Browsing by Author "Webster, Matthew T."
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- Adaptação local na abelha ibéricaPublication . Henriques, Dora; Wallberg, Andreas; Chávez-Galarza, Julio; Neves, Cátia J.; Costa, Filipe Oliveira; Webster, Matthew T.; Pinto, M. AlicePerceber a base genética do processo de adaptação permite uma previsão de como os organismos poderão responder a mudanças ambientais. A sequenciação de genomas a baixo custo, juntamente com os avanços das ferramentas estatísticas e computacionais possibilitam a compreensão da base genética da adaptação. O objectivo deste trabalho é o estudo da adaptação local da abelha ibérica, tendo como base algoritmos que permitem a incorporação de dados genéticos e ambientais. A Península Ibérica constituiu um local de interesse para este tipo de estudos por ser constituída por uma diversidade climática como Mediterrânico e Atlântico. Foram sequenciados 86 genomas de indivíduos distribuídos em 3 transectos (Atlântico, Central e Mediterrâneo) de forma a representar a diversidade climática existente na Península Ibérica. Em cada ponto de amostragem os dados de latitude e longitude foram recolhidos e variáveis ambientais foram retiradas das bases de dados WorldClim e Climatic Research Unit. Os métodos LFMM e Samβada, que integram informação genética e ambiental foram utilizados para procurar sinais de selecção. A vantagem destes métodos é que se pode perceber quais as variáveis ambientais que exercem uma pressão selectiva e que genes estão associados a cada variável. No total foram identificados 1289449 SNPs, dos quais 2193 mostraram estar significativamente associados com variáveis ambientais. Estes estão localizados em 826 genes. No conjunto das variáveis ambientais utilizadas, a longitude, latitude e precipitação apresentaram um maior num de SNPs associados. Foram encontrados genes com diversas funções, por exemplo quatro genes parecem relacionados com o desenvolvimento do sistema imunitário e este encontram associados à longitude, para a latitude proteínas de ligação parecem ser predominantes, já na precipitação aparecem genes relacionados com a morfogénese, actividade transportadora transmembranar e actividade olfactória. Este estudo representa primeira tentativa de compreender a base genética da adaptação local a partir de genomas completos.
- An unprecedented large-scale survey of honey bee mitochondrial diversity in Europe: c-lineage dominance and the need for conservation effortsPublication . Li, Fernanda; Costa, Maíra; Lopes, Ana Rita; Gonçalves, Telma; Henriques, Dora; Quaresma, Andreia; Yadró Garcia, Carlos A.; Albo, Alexandre; Blažytė-Čereškienė, Laima; Brodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Charistos, Leonidas; Chlebo, Robert; Coffey, Mary F.; Dahle, Bjørn; Danneels, Ellen; Dobrescu, Constantin; Dupleix-Marchal, Anna; Filipi, Janja; Gajda, Anna; Gratzer, Kristina; Groeneveld, Linn Fenna; Hatjina, Fani; Johannesen, Jes; Kolasa, Michal; Körmendy-Rácz, János; Kovačić, Marin; Kristiansen, Preben; Martikkala, Maritta; McCormack, Grace P.; Martín-Hernández, Raquel; Pavlov, Borce; Pietropaoli, Marco; Poirot, Benjamin; Radev, Zheko; Raudmets, Aivar; René-Douarre, Vincent; Roessink, Ivo; Škerl, Maja Ivana Smodiš; Soland-Reckeweg, Gabriele; Titera, Dalibor; Steen, Jozef van der; Varnava, Andri; Vejsnæs, Flemming; Webster, Matthew T.; Fedoriak, Mariia M.; Zarochentseva, Oksana; Graaf, Dirk C.; Pinto, M. AliceEurope is home to ten Apis mellifera subspecies, which belong to three mitochondrial lineages: the Western European (M), Eastern European (C), and African (A). However, the long-standing human-mediated movement of queens, primarily of C-lineage ancestry, has threatened the genetic integrity of many of these native subspecies through introgression and replacement. This has led to the establishment of conservation programs to recover the native lines in some European countries. The maternally-inherited mitochondrial DNA (mtDNA), particularly the highly polymorphic intergenic region tRNAleu-cox2, has been the marker of choice for assessing honey bee variation and introgression at large geographical scales. Herein, we will show the results of the tRNAleu-cox2 variation obtained from over 1200 colonies sampled across the range of the ten subspecies and covering 33 European countries. These revealed that apart from a few countries (Portugal, Spain, and Ireland) and isolated protected populations, European populations are predominantly dominated by C-lineage haplotypes, and many native subspecies exhibit a signature of C-derived introgression. In conclusion, this unprecedented survey of honey bee diversity across Europe underscores the concerning dominance of C-lineage genetic variation, highlighting the urgent need for strategic conservation efforts to preserve the native genetic diversity of Apis mellifera.
- 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.
