Browsing by Author "Quaresma, Andreia"
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- An unprecedented large-scale survey of honey bee mitochondrial diversity in Europe: c-lineage dominance and the need for conservation effortsPublication . Li, Fernanda; Costa, Maíra; Lopes, Ana Rita; Gonçalves, Telma; Henriques, Dora; Quaresma, Andreia; Yadró Garcia, Carlos A.; Albo, Alexandre; Blažytė-Čereškienė, Laima; Brodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Charistos, Leonidas; Chlebo, Robert; Coffey, Mary F.; Dahle, Bjørn; Danneels, Ellen; Dobrescu, Constantin; Dupleix-Marchal, Anna; Filipi, Janja; Gajda, Anna; Gratzer, Kristina; Groeneveld, Linn Fenna; Hatjina, Fani; Johannesen, Jes; Kolasa, Michal; Körmendy-Rácz, János; Kovačić, Marin; Kristiansen, Preben; Martikkala, Maritta; McCormack, Grace P.; Martín-Hernández, Raquel; Pavlov, Borce; Pietropaoli, Marco; Poirot, Benjamin; Radev, Zheko; Raudmets, Aivar; René-Douarre, Vincent; Roessink, Ivo; Škerl, Maja Ivana Smodiš; Soland-Reckeweg, Gabriele; Titera, Dalibor; Steen, Jozef van der; Varnava, Andri; Vejsnæs, Flemming; Webster, Matthew T.; Fedoriak, Mariia M.; Zarochentseva, Oksana; Graaf, Dirk C.; Pinto, M. AliceEurope is home to ten Apis mellifera subspecies, which belong to three mitochondrial lineages: the Western European (M), Eastern European (C), and African (A). However, the long-standing human-mediated movement of queens, primarily of C-lineage ancestry, has threatened the genetic integrity of many of these native subspecies through introgression and replacement. This has led to the establishment of conservation programs to recover the native lines in some European countries. The maternally-inherited mitochondrial DNA (mtDNA), particularly the highly polymorphic intergenic region tRNAleu-cox2, has been the marker of choice for assessing honey bee variation and introgression at large geographical scales. Herein, we will show the results of the tRNAleu-cox2 variation obtained from over 1200 colonies sampled across the range of the ten subspecies and covering 33 European countries. These revealed that apart from a few countries (Portugal, Spain, and Ireland) and isolated protected populations, European populations are predominantly dominated by C-lineage haplotypes, and many native subspecies exhibit a signature of C-derived introgression. In conclusion, this unprecedented survey of honey bee diversity across Europe underscores the concerning dominance of C-lineage genetic variation, highlighting the urgent need for strategic conservation efforts to preserve the native genetic diversity of Apis mellifera.
- Applying reduce SNP assays for inferring C-lineage introgression patterns in Iberian honeybee populations of the Azores archipelagoPublication . Lopes, Ana; Neves, Cátia J.; Ferreira, Helena; Henriques, Dora; Quaresma, Andreia; Martín-Hernández, Raquel; Azevedo, João; Pinto, M. AliceThe genetic composition of the honeybee populations of the Macaronesian archipelago of the Azores is poorly known. Until now, only honeybee populations of the island of São Miguel have been surveyed for genetic variation through the use of the tRNAleu-cox2 intergenic mitochondrial DNA region and microsatellites. Here, we combine data from the mtDNA obtained with the DraI test (intergenic region) and from the nuclear DNA obtained with newly developed reduced SNP assays to provide a complete picture of introgression patterns in the Azorean honeybee populations at both mitochondrial and nuclear compartments. The sampling was carried out in 2014 and 2015 and comprised 474 colonies widely distributed across the 8 islands populated by honeybees. Our cyto-nuclear results show that C-derived introgression varies across the archipelago ranging from virtually pure populations of the Iberian honeybee in the island of Santa Maria (Q-values <5%) to highly introgressed populations in the island of Graciosa (Q-values>30%). The introgression levels are alarming and contrast with those of the Iberian honeybee populations of the mainland in Iberia, which are still virtually free of C-derived introgression, despite frequent importation of commercial queens.
