Large-scale mitochondrial DNA analysis of native honey bee Apis mellifera populations reveals a new African subgroup private to the South West Indian Ocean islands

Distribution of honey bee mitochondrial DNA haplotypes in an Italian region where a legislative act is protecting the Apis mellifera ligustica subspecies

The conservation of the genetic integrity of Apis mellifera subspecies has emerged as an important objective. In 2019, the Emilia-Romagna region became the first Italian regional authority to issue a law specifically addressing the protection of the native Apis mellifera ligustica subspecies. In this study we analysed a highly informative portion of the mitochondrial DNA (mtDNA), widely used for assessing genetic diversity of honey bee populations. By analysing 1143 honey bees sampled after the introduction of this law, we provided a snapshot of the distribution of mtDNA haplotypes in this region. The two most frequent mtDNA haplotypes were C1 (characteristic of A. m. ligustica) and C2 (characteristic of A. m. carnica), reported in 86.5% and 11.0% of the analysed bees, respectively. About 1.3% and 1.1% of the analysed bees carried mtDNA haplotypes of the A and M lineages (haplotypes A1a, A1e, A4, A26, A65 and two novel ones, A2w and A6a; M3, M3a, M4 and M79). Continued genetic monitoring will be important to assess the impact of this regional law over the coming years. Based on the obtained results, we recommend a more stringent policy to prevent the erosion of the genetic integrity of the native subspecies A. m. ligustica.

HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations

BACKGROUND

Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited.

RESULTS

We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples.

CONCLUSION

HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.

New COI-COII mtDNA Region Haplotypes in the Endemic Honey Bees Apis mellifera intermissa and Apis mellifera sahariensis (Hymenoptera: Apidae) in Algeria

The practice of beekeeping in Algeria is of great cultural, social, and economic importance. However, the importation of non-local subspecies reported by beekeepers has disrupted the natural geographical distribution area and the genetic diversity of the native honey bees. To assess the genetic diversity of A. m. intermissa and A. m. sahariensis, and their relationships with African and European subspecies, the COI-COII intergenic region was analyzed in 335 individuals, 68 sampled in Algeria, 71 in Europe, Madagascar, and the South West Indian Ocean archipelagos, and 196 sequences recovered from GenBank. The results show the presence of the A lineage exclusively in Algerian samples with the identification of 24 haplotypes of which 16 are described for the first time. These haplotypes were found to be shared by both subspecies, with A74 being the most common haplotype in the population studied. The sequence comparison indicates the existence of three polymorphisms of the COI-COII marker: P0Q, P0QQ, and P0QQQ. One new haplotype was identified in the M lineage in samples from France. No evidence of genetic introgression within the Algerian honey bee population was detected. These data enhance our knowledge of the genetic diversity and emphasize the importance of protecting these local subspecies.

Parasite and virus dynamics in the honeybee Apis mellifera unicolor on a tropical island recently invaded by Varroa destructor

In La Réunion, the established honeybee subspecies Apis mellifera unicolor, an endemic subspecies of African lineage, is facing considerable challenges. Since the introduction of the Varroa destructor mite in 2017 high colony losses have been recorded. We investigated the dynamics of V. destructor and two viruses, the Deformed Wing Virus (DWV), known to be transmitted by the mite, and the Chronic Bee Paralysis Virus (CBPV), in A. m. unicolor. Colonies from two apiaries located at 300 and 900 m a.s.l were monitored twice for one year without any acaricide treatment. The brood area, V. destructor infestation rates, DWV and CBPV prevalence and load were recorded monthly. A. m. unicolor maintained brood rearing throughout the year. Varroa destructor infestation resulted in high colony mortality (up to 85 %) and high phoretic mite rates (up to 52 mites per hundred bees). The establishment of DWV in colonies occurred after that of V. destructor and the mite infestation rate had a significant effect on the virus prevalence and load. CBPV appeared only transiently throughout the surveys. The data showed that, in tropical colonies with permanent brood rearing, V. destructor and DWV can reach high levels, but are still subject to seasonal variations that appear to be influenced by environmental conditions. This suggests that beekeeping practices could be adapted by favouring sites and periods for transhumance or acaricide treatment.