- Função de genes associados à precipitação envolvidos na adaptação local da abelha ibéricaPublication . Ferreira, Helena; Neves, Cátia J.; Henriques, Dora; Chávez-Galarza, Julio; Wallberg, Andreas; Webster, Matthew T.; Pinto, M. AliceO aparecimento de novas tecnologias em estudos genómicos permite-nos realizar análises mais aprofundadas e compreender de que modo as forças evolutivas atuam sobre o genoma dos organismos. Um scan genómico realizado previamente na abelha ibérica, revelou genes associados a imunidade, detoxificação e mecanismo da visão, estando alguns deles associados a variáveis ambientais (Chávez-Galarza et al. 2013). Na sequência deste estudo procurou se sinais de seleção em genomas completos de 84 indivíduos de abelha ibérica, integrando informação genética, geográfica e ambiental. Detetou-se a presença 315 genes associados à precipitação. O principal objetivo é caracterizar a função destes genes, e também tentar perceber que tipos de substituições nucleotídicas ocorrem nas sequências codificantes das proteínas. Para isso utilizaram se diversas bases genómicas, como o NCBI, BeeBase e Flybase, as quais mostraram que 51 das variações, presentes em 28 genes, são não-sinónimas, originando aminoácidos diferentes.
- Genome-wide detection of signatures of selection in non- synonymous positions of iberian honey bee (Apis mellifera iberiensis)Publication . Henriques, Dora; Chávez-Galarza, Julio; Wallberg, Andreas; Neves, Cátia J.; Rufino, José; Costa, Filipe Oliveira; Webster, Matthew T.; Pinto, M. AliceMaternal and biparental genetic surveys of the Iberian honey bee (Apismelliferaiberiensis) populations have revealed complex and incongruent patterns of variation which have yet to be completely understood. Complex patternsare expected inregions like the Iberian Peninsulabecause (1) itcomprises a diverse range of habitats and climates,(2) it has served as a glacial refugium during the Pleistocene, and (3) it has functioned as a bridge for populations migrating between Africa and Europe. While the demographic history played an important role in shaping the genome of the Iberian honey bee, selection is an evolutionary force that cannot be discarded. In this study we used Illumina technology to sequence the whole genomes of 87 Iberian honey bees collected across three longitudinal transects in the Iberian Peninsula. The whole-genome dataset was scanned for signatures of selection using two genetic-environment association methods (LFMM and Samβada). A total of 828 SNPs, spanning 308 genes, were detected by both methods. Of the 308 genes,25 have SNPs in non-synonymous positions which were analyzed for positive selectionusing eight codon-substitution models (four neutral and four under selection) implemented by PAML and Selecton softwares.Of the 25 genes, 13 out show signals of positive selection. Functional annotation indicates that these genes are involved in various biological processes such as sensory perception of smell (2 genes), oxidation-reduction (2 genes), neurogenesis (1 gene) and cellular response to starvation (1 gene). This study represents an important first step into understanding local adaptation of Iberian honey bees.
- Large Scale Mitochondrial Evidence of C-lineage Dominance in European Honey BeesPublication . Li, Fernanda; Lopes, Ana; Costa, Maíra; Henriques, Dora; Quaresma, Andreia; Yadró García, Carlos A.; Albo, Alexandre; Čereškienė, Laima Blažytė; Brodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Charistos, Leonidas; Chlebo, Robert; Coffey, Mary F.; Dahle, Bjørn; Danneels, Ellen; Dobrescu, Constantin; Dupleix-Marchal, Anna; Filipi, Janja; Gajda, Anna; Gratzer, Kristina; Groeneveld, Linn Fenna; Hatjina, Fani; Johannesen, Jes; Kolasa, Michal; Körmendy-Rácz, János; Kovačić, Marin; Kristiansen, Preben; Martikkala, Maritta; McCormack, Grace P.; Martín-Hernández, Raquel; Pavlov, Borce; Poirot, Benjamin; Pietropaoli, Marco; Radev, Zheko; Raudmets, Aivar; René-Douarre, Vincent; Roessink, Ivo; Škerl, Maja Ivana Smodiš; Soland, Gabriele; Titera, Dalibor; Steen, Jozef van der; Varnava, Andri; Vejsnæs, Flemming; Fedoriak, Mariia M.; Zarochentseva, Oksana; Webster, Matthew T.; Graaf, Dirk C.; Pinto, M. AliceIn Europe, distribution of the several endemic honey bee (Apis mellifera) subspecies has suffered a considerable shift in the last century. In particular, beekeepers tend to favour subspecies of Eastern European ancestry (C-lineage), such as the Italian honey bee (A. m. ligustica), due to their perceived docility and high honey production. As a result, large scale migratory beekeeping and trade of C-lineage queens have exposed the native European honey bees to introgression and replacement, jeopardizing their genetic integrity and locally adapted traits. The maternally-inherited and highly polymorphic mitochondrial intergenic region tRNAleu-cox2 is routinely used for the assessment of honey bee diversity and introgression at large geographical scales. In this study, we conducted a survey on tRNAleu-cox2 variation in more than 1300 colonies from 33 European countries to assess current status of mitochondrial diversity patterns in Europe. Total genomic DNA was extracted from the bee thorax followed by PCR amplification of the tRNAleu-cox2 region and sequencing. The haplotypes were identified using alignments in MEGA 11. A clear dominance of C-lineage haplotypes was found (65%). The most prevalent C-lineage haplotype was C2 (54%) followed by C3 (23%) and C1(22%). Contrary to this trend, in Portugal, Spain and Ireland, less than 10% of the colonies exhibit the C-haplotype. Furthermore, the analysed apiaries in isolated protected areas (n=7) revealed a high proportion of colonies of western European (M-lineage) ancestry (80%) with M4 as the most frequent haplotype. African haplotypes (A lineage) were also found, albeit at lower frequencies, and were mainly concentrated in the Iberian Peninsula (9%). Intensive queen breeding and migratory beekeeping is homogenizing the gene pool of European bee populations. This survey of honey bee maternal diversity across Europe highlights the alarming dominance of C-lineage haplotypes and underscores the importance of conservation apiaries, as they have effectively preserved the autochthonous M-lineage subspecies in different countries. This work was conducted in the framework of the project Better-B, funded by the European Union, the Swiss State Secretariat for Education, Research, and Innovation, and UK Research and Innovation under the UK government's Horizon Europe funding guarantee (grant number 10068544).
