroa and has been replaced by the variants A and B, due to their superior adaptation to varroamediated transmission. Also of interest is the distinct clade formed by the BQCV and LSV sequences of São Miguel and Santa Maria, as well as the independent cluster formed by Flores sequences supporting the previous scenario. All these Ƥndings will be discussed in this communication.
- 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.
- 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.
- Epidemiology of the microsporidium nosema ceranae in four mediterranean countriesPublication . Jabal-Uriel, Clara; Barrios, Laura; Bonjour-Dalmon, Anne; Caspi-Yona, Shiran; Chejanovsky, Nor; Erez, Tal; Henriques, Dora; Higes, Mariano; Le Conte, Yves; Lopes, Ana; Meana, Aranzazu; Alice Pinto, M.; Teixeira, Amílcar; Reyes-Carreño, Maritza; Soroker, Victoria; Martín-Hernández, RaquelNosema ceranae is a highly prevalent intracellular parasite of honey bees’ midgut worldwide. This Microsporidium was monitored during a long-term study to evaluate the infection at apiary and intra-colony levels in six apiaries in four Mediterranean countries (France, Israel, Portugal, and Spain). Parameters on colony strength, honey production, beekeeping management, and climate were also recorded. Except for São Miguel (Azores, Portugal), all apiaries were positive for N. ceranae, with the lowest prevalence in mainland France and the highest intra-colony infection in Israel. A negative correlation between intra-colony infection and colony strength was observed in Spain and mainland Portugal. In these two apiaries, the queen replacement also influenced the infection levels. The highest colony losses occurred in mainland France and Spain, although they did not correlate with the Nosema infection levels, as parasitism was low in France and high in Spain. These results suggest that both the effects and the level of N. ceranae infection depends on location and beekeeping conditions. Further studies on host-parasite coevolution, and perhaps the interactions with other pathogens and the role of honey bee genetics, could assist in understanding the difference between nosemosis disease and infection, to develop appropriate strategies for its control.
- Standard methods and good practices in Apis honey bee omics researchPublication . Techer, Maeva A.; Chakrabarti, Priyadarshini; Caesar, Lílian; Eynard, Sonia E.; Farrell, M. Catherine; Foster, Leonard J.; Gorrochategui-Ortega, June; Henriques, Dora; Li-Byarlay, Hongmei; Morré, Jeffrey T.; Newton, Irene L. G.; Parejo, Melanie; Pinto, M. Alice; Vignal, Alain; Zarraonaindia, Iratxe; McAfee, AlisonIn the past decades, COLOSS members have joined forces multiple times to develop and condense standard methods related to research on honey bees, their pests, pathogens, and colony products. This led to the publication of four open-access BEEBOOK volumes that have been utilized by researchers worldwide. Among the chapters, “Standard methods for molecular research in Apis mellifera,” written by Evans and collaborators in 2013, has been a cornerstone for the standardization of honey bee molecular studies. However, since sequencing technologies and analyzing algorithms have made tremendous progress, many described methods require updating. In parallel, other Apis species’ genomes have now been sequenced, thus opening new research avenues in a comparative framework. In this chapter, we add to the methods previously covered by Evans et al. in 2013 and provide updated methodology where necessary, including worked examples and bioinformatic analysis pipe-lines. We also cover topics which were not previously covered in depth, such as sequencing ancient samples, population genomics, proteomics, and sampling honey bee colony products for microbiome studies, among others. Our hope is for this to become a lasting resource for honey bee scientists as the field continues to advance.
- Genomic DNA extraction from honey bee (Apis mellifera) queen spermathecal contentPublication . Yadró, Carlos A.; Lopes, Ana Rita; Henriques, Dora; Musin, Eduard; Wegener, Jakob; Pinto, M. AliceGenetic analysis of the honey bee spermathecal content can be particularly useful to provide an estimate of the genetic diversity and purity of the surrounding populations. Here we compared the concentration and quality of DNA extracted from queen spermatheca using four commercial kits to determine the best method to obtain DNA suitable for single nucleotide polymorphism genotyping by next-generation sequencing. The four kits were tested with different adjustments in the lysis incubation time, use of RNA-carrier, elution conditions and number of re-elutions. Only the use of QIAamp DNA Microkit with 3 h of lysis incubation, the addition of RNA-carrier and multiple re-elutions produced a DNA concentration over the required threshold.
- Maternal diversity patterns of Ibero-Atlantic populations reveal further complexity of Iberian honeybeesPublication . Pinto, M. Alice; Henriques, Dora; Neto, Margarida; Guedes, Helena; Muñoz, Irene; Azevedo, João; De la Rúa, PilarDissecting complex diversity patterns typically exhibited by organisms of hybrid zones is among the greatest challenges in evolutionary biology. This has been a long-standing goal of numerous Iberian honeybee studies. Herein, we further contribute to this goal by a fine-scale maternal survey of the Portuguese honeybee populations. In addition to confirm a predicted African ancestry of Portuguese populations and negligible levels of C-lineage introgression, our fine-scale survey revealed unparalleled levels of African maternal diversity and a remarkable north–south cline formed by African haplotypes of distinct ancestry. This survey further highlights the distinctiveness of Apis mellifera iberiensis by showing the existence of highly contrasting diversity patterns between the Atlantic and Mediterranean populations. Our findings further support an ancient natural invasion of the Iberian Peninsula possibly by Apis mellifera intermissa and also by Apis mellifera sahariensis. Protecting this African legacy is of unquestionable importance, especially with Iberia becoming warmer and dryer.
- A landscape genetics approach to unravel the complex evolutionary history of the Iberian honey bee hybrid zonePublication . Pinto, M. Alice; Johnston, J. Spencer; Azevedo, João; Brandão, Andreia; Moura, Inês; Muñoz, Irene; De la Rúa, Pilar; Patton, John C.While landscape genetics is in its infancy, it is a rapidly growing research field in part owing to the increasing availability of powerful molecular and analytical tools. By integrating landscape ecology, spatial statistics and population genetics, landscape genetics is allowing an unprecedented understanding of the microevolutionary processes shaping genetic variation, which has important implications for the advance of ecological and evolutionary knowledge. The Iberian honey bee provides a great model system to address evolutionary questions using a landscape genetics framework. First, previous studies suggest that the Iberian honey bee has a hybrid origin and hybrid zones have been favored by evolutionary biologists as powerful natural laboratories to study evolutionary processes. Second, with the publication of the honey bee genome and development of high‐density SNP markers, powerful tools are now available to dissect the relative importance of neutral and adaptive forces in shaping the Iberian honey bee hybrid zone, a goal of central importance as it leads to more robust inferences of demographic history and to identification of adaptive divergence. Herein, we will present an ongoing research project on the Iberian honey bee hybrid zone where the tools of landscape genetics and population genomics will be combined to unravel the challenging evolutionary history of the Iberian honey bee.