Percorrer por autor "Coffey, Mary F."
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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; Van der Steen, Jozef; Varnava, Andri; Vejsnæs, Flemming; Webster, Matthew T.; Fedoriak, Mariia M.; Zarochentseva, Oksana; Graaf, Dirk C. de; 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.
- Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPsPublication . Momeni, Jamal; Parejo, Melanie; Nielsen, Rasmus O.; Langa, Jorge; Montes, Iratxe; Papoutsis, Laetitia; Farajzadeh, Leila; Bendixen, Christian; Căuia, Eliza; Charrière, Jean Daniel; Coffey, Mary F.; Costa, Cecilia; Dall'Olio, Raffaele; De la Rúa, Pilar; Dražić, Marica Maja; Filipi, Janja; Galea, Thomas; Golubovski, Miroljub; Gregorc, Aleš; Grigoryan, Karina; Hatjina, Fani; Ilyasov, Rustem; Ivanova, Evgeniya Neshova; Janashia, Irakli; Kandemir, Irfan; Karatasou, Aikaterini; Kekecoglu, Meral; Kezic, Nikola; Matray, Enikö Sz; Mifsud, David; Moosbeckhofer, Rudolf; Nikolenko, Alexei G.; Papachristoforou, Alexandros; Petrov, Plamen; Pinto, M. Alice; Poskryakov, Aleksandr V.; Sharipov, Aglyam Y.; Siceanu, Adrian; Soysal, M. Ihsan; Uzunov, Aleksandar; Zammit Mangion, Marion; Vingborg, Rikke; Bouga, Maria; Kryger, Per; Meixner, Marina D.; Estonba, AndoneWith numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference. Results: Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. Conclusions: The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.
- INSIGNIA: um projeto de monitorização ambiental de pesticidas através da utilização da abelha melliferaPublication . Pinto, M. Alice; Amaral, Joana S.; Baveco, Hans; Biron, David G.; Brodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Charistos, Leonidas; Coffey, Mary F.; Fernández-Alba, Amadeo R.; Formato, Giovanni; Graaf, Dirk C. de; Gratzer, Kristina; Gray, Alison; Hatjina, Fani; Kasiotis, Konstantinos; Kilpinen, Ole; Pietropaoli, Marco; Roessink, Ivo; Rufino, José; Vejsnæs, Flemming; Van der Steen, JozefINSIGNIA ("cItizeN Science InvestiGatioN for pestIcIcides in Apicultutarl products"; https://www.insignia-bee,eu/) é um projecto financiado pela agência "Directorate General for Health and Food Safety" da Comissão Europeia, e que teve início em Outubro de 2018. O consórcio INSIGNIA é coordenado por Jozef van der Steen e integra 16 instituições parceiras de 12 países Europeus, entre as quais está o Centro de Investigação e Montanha (CIMO) do Instituto Politécnico de Bragança (IPB).
- Introducing the INSIGNIA project: environmental monitoring of pesticide use through honey beesPublication . Van der Steen, Jozef; Brodschneider, Robert; Gratzer, Kristina; Bieszczad, Sarah; Hatjina, Fani; Charistos, Leonidas; Carreck, Norman L.; Gray, Alison; Pinto, M.Alice; Amaral, Joana S.; Rufino, José; Quaresma, Andreia; Roessink, Ivo; Baveco, Hans; Formato, Giovanni; Pietropaoli, Marco; Kasiotis, Konstantinos; Anagnostopoulos, Christ; Zafeiraki, Effrosyni; Fernández-Alba, Amadeo R.; Eulderink, Caroline; Vejsnæs, Flemming; Kilpinen, Ole; Coffey, Mary F.; Biron, David G.; Brusbardis, Valters; Graaf, Dirk C. deINSIGNIA aims to design and test an innovative, non-invasive, scientifically proven citizen science environmental monitoring protocol for the detection of pesticides by honey bees. It is a 30-month pilot project initiated and financed by the EC (PP-1-1-2018; EC SANTE). The study is being carried out by a consortium of specialists in honey bees, apiculture, statistics, analytics, modelling, extension, social science and citizen science from twelve countries. Honey bee 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. Honey bee colonies forage over a circle of 1 km radius, increasing to several km if required, depending on the availability and attractiveness of food. All material collected is accumulated in the hive.