Ecology and Management of African Honey Bees (Apis mellifera L.)

In Africa, humans evolved as honey hunters of honey bee subspecies adapted to diverse geographical regions. Beekeeping today is practiced much as it was when Africans moved from honey hunting to beekeeping nearly 5,000 years ago, with beekeepers relying on seasonally available wild bees. Research suggests that populations are resilient, able to resist diseases and novel parasites. Distinct biomes, as well as environmental pressures, shaped the behavior and biology of these bees and in turn influenced how indigenous beekeeping developed. It appears that passive beekeeping practices that enabled free-living populations contributed to the overall resilience and health of the bee. There is clearly a need for research aimed at a deeper understanding of bee biology and the ecosystems from which they benefit and on which humans depend, as well as a growing realization that the management of these bees requires an indigenous approach that reflects a broader knowledge base and the economics of local communities and markets.

Geographic population structure of the honeybee microsporidian parasite Vairimorpha (Nosema) ceranae in the South West Indian Ocean

The microsporidian Vairimorpha (Nosema) ceranae is one of the most common parasites of the honeybee. A single honeybee carries many parasites and therefore multiple alleles of V. ceranae genes that seem to be ubiquitous. As a consequence, nucleotide diversity analyses have not allowed discriminating genetic structure of parasite populations. We performed deep loci-targeted sequencing to monitor the haplotype frequencies of genome markers in isolates from discontinuous territories, namely the tropical islands of the South West Indian Ocean. The haplotype frequency distribution corroborated the suspected tetraploidy of the parasite. Most major haplotypes were ubiquitous in the area but with variable frequency. While oceanic isolates differed from European and Asian outgroups, parasite populations from distinct archipelagoes also differed in their haplotype distribution. Interestingly an original and very divergent Malagasy isolate was detected. The observed population structure allowed formulating hypotheses upon the natural history of V. ceranae in this oceanic area. We also discussed the usefulness of allelic distribution assessment, using multiple informative loci or genome-wide analyses, when parasite population is not clonal within a single host.

Africanized honeybee population (Apis mellifera L.) in Nicaragua: Forewing length and mitotype lineages

Various subspecies of Apis mellifera L. were introduced to Central America since colonization 500 years ago. Hybridization increased with the entrance of the Africanized bee in Nicaragua in 1984. Rustic beekeeping activities and numerous feral swarms define the genetic pattern, reflected in phenotypic heterogeneity and remarkable differences in the behaviour of the bee colonies, especially the nest defence. Due to these facts, the question emerge about the degree of Africanization of honeybee colonies in Nicaragua. In this study, we identified Africanized honeybee colonies based on the single character "mean forewing length" and we corroborated our results by determining mitotypes using mtDNA analysis. Morphometric and genetic approaches were realized in three different geographical zones of Nicaragua and related to beehive characteristics and management. Worker bee samples were taken from the inside of 146 hives from 26 apiaries. Abdominal colour as phenotypic character was the first examination, followed by measurement of 1460 right forewings to determine corresponding probability of Africanization. More than 60% of the beehives showed phenotypic heterogeneity and mean forewing length of 8.74 mm (SD 0.16 mm) indicated a high degree of Africanization. Those results provided a selection of 96 worker bees to perform PCR of two worker bees per hive. For mitochondrial DNA analysis 14 samples from sentinel apiaries were added. Three from 61 beehives presented bees with different mtDNA. Throughout, three mitotypes of the African (A) lineage were detected; one mitotype is still unidentified. Mitotype A1 A. mellifera iberiensis was represented by 88 bees and mitotype A4 A. mellifera scutellata by 21 bees. Phylogenetic analysis confirmed the PCR findings. No associations were found between mitotypes, forewing length, beehive characteristics and management. A high degree of Africanization in A. mellifera colonies represented by two predominating mitotypes from the A lineage, prevail in Neotropical Nicaragua, with mitotype A4 predominating at higher altitudes.

