Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera)

Population-wide modelling reveals prospects of marker-assisted selection for parasitic mite resistance in honey bees

In 2019, a joint eight-variant model was published in which eight single nucleotide polymorphisms (SNPs) in seven Apis mellifera genes were associated with Varroa destructor drone brood resistance (DBR, i.e. mite non-reproduction in drone brood). As this model was derived from only one Darwinian Black Bee Box colony, it could not directly be applied on a population-overarching scale in the northern part of Belgium (Flanders), where beekeepers prefer the carnica subspecies. To determine whether these eight SNPs remained associated with the DBR trait on a Flemish colony-broad scope, we performed population-wide modelling through sampling of various A. mellifera carnica colonies, DBR scoring of Varroa-infested drone brood and variant genotyping. Novel eight-variant modelling was performed and the classification performance of the eight SNPs was evaluated. Besides, we built a reduced three-variant model retaining only three genetic variants and found that this model classified 76% of the phenotyped drones correctly. To examine the spread of beneficial alleles and predict the DBR probability distribution in Flanders, we determined the allelic frequencies of the three variants in 292 A. mellifera carnica queens. As such, this research reveals prospects of marker-assisted selection for Varroa drone brood resistance in honeybees.

Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution of Honey Bees (Apis mellifera)

Previous morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a meta-analysis of complete mitochondrial DNA coding regions (11.0 kbp) from 22 nominal subspecies represented by 78 individual sequences in A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Molecular clock-calibrated phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe ~ 780 Kya, and expansion to Southeast Europe and Asia Minor ~ 720 Kya. Eurasian bees spread southward via a Levantine/Nilotic/Arabian corridor into Africa ~ 540 Kya. An African clade re-established in Iberia ~ 100 Kya spread thereafter to westerly Mediterranean islands and back into North Africa. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies. Names matter: paraphyletic anomalies are artefacts of mis-referral in GenBank of sequences to the wrong subspecies, or use of faulty sequences, which are clarified by inclusion of multiple sequences from available subspecies.

When One's Not Enough: Colony Pool-Seq Outperforms Individual-Based Methods for Assessing Introgression in Apis mellifera mellifera

The human management of honey bees (Apis mellifera) has resulted in the widespread introduction of subspecies outside of their native ranges. One well known example of this is Apis mellifera mellifera, native to Northern Europe, which has now been significantly introgressed by the introduction of C lineage honey bees. Introgression has consequences for species in terms of future adaptive potential and long-term viability. However, estimating introgression in colony-living haplodiploid species is challenging. Previous studies have estimated introgression using individual workers, individual drones, multiple drones, and pooled workers. Here, we compare introgression estimates via three genetic approaches: SNP array, individual RAD-seq, and pooled colony RAD-seq. We also compare two statistical approaches: a maximum likelihood cluster program (ADMIXTURE) and an incomplete lineage sorting model (ABBA BABA). Overall, individual approaches resulted in lower introgression estimates than pooled colonies when using ADMIXTURE. However, the pooled colony ABBA BABA approach resulted in generally lower introgression estimates than all three ADMIXTURE estimates. These results highlight that sometimes one individual is not enough to assess colony-level introgression, and future studies that do use colony pools should not be solely dependent on clustering programs for introgression estimates.

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.

The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies

Simple Summary

The western honeybee, Apis mellifera, is a globally distributed bee species with many recognised subspecies, one of which is Apis mellifera carnica, the Carniolan honeybee. Apis m. carnica is native to southern Central Europe and parts of the Balkans, with the locus classicus in Slovenia. It is also widely popular with beekeepers in parts of Central and Northern Europe and other parts of the world, including the USA, Canada, and even New Zealand. In Slovenia, A. m. carnica is protected, with measures to conserve the subspecies’ autochthonous domestic population in place. Such efforts depend heavily upon genomic and phylogenetic information. In this study, we sequenced and annotated the mitochondrial genome of a specimen from Slovenia and compared the obtained data with a previously published sample of the A. m. carnica from Austria and the closely related Italian honeybee A. m. ligustica. We found several features unique to the new mitochondrial genome. We also phylogenetically analyzed the relationship between our sequence and the selected available A. mellifera mitochondrial sequences. The acquired position of the sequenced A. m. carnica from Slovenia on the phylogenetic tree brings new evidence for close relationships among C and O lineages and reflects their recent historical matrilinear ancestry.

Abstract

The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.

Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

The deep sea (> 200 m) is considered as the largest and most remote biome, which characterized by low temperatures, low oxygen level, scarce food, constant darkness, and high hydrostatic pressure. The sea stars (class Asteroidea) are ecologically important and diverse echinoderms in all of the world’s oceans, occurring from the intertidal to the abyssal zone (to about 6000 m). To date, the phylogeny of the sea stars and the relationships of deep-sea and shallow water groups have not yet been fully resolved. Here, we recovered five mitochondrial genomes of deep-sea asteroids. The A+T content of the mtDNA in deep-sea asteroids were significantly higher than that of the shallow-water groups. The gene orders of the five new mitogenomes were identical to that of other asteroids. The phylogenetic analysis showed that the orders Valvatida, Paxillosida, Forcipulatida are paraphyletic. Velatida was the sister order of all the others and then the cladeValvatida-Spinulosida-Paxillosida-Notomyotida versus Forcipulatida-Brisingida. Deep-sea asteroids were nested in different lineages, instead of a well-supported clade. The tropical Western Pacific was suggested as the original area of asteroids, and the temperate water was initially colonized with asteroids by the migration events from the tropical and cold water. The time-calibrated phylogeny showed that Asteroidea originated during Devonian-Carboniferous boundary and the major lineages of Asteroidea originated during Permian–Triassic boundary. The divergence between the deep-sea and shallow-water asteroids coincided approximately with the Triassic-Jurassic extinction. Total 29 positively selected sites were detected in fifteen mitochondrial genes of five deep-sea lineages, implying a link between deep-sea adaption and mitochondrial molecular biology in asteroids.

Further Evidence of Population Admixture in the Serbian Honey Bee Population

Simple Summary

The western honey bee is one of the most ecologically and economically important pollinator species. Due to human interference, it faces serious challenges, not only in number decline and habitat loss, but also in natural subspecies diversity and distribution. The conservation of genetic diversity and perseverance of locally adapted populations and subspecies becomes a crucial task in the face of rapid environmental changes. In order to further assess present genetic variability in Serbian honey bee populations, we analyzed 14 microsatellite loci and then compared nine of them with previously published data. Our results suggest that Serbia now harbors a distinct, relatively homogenous honey bee population, although some local differences are still preserved.

Abstract

Socioeconomic interests and beekeeper preferences have often taken precedence over the conservation of locally native honey bee subspecies, leading to the predominance of admixture populations in human-dominated areas. To assess the genetic diversity of contemporary managed Serbian honey bee colonies, we used 14 microsatellite loci and analyzed 237 worker bees from 46 apiaries in eight localities of northern and southern Serbia. Furthermore, we compared data for nine microsatellite loci with 338 individuals from Italy, Hungary, Poland, and Spain. The standard parameters of genetic diversity in Serbian honey bee populations were in line with other analyses, although somewhat smaller. STRUCTURE analysis showed the existence of two equally distributed genetic clusters and Analysis of molecular variances could not confirm the presence of a geographically discrete population but showed local differences. Discriminant analysis of principal components showed overlapping of worker bees from different parts of Serbia. Clear genetic differentiation can be observed when comparing all populations between geographical regions and their corresponding subspecies. The absence of the A. m. macedonica subspecies from its historical distribution range in southern Serbia as well as the lack of distinctive geographical groups suggest that selective breeding, queen import, and migratory beekeeping practices strongly influence the genetic structure and diversity of honey bees, leading to the genetic uniformization and creation of the admixture population.

Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica)

Mitochondrial genomes (mitogenomes) are involved in cellular energy metabolism and have been shown to undergo adaptive evolution in organisms with increased energy-consuming activities. The genetically selected high royal jelly-producing bees (RJBs, Apis mellifera ligustica) in China can produce 10 times more royal jelly, a highly nutritional and functional food, relative to unselected Italian bees (ITBs). To test for potential adaptive evolution of RJB mitochondrial genes, we sequenced mitogenomes from 100 RJBs and 30 ITBs. Haplotype network and phylogenetic analysis indicate that RJBs and ITBs are not reciprocally monophyletic but mainly divided into the RJB- and ITB-dominant sublineages. The RJB-dominant sublineage proportion is 6-fold higher in RJBs (84/100) than in ITBs (4/30), which is mainly attributable to genetic drift rather than positive selection. The RJB-dominant sublineage exhibits a low genetic diversity due to purifying selection. Moreover, mitogenome abundance is not significantly different between RJBs and ITBs, thereby rejecting the association between mitogenome copy number and royal jelly-producing performance. Our findings demonstrate low genetic diversity levels of RJB mitogenomes and reveal genetic drift and purifying selection as potential forces driving RJB mitogenome evolution.