- Autent+ Desenvolvimento de abordagem inovadoras com vista à valorização e exploração do potencial de mercado do mel PortuguêsPublication . Amaral, Joana S.; Quaresma, Andreia; Rodrigues, Pedro João; Rufino, José; Henriques, Dora; Calaim, Luís; Gaspar, Albino; Pinto, M. AliceA FENAPICOLA candidatou-se, como proponente, a uma medida de investigação aplicada, tendo convidado o Instituto Politécnico de Bragança (IPB) como entidade parceira, envolvendo este último uma equipa multidisciplinar de 6 investigadores provenientes dos centros de investigação CIMO (Centro de Investigação de Montanha) e CEDRI (Centro de Investigação em Digitalização e Robótica Inteligente). Assim foi criado o projeto AUTENT+, um projeto financiado pelo Instituto de Financiamento da Agricultura e Pescas (IFAP), em resultado da candidatura submetida ao Plano Apícola Nacional (PAN) 2020/2022, medida 5.1 "Apoio a projetas de investigação aplicada”. O AUTENT + tem como principal objetivo a valorização do mel nacional como um produto autêntico e sustentável, através de abordagens que visam diferenciar, acrescentar valor e o potencial de mercado a este produto. Para tal, o projeto centra-se no desenvolvimento de metodologias inovadoras com vista à deteção de adulterações do mel, em particular no que respeita à origem botânica e entomológica/geográfica, e no desenvolvimento de ferramentas que permitam , de uma forma simples, informar o consumidor sobre as caraterísticas do produto que adquirem.
- Bio-Monitoring of environmental pollution using the citizen science approachPublication . Steen, Jozef van der; Amaral, Joana S.; Baveco, Hans; Blanco Muñoz, Patricia; Brodschneider, Robert; Brusbardis, Valters; Buddendorf, Bas; Carreck, Norman L.; Danneels, Ellen; Charistos, Leonidas; Graaf, Dirk C.; Díaz Galiano, Francisco José; Fernandez-Alba, Amadeo; Ferrer-Amate, Carmen; Formato, Giovanni; Gómez Ramos, María José; Gratzer, Kristina; Gray, Alison; Hatjina, Fani; Henriques, Dora; Kasiotis, Konstantinos; Kilpinen, Ole; Lopes, Ana; Martínez Bueno, María Jesús; Murcia-Morales, María; Pietropaoli, Marco; Pinto, M. Alice; Quaresma, Andreia; Rufino, José; Roessink, Ivo; Vejsnæs, Flemming; Zafeiraki, EffrosyniHoneybee colonies are excellent bio-samplers of biological material such as nectar, pollen, and plant pathogens, as well as non-biological material such as pesticides or airborne contamination. The INSIGNIA-EU project aims to design and test an innovative, non-invasive, scientifically proven citizen science environmental monitoring protocol for the detection of pesticides, microplastics, heavy metals, and air pollutants by honey bee colonies http://insignia-eu.eu. In the pilot INSIGNIA project (2018-2021), a protocol was developed and tested for citizen-science-based monitoring of pesticides using honeybees. As part of the project, biweekly pollen was obtained from sentinel apiaries over a range of European countries and landscapes and analysed for botanical origin, using state-of-theart molecular techniques such as metabarcoding. An innovative non-biological matrix, the “APIStrip”, was also proved to be very efficient for detecting the residues of 273 agricultural pesticides and veterinary products, both authorized and unauthorized. The data collected are used to develop and test a spatial modelling system aimed at predicting the spatiallyexplicit environmental fate of pesticides and honeybee landscape-scale pollen foraging, with a common underlying geo-database containing European land-use and land-cover data (CORINE), the LUCAS database (landcover) supplemented with national data sets on agricultural and (semi-) natural habitats. After a call by the European Commission, a new 2 years project was granted aiming to present a comprehensive pan-European environmental pollution monitoring study with honey bees. Although pesticides used in agriculture, are a known hazard due to their biological activity, other pollutants, have even been recognized as such, for which we have not been aware of their impact for many years. An example is air pollution which increased while our societies industrialized and is currently regarded as the single largest environmental health risk in Europe (https://www.eea.europa.eu/). Unfortunately, other pollutants such as heavy metals, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, airborne particulate matter, and microplastics have also reached our environment. The outcome of this project will provide the first standardized EU-wide monitoring of all types of environmental pollutants with honey bee colonies. The project is funded by the EU, under the N° 09.200200/2021/864096/SER/ ENV.D.2 contract.