- Introducing the INSIGNIA project: Environmental monitoring of pesticides use through honey beesPublication . Carreck, Norman L.; Amaral, Joana S.; Anagnostopoulos, Christ; Baveco, Hans; Bieszczad, Sarah; Biron, David G.; Brodschneider, Robert; Brusbardis, Valters; Charistos, Leonidas; Coffey, Mary F.; Eulderink, Caroline; Fernández-Alba, Amadeo R.; Formato, Giovanni; Graaf, Dirk C. de; Gratzer, Kristina; Gray, Alison; Hatjina, Fani; Kasiotis, Konstantinos; Kilpinen, Ole; Murcia-Morales, Maria; Pietropaoli, Marco; Pinto, M. Alice; Quaresma, Andreia; Roessink, Ivo; Rufino, José; Vejsnæs, Flemming; Zafeiraki, Effrosyni; Van der Steen, JozefINSIGNIA aims to design and test an innovative, non-invasive, scientifically proven citizen science environmental monitoring protocol for the detection of pesticides via honey bees. It is a pilot project initiated and financed by the European Commission (PP-1-1-2018; EC SANTE). The study is being carried out by a consortium of specialists in honey bees, apiculture, chemistry, molecular biology, statistics, analytics, modelling, extension, social science and citizen science from twelve countries. Honey bee 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. Honey bee colonies forage over a circle of about 1 km radius, increasing to several km if required depending on the availability and attractiveness of food. All material collected is concentrated in the hive, and the honey bee colony can provide four main matrices for environmental monitoring: bees, honey, pollen and wax. For pesticides, pollen and wax are the focal matrices. Pollen collected in pollen traps will be sampled every two weeks to record foraging conditions. During the season, most of pollen is consumed within days, so beebread can provide recent, random sampling results. On the other hand wax acts as a passive sampler, building up an archive of pesticides that have entered the hive. Alternative in-hive passive samplers will be tested to replicate wax as a “pesticide-sponge”. Samples will be analysed for the presence of pesticides and the botanical origin of the pollen using an ITS2 DNA metabarcoding approach. Data on pollen and pesticides will be then be combined to obtain information on foraging conditions and pesticide use, together with evaluation of the CORINE database for land use and pesticide legislation to model the exposure risks to honey bees and wild bees. All monitoring steps from sampling through to analysis will be studied and tested in four countries in year 1, and the best practices will then be ring-tested in nine countries in year 2. Information about the course of the project and its results and publications will be available in the INSIGNIA website www.insignia-bee.eu.
- Large Scale Mitochondrial Evidence of C-lineage Dominance in European Honey BeesPublication . Li, Fernanda; Lopes, Ana Rita; Costa, Maíra; Henriques, Dora; Quaresma, Andreia; Yadró Garcia, Carlos A.; Albo, Alexandre; Čereškienė, Laima Blažytė; 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; Poirot, Benjamin; Pietropaoli, Marco; Radev, Zheko; Raudmets, Aivar; René-Douarre, Vincent; Roessink, Ivo; Škerl, Maja Ivana Smodiš; Soland, Gabriele; Titera, Dalibor; Van der Steen, Jozef; Varnava, Andri; Vejsnæs, Flemming; Fedoriak, Mariia M.; Zarochentseva, Oksana; Webster, Matthew T.; Graaf, Dirk C. de; Pinto, M. AliceIn Europe, distribution of the several endemic honey bee (Apis mellifera) subspecies has suffered a considerable shift in the last century. In particular, beekeepers tend to favour subspecies of Eastern European ancestry (C-lineage), such as the Italian honey bee (A. m. ligustica), due to their perceived docility and high honey production. As a result, large scale migratory beekeeping and trade of C-lineage queens have exposed the native European honey bees to introgression and replacement, jeopardizing their genetic integrity and locally adapted traits. The maternally-inherited and highly polymorphic mitochondrial intergenic region tRNAleu-cox2 is routinely used for the assessment of honey bee diversity and introgression at large geographical scales. In this study, we conducted a survey on tRNAleu-cox2 variation in more than 1300 colonies from 33 European countries to assess current status of mitochondrial diversity patterns in Europe. Total genomic DNA was extracted from the bee thorax followed by PCR amplification of the tRNAleu-cox2 region and sequencing. The haplotypes were identified using alignments in MEGA 11. A clear dominance of C-lineage haplotypes was found (65%). The most prevalent C-lineage haplotype was C2 (54%) followed by C3 (23%) and C1(22%). Contrary to this trend, in Portugal, Spain and Ireland, less than 10% of the colonies exhibit the C-haplotype. Furthermore, the analysed apiaries in isolated protected areas (n=7) revealed a high proportion of colonies of western European (M-lineage) ancestry (80%) with M4 as the most frequent haplotype. African haplotypes (A lineage) were also found, albeit at lower frequencies, and were mainly concentrated in the Iberian Peninsula (9%). Intensive queen breeding and migratory beekeeping is homogenizing the gene pool of European bee populations. This survey of honey bee maternal diversity across Europe highlights the alarming dominance of C-lineage haplotypes and underscores the importance of conservation apiaries, as they have effectively preserved the autochthonous M-lineage subspecies in different countries. This work was conducted in the framework of the project Better-B, funded by the European Union, the Swiss State Secretariat for Education, Research, and Innovation, and UK Research and Innovation under the UK government's Horizon Europe funding guarantee (grant number 10068544).
