Browsing by Author "Cilia, Giovanni"
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- Climate change-induced stress in the honey bee Apis mellifera L.- a genetic reviewPublication . Sagastume, Soledad; Cilia, Giovanni; Henriques, Dora; Yadró García, Carlos A.; Corona, Miguel; Higes, Mariano; Pinto, M. Alice; Nanetti, Antonio; Martín-Hernández, RaquelClimate change is a powerful driver of stress, as it reinforces hotter and drier environments. For bees, the most concerning aspects of these new environmental conditions are the resistance and resilience of bees to changes in temperature, humidity and ultraviolet radiation, as well as the negative effect on diversity of food resources which can lead in nutritional stress. The climatic vulnerability of various bee species and subspecies varies worldwide, as they experience varying levels of stress and display distinct behaviors, weaknesses, and lifespans. To understand these differences, it is crucial to consider both the genetics and epigenetics of bees, as these factors play a key role in their response, resistance, and adaptation to new stressors. This review provides a guide of genetic and epigenetic markers involved in the cellular response of Apis mellifera to most common stressors derived from climate change. Understanding how the various molecular mechanisms interact to restore homeostasis during the stress response is essential for designing future studies based on molecular markers.
- 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.
- Estrutura populacional e estado de conservação das subespécies de Apis mellifera no Oriente Próximo e MédioPublication . Yadró Garcia, Carlos A.; Henriques, Dora; Honrado, Mónica; Amaral, Joana S.; Eissa, Asmaa Anwar; Haddad, Nizar; Obeidat, Wisam; Arruda, James; Lamghari, Fouad; Cilia, Giovanni; Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. AliceA abelha melífera, Apis mellifera, é composta por 31 subespécies que se encontram distribuídas na Ásia, África e Europa. O objetivo deste trabalho é desvendar a estrutura populacional e verificar o estado de conservação de três subespécies do Médio Oriente, as quais têm sido pouco estudadas. Para isso, foi extraído o DNA a partir de tóraxes inteiros de machos de 329 amostras de A. m. lamarckii (Egito, 68 amostras), A. m. syriaca (Jordânia, 238 amostras) e A. m. jemenitica (Omã e Emirados Árabes Unidos, 23 amostras). Foram adicionadas 21 amostras de A. m. ligustica, que é uma subespécie amplamente utilizada pelos apicultores no mundo inteiro e por isso fonte de introgressão genética. O genoma completo das 329 amostras foi sequenciado na plataforma Illumina NovaSeq 600 tendo como objetivo uma cobertura de 20X. Os 329 genomas foram mapeados usando o genoma de referência Amel_HAv3.1 e foi implementada uma pipeline que garante a qualidade dos dados. No final, obteve-se um total de 4.030.485 de SNPs que foram usados na reconstrução da estrutura populacional com o ADMIXTURE e PCA. As amostras egípcias mostraram que apesar de terem alguma introgressão de A. m. ligustica, essa não é relevante e é variável (Q-values entre 1E-05 e 0.44), com a maior parte (97%) das amostras apresentando um valor médio de 0.07 ± 0.06 (Q-values, meia ± DP). A. m. syriaca apresenta uma estrutura complexa, tendo sido observados dois grupos distintos pelo PCA e três pelo ADMIXTURE. Relativamente seu ao estado de conservação, foram detetados 76 indivíduos com uma proporção considerável (Q-values entre 0.15 e 0.47) de introgressão com A. m. ligustica. No caso de A. m. jemenitica, foram observados dois cenários diferentes. Em Omã, todas as amostras estudadas mostraram ser puras. Por outro lado, apenas sete amostras dos Emirados Árabes Unidos foram classificadas como tal, enquanto as restantes mostraram proporções de introgressão semelhantes às do Egito. Estes resultados evidenciam o estado precário de integridade genética que estas subespécies apresentam nos locais estudados. No entanto, a existência de indivíduos que podem ser considerados puros para suas respetivas subespécies pode servir como ponto de partida para o desenvolvimento de planos de conservação.
- Exploring population structure and adaptation in honey bee subspecies from southern glacial refugia: A. M. Iberiensis and A. M. LigusticaPublication . Yadró Garcia, Carlos A.; Henriques, Dora; Cilia, Giovanni; Rufino, José; Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. AliceGlacial refugia harbor populations with complex diversity patterns. In honey bees, the Iberian and Italian Peninsulas served as two of the most important glacial refugia in Europe. Here, we analyzed whole genomes generated from drones to infer population structure, genetic diversity, and the molecular basis of the local adaptation for the two native subspecies of these Peninsulas: A. m. iberiensis (N=86; M-lineage) and A. m. ligustica (N=225; C-lineage). For A. m. iberiensis, Admixture analysis revealed a strong cline between two genetic backgrounds from Southwest to Northeast and no C-lineage introgression was detected. For A. m. ligustica, introgression with A. m. carnica occurred in Central and Southern Italy (median q-valuecarnica=0.069; IQR=0.187), away from the natural hybridization zone in Northeastern Italy where higher admixture proportions were detected (median q-valuecarnica=0.229; IQR=0.262). A. m. mellifera introgression was detected especially in the Northwest (median q-valuemellifera 0.053; IQR=0.030), and with lower values in Central and Southern Italy (median q-valuemellifera 0.014; IQR=0.041). A. m. iberiensis showed higher diversity when compared to A. m. ligustica: π (πiberiensis=0.325, πligustica= 0.245, p-value<0.001); He (Heiberiensis=0.319, Heligustica=0.319; p-value<0.001) but lower relatedness (IBD kinshipiberiensis=0.002, IBD kinshipligustica=0.014; p-value<0.001). Selection signatures were detected and cross-validated using PCAdapt, SAMBADA, and RDA. SNPs with q-adjusted p-values < 0.01 detected by at least two methods were considered strong candidates. For A. m. ligustica, 133 candidate SNPs annotated to 125 genes were detected by all three methods, including dnaJ homolog subfamily C member 9, nephrin, and the diuretic hormone receptor, and these were correlated with precipitation. For A. m. iberiensis, 528 SNPs annotated to 527 genes were detected, and these included proteins related to heat-shock response, such as Cyp40 and rrp45. While no common candidate SNPs were detected between both subspecies, 20 common genes containing candidate SNPs were detected, such as 4-coumarate-CoA ligase 1, CPR9, and alpha-mannosidase 2.
- General beekeeping practices and main stressors identified by beekeepers in the MediterraneanPublication . Nanetti, Antonio; Martín-Hernández, Raquel; Zammit Mangion, Marion; Alice Pinto, M.; 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: 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.