Browsing by Author "Costa, Cecilia"
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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.
- Complex population structure and haplotype patterns in the Western European honey bee from sequencing a large panel of haploid dronesPublication . Wragg, David; Eynard, Sonia E.; Basso, Benjamin; Canale‐Tabet, Kamila; Labarthe, Emmanuelle; Bouchez, Olivier; Bienefeld, Kaspar; Bieńkowska, Małgorzata; Costa, Cecilia; Gregorc, Aleš; Kryger, Per; Parejo, Melanie; Pinto, M. Alice; Bidanel, Jean‐Pierre; Servin, Bertrand; Le Conte, Yves; Vignal, AlainHoney bee subspecies originate from specific geographical areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of the bees' original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environ-ment and mate naturally with queens from the local subspecies. The resulting ad-mixture complicates population genetics analyses, and population stratification can be a major problem for association studies. To better understand Western European honey bee populations, we produced a whole genome sequence and single nucleotide polymorphism (SNP) genotype data set from 870 haploid drones and demonstrate its utility for the identification of nine genetic backgrounds and various degrees of admixture in a subset of 629 samples. Five backgrounds identified correspond to sub-species, two to isolated populations on islands and two to managed populations. We also highlight several large haplotype blocks, some of which coincide with the position of centromeres. The largest is 3.6 Mb long and represents 21% of chromosome 11, with two major haplotypes corresponding to the two dominant genetic backgrounds identified. This large naturally phased data set is available as a single vcf file that can now serve as a reference for subsequent populations genomics studies in the honey bee, such as (i) selecting individuals of verified homogeneous genetic backgrounds as references, (ii) imputing genotypes from a lower-density data set generated by an SNP- chip or by low- pass sequencing, or (iii) selecting SNPs compatible with the re-quirements of genotyping chips.
- Deciphering the variation in cuticular hydrocarbon profiles of six European honey bee subspeciesPublication . Rodríguez-León, Daniel Sebastián; Uzunov, Aleksandar; Costa, Cecilia; Elen, Dylan; Charistos, Leonidas; Galea, Thomas; Gabel, Martin; Scheiner, Ricarda; Pinto, M. Alice; Schmitt, ThomasThe Western honey bee (Apis mellifera) subspecies exhibit local adaptive traits that evolved in response to the different environments that characterize their native distribution ranges. An important trait is the cuticular hydrocarbon (CHC) profile, which helps to prevent desiccation and mediate communication. We compared the CHC profiles of six European subspecies (A. m. mellifera, A. m. carnica, A. m. ligustica, A. m. macedonica, A. m. iberiensis, and A. m. ruttneri) and investigated potential factors shaping their composition. We did not find evidence of adaptation of the CHC profiles of the subspecies to the climatic conditions in their distribution range. Subspecies-specific differences in CHC composition might be explained by phylogenetic constraints or genetic drift. The CHC profiles of foragers were more subspecies-specific than those of nurse bees, while the latter showed more variation in their CHC profiles, likely due to the lower desiccation stress exerted by the controlled environment inside the hive. The strongest profile differences appeared between nurse bees and foragers among all subspecies, suggesting an adaptation to social task and a role in communication. Foragers also showed an increase in the relative amount of alkanes in their profiles compared to nurses, indicating adaptation to climatic conditions.
- Evaluation of suppressed mite reproduction (Smr) reveals potential for varroa resistance in european honey bees (apis mellifera l.)Publication . Mondet, Fanny; Parejo, Melanie; Meixner, Marina D.; Costa, Cecilia; Kryger, Per; Andonov, Sreten; Servin, Bertrand; Basso, Benjamin; Bieńkowska, Małgorzata; Bigio, Gianluigi; Căuia, Eliza; Cebotari, Valentina; Dahle, Bjørn; Dražić, Marica Maja; Hatjina, Fani; Kovačić, Marin; Kretavicius, Justinas; Lima, Ana S.; Panasiuk, Beata; Pinto, M. Alice; Uzunov, Aleksandar; Wilde, Jerzy; Büchler, RalphIn the fight against the Varroa destructor mite, selective breeding of honey bee (Apis mellifera L.) populations that are resistant to the parasitic mite stands as a sustainable solution. Selection initiatives indicate that using the suppressed mite reproduction (SMR) trait as a selection criterion is a suitable tool to breed such resistant bee populations. We conducted a large European experiment to evaluate the SMR trait in different populations of honey bees spread over 13 different countries, and representing different honey bee genotypes with their local mite parasites. The first goal was to standardize and validate the SMR evaluation method, and then to compare the SMR trait between the different populations. Simulation results indicate that it is necessary to examine at least 35 single-infested cells to reliably estimate the SMR score of any given colony. Several colonies from our dataset display high SMR scores indicating that this trait is present within the European honey bee populations. The trait is highly variable between colonies and some countries, but no major differences could be identified between countries for a given genotype, or between genotypes in different countries. This study shows the potential to increase selective breeding efforts of V. destructor resistant populations.
- From the popular tRNAleu-COX2 intergenic region to the mitogenome: insights from diverse honey bee populations of Europe and North AfricaPublication . Henriques, Dora; Chávez-Galarza, Julio; Quaresma, Andreia; Neves, Cátia J.; Lopes, Ana Rita; Costa, Cecilia; Costa, Filipe Oliveira; Rufino, José; Pinto, Maria A.The tRNAleu-COX2 intergenic region of the mitochondrial DNA has been used for assessing diversity in honey bee (Apis mellifera L.) populations worldwide. However, differential mutation rates in different partitions of the mitogenome may produce incongruent results. In this study, we sequenced 123 mitogenomes of 7 subspecies from lineages A, M, and C. This allowed generating a comprehensive dataset to investigate the phylogenetic and phylogeographic congruence among the mitogenome, individual genes, and the tRNAleu-COX2 region.We showed that the diversity patterns inferred fromthe tRNAleu-COX2 marker are not fully paralleled by those obtainedwith the mitogenome and the individual genes; while the three lineages are supported by these, the African sub-lineages and the haplotypes are not. Thus, conclusions drawn from the tRNAleu-COX2 region need to be taken with caution and this marker may not be appropriate to infer phylogenetic relationships between honey bee colonies.
- The mitochondrial genome of Apis mellifera sicilianaPublication . Henriques, Dora; Costa, Cecilia; Rufino, José; Pinto, M. AliceWe assembled the mitogenome of Apis mellifera siciliana, which was previously identified as African by the tRNA-leu-cox2 intergenic region. The mitogenome is 16,590 bp long. The gene content and organization are identical to other A. mellifera mitogenomes, containing 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic analysis showed a close mitochondrial relationship between A. m. siciliana and other African subspecies such as Apis mellifera sahariensis, Apis mellifera intermissa, and Apis mellifera ruttneri.