Percorrer por autor "Zammit Mangion, Marion"
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- 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.
- Conservation status of Apis mellifera ruttneri inferred from whole genome sequencesPublication . Pinto, M. Alice; Ariel Yadró, Carlos; Henriques, Dora; Zammit Mangion, Marion; Galea, Thomas; Farrugia, Dylan; Cilia, Giovanni; Noureddine, Adjlane; Rufino, José; Nanetti, Antonio; Martín-Hernández, RaquelApis mellifera ruttneri is the native honey bee subspecies from the Maltese islands (Malta, Comino and Gozo). This African-lineage subspecies is adapted to the harsh environmental conditions and to the limited forage season of these islands. For many years, it was considered highly hybridized, due to the large and sustained importation of foreign subspecies, especially A. m. ligustica, perceived by many beekeepers as superior or for commercial reasons. Recent studies based on morphometry and mitochondrial DNA have suggested the occurrence of A. m. ruttneri, particularly in the main island. Conservation initiatives and a breeding program have been developed, but to date its conservation status is not fully known. As part of the MEDIBEES project, here, over 50 A. m. ruttneri georeferenced colonies collected from across Malta, as well as 50 several reference subspecies (A. m. ligustica, A. m. siciliana, A. m. iberiensis, A. m. sahariensis, and A. m. intermissa) were whole genome sequenced. The population structure and admixture were assessed from genome-wide single nucleotide polymorphisms using model and distance based-methods. The results show varying levels of admixture proportions of A. m. ruttneri with C-lineage honey bees across Malta but also a shared ancestry with the honey bees of north Africa, consistent with the putative natural colonization from Africa in ancient times.
- Exploiting the mitogenomes of apis mellifera subspecies to develop an authentication tool to verify the entomological origin of mediterranean honeysPublication . Honrado, Mónica; Henriques, Dora; Santos, Joana; Yadró Garcia, Carlos A.; Martín-Hernández, Raquel; Nanetti, Antonio; González, Amelia Virginia; Al Shagour, Banan; Hosri, Chadi; Farrugia, Dylan; Giovanni, Cilia; Zammit Mangion, Marion; Muz, Mustafa Necati; Haddad, Nizar; Galea, Thomas; Haider, Yamina; Obeidat, Wisam; Aglagane, Abdessamad; Arab, Alireza; Varnava, Andri; Eissa, Asmaa Anwar; Muz, Dilek; Hatjina, Fani; Lamghari, Fouad; Arruda, James; Caristos Caristos, Leonidas; Pinto, M. Alice; Amaral, Joana S.Honey is highly susceptible to adulteration. Currently, the assessment of its geographical origin remains one of the most difficult tasks, which is typically performed by melyssopalynology. Recently, the attention has shifted towards indirect approaches such as the entomological origin based on geographical distribution patterns of honey bee subspecies. Although queens’ trade has impacted the natural subspecies distribution, honeys produced with autochthonous bees or bearing a Protected Designation of Origin specifying the producing honey bee subspecies, offer a unique avenue for authentication. In the MEDIBEES project, we aim to develop a DNA-metabarcoding approach to authenticate honey's entomological origin focusing on mitochondrial lineages A, M, C, and O. To achieve this goal, the DNA from 1251 honey bees representing 16 subspecies (A.m. sahariensis, A.m. intermissa, A.m. siciliana, A.m. ruttneri, A.m. iberiensis, A.m. ligustica, A.m. macedonica, A.m. adami, A.m. cecropia, A.m. cypria, A.m. caucasia, A.m. meda, A.m. anatoliaca, A.m. syriaca, A.m. jemenitica, A.m. lamarcki) was extracted and the whole genome sequenced. From those, 740 mitogenomes were assembled using the MitoZ software. The quality of the assembled mitogenome was assessed by aligning all the sequences using MEGA and 348 samples were deleted. Finally, a phylogenetic analysis was conducted to eliminate non-local subspecies, resulting in a total of 326 mitogenomes. This dataset was used for calculating the fixation index (FST) pairwise values, and a sliding window of 400bp was used to identify single nucleotide polymorphisms that effectively differentiate (FST>0.98) the four lineages, enabling the identification of promising regions for primer design. In this study, three regions were identified that discriminate the four maternal lineages while showing an appropriate length for metabarcoding, namely in the COI, ND1 gene, and CYTB genes.