- Maternal origin of honeybee (Apis mellifera) colonies from across EuropePublication . Lopes, Ana; Costa, Maíra; Tounakti, Sahar; Henriques, Dora; Quaresma, Andreia; Yadró Garcia, Carlos A.; Albo, Alexandre; Blažytė-Čereškienė, Laima; Broodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Charistos, Leonidas; Chlebo, Robert; Coffey, Mary F.; Danneels, Ellen; Dobrescu, Constantin; Filipi, Janja; Gajda, Anna; Galea, Thomas; Gratzer, Kristina; Hatjina, Fani; Johannesen, Jes; Körmendy-Rácz, János; Kovačić, Marin; Preben, Kristiansen; Martikkala, Maritta; Martín-Hernández, Raquel; Pietropaoli, Marco; Poirot, Benjamin; Radev, Zheko; Raudmets, Aivar; Douarre, Vincent; Rodriguez-Flores, Maria Shantal; Roessink, Ivo; Ivana, Maja; Škerl, Maja Ivana Smodiš; Titera, Dalibor; Van der Steen, Jozef; Varnava, Andri; Vejsnæs, Flemming; Webster, Matthew T.; Graaf, Dirk C. de; Pinto, M. AliceWorldwide commercial beekeeping poses a threat to the native origin of the honeybee (Apis mellifera), with beekeepers favouring subspecies of Eastern European C-lineage ancestry, due to their docile behaviour and high honey production traits. In many parts of western and northern Europe, queens of Western European M-lineage ancestry have been massively replaced by queens of C-lineage ancestry, and this has led to the development of conservation programs aiming at recovering native lines. The maternally-inherited mitochondrial DNA (mtDNA), particularly the intergenic region tRNAleu-cox2, has been the marker of choice for assessing honey bee variation at large geographical scales. Herein, we will show the results of the mtDNA analysis of over 850 colonies collected across 28 European countries. These samples were subjected to DNA extraction, followed by PCR, and Sanger sequencing. The analysis of the sequences was conducted in Mega 11. The results indicated that, apart from Portugal, Spain, and the conservation centres in France and Denmark, where the colonies exhibited African or M haplotypes, the remaining countries are dominated by colonies of C-lineage maternal ancestry. In conclusion, this unprecedented mtDNA analysis conducted across Europe underscores the worrying dominance of C-lineage genetic variation, highlighting the urgent need for strategic conservation efforts to preserve the native genetic diversity of Apis mellifera.