MtDNA Analysis Indicates Human-Induced Temporal Changes of Serbian Honey Bees Diversity

Simple Summary

The western honey bee is one of the most economically and ecologically important species currently facing serious challenges in its whole area of distribution. The honey bee is a highly diverse species with about 30 subspecies that are adapted to regional climate factors, vegetation, pests and pathogens. The local populations of honey bees are rapidly changing and their diversity is constantly manipulated by beekeepers through the import of foreign queens, selection and migratory beekeeping. This manipulation may lead to such changes that honey bees lose their ability to thrive in the areas that were previously suitable for their wellbeing. To see how this human interference changed the genetic variability of native honey bee populations from Serbia, we sequenced part of the mitochondrial genome and compared them with published sequences. Our results suggest that human influence significantly changes the natural composition of honey bees in Serbia and that the presence of some previously reported subspecies could not be confirmed.

Abstract

Local populations of Apis mellifera are rapidly changing by modern beekeeping through the introduction of nonnative queens, selection and migratory beekeeping. To assess the genetic diversity of contemporary managed honey bees in Serbia, we sequenced mitochondrial tRNA^leu-cox2 intergenic region of 241 worker bees from 46 apiaries at eight localities. Nine haplotypes were observed in our samples, with C2d being the most common and widespread. To evaluate genetic diversity patterns, we compared our data with 1696 sequences from the NCBI GenBank from neighbouring countries and Serbia. All 32 detected haplotypes belonged to the Southeast Europe lineage C, with two newly described haplotypes from our sample. The most frequent haplotype was C2d, followed by C2c and C1a. To distinguish A. m. carnica from A. m. macedonica, both previously reported in Serbia, PCR-RFLP analysis on the COI gene segment of mtDNA was used, and the result showed only the presence of A.m. carnica subspecies. An MDS plot constructed on pairwise F_ST values showed significant geographical stratification. Our samples are grouped together, but distant from the Serbian dataset from the GenBank. This, with the absence of A. m. macedonica subspecies from its historic range of distribution in southern Serbia, indicates that honey bee populations are changing rapidly due to the anthropogenic influence.

Mitochondrial DNA Variation in Peruvian Honey Bee (Apis mellifera L.) Populations Using the tRNAleu-cox2 Intergenic Region

Simple Summary

Currently, the genetic diversity of Peruvian honey bee populations is unknown. Only two studies were carried out and suggest that many regions of Peru present Africanized honey bee colonies and a varied degree of Africanization. To molecularly characterize and know more about the genetic background of Peruvian honey bees, the highly polymorphic tRNAleu-cox2 was used. This study analyzed 512 colonies in three regions of Peru: Lima, Piura, and Junín. The results indicated that 65% colonies correspond to lineage A (African), 33.8% colonies to lineage C (Eastern European), and 1.2% colonies to lineage M (Western European). A total of 24 haplotypes were identified: 16 haplotypes belong to lineage A (sub-lineage A_I (13), sub-lineage A_III (03)), lineage C (06), and lineage M (02), and 15 of them are for the first time reported and represented by A1t, A1u, A1w, A4p, A4q, A4s, A4t, A4u, A4v, A4w, 30d, A30e, A65, M7b, and M7c. Piura and Lima presented higher proportions of African haplotypes and lower proportions of haplotypes from lineage C than Lima. Very few haplotypes of lineage M were identified, whose presence could be due to accidental purchases or traces of honey bee introductions from lineage M in the 19th century. Hence, studies about the diversity and genetic structure of Peruvian honey bee populations are necessary to promote adequate, sustainable management and establish conservation and breeding programs.

Abstract

Mitochondrial DNA variations of Peruvian honey bee populations were surveyed by using the tRNA^leu-cox2 intergenic region. Only two studies have characterized these populations, indicating the presence of Africanized honey bee colonies in different regions of Peru and varied levels of Africanization, but the current status of its genetic diversity is unknown. A total of 512 honey bee colonies were sampled from three regions to characterize them. Our results revealed the presence of European and African haplotypes: the African haplotypes identified belong to sub-lineage A_I (13) and sub-lineage A_III (03), and the European haplotypes to lineages C (06) and M (02). Of 24 haplotypes identified, 15 new sequences are reported here (11 sub-lineage A_I, 2 sub-lineage A_III, and 2 lineage M). Peruvian honey bee populations presented a higher proportion from African than European haplotypes. High proportions of African haplotype were reported for Piura and Junín, unlike Lima, which showed more European haplotypes from lineage C. Few colonies belonging to lineage M would represent accidental purchase or traces of the introduction into Peru in the 19th century.

