Percorrer por autor "Nanetti, Antonio"
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- Beekeeping in the Mediterranean: a medibees survey on practices, trends and challengesPublication . Mangion, Marion Zammit; Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. Alice; Noureddine, Adjlane; Anwer, Asmaa; Haddad, Nizar; Hosri, Chadi; Muz, Mustafa Necati; Daour, Ahmad Yousef; Sagastume, SoledadMEDIBEES is a PRIMA funded project that aims to identify honeybee colonies and subspecies that are most resilient to climate change and common pathogens throughout the Mediterranean region. Honeybees are critical to sustainable agricultural systems and the project aims to contribute to sustainability in the context of the increased desertification of the region due to climate change. As part of this project an intensive investigation of beekeeping was carried out within the consortium, with the objectives of 1) understanding the main practices in place, 2) identifying trends and challenges faced by beekeepers. This would help guide the consortium in framing research questions that are rooted in the requirements of the stakeholders. A questionnaire was therefore developed and circulated among beekeepers from Algeria, Egypt, Italy, Jordan, Lebanon, Malta, Portugal, Spain and Turkey in late June 2021. To date, over 1300 detailed responses have been collected. This study has yielded an important first profile of the nature of the apicultural industry for many of these participating countries. In this presentation, a description of the socio-demographics and the diverse management practice in place among beekeepers across the Mediterranean will be presented. In addition, important first-time data on the distribution of hives, the main sources of losses including current biotic and abiotic threats, the characteristics and ecological trends of both native and introduced honey bee subspecies in the different geographical regions will be described as experienced by the major stakeholders ie beekeepers. Finally, notably and overwhelmingly, beekeepers from the Mediterranean region list changes in weather patterns as the major factor affecting colony losses and profitability. This was followed closely by indiscriminant use of agricultural insecticides and urbanisation.
- Climate change-induced stress in the honey bee Apis mellifera L.- a genetic reviewPublication . Sagastume, Soledad; Cilia, Giovanni; Henriques, Dora; Yadró Garcia, 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.
- Conservation status of the honey bee subspecies native to the Mediterranean islandsPublication . Henriques, Dora; Yadró Garcia, Carlos A.; Yadró García, Carlos A.; Mangion, Marion Zammit; Galea, Thomas; Cilia, Giovannni; Nanetti, Antonio; Muz, Mustafa Necati; Muz, Dilek; Varnava, Andri; Hatjina, Fani; Charistos, Leonidas; Rufino, José; Martín Hernández, Raquel; Pinto, M. AliceThe Mediterranean islands have been a stage for honey bee diversification, hosting four of the 31 recognized subspecies: Apis mellifera siciliana in Sicily, A. m. ruttneri in Malta, A. m. cypria in Cyprus, and A. m. adami in Crete. However, owing to small population sizes, island subspecies are particularly vulnerable to introgressive hybridization when exotic queens or colonies are introduced into their geographically isolated territories. While previous genetic surveys—typically based on mitochondrial and/or microsatellite markers—have provided valuable insights, the current conservation status of these subspecies remains uncertain. Here, we sequenced the whole genomes of 327 samples collected from Sicily (n=97), Malta (n=79), Cyprus (n=37), and Crete (n=36), along with probable source populations (A. m. intermissa, A. m. sahariensis, A. m. media, A. m. anatoliaca, A. m. macedonica, A. m. cecropia, A. m. ligustica, A. m. carnica, A. m. caucasia), to provide a comprehensive and up-to-date assessment of the ancestry and diversity patterns of these insular subspecies. Whole-genome data were analysed using the software Admixture and additional analytical tools to explore ancestry and introgression patterns. For A. m. siciliana, 32 out of 97 samples (32.99%) exhibited high purity levels based on a threshold of 0.9. The situation in Malta was more concerning, with only 11 out of 79 samples (13.92%) classified as pure A. m. ruttneri. The most severe admixture was observed in Crete, where just 2 out of 36 samples (5.56%) were identified as pure A. m. adami, highlighting extensive hybridization with mainland subspecies. Meanwhile, A. m. cypria appears to be the best-preserved Mediterranean subspecies, with genetic integrity largely maintained except in the northwestern population, which exhibited shared ancestry with mainland A. m. anatoliaca. Overall, our findings highlight the urgent need for conservation efforts across these islands. While the native subspecies remain threatened by hybridization, their preservation might still be possible, provided that further importations of non-native colonies are effectively prevented.