- An unparalleled survey of honey bee genetic diversity in Europe – insights from wing shape, nuclear whole genome, and mitochondrial DNA dataPublication . Pinto, M. Alice; Li, Fernanda; Lopes, Ana Rita; Taliadoros, Demetris; Costa, Maíra; Yadró Garcia, Carlos A.; Cunha, Larissa; Henriques, Dora; Martin Hernandez, Giselle; Albo, Alexandre; Blažytė-Čereškienė, Laima; Brodschneider, Robert; Brusbardis, Valters; Carreck, Norman; Charistos, Leonidas; Chlebo, Robert; Cillia, Giovanni; Coffey, Mary F.; Dahle, Bjorn; Danneels, Ellen; Dobrescu, Constantin; Filipi, Janja; Gajda, Anna; Gratzer, Kristina; Groeneveld, Linn; Hatjina, Fani; Johannesen, Jes; Kolasa, Michal; Körmendy-Rácz, János; Kovačić, Marin; Kristiansen, Preben; Dupleix-Marchal, Anna; Martikkala, Maritta; McCormack, Grace; Martín-Hernández, Raquel; Nanetti, Antonio; Pavlov, Borce; Pietropaoli, Marco; Poirot, Benjamin; Radev, Zheko; Raudmets, Aivar; René-Douarre, Vincent; Roessink, Ivo; Škerl, Maja Ivana Smodiš; Soland, Gabriele; Titera, Dalibor; Van der Steen, Jozef; Varnava, Andri; Vejsnæs, Flemming; Graaf, Dirk C. de; Webster, MathewEurope is home to 10 subspecies of Apis mellifera, classified into four main lineages sensu Ruttner: M (western and northern European), C (southeastern European), A (African), and O (Middle Eastern). However, large-scale movements of honey bee genetic material—driven by transhumance and, more importantly, queen trading—has intensified gene flow, particularly from the C-lineage subspecies A. m. carnica and A. m. ligustica, threatening the genetic integrity of several subspecies and blurring the genetic boundaries between subspecies. Here, we analyzed over 1,200 recently collected samples from apiaries in 33 countries using a multi-marker approach: maternally inherited mitochondrial DNA (tRNAleu-cox2 intergenic region), nuclear genome-wide single nucleotide polymorphisms (SNPs), and wing shape (DeepWings©) to provide the most updated and extensive account of honey bee genetic variation in Europe. Our results reveal a strong dominance of C-lineage ancestry across Europe, with noteworthy introgression signals in island subspecies and A. m. mellifera populations outside conservation apiaries. Notably, all three markers consistently captured these broad introgression patterns. This unprecedented survey highlights a worrying trend of genetic homogenization in European honey bee populations. Moreover, the widespread prevalence of C-lineage genetic introgression underscores the need for conservation efforts to preserve the diversity shaped by evolution, which is crucial for adaptation to growing environmental challenges.
- Wing geometric morphometrics of european honey bee populationsPublication . Costa, Maíra; Gonçalves, Telma; Lopes, Ana; Vitrio, Nathalia; Albo, Alexandre; Blažytė-Čereškienė, Laima; Brodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Charistos, Leonidas; Chlebo, Robert; Coffey, Mary F.; Danneels, Ellen; Graaf, Dirk C. de; Dobrescu, Constantin; Filipi, Janja; Gajda, Anna; Gratzer, Kristina; Hatjina, Fani; Johannesen, Jes; Körmendy-Rácz, János; Kovačić, Marin; Kristiansen, Preben; Martikkala, Maritta; Martín-Hernández, Raquel; Pietropaoli, Marco; Poirot, Benjamin; Radev, Zheko; Raudmets, Aivar; Douarre, Vincent; Roessink, Ivo; Škerl, Maja Ivana Smodiš; Titera, Dalibor; Van der Steen, Jozef; Varnava, Andri; Vejsnæs, Flemming; Webster, Matthew T.; Rodrigues, Pedro João; Henriques, Dora; Pinto, M. AliceWing venation patterns have long been used to identify honey bee subspecies, singly or in combination with other morphological traits, using different approaches. Beekeepers have traditionally used identification methods that only require estimations of the Cubital Index, Hantel Index, and/or Discoidal Shift Angle. However, these measures do not consider all the information carried by wing patterns, and a more accurate approach is geometric morphometrics, which requires the annotation of 19 landmarks in the forewing vein junctions. While manual wing annotation is a time-consuming and error-prone endeavour, the recently developed software DeepWings© performs this task automatically, allowing a fast and relatively accurate identification of European honey bee subspecies, and is appropriate for large-scale projects. In this study, we analyse the patterns of forewings extracted from over 850 colonies sampled across 29 European countries. To that end, the right forewings of five workers per colony are photographed with a digital camera attached to a stereomicroscope. The images are then analysed using DeepWings©. Our main objective is to assess (i) how closely the colonies identified by DeepWings© match the endemic evolutionary lineages and subspecies; and (ii) the association between the identification produced by DeepWings© and that inferred from mitochondrial DNA. While geometric morphometrics does not replace molecular tools for the identification of colonies, it can provide a preliminary estimation of their genetic integrity.