Characterization of the native honey bee (Apis mellifera jemenitica) in the south western region of Saudi Arabia using morphometric and genetic (mtDNA COI) characteristics

Apis mellifera jemenitica incorporates a few perceived subspecies that vary in their natural properties and farming qualities. Mitochondrial COI gene sequence (mtCOI) has not been used before for bee identification in the southwestern region of Saudi Arabia. The aim of this work was to study the morphometry and analyzing the mtCOI of all collected bees. The nucleotide sequence of the mtCOI gene was analyzed. Similarity searches and distances between each obtained DNA and sequences available in GenBank were made. Morphometric analysis revealed close similarities among the studied bees, but these similarities are different from those previously indicated in earlier studies of the same region. Molecular studies revealed that the collected bees are similar to each other and some other sequences found in GenBank, but these bees are a new hybrid or subspecies that are different from those previously reported in the same region, indicating the emergence of a new hybrid.

Coexistence of honeybees with distinct mitochondrial haplotypes and hybridised nuclear genomes on the Comoros Islands

The honeybee, Apis mellifera, is a globally distributed species that has spread both naturally and by humans across the globe resulting in many natural and secondary contact zones. The geographic isolation of honeybees is likely to contribute to genetic differentiation. Secondary contact has resulted in hybridization at the nuclear genome, but replacement of mitochondrial. Here, we used a mitochondrial marker and 19 microsatellite markers to test for the variations in the mitochondrial and nuclear genomes of honeybee populations on the Comoros islands. We used samples of 160 workers for mtDNA analysis and 288 workers from 16 colonies spread across the three islands for microsatellite analyses. Our results showed that the wild honeybee populations of the Comoros Islands consist of coexisting mitochondrial haplotypes. One belongs to the typical African A-lineage, and the other, the newly described L-lineage, is closely related to Apis koschevnikovi, a honeybee species native to Southeast Asia. The nuclear genomes show complete hybridization, high genetic diversity, and strong differentiation according to the island of origin. Based on our results, we hypothesise that the Asian honeybee could have been transported from Southeast Asia to Madagascar and Comoros via the human migrations that occurred 6000 years ago, and has hybridised with African honeybees at the nuclear genome, but maternal ancestry still can be traced using the mtDNA markers. We conclude that mtDNA plays a pivotal role in adaptation to the local environment, with both haplotypes of the honeybees of Comoros contributing significantly to the mito-nuclear coadaptation resulting in maintenance at almost equal frequency.

When European meets African honeybees (Apis mellifera L.) in the tropics: Morphological changes related to genetics in Mauritius Island (South-West Indian Ocean)

The previous genetic characterization of the honeybee population of Mauritius Island (Indian Ocean) revealed an ongoing process of hybridization between the first established African subspecies Apis mellifera unicolor and recently imported European subspecies (A. m. ligustica, A. m. carnica and A. m. mellifera). This context offers the rare opportunity to explore the influence of hybridization between African and European honeybees on phenotypic traits out of the case largely studied of the Africanized honeybee (hybrid between A. m. scutellata from South Africa and European subspecies). We thus conducted geometric morphometric analyses on forewings of 283 workers genetically characterized at 14 microsatellite loci to evaluate (1) if the morphological variability coincides well with the neutral genetic variability, (2) if hybrids exhibited rather parental, intermediate or transgressive traits, and (3) to test if fluctuating asymmetry (FA) of size and shape, as a measure of developmental stability, was elevated in hybrids (due to genetic stress) and/or European bees (due to unsuitable environment) compared to African bees. A strong concordance was found between morphological variability and neutral genetic variability, especially for wing shape, based on partial least-square analyses (PLS). However, on average, the morphology of hybrids was more similar to the African bees, potentially reflecting the dynamics and direction of introgression. Significant FA for wing size as well as wing shape was detected, suggesting the overall presence of stress during the development of the studied individuals. In contrast, the asymmetry levels do not differ according to the ancestry (African, European or hybrid) of the individuals. Therefore, if ongoing hybridization contributed to increasing the genetic and phenotypic diversity of the populations and influences its adaptive potential, developmental stressors could not be identified and their evolutionary consequences remain uncertain.

