Browsing by Author "Vignal, Alain"
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- 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.
- Desenvolvimento de painéis de SNPs ultra-reduzidos a partir de dados de sequenciaçãoPublication . Henriques, Dora; Parejo, Melanie; Vignal, Alain; Wragg, David; Wallberg, Andreas; Webster, Matthew T.; Pinto, M. AliceA abelha melífera, Apis mellifera L., tem um papel fundamental no funcionamento dos ecossistemas e na produção de alimentos, no entanto, está sujeita a diversas ameaças. Entre outras, a introdução em larga escala de raças comerciais (normalmente com ancestralidade da Europa Oriental ou linhagem C) leva a uma hibridação introgressiva quebrando os complexos de genes adaptados localmente, os quais são cruciais para uma sustentabilidade a longo prazo das populações nativas. Esta ameaça tem sido alvo de preocupação na Europa Ocidental onde a subespécie nativa A. m. mellifera está seriamente ameaçada pela introgressão e a outra, a abelha ibérica, A. m. iberiensis, pode vir a ter o mesmo destino. Foram desenvolvidos quatro painéis ultra-reduzidos do marcador molecular designado polimorfismo de nucleótido simples (SNPs; 37-40 SNPs, cada) que podem ser usados de forma independente ou combinada para estimar introgressão genética na abelha ibérica. Como base usamos o genoma completo de 176 indivíduos (117 A. m. iberiensis e 59 linhagem C). A seleção dos SNPs foi feita usando o índice de diferenciação (FST), sendo apenas utilizados os SNPs fixos (FST=1). Adicionalmente, avaliamos os efeitos do tamanho da amostra e da amostragem geograficamente confinada no número de SNPs fixos. Verificamos que existe um enviesamento quando o tamanho da amostra é ≤10 e quando a amostragem representa uma pequena porção da diversidade genética. Finalmente, demonstramos que os painéis ultra-reduzidos, individualmente ou combinados, são rigorosos na estimação da introgressão da linhagem C em A. m. iberiensis, apresentando-se como uma ferramenta de grande utilidade na monitorização da integridade genética desta subespécie.
- Developing reduced SNP assays from whole-genome sequence data to estimate C-lineage introgression in the Iberian honeybee (Apis mellifera iberiensis)Publication . Henriques, Dora; Parejo, Melanie; Vignal, Alain; Wragg, David; Wallberg, Andreas; Webster, Matthew T.; Pinto, M. AliceThe honeybee has been subject to a growing number of threats. In Western Europe one such threat is large-scale introductions of commercial strains (C-lineage), which is leading to introgressive hybridization and even the local extinction of native populations (M-lineage). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in ;M-lineage subspecies Apis mellifera iberiensis. We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST=1) is introduced when the sample size is small (N≤10) and when sampling only captures a small fraction of a population’s genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training dataset to design four independent SNP assays selected from pairwise FST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid datasets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia, and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.
- Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)Publication . Henriques, Dora; Parejo, Melanie; Vignal, Alain; Wragg, David; Wallberg, Andreas; Webster, Matthew T.; Pinto, M. AliceThe most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large- scale introductions of commercial strains (C- lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M- lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C- lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N ≤ 10) and when sampling only captures a small fraction of a population’s genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C- lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time- and cost- effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.
- Genome-wide scans between two honeybee populations reveal putative signatures of human-mediated selectionPublication . Parejo, Melanie; Wragg, David; Henriques, Dora; Vignal, Alain; Neuditschko, MarkusAnimal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics. Human-mediated selection has left signatures in the genomes of many domesticated animals, including the European dark honeybee, Apis mellifera mellifera, which has been selected by apiculturists for centuries. Using whole-genome sequence information, we investigated selection signatures in spatially separated honeybee subpopulations (Switzerland, n = 39 and France, n = 17). Three different test statistics were calculated in windows of 2 kb (fixation index, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio) and combined into a recently developed composite selection score. Applying a stringent false discovery rate of 0.01, we identified six significant selective sweeps distributed across five chromosomes covering eight genes. These genes are associated with multiple molecular and biological functions, including regulation of transcription, receptor binding and signal transduction. Of particular interest is a selection signature on chromosome 1, which corresponds to the WNT4 gene, the family of which is conserved across the animal kingdom with a variety of functions. In Drosophila melanogaster, WNT4 alleles have been associated with differential wing, cross vein and abdominal phenotypes. Defining phenotypic characteristics of different Apis mellifera ssp., which are typically used as selection criteria, include colour and wing venation pattern. This signal is therefore likely to be a good candidate for human mediated-selection arising from different applied breeding practices in the two managed populations.
- Standard methods and good practices in Apis honey bee omics researchPublication . Techer, Maeva A.; Chakrabarti, Priyadarshini; Caesar, Lílian; Eynard, Sonia E.; Farrell, M. Catherine; Foster, Leonard J.; Gorrochategui-Ortega, June; Henriques, Dora; Li-Byarlay, Hongmei; Morré, Jeffrey T.; Newton, Irene L. G.; Parejo, Melanie; Pinto, M. Alice; Vignal, Alain; Zarraonaindia, Iratxe; McAfee, AlisonIn the past decades, COLOSS members have joined forces multiple times to develop and condense standard methods related to research on honey bees, their pests, pathogens, and colony products. This led to the publication of four open-access BEEBOOK volumes that have been utilized by researchers worldwide. Among the chapters, “Standard methods for molecular research in Apis mellifera,” written by Evans and collaborators in 2013, has been a cornerstone for the standardization of honey bee molecular studies. However, since sequencing technologies and analyzing algorithms have made tremendous progress, many described methods require updating. In parallel, other Apis species’ genomes have now been sequenced, thus opening new research avenues in a comparative framework. In this chapter, we add to the methods previously covered by Evans et al. in 2013 and provide updated methodology where necessary, including worked examples and bioinformatic analysis pipe-lines. We also cover topics which were not previously covered in depth, such as sequencing ancient samples, population genomics, proteomics, and sampling honey bee colony products for microbiome studies, among others. Our hope is for this to become a lasting resource for honey bee scientists as the field continues to advance.