A note to transfer a generic database pseudocode for storing chronological data from research in apiaries

In honey bee research conducted in apiaries, a large amount of information is usually generated requiring a flexible database for storing and retrieving data. Here, we developed a generic database pseudocode, based on the abstraction of the apiary system, for data collected from the colonies through time.We thank J Chávez-Galarza for the fruitful discussions during the design of the database architecture. This research was funded through the 2013-2014 BiodivERsA/FACCE-JPI joint call for research proposals, with the national funders “Fundação para a Ciência e Tecnologia” (Portugal), “Agence Nationale de la Recherche” (France), and “Ministério de Economia y Competividade” (Spain).info:eu-repo/semantics/publishedVersio

Historical and contemporaneous human-mediated processes left a strong genetic signature on honey bee populations from the Macaronesian archipelago of the Azores

In this study, honey bees fromthe Macaronesian archipelago of the Azoreswere extensively surveyed to unveil diversity patterns. A total of 638 colonies were analyzed over two time periods using mtDNA and wing geometric morphometrics. The genetic composition revealed to be heterogeneous and related to historical and contemporary human-mediated introductions. The close relationship of Azorean populations with those from northern Portugal supports historical introductions by Portuguese settlers. The African sublineage AIII prevailed on five islands, contrasting with three islands where C haplotypes were dominant. On Pico and Graciosa, C haplotypes are due to recent imports of commercial queens. On Faial, the sudden replacement of AIII by C haplotypes coincided with arrival of Varroa destructor . This study deepens the current understanding of Macaronesian honey bees, suggesting that they are variants of the Iberian honey bee with differential levels of Cderived introgression.CASM was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001. Financial support was provided through the program COMPETE 2020 – POCI (Programa Operacional para a Competividade e Internacionalização) and by Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871).info:eu-repo/semantics/publishedVersio

Wing geometric morphometrics of workers and drones and single nucleotide polymorphisms provide similar genetic structure in the Iberian honey bee (Apis mellifera iberiensis)

Wing geometric morphometrics has been applied to honey bees (Apis mellifera) in identification of evolutionary lineages or subspecies and, to a lesser extent, in assessing genetic structure within subspecies. Due to bias in the production of sterile females (workers) in a colony, most studies have used workers leaving the males (drones) as a neglected group. However, considering their importance as reproductive individuals, the use of drones should be incorporated in these analyses in order to better understand diversity patterns and underlying evolutionary processes. Here, we assessed the usefulness of drone wings, as well as the power of wing geometric morphometrics, in capturing the signature of complex evolutionary processes by examining wing shape data, integrated with geographical information, from 711 colonies sampled across the entire distributional range of Apis mellifera iberiensis in Iberia. We compared the genetic patterns reconstructed fromspatially-explicit shape variation extracted fromwings of both sexes with that previously reported using 383 genome-wide SNPs (single nucleotide polymorphisms). Our results indicate that the spatial structure retrieved from wings of drones and workers was similar (r = 0.93) and congruent with that inferred from SNPs (r = 0.90 for drones; r = 0.87 for workers), corroborating the clinal pattern that has been described for A. m. iberiensis using other genetic markers. In addition to showing that drone wings carry valuable genetic information, this study highlights the capability of wing geometric morphometrics in capturing complex genetic patterns, o ering a reliable and low-cost alternative for preliminary estimation of population structure.This research was funded by the program COMPETE 2020—POCI (Programa Operacional para a Competividade e Internacionalização) and by Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871). FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) provided funds for TMF (2011/07857-9) and JSGT (2011/02434-2).info:eu-repo/semantics/publishedVersio

Does geometric morphometrics provide congruent results with SNP data? The case of Iberian honey bee (Apis mellifera iberiensis)

While molecular markers are usually preferred to infer population structure, geometric morphometrics is a cheap method that has been widely applied to the wings of female honey bees to identify subspecies or lineages and can be used alternatively or complementarily to molecular markers. However, the power of geometric morphometrics to capture the signature of complex evolutionary processes has not been tested in honey bees. In this study, we applied geometric morphometrics, combined with geographical information, to the right forewings of female individuals from 711 colonies distributed along the Iberian Peninsula, which contains a complex population structure. The results were further compared with those obtained using 383 SNPs. Our data showed that geometric morphometrics provided a similar spatial structure of SNPs data (r=0.90). Our findings reinforce the power of spatially explicit wing geometric morphometrics data to capture the signature of complex evolutionary processes. Thus, this method could be used as a low-cost alternative for preliminary estimation of population structure.info:eu-repo/semantics/publishedVersio

Can introgression in M-lineage honey bees be detected by abdominal colour patterns?