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.

Distribution of the Main Apis mellifera Mitochondrial DNA Lineages in Italy Assessed Using an Environmental DNA Approach

Growing interest has been emerging on the need to monitor the genetic integrity of the European Apis mellifera subspecies that could be threatened by the human-mediated dispersion of non-native populations and lines. Mitochondrial DNA (mtDNA) lineages can provide useful information for this purpose. In this study, we took advantage of the environmental DNA (eDNA) contained in the honey, which can be analyzed to detect the main groups of mitotypes of the honey bees that produced it. In this study, we applied this eDNA to produce a distribution map all over the Italian peninsula and the two major islands (Sicily and Sardinia) of the following three honey bee mtDNA lineages: A, C and M. A total of 607 georeferenced honey samples, produced in all Italian regions, was analyzed to detect these lineages. The A lineage was widespread in Sicily, as expected, considering that A. m. siciliana carries the African lineage. Surprisingly, this lineage was also reported in about 14% of all other samples produced in almost all continental regions, and in Sardinia. The applied method obtained an updated distribution map of honey bee mtDNA lineages that could be useful to design policies for the conservation of Italian honey bee genetic resources.

Chemical Composition of Volatile Compounds in Apis mellifera Propolis from the Northeast Region of Pará State, Brazil

Propolis is a balsamic product obtained from vegetable resins by exotic Africanized bees Apis mellifera L., transported and processed by them, originating from the activity that explores and maintains these individuals. Because of its vegetable and natural origins, propolis is a complex mixture of different compound classes; among them are the volatile compounds present in the aroma. In this sense, in the present study we evaluated the volatile fraction of propolis present in the aroma obtained by distillation and simultaneous extraction, and its chemical composition was determined using coupled gas chromatography, mass spectrometry, and flame ionization detection. The majority of compounds were sesquiterpene and hydrocarbons, comprising 8.2-22.19% α-copaene and 6.2-21.7% β-caryophyllene, with additional compounds identified in greater concentrations. Multivariate analysis showed that samples collected from one region may have different chemical compositions, which may be related to the location of the resin's production. This may be related to other bee products.

The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers

The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.

Mitochondrial DNA Suggests the Introduction of Honeybees of African Ancestry to East-Central Europe

Simple Summary

In Europe, a well-known threat to the conservation of honeybee diversity is the loss of genetic uniqueness of local populations due to beekeepers’ preference for a few genetic lineages. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees of African origin could represent another threat. This issue has not yet been recognised in detail, although bees bearing African mitochondrial DNA occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mitochondrial DNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35%) had African mitochondrial DNA. It is unlikely that their presence in the area resulted from natural migration but instead human-driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.

Abstract

In Europe, protecting the genetic diversity of Apis mellifera is usually perceived in the context of limiting the spread of the evolutionary C-lineage within the original range of the M-lineage. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees from the African A-lineage could represent another threat. This issue has not yet been investigated in detail, although A-mitotypes occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mtDNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35 %) had A-mitotypes. It is unlikely that their presence in the area resulted from natural migration but instead human driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.

Viral impacts on honey bee populations: A review

Honey bee is vital for pollination and ecological services, boosting crops productivity in terms of quality and quantity and production of colony products: wax, royal jelly, bee venom, honey, pollen and propolis. Honey bees are most important plant pollinators and almost one third of diet depends on bee's pollination, worth billions of dollars. Hence the role that honey bees have in environment and their economic importance in food production, their health is of dominant significance. Honey bees can be infected by various pathogens like: viruses, bacteria, fungi, or infested by parasitic mites. At least more than 20 viruses have been identified to infect honey bees worldwide, generally from Dicistroviridae as well as Iflaviridae families, like ABPV (Acute Bee Paralysis Virus), BQCV (Black Queen Cell Virus), KBV (Kashmir Bee Virus), SBV (Sacbrood Virus), CBPV (Chronic bee paralysis virus), SBPV (Slow Bee Paralysis Virus) along with IAPV (Israeli acute paralysis virus), and DWV (Deformed Wing Virus) are prominent and cause infections harmful for honey bee colonies health. This issue about honey bee viruses demonstrates remarkably how diverse this field is, and considerable work has to be done to get a comprehensive interpretation of the bee virology.