- Bioinformatics pipeline to evaluate patterns of diversity in detoxification genes in Western Honey BeePublication . Barbosa, Daniela; Li, Fernanda; Bashir, Sana; Lopes, Ana; Yadró García, Carlos A.; Quaresma, Andreia; Rufino, José; Rosa-Fontana, Annelise; Verbinnen, Gilles; Graaf, Dirk C.; Smet, Lina de; Pinto, M. Alice; Henriques, DoraThe Western honey bee, Apis mellifera, displays significant genetic diversity in detoxification genes, which is pivotal for environmental adaptation and resilience. Herein, we developed a bioinformatics pipeline to investigate patterns of diversity in these genes, focusing on single nucleotide polymorphisms (SNPs) across A. mellifera populations, with variant annotation performed using both snpEff and the Variant Effect Predictor (VEP). Our pipeline integrates GATK, VCFtools, PLINK, bcftools, snpEff, and VEP to process genomic data systematically. Regions of interest were defined in a BED file for variant filtering. Using GATK, SNPs were extracted from a VCF file and conversion to PLINK format for population genetics analyses. Variants were filtered by minor allele frequency (MAF) and population differentiation (FST index) to identify SNPs with considerable. Variants were annotated with snpEff and VEP to predict functional impacts, enabling a comparative analysis of their annotation consistency and depth. Custom scripts were developed to map SNPs to detoxification genes, quantify SNP density, and integrated gene descriptions and lineage data. The resulting data were visualized using a combination of and generate different graphs using ggplot2 and chromoMap for chromossomal maps. Quality control steps were applied through the pipeline ensuring data reliability. Our findings reveal distinct SNP patterns in detoxification genes, highlighting candidate SNPs associated with A. mellifera subspecies-specific adaptations. The comparison of snpEff and VEP annotations provides insights into their strengths and limitations, which can help optimize software selection for genomic studies. This pipeline offers a reproducible framework for studying genetic diversity in A. mellifera that is adaptable to other species, advancing conservation and evolutionary genomics.
- Can introgression in M-lineage honey bees be detected by abdominal colour patterns?Publication . Henriques, Dora; Lopes, Ana; Ferrari, Roberto; Neves, Cátia J.; Quaresma, Andreia; Browne, Keith A.; McCormack, Grace P.; Pinto, M. AliceHoney bee abdominal pigmentation is one of the most recognisable traits and it is often used by beekeepers as an indicator of M-lineage subspecies purity. However, this approach may negatively impact population diversity and is futile if there is no association between tergite colour patterns and the genetic background. To assess whether this trait can be used as a proxy for introgression proportions in M-lineage subspecies, we genotyped, with highly informative SNP assays, A. m. mellifera and A. m. iberiensis individuals displaying four different colour phenotypes. The SNP data detected highly introgressed bees exhibiting a black phenotype and, at the same time, pure or marginally introgressed bees with yellow banding patterns, in both subspecies. Despite these observations, contrary to A. m. iberiensis , in A. m. mellifera , introgression proportions revealed to be a significant predictor of abdominal pigmentation. Therefore, abdominal pigmentation could be used by A. m. mellifera conservationists to guide colony selection when genetic tools are unavailable.
- Caracterização genética da Vespa velutina em PortugalPublication . Quaresma, Andreia; Henriques, Dora; Godinho, Joana; Pinto, M. AliceA vespa asiática (Vespa velutina nigrithorax) é originária do Sudeste Asiático. Em 2004 foi vista pela primeira vez em território Francês, onde foi introduzida acidentalmente, e onde, na última década, se espalhou rapidamente, tendo começado a invadir outros territórios europeus. Na Península Ibérica, foi vista pela primeira vez em 2010 em Espanha e em 2011 em Portugal. Através da genética das populações é possível inferir sobre os padrões de invasão desta espécie em Portugal. Assim, de forma a ter uma amostragem representativa do território invadido, foram recolhidas um total de 191 amostras, cada uma representando uma colonia. Com o fim de estimar a estrutura populacional e a forma de invasão desta espécie em Portugal, a sua variabilidade genética foi estudada através de 17 microssatélites. Os resultados obtidos mostram que esta população sofreu um bottleneck apresentando um reduzido número de alelos, o que está de acordo com outros estudos europeus. Estes resultados sugerem ainda a entrada de um pequeno número de indivíduos ou de uma rainha fecundada por vários machos na Europa. Com esta informação é possível inferir dados sobre o ciclo de vida da V. velutina que poderão ajudar a explicar o seu sucesso demográfico nas áreas invadidas.