Honey bee abdominal pigmentation is one of the most recognisable traits and it is often used by beekeepers as an indicator of M-lineage subspecies purity. However, this approach may negatively impact population diversity and is futile if there is no association between tergite colour patterns and the genetic background. To assess whether this trait can be used as a proxy for introgression proportions in M-lineage subspecies, we genotyped, with highly informative SNP assays, A. m. mellifera and A. m. iberiensis individuals displaying four different colour phenotypes. The SNP data detected highly introgressed bees exhibiting a black phenotype and, at the same time, pure or marginally introgressed bees with yellow banding patterns, in both subspecies. Despite these observations, contrary to A. m. iberiensis , in A. m. mellifera , introgression proportions revealed to be a significant predictor of abdominal pigmentation. Therefore, abdominal pigmentation could be used by A. m. mellifera conservationists to guide colony selection when genetic tools are unavailable.KAB was funded by Dr. Tony Ryan research scholarship and an Irish Research Council scholarship. This work was financed by the Native Irish Honeybee Society (NIHBS), Federation of Irish Beekeeping Associations (FIBKA) and FEDER (Fundo Europeu de Desenvolvimento Regional) through the program COMPETE 2020–POCI (Programa Operacional para a Competividade e Internacionalização) and by the Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871).info:eu-repo/semantics/publishedVersio

Conservation of European M-lineage honey bees using abdominal colour as an indicator of subspecies purity has pitfalls

There are 31 honey bee (Apis mellifera) recognized subspecies, which have been grouped into four main lineages. Two of these lineages occur naturally in Europe: M in western and northern Europe and C in southeastern Europe. In Europe, M-lineage groups only two subspecies, Apis mellifera mellifera and Apis mellifera iberiensis, both being black in colour. C-Lineage groups have instead eight subspecies, including one of the beekeepers-favored and phenotypically distinct, the yellow Apis mellifera ligustica from Italy. M-lineage honey bees’ distribution has been changing and in some countries, the native bee is being replaced or hybridised with C-lineage subspecies. Honey bee abdominal pigmentation is one of the most recognisable traits and it has been used by beekeepers as an indicator of subspecies identity. However, this approach may negatively impact population diversity and is futile if there is no association between tergite colour patterns and genetic background. To test this approach, we calculated the introgression level of A. m. mellifera (N=162) and A. m. iberiensis individuals (N=559) with different colour phenotypes and from a wide geographical range using informative SNPs. In this study, many A. m. mellifera samples showed high levels of C-lineage introgression. The individuals collected in Iberia were revealed to be pure. Introgressed A. m. iberiensis individuals were all from the Azores, where a high frequency of C-lineage mitotypes exists in several islands. Our results showed that for both subspecies, it is not possible to directly identify introgressed individuals from observed colour patterns, as we found black honey bees with a considerable amount of introgression and honey bees with yellow banding that were pure or marginally introgressed. With this study, we hope to increase awareness among stakeholders of the need to use other tools to select honey bees for conservation and breeding purposes.This work was financed by the Native Irish Honeybee Society (NIHBS), Federation of Irish Beekeeping Associations (FIBKA) and FEDER (Fundo Europeu de Desenvolvimento Regional) through the program COMPETE 2020–POCI (Programa Operacional para a Competividade e Internacionalização) and by the Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871). FCT provided financial support by national funds (FCT/MCTES) to CIMO (UIDB/00690/2020). Dora Henriques is funded by BeeHappy and MEDIBEES which is part of the PRIMA programme supported by the European Union.info:eu-repo/semantics/publishedVersio

Composição genética das populações de abelha melífera (Apis mellifera L.) da Macaronésia

A região biogeográfica da Macaronésia engloba as ilhas do Atlântico Norte situadas perto da Europa e África e é composta pelos arquipélagos dos Açores e da Madeira, Canárias e Cabo Verde. As ilhas são locais com uma biogeografia única associada a elevados níveis de endemismo, sendo, por isso, um verdadeiro laboratório para o estudo da diversidade. Apesar de atualmente a abelha melífera (Apis mellifera L.) se encontrar em todo o mundo, a sua distribuição natural está restrita a África, Europa, Médio Oriente e a algumas regiões das Ásia. Nesta ampla área geográfica encontram-se 31 subespécies que estão agrupadas em quatro linhagens evolutivas: A (África), M (Europa Ocidental), C (Europa Oriental) e O (Médio Oriente). Das 31 subespécies até hoje descritas, cinco delas são nativas de ilhas. No entanto, apesar de existirem abelhas nas ilhas da Macaronésia, estas não atingiram o estatuto de subespécie. Embora existam vários estudos de diversidade genética nos diferentes arquipélagos da Macaronésia, uma compreensão mais completa da história evolutiva das populações insulares requer uma amostragem representativa de todos os arquipélagos. Nesta comunicação irão apresentar-se os resultados de um estudo genético levado a cabo por uma equipa do CIMO sobre a composição genética das populações dos Açores e da Madeira. Entre 2014 e 2015 foram amostradas 474 colónias nos Açores, e na Madeira foram amostradas 50 colónias. A composição genética foi determinada usando uma região do ADN mitocondrial (que tem uma herança materna) muito variável designada por tRNAleu-cox2. As 474 amostras dos Açores foram também analisadas usando um marcador do ADN nuclear designado por “polimorfismo de nucleótido simples, ou SNP, (com herança biparental). Os nossos resultados revelam que a semelhança genética entre as populações dos Açores e Madeira com as populações do Norte de Portugal é concordante com a hipótese da introdução histórica de abelha melífera a partir do século XV pelos colonizadores Portugueses. Além disso, a composição genética é marcada por uma forte componente materna de origem Africana sendo também bastante heterogénea entre ilhas, fundamentalmente em resultado da introdução de abelhas comerciais a partir da Europa oriental na década de 1980, no âmbito de um programa de modernização da apicultura apoiado pelo Governo Regional dos Açores. Este estudo aprofunda a compreensão da diversidade genética das abelhas melíferas existentes na Macaronésiainfo:eu-repo/semantics/publishedVersio