- General beekeeping practices and main stressors identified by beekeepers in the MediterraneanPublication . Nanetti, Antonio; Martín-Hernández, Raquel; Zammit Mangion, Marion; Pinto, M. Alice; Farrugia, Dylan; Zammit Mangion, Rachel; Noureddine, Adjlane; Eissa, Asmaa Anwar; Cilia, Giovanni; Daour, Ahmad Yousef; Garrido, Claudia; Haddad, Nizar; Henriques, Dora; Hosri, Chadi; Muz, Mustafa Necati; Sagastume, Soledad; Galea, Thomas; Medibees ConsortiumBeekeeping is an ecologically and economically important activity in the Mediterranean that is increasingly under threat from a combination of factors. In the MEDIBEES (Monitoring the Mediterranean honey bee subspecies and their resilience to climate change for the improvement of sustainable agro-ecosystems) PRIMA project we aim to identify honey bees that show resilience to stressors associated with climate change. An important first step in our work was to establish baseline data of practices in the region through the administering of a questionnaire on the beekeeping practices. Over 1022 responses were received from beekeepers in Algeria, Egypt, Jordan, Italy, Lebanon, Malta, Spain, Portugal and Turkey. Beekeeping was overwhelmingly male dominated (ratio 9:1) and practiced largely by the middle-aged (mainly between 40-50 years). The majority of beekeepers reported having 10-50 boxes with the exceptions of Algeria and Jordan where the majority reported keeping more than 100 hive boxes. Across the Mediterranean the Langstroth hive box was most commonly used. Despite the perception of migratory beekeeping being frequently practiced, only Lebanon and Turkey reported significant levels of transhumance (>50.0 and 70.0% of beekeepers respectively). 51.2% of beekeepers reported practicing queen rearing with the majority of these (51.4%) reporting re-queening their colonies every 2 years. Interestingly, the majority of all beekeepers agreed with the statement that their native honey bee is endangered where pesticide use, lack of adequate forage and parasite infestations such as the Varroa mite were repeatedly cited as causing the greatest losses to honey bees in general. Climate change and urbanisation were also linked with colony losses by causing habitat loss. Supplementary feeding was reported to be an integral part of beekeeping in this region, with beekeepers reporting using between 0-5kg, closely followed by 6-10 kg of additional sugars.
- Medibees Project: disentangling diversity patterns and processes of mediterranean honey bee subspecies by whole-genome sequencingPublication . Ariel Yadró, Carlos; Henriques, Dora; Martín-Hernández, Raquel; Nanetti, Antonio; Haddad, Nizar; Muz, Mustafa Necati; Hosri, Chadi; Zammit Mangion, Marion; Noureddine, Adjlane; Pinto, M. AliceApis mellifera is represented by 31 presently acknowledged subspecies that are native to Asia, Africa, and Europe. Approximately 40% of that richness evolved in the Mediterranean region, as the result of adaptation to diverse environmental conditions. Understanding and preserving such diversity will help to promote the honey bee’s resilience to climate change and biotic stressors, which is the main goal of the MEDIBEES project. This goal will be addressed by the following objectives: a) elucidate the genetic background of the Mediterranean subspecies, b) uncover the genetic basis of their adaptation to the local conditions, c) evaluate the respective conservation status, and d) assess their resilience to climate change. To that end, over 1300 geo-referenced colonies representing 9 subspecies (A. m. ligustica, A. m. siciliana, A. m. ruttneri, A. m. sahariensis, A. m. intermissa, A. m. syriaca, A. m. anatoliaca, A. m. caucasia and A. m. meda) are being sampled in 6 Mediterranean countries (Algeria, Italia, Jordan, Lebanon, Malta and Turkey). The samples will be whole-genome sequenced using Illumina technology. These newly generated genome datasets will be combined with those previously obtained for A. m. iberiensis from Spain and Portugal, and the data will be subjected to a battery of analytical tools. Here, we describe how the massive whole-genome dataset will be scrutinized to fully address the MEDIBEES objectives. This project promises to generate unprecedented knowledge on the differential vulnerability and resilience of the Mediterranean honey bee subspecies to the main environmental stressors typical of this region.
