Percorrer por autor "Muz, Dilek"
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- 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.
- 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.
- 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.
- Implementation of an extended SNP Panel for the genetic monitoring of honeybees and its application to A. mellifera mellifera and A. mellifera carnica samples across EuropePublication . Huml, Jana Vanessa; Bernstein, Richard; Hoppe, Andreas; Knight, Mairi E.; Ellis, Jonathan S.; Buswell, Victoria G.; Henriques, Dora; Pinto, M. Alice; Mccormack, Grace; Abdessamad, Aglagane; Anwar, Asmaa; Arab, Alireza; Muz, Dilek; Muz, Mustafa Necati; Mangion, Marion Zammit; Salome, James Arruda; Reckeweg, Gabriele SolandA number of methods have been established for the routine genetic monitoring of honeybees. These mainly focus on the estimation of hybridization between subspecies, as introgression is a major threat to the genetic integrity of native subspecies, leading to the replacement of locally adapted forms and the loss of species’ genetic diversity through homogenization. Given this focus, intra-subspecies diversity of markers is limited, making them less suitable for the estimation of other measures relevant in a conservation monitoring scheme, such as genetic diversity, inbreeding and effective population size. In this project, we evaluate a new tool for the genetic monitoring of honeybees, a 70K SNP-chip based on Jones et al. (2021). This has the advantage of including markers identified in previous studies that reflect phenotypic differences, such as variation in immune response or associations with traits such as hygienic behaviour, honey production and varroa tolerance. It also includes previously published marker sets for the estimation of introgression. The inclusion of markers that show intra-subspecies variation of functional relevance, as well as the higher marker density compared to previous honeybee SNP-chips, makes this a promising tool including a wide range of applications. These are the estimation of genetic diversity, inbreeding and effective population size, parentage analysis and possible genomic selection in breeding programs. Further, the analysis of introgression was optimized to distinguish between six clusters comprising of the A-, O- and Y-Lineages, A. mellifera mellifera, A. mellifera carnica and A. mellifera ligustica, using a comprehensive database of 1270 reference samples, built considering a total of 20 subspecies and ~4600 samples across Europe, the Middle East and Africa. Here, we report on the optimization and validation of these applications on the basis of the 70K SNP-chip and present results on ~4200 samples targeting A. m. mellifera and A. m. carnica across 20 European countries.
- 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.