Applying reduce SNP assays for inferring C-lineage introgression patterns in Iberian honeybee populations of the Azores archipelago

The genetic composition of the honeybee populations of the Macaronesian archipelago of the Azores is poorly known. Until now, only honeybee populations of the island of São Miguel have been surveyed for genetic variation through the use of the tRNAleu-cox2 intergenic mitochondrial DNA region and microsatellites. Here, we combine data from the mtDNA obtained with the DraI test (intergenic region) and from the nuclear DNA obtained with newly developed reduced SNP assays to provide a complete picture of introgression patterns in the Azorean honeybee populations at both mitochondrial and nuclear compartments. The sampling was carried out in 2014 and 2015 and comprised 474 colonies widely distributed across the 8 islands populated by honeybees. Our cyto-nuclear results show that C-derived introgression varies across the archipelago ranging from virtually pure populations of the Iberian honeybee in the island of Santa Maria (Q-values 30%). The introgression levels are alarming and contrast with those of the Iberian honeybee populations of the mainland in Iberia, which are still virtually free of C-derived introgression, despite frequent importation of commercial queens.info:eu-repo/semantics/publishedVersio

A study of local adaptation in the Iberian honeybee (Apis mellifera iberiensis) using a reciprocal translocation experiment

In Europe, several translocation experiments suggested that native populations of Apis mellifera are adapted to local climate and flora. However, so far, no study has been conducted on the Iberian honeybee, Apis mellifera iberiensis. The goal of this study was to assess the existence of genotype-environment interaction (GEI), and consequently local adaptation, in the Iberian honeybee. In 2015 two apiaries were set up, each one with 36 colonies (18 of the origin Bragança and 18 of the origin Vila do Bispo), in two latitudinal extremes of Portugal: Bragança (north) and Vila do Bispo (south). Several traits of the 36 colonies were measured for almost 2 years, including: number of brood and pollen cells, honey yield, survival, and Varroa destructor infestation. The analyses were performed using t-Student and Mann-Whitney tests to compare those traits between the two origins in the same apiary and the same origin between the two apiaries. The survival analysis was performed using the Cox proportional hazard model in R. Colonies of the southern origin Vila do Bispo showed a tendency to collect more pollen and consequently they produced a higher number of brood cells, had a higher varroa infestation level and a lower survival rate than colonies of the origin Bragança in both locations. Honey yield was the only trait that showed existence of GEI, and therefore local adaptation, since the local honeybees had a higher honey production in their apiary of origin. Additionally, the differences between the two origins were sharper in more favourable environments where the honeybees can better express their genetic potential. Our findings highlight the importance of protecting local honeybee diversity in a period of increasing selection pressures such as climate change, agricultural land overuse and novel pathogens and parasites.Thisresearchwas funded through the 2013-2014~'BiodivERsA/FACCE-JPI Joint call for research proposals, with the national funders FCT(Portugal), CNRS (France), and MEC(Spain).info:eu-repo/semantics/publishedVersio

Assessment of honey bee cells using deep learning

Temporal assessment of honey bee colony strength is required for different applications in many research projects. This task often requires counting the number of cells with brood and food reserves multiple times a year from images taken in the apiary. There are thousands of cells in each frame, which makes manual counting a time-consuming and tedious activity. Thus, the assessment of frames has been frequently been performed in the apiary in an approximate way by using methods such as the Liebefeld. The automation of this process using modern imaging processing techniques represents a major advance. The objective of this work was to develop a software capable of extracting each cell from frame images, classify its content and display the results to the researcher in a simple way. The cells’ contents display a high variation of patterns which added to light variation make their classification by software a challenging endeavor. To address this challenge, we used Deep Neural Networks (DNNs) for image processing. DNNs are known by achieving the state-of-art in many fields of study including image classification, because they can learn features that best describe the content being classified, such as the interior of frame cells. Our DNN model was trained with over 60,000 manually labeled images whose cells were classified into seven classes: egg, larvae, capped larvae, honey, nectar, pollen, and empty. Our contribution is an end-to-end software capable of doing automatic background removal, cell detection, and classification of its content based on an input image. With this software the researcher is able to achieve an average accuracy of 94% over all classes and get better results compared with approximation methods and previous techniques that used handmade features like color and texture.This research was funded through the 2013-2014 BiodivERsA/FACCE-JPJ joint call for research proposals,witht he national funders FCT (Portugal), CNRS (France), and MEC (Spain).info:eu-repo/semantics/publishedVersio