Browsing by Author "Dall'Olio, Raffaele"
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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.
- Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence dataPublication . Pinto, M. Alice; Henriques, Dora; Chávez-Galarza, Julio; Kryger, Per; Garnery, Lionel; Zee, Romée van der; Dahle, Bjørn; Soland-Reckeweg, Gabriele; De la Rúa, Pilar; Dall'Olio, Raffaele; Carreck, Norman L.; Johnston, J. SpencerThe recognition that the Dark European honey bee, Apis mellifera mellifera, is increasingly threatened in its native range has led to the establishment of conservation programmes and protected areas throughout western Europe. Previous molecular surveys showed that, despite management strategies to preserve the genetic integrity of A. m. mellifera, protected populations had a measurable component of their gene pool derived from commercial C-lineage honey bees. Here we used both sequence data from the tRNAleu-cox2 intergenic mtDNA region and a genome-wide scan, with over 1183 single nucleotide polymorphisms (SNPs), to assess genetic diversity and introgression levels in several protected populations of A. m. mellifera, which were then compared with samples collected from unprotected populations. MtDNA analysis of the protected populations revealed a single colony bearing a foreign haplotype, whereas SNPs showed varying levels of introgression ranging from virtually zero in Norway to about 14% in Denmark. Introgression overall was higher in unprotected (30%) than in protected populations (8%), and is reflected in larger SNP diversity levels of the former, although opposite diversity levels were observed for mtDNA. These results suggest that, despite controlled breeding, some protected populations still require adjustments to the management strategies to further purge foreign alleles, which can be identified by SNPs.
- Introgression of lineage c honey bees into black honey bee populations: a genome-wide estimation using single nucleotide polymorphisms (SNPS)Publication . Henriques, Dora; Chávez-Galarza, Julio; Kryger, Per; Johnston, J. Spencer; De la Rúa, Pilar; Rufino, José; Dall'Olio, Raffaele; Garnery, Lionel; Pinto, M. AliceThe black honey bee, Apis mellifera mellifera L., is probably the honey bee subspecies more threatened by introgression from foreign subspecies, specially lineage C A. m. carnica and A. m. ligustica. In fact, in some areas of its distributional range, intensive beekeeping with foreign subspecies has driven A. m. mellifera populations to nearly replacement. While massive and repeated introductions may lead to loss of native genetic patrimony, a low level of gene flow can also be detrimental because it may compromise honey bee survival and local adaptation by disrupting co-evolved gene complexes. Assessing levels of introgression is an important activity in breeding programs, especially when conservation of native races is a major concern. Previous surveys of A. m. mellifera populations estimated the introgression of lineage C honey bees by using mtDNA and microsatellites markers. In this presentation we used both mtDNA (sequence data of the tRNAleu-cox2 intergenic region) and over 1245 SNPs to ascertain introgression levels of A. m. carnica and A. m. ligustica in A. m. mellifera populations (some included in conservation programs) sampled in France, Switzerland, Denmark, Holland, Norway, England, and Scotland. We used different model-based approaches, implemented by different software applications (Structure, Admixture, NewHybrids). We found varying levels of introgression ranging from less than 3% (in Norway) to over 65% (in France).
- Introgression of lineage c honey bees into black honey bee populations: a genome-wide estimation using single nucleotide polymorphisms (SNPS)Publication . Henriques, Dora; Chávez-Galarza, Julio; Kryger, Per; Johnston, J. Spencer; De la Rúa, Pilar; Rufino, José; Dall'Olio, Raffaele; Garnery, Lionel; Pinto, M. AliceThe black honey bee, Apis mellifera mellifera L., is probably the honey bee subspecies more threatened by introgression from foreign subspecies, specially lineage C A. m. carnica and A. m. ligustica. In fact, in some areas of its distributional range, intensive beekeeping with foreign subspecies has driven A. m. mellifera populations to nearly replacement. While massive and repeated introductions may lead to loss of native genetic patrimony, a low level of gene flow can also be detrimental because it may compromise honey bee survival and local adaptation by disrupting co-evolved gene complexes. Assessing levels of introgression is an important activity in breeding programs, especially when conservation of native races is a major concern. Previous surveys of A. m. mellifera populations estimated the introgression of lineage C honey bees by using mtDNA and microsatellites markers. In this presentation we used both mtDNA (sequence data of the tRNAleu-cox2 intergenic region) and over 1245 SNPs to ascertain introgression levels of A. m. carnica and A. m. ligustica in A. m. mellifera populations (some included in conservation programs) sampled in France, Switzerland, Denmark, Holland, Norway, England, and Scotland. We used different model-based approaches, implemented by different software applications (Structure, Admixture, NewHybrids). We found varying levels of introgression ranging from less than 3% (in Norway) to over 65% (in France).