- MEDIBEES: Monitoring the Mediterranean honey bee subspecies and their resilience to climate change for the improvement of sustainable agro-ecosystemsPublication . Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. Alice; Noureddine, Adjlane; Haddad, Nizar; Hosri, Chadi; Muz, Mustafa Necati; Zammit Mangion, Marion; Daour, Ahmad Yousef; Sagastume, Soledad; Cilia, Giovanni; Medibees ConsortiumBeekeeping provides livelihood for hundreds of thousands of beekeepers in the Mediterranean area. This activity relies on a number of different indigenous Apis mellifera subspecies, adapted to the very diverse and harsh conditions of the region. Climate change is expected to increase the stress factors affecting bees, especially in this region, reducing both pollination efficiency and production potential. Unfortunately, our ability to address this problem is limited by the incomplete knowledge of the natural adaptation mechanisms developed by the different subspecies. In order to increase the knowledge base for future selection programs to improve bee populations for environmental changes, the MEDIBEES project is being developed. It includes 9 partners from 8 Mediterranean countries on all three shores of the Mediterranean, covering 10 local A. mellifera subspecies, which represents a remarkable though understudied proportion of the species genetic diversity. The project aims to: a) unravel the differential genetic background of Mediterranean subspecies, b) understand their adaptation to local conditions, and c) characterize their resistance to climate change. To achieve the objectives, colonies belonging to the local subspecies will be studied phenotypically to determine their behavior under environmental conditions, covering survival, sensitivity to pests/pathogens, behavior, physiology and reproduction which will be completed by gene expression and transcriptomic assays. In addition, complete genomes of field and laboratory samples will be sequenced to find genes putatively involved in adaptation and to develop new genetic tools to characterize honey bee populations according to their resistance to environmental stress factors. This effort will encourage the use of local subspecies, to make them more attractive and avoid importing foreign breeds, and will lay the foundation for future selection programs. Besides, the valorization of honey by both promoting its use and developing quality labels, and the evaluation of beekeeping by-products as modifiers of soil fertility and biota are also approached to help the beekeepers improve the sustainability of their farms in an economical and environmental sound manner.
- Mitochondrial DNA Variability in the Honey bee Apis mellifera L., Implications for ConservationPublication . Vella, Cristina; Lanfranco, Sandro; Hernández, Raquel Martín; Higes, Mariano; Nanetti, Antonio; Pinto, M. Alice; Yadró Garcia, Carlos A.; Henriques, Dora; Cilia, Giovanni; Sagastume De Andrés, Soledad; Adjlane, Noureddine; Al Shagour, Banan; Al Daour, Ahmad; Muz, Mustafa Necati; Muz, Dilek; Hosri, Chadi; Zammit Mangion, Marion; Galea, ThomasThe Western honey bee (Apis mellifera L.) is a keystone species that plays a vital role in maintaining environmental health and agricultural productivity. However, it faces significant threats, including indiscriminate pesticide use, parasite ecosystem expansion, climate change, and the uncontrolled importation of non-native subspecies. The PRIMA project MEDIBEES (Monitoring the Mediterranean Honey Bee Subspecies and Their Resilience to Climate Change for Sustainable Agro-Ecosystems) aims to identify the current genetic structure of native honey bee populations across the Mediterranean and neighbouring regions to help support breeding programmes and conservation efforts. A. mellifera subspecies may be classified into four major mitochondrial DNA lineages: A (Africa), M (Western and Northern Europe), C (Eastern and Central Europe) and O (Western and Central Asia), each of which is sub-divided into a number of haplotypes. The occurrence of non-native lineages is a strong indicator of introduction of foreign subspecies. In this study, the mtDNA tRNA-COII region of over 1,344 DNA samples was amplified using standard PCR methods, sequenced and then analysed using Geneious Prime 2024 software. These samples were collected from the Mediterranean and neighbouring regions including A.m. ligustica (Italy), A.m. siciliana (Italy, Sicily), A.m. cypria (Cyprus), A.m. syriaca (Jordan and Lebanon), A.m. ruttneri (Malta), A.m. meda (Iran), A.m. anatoliaca and A.m. caucasica (Turkey), A.m. jemenitica (UAE and Oman), A.m. sahariensis (Morocco and Algeria), A.m. macedonica (Greece) and A.m. intermissa (Algeria). Results indicate that lineage C, typical of A.m. ligustica and A.m. carnica, was present in a number of studied samples, suggesting the introduction of non-native C lineage subspecies through the importation of commercially managed colonies. This presentation will focus on describing the current distribution of mtDNA haplotypes within these subspecies as well as evidence of non-native lineages, indicating the possible introduction of other subspecies into these regions. The implications of the data including insights into the movement and transfer of subspecies in these areas and potential impact on local beekeeping practices will be discussed.