The complete mitochondrial genome of Apis mellifera unicolor (Insecta: Hymenoptera: Apidae), the Malagasy honey bee

The complete mitochondrial genome of the endemic Malagasy honey bee Apis mellifera unicolor is 16,373 bp and comprises 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The mitochondrial genome closely resembles mitogenomes of other published Apis mellifera subspecies, and the phylogenetic analysis suggests that A. m. unicolor is distinct from other African (A) lineage honey bees but is most closely related to the honey bees from southern African: A. m. scutellata and A. m. capensis.

Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors

Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.

Autosomal and Mitochondrial Adaptation Following Admixture: A Case Study on the Honeybees of Reunion Island

The honeybee population of the tropical Reunion Island is a genetic admixture of the Apis mellifera unicolor subspecies, originally described in Madagascar, and of European subspecies, mainly A. m. carnica and A. m. ligustica, regularly imported to the island since the late 19th century. We took advantage of this population to study genetic admixing of the tropical-adapted indigenous and temperate-adapted European genetic backgrounds. Whole genome sequencing of 30 workers and 6 males from Reunion, compared with samples from Europe, Madagascar, Mauritius, Rodrigues, and the Seychelles, revealed the Reunion honeybee population to be composed on an average of 53.2 ± 5.9% A. m. unicolor nuclear genomic background, the rest being mainly composed of A. m. carnica and to a lesser extent A. m. ligustica. In striking contrast to this, only 1 out of the 36 honeybees from Reunion had a mitochondrial genome of European origin, suggesting selection has favored the A. m. unicolor mitotype, which is possibly better adapted to the island’s bioclimate. Local ancestry was determined along the chromosomes for all Reunion samples, and a test for preferential selection for the A. m. unicolor or European background revealed 15 regions significantly associated with the A. m. unicolor lineage and 9 regions with the European lineage. Our results provide insights into the long-term consequences of introducing exotic specimen on the nuclear and mitochondrial genomes of locally adapted populations.

Genetic diversity and differentiation among insular honey bee populations in the southwest Indian Ocean likely reflect old geographical isolation and modern introductions

With globalization the Western honey bee has become a nearly cosmopolitan species, but it was originally restricted to the Old World. This renowned model of biodiversity has diverged into five evolutionary lineages and several geographic “subspecies.” If Apis mellifera unicolor is indubitably an African subspecies endemic to Madagascar, its relationship with honey bees from three archipelagos in the southwest Indian Ocean (SWIO) hotspot of biodiversity is misunderstood. We compared recent mtDNA diversity data to an original characterization of the nuclear diversity from honey bees in the Mascarenes and Comoros archipelagos, using 14 microsatellites, but also additional mtDNA tRNA^Leu-cox2 analysis. Our sampling offers the most comprehensive dataset for the SWIO populations with a total of 3,270 colonies from 10 islands compared with 855 samples from Madagascar, 113 from Africa, and 138 from Europe. Comprehensive mitochondrial screening confirmed that honey bees from La Réunion, Mauritius, and Comoros archipelagos are mainly of African origin (88.1% out of 2,746 colonies) and that coexistence with European lineages occurs only in the Mascarenes. PCA, Bayesian, and genetic differentiation analysis showed that African colonies are not significantly distinct on each island, but have diversified among islands and archipelagos. F_ST levels progressively decreased in significance from European and African continental populations, to SWIO insular and continental populations, and finally among islands from the same archipelago. Among African populations, Madagascar shared a nuclear background with and was most closely related to SWIO island populations (except Rodrigues). Only Mauritius Island presented clear cytoplasmic disequilibrium and genetic structure characteristic of an admixed population undergoing hybridization, in this case, between A. m. unicolor and A. m. ligustica, A. m. carnica and A. m. mellifera-like individuals. Finally, global genetic clustering analysis helped to better depict the colonization and introduction pattern of honey bee populations in these archipelagos.