- COI Metabarcoding as a Novel Approach for Assessing the Honey Bee Source of European HoneyPublication . Honrado, Mónica; Quaresma, Andreia; Henriques, Dora; Pinto, M. Alice; Amaral, Joana S.Honey is a widely consumed food product frequently subjected to adulteration, with the mislabeling of its botanical or geographical origin being one of the most common practices. Determining the entomological origin of honey is particularly challenging but of high relevance for ensuring its authenticity, especially for products with protected designation of origin (PDO) labels. This study presents a novel DNA metabarcoding approach targeting a highly informative 406 bp fragment of the cytochrome c oxidase I (COI) gene to differentiate among the three major mitochondrial lineages (A, M, and C) of honey bees (Apis mellifera L.) native to Europe. The target region was selected based on the calculated fixation index (FST), which is frequently used in Population Genetics as a measure of differentiation between populations. The approach was validated with 11 honey samples of known entomological origin and applied to 44 commercial honeys from 13 countries. The approach demonstrated high sensitivity, accurately identifying the entomological origin of honey, including samples produced by honey bees of varying ancestries, which could not be resolved by previous methods based on real-time PCR coupled with high-resolution melting (PCR-HRM) analysis. The results demonstrate the effectiveness of COI metabarcoding in verifying honey authenticity and highlight the predominance of C-lineage honey bees in the production of commercial honeys from northwestern Europe. This finding suggests a limited presence of the native M-lineage ancestry, underscoring the need for conservation efforts.
- Conservation of European M-lineage honey bees using abdominal colour as an indicator of subspecies purity has pitfallsPublication . Henriques, Dora; Lopes, Ana; Ferrari, Roberto; Neves, Cátia J.; Quaresma, Andreia; Browne, Keith A.; McCormack, Grace P.; Pinto, M. AliceThere are 31 honey bee (Apis mellifera) recognized subspecies, which have been grouped into four main lineages. Two of these lineages occur naturally in Europe: M in western and northern Europe and C in southeastern Europe. In Europe, M-lineage groups only two subspecies, Apis mellifera mellifera and Apis mellifera iberiensis, both being black in colour. C-Lineage groups have instead eight subspecies, including one of the beekeepers-favored and phenotypically distinct, the yellow Apis mellifera ligustica from Italy. M-lineage honey bees’ distribution has been changing and in some countries, the native bee is being replaced or hybridised with C-lineage subspecies. Honey bee abdominal pigmentation is one of the most recognisable traits and it has been used by beekeepers as an indicator of subspecies identity. However, this approach may negatively impact population diversity and is futile if there is no association between tergite colour patterns and genetic background. To test this approach, we calculated the introgression level of A. m. mellifera (N=162) and A. m. iberiensis individuals (N=559) with different colour phenotypes and from a wide geographical range using informative SNPs. In this study, many A. m. mellifera samples showed high levels of C-lineage introgression. The individuals collected in Iberia were revealed to be pure. Introgressed A. m. iberiensis individuals were all from the Azores, where a high frequency of C-lineage mitotypes exists in several islands. Our results showed that for both subspecies, it is not possible to directly identify introgressed individuals from observed colour patterns, as we found black honey bees with a considerable amount of introgression and honey bees with yellow banding that were pure or marginally introgressed. With this study, we hope to increase awareness among stakeholders of the need to use other tools to select honey bees for conservation and breeding purposes.
- Correction to: Invasion genetics of the Asian hornet Vespa velutina nigrithorax in Southern EuropePublication . Quaresma, Andreia; Henriques, Dora; Godinho, Joana; Maside, Xulio; Bortolotti, Laura; Pinto, M. AliceIn the original publication of the article, the fourth author’s family name and affiliations were published incorrectly. The correct author’s name and affiliations are given in this correction. The original article has been corrected.