Percorrer por autor "Kandemir, Irfan"
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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.
- Hinf-I digestion of cytochrome oxidase I region is not a diagnostic test for A-m. lamarckiiPublication . Kandemir, Irfan; Pinto, M. Alice; Meixner, Marina D.; Sheppard, Walter S.Restriction fragment length polymorphism of whole mitochondrial DNA or PCR amplified mtDNA regions are known to be useful in discriminating among honey bee lineages and also some individual subspecies. In this study, PCR-amplified fragments of cytochrome oxidase I (CO-I) and cytochrome B (Cyt B) of honey bees sampled from different countries (Cyprus, Turkey, Ethiopia, Syria and Egypt) were digested with Hinf I and Bgl II restriction enzymes, respectively. Eastern Europe and Mediterranean honey bee subspecies were separated by the Cyt B/Bgl II analysis, although Hinf I digestion of the CO-I region yielded much finer resolution within different honey bee lineages. Here we report that CO-I/Hinf-I is a discriminative test for the mitochondrial “O” lineage, rather than a diagnostic site for A. m. lamarckii.
- Honey bee (Apis mellifera) wing images: a tool for identification and conservationPublication . Oleksa, Andrzej; Cauia, Eliza; Siceanu, Adrian; Puskadija, Zlatko; Kovačić, Marin; Pinto, M. Alice; Rodrigues, Pedro J.; Hatjina, Fani; Charistos, Leonidas; Bouga, Maria; Presern, Janez; Kandemir, Irfan; Rasic, Sladan; Kusza, Szilvia; Tofilski, AdamThe honey bee (Apis mellifera) is an ecologically and economically important species that provides pollination services to natural and agricultural systems. The biodiversity of the honey bee in parts of its native range is endangered by migratory beekeeping and commercial breeding. In consequence, some honey bee populations that are well adapted to the local environment are threatened with extinction. A crucial step for the protection of honey bee biodiversity is reliable differentiation between native and nonnative bees. One of the methods that can be used for this is the geometric morphometrics of wings. This method is fast, is low cost, and does not require expensive equipment. Therefore, it can be easily used by both scientists and beekeepers. However, wing geometric morphometrics is challenging due to the lack of reference data that can be reliably used for comparisons between different geographic regions. Here, we provide an unprecedented collection of 26,481 honey bee wing images representing 1,725 samples from 13 European countries. The wing images are accompanied by the coordinates of 19 landmarks and the geographic coordinates of the sampling locations. We present an R script that describes the workflow for analyzing the data and identifying an unknown sample. We compared the data with available reference samples for lineage and found general agreement with them. The extensive collection of wing images available on the Zenodo website can be used to identify the geographic origin of unknown samples and therefore assist in the monitoring and conservation of honey bee biodiversity in Europe.
- Honey bees (Hymenoptera: Apidae) of african origin exist in non-africanized areas of the Southern United States: evidence from mitochondrial DNAPublication . Pinto, M. Alice; Sheppard, Walter S.; Johnston, J. Spencer; Rubink, William L.; Coulson, Robert N.; Schiff, Nathan M.; Kandemir, Irfan; Patton, John C.Descendents of Apis mellifera scutellata Lepeletier (Hymenoptera: Apidae) (the Africanized honey bee) arrived in the United States in 1990. Whether this was the Þrst introduction is uncertain. A survey of feral honey bees from non-Africanized areas of the southern United States revealed three colonies (from Georgia, Texas, and New Mexico) with a diagnostic African mitochondrial DNA cytochrome b/BglII fragment pattern. To assess maternal origin of these colonies, we developed a primer pair for ampliÞcation of a cytochrome b fragment and sequenced using internal sequencing primers. Samples of the three reported honey bee colonies plus another 42 representing the 10 subspecies known to have been introduced in the United States were sequenced. Of the three colonies, the colonies from Texas and New Mexico matched subspecies of European maternal ancestry, whereas the colony from Georgia was of African ancestry. Contrary to expectations, the mitotype of the latter colony was more similar to that exhibited by sub-Saharan A. m. scutellata than to the mitotypes common in north African A. m. intermissa Maa or Portuguese and Spanish A. m. iberiensis Engel. This Þnding was consistent with anecdotal evidence that A. m. scutellata has been sporadically introduced into the United States before the arrival of the Africanized honey bee from South America.
- The Journal of Apicultural Research welcomes the publication of research findings from around the globePublication . Parejo, Melanie; Alippi, Adriana M.; Bobis, Otilia; Broodschneider, Robert; Harris, Vanessa Corby; Dimou, Maria; Duangphakdee, Orawan; Gajda, Anna; Henriques, Dora; Kandemir, Irfan; Pickard, Robert; Rangel, Juliana; Roberts, Stuart; Soroker, Victoria; Stevanovic, Jevrosima; Bouga, MariaThe Journal of Apicultural Research (JAR) is a peer-reviewed, scientific journal dedicated to examining and publishing the latest research on bees from around the world. JAR publishes many different types of articles to reach different international audiences, from career scientists to students and well-informed beekeepers. These comprise original, theoretical, and experimental research papers, as well as authoritative notes, comments, and reviews on scientific aspects of all types of bees (superfamily Apoidea). As of 2021, JAR has an Impact Factor of 2.407 and is ranked 33rd out of 100 in the Entomology category (© InCites Journal Citation Reports®, Clarivate Analytics, 2022). Five regular issues are published per year and special issues are added when timely topics arise, the latest being a special issue on stingless bees (2022) and review papers (2023). In the last decade, COLOSS BEEBOOK chapters are published in JAR. These open-access chapters are a collection of the Standard Methods used in honey bee research, including the study of parasites, pests, and hive products. They are a primary reference resource for bee researchers across the globe and facilitate new projects that might not otherwise be undertaken by laboratories that are new to apidology (236,516 downloads - Taylor & Francis 3,028 citations - Web of Science, 2022). The Journal of Apicultural Research was founded by the International Bee Research Association (IBRA) in 1962. The very first issue included a Note from the first Editors, Dr. Eva Crane & Dr. James Simpson, who introduced JAR as a new opportunity for publication: “The journal will cover all aspects of bees, Apis and non-Apis, and substances used or produced by them, their pollinating activities, and organisms causing diseases or injuries to them.” Since the first issue, this legacy has been maintained in more than 2,800 scientific articles, co-authored by some 1,900 researchers, published so far in JAR, making our journal a key forum for the international exchange of scientific data in apidology. We encourage colleagues from around the globe to continue to participate in sharing their research with the scientific community by publishing in JAR.