- Maternal origin of honeybee (Apis mellifera) colonies from across EuropePublication . Lopes, Ana; Costa, Maíra; Tounakti, Sahar; Henriques, Dora; Quaresma, Andreia; Yadró Garcia, Carlos A.; Albo, Alexandre; Blažytė-Čereškienė, Laima; Broodschneider, Robert; Brusbardis, Valters; Carreck, Norman L.; Charistos, Leonidas; Chlebo, Robert; Coffey, Mary F.; Danneels, Ellen; Dobrescu, Constantin; Filipi, Janja; Gajda, Anna; Galea, Thomas; Gratzer, Kristina; Hatjina, Fani; Johannesen, Jes; Körmendy-Rácz, János; Kovačić, Marin; Preben, Kristiansen; Martikkala, Maritta; Martín-Hernández, Raquel; Pietropaoli, Marco; Poirot, Benjamin; Radev, Zheko; Raudmets, Aivar; Douarre, Vincent; Rodriguez-Flores, Maria Shantal; Roessink, Ivo; Ivana, Maja; Škerl, Maja Ivana Smodiš; Titera, Dalibor; Steen, Jozef van der; Varnava, Andri; Vejsnæs, Flemming; Webster, Matthew T.; Graaf, Dirk C.; Pinto, M. AliceWorldwide commercial beekeeping poses a threat to the native origin of the honeybee (Apis mellifera), with beekeepers favouring subspecies of Eastern European C-lineage ancestry, due to their docile behaviour and high honey production traits. In many parts of western and northern Europe, queens of Western European M-lineage ancestry have been massively replaced by queens of C-lineage ancestry, and this has led to the development of conservation programs aiming at recovering native lines. The maternally-inherited mitochondrial DNA (mtDNA), particularly the intergenic region tRNAleu-cox2, has been the marker of choice for assessing honey bee variation at large geographical scales. Herein, we will show the results of the mtDNA analysis of over 850 colonies collected across 28 European countries. These samples were subjected to DNA extraction, followed by PCR, and Sanger sequencing. The analysis of the sequences was conducted in Mega 11. The results indicated that, apart from Portugal, Spain, and the conservation centres in France and Denmark, where the colonies exhibited African or M haplotypes, the remaining countries are dominated by colonies of C-lineage maternal ancestry. In conclusion, this unprecedented mtDNA analysis conducted across Europe underscores the worrying dominance of C-lineage genetic variation, highlighting the urgent need for strategic conservation efforts to preserve the native genetic diversity of Apis mellifera.
- Patterns of Iberian honey bee variation inferred from the coding regions of whole mtDNA genomes: comparison with the popular intergenic tRNAleu-cox2 regionPublication . Pinto, M. Alice; Henriques, Dora; Wallberg, Andreas; Chávez-Galarza, Julio; Webster, Matthew T.Iberian honey bees (Apis mellifera iberiensis) are well-known for their complex patterns of variation, which have been extensively reported by PCR-RFLP data of the intergenic tRNAleu-cox2 region of the mitochondrial DNA. This mtDNA marker has revealed a highly structured and diverse subspecies characterized by the presence of western European (M) and African (A) haplotypes belonging to three African sublineages (AI, AII, AIII) forming a cline possibly originated from secondary contact. While the African-derived haplotypes occur in the southwestern half of Iberia, with sublineage AIII mostly present in the northern Atlantic coast, the northeastern half of Iberia is occupied by haplotypes of M ancestry. Here we report on the diversity patterns inferred from the coding portion of 87 mitochondrial whole genomes of Iberian honey bees and 20 of two reference subspecies: the North African A. m. intermissa and the western European A. m. mellifera. The whole mtDNA patterns were compared with those obtained with the intergenic tRNAleu-cox2 region. As expected, a concordant northeastern-southwestern cline formed by the two highly divergent lineages A and M was observed. However, the previously grouping of haplotypes into the three African sublineages is not supported by the entire coding portion of the mitochondrial molecule. This finding suggests that the tRNAleu-cox2 region is still a good marker for understanding the big picture of variation patterns.