- Contrasting whole-genome diversity patterns and adaptation in honeybees from two southern European glacial refugiaPublication . Yadró Garcia, Carlos A.; Henriques, Dora; Cilia, Giovanni; Rufino, José; Vella, Cristina; Aglagane, Abdessamad; Sagastume, Soledad; Zammit-Mangion, Marion; Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. AliceHuman-driven environmental change makes understanding genetic variation essential for protecting keystone species such as the honeybee, Apis mellifera. We compared whole-genome mitonuclear variation in subspecies inhabiting the Iberian and Italian Peninsulas, which have been shaped by distinct glacial histories and modern beekeeping pressures. Italian honeybees showed a stronger anthropogenic imprint, driven largely by recent human-mediated gene flow. Both subspecies showed mitonuclear asymmetry, approximate south-to-northeast clinal pattern, evidence of ancient or recent admixture with other subspecies and lineages, and genomic signatures of a 20th-century bottleneck. African ancestry was present both, though ancient and predominantly mitochondrial in Iberia, but recent and predominantly nuclear Italy. Italian honeybees also had persistently lower historical effective population sizes, lower nucleotide versity, and higher kinship. Shared and subspecies-specific enriched genes suggest both convergent and unique adaptive responses. These results highlight complex evolutionary dynamics and the significant netic impact of modern beekeeping.
- 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.
- 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.
- 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.
- Genomic insights into middle eastern honey bee subspecies: population structure and genetic integrityPublication . Henriques, Dora; Yadró Garcia, Carlos A.; Honrado, Mónica; Amaral, Joana S.; Muz, Mustafa Necati; Muz, Dilek; Haddad, Nizar; Al Shagour, Banan; Obeidat, Wisam; Hosri, Chadi; Arab, Alireza; Arruda, James; Lamghari, Fouad; Rufino, José; Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. AliceThe genetic patterns of Middle Eastern A. mellifera subspecies have been understudied, hindering a comprehensive understanding of honey bee evolutionary history. Here, we studied the genetic integrity of five Middle Eastern subspecies across a broad geographical range: Turkey (A. m. anatoliaca, N=97; A. m. caucasia, N=75; A. m. syriaca, N=18), Jordan and Lebanon (A. m. syriaca, N=238 and N=29), Iran (A. m. meda, N=75), Oman, and the UAE (A. m. jemenitica, N=13 and N=10). ADMIXTURE and PCA analyses were conducted on SNPs detected from whole-genomes. Our findings reveal concerning conservation statuses for many populations/subspecies. In A. m. caucasia and A. m. anatoliaca, only 10 and 28 samples, respectively, were pure (introgression < 90%). In the A. m. caucasia range, 60 samples were hybrids of A. m. caucasia, A. m. syriaca, and A. m. ligustica. In the A. m. anatoliaca range, 69 samples showed high hybridization degrees with A. m. syriaca, and A. m. caucasia. Only six samples in the Turkish range of the A. m. syriaca range were identified as pure, while the rest were also hybrids. All samples from Jordan and Lebanon showed variable A. m. ligustica introgression. In Iran, 23 samples were classified as pure A. m. meda. The rest showed introgression primarily due to A. m. ligustica and A. m. caucasia. In the UAE, two main groups were identified: the first comprised hybrids of A. m. jemenitica, A. m. lamarckii and A. m. ligustica, and the second group mainly consisted of hybrids of A. m. lamarckii and A. m. ligustica. Oman stands out as the sole location where all samples were identified as pure A. m. jemenitica. This study indicates widespread hybridization across various regions and underscores the urgent need for targeted conservation efforts for Middle Eastern subspecies.