Characterization of (GT)n and (CT)n microsatellites in two insect species: Apis mellifera and Bombus terrestris

Genetic Characterizations of the Iranian Honey Bee (Apis mellifera meda Skorikov 1929) Populations Using the Microsatellite DNA Markers

The genetic characterization of the Iranian honey bee was investigated by analyzing 10 polymorphic DNA microsatellite loci in 300 honey bee samples representative of twenty Iranian provinces. This study evaluated the heterozygosity (Ho and He), the Shannon index, the number of observed alleles, and F-statistics among tested populations as genetic parameters. Our finding demonstrated that the Iranian honey bee populations were described by low genetic diversity in terms of the number of observed alleles, Shannon index, and Heterozygosity values. Most populations had significant deviations from Hardy Weinberg equilibrium cause of heterozygote shortage. Low FST and FIS values proposed the absence or very low genetic diversity within and among A. m. meda populations in the present study. The cluster analysis has categorized the honey bee samples gathered from various regions of Iran into two main groups, including honey bees in the North-West (i.e., North, Northwest, and West) provinces and honey bees in the East-South (i.e., Eastern North, Central part, and Southern) provinces of Iran. Our results also revealed lower genetic differentiation and heterozygosity among tested honey bee populations. The results from this study are consistent with previous investigations in Iran, alarming the loss of genetic diversity in the Iranian honey bee populations, which leads to more homozygosity. This study presented new data and reports on genetic structure in investigated native Iranian honey bee populations, and it will benefit future studies on selection, native biodiversity preservation and other conservation breeding projects.

Tragedy of the commons in Melipona bees revisited

Melipona stingless bees display a paradoxical overproduction of queens, which are later eliminated by nest-mate workers. Mechanistically, it was suggested that the monoterpenoid geraniol deposited into newly provisioned cells by adult bees would cause larvae to develop into queens in Melipona beecheii. This system could be evolutionarily stable if many of these new queens were to leave the nest and parasitize other genetically unrelated colonies nearby, as was shown to occur in a congeneric species. Here, we use microsatellite markers to test whether queen overproduction could be a strategy by which adult workers control the caste fate of the developing larvae to export copies of their own genes to the rest of the population via queen parasitism in M. beecheii. In addition, we re-examined whether artificially increasing the levels of geraniol indeed caused larvae to develop as queens rather than workers. Contrary to our prediction, we found no evidence for queen parasitism in M. beecheii and observed no effect of geraniol on the rearing of new queens. Together, these results support the original 'tragedy of the commons' hypothesis for queen overproduction in Melipona bees, where individual larvae selfishly bias their development towards the queen pathway according to their best evolutionary interests.

Pattern of population structuring between Belgian and Estonian bumblebees

Several population genetic studies investigated the extent of gene flow and population connectivity in bumblebees. In general, no restriction in gene flow is considered for mainland populations of common bumblebee species. Whether this assumption holds true for all species is not known. An assessment of bumblebee genetic structure in the context of their geographic distribution is needed to prioritize conservation and management needs. Here, we conducted a genetic study on seven bumblebee species occurring in Belgium and Estonia. Using 16 microsatellite markers, we investigated genetic diversity and population structuring in each species. This is the first study investigating population structuring of both declining and stable bumblebee species on both small and large geographic scales. Our results showed no or only low population structuring between the populations of the restricted and declining bumblebee species on both scales, while significant structuring was found for populations of the common species on the larger scale. The latter result, which may be due to human or environmental changes in the landscape, implies the need for the conservation of also widespread bumblebee species. Conservation strategies to improve gene flow and connectivity of populations could avoid the isolation and future losses of populations of these important species.

Genetic Diversity in the Progeny of Commercial Australian Queen Honey Bees (Hymenoptera: Apidae) Produced in Autumn and Early Spring

Honey bee [Apis mellifera L. (Hymenoptera: Apidae)] queens are polyandrous, mating with an average 12 males (drones). Polyandry has been shown to confer benefits to queens and the colonies they head, including avoidance of inviable brood that can arise via sex locus homozygosity, increased resilience to pests and pathogens, and increased survival and productivity, leading to improved colony-level fitness. Queens with an effective mating frequency (ke) greater than 7 are considered adequately mated, whereas queens that fall below this threshold head colonies that have increased likelihood of failure and may be less productive for beekeepers. We determined ke in queens produced in early Spring and Autumn by five Australian commercial queen producers to determine whether the queens they produced were suitably mated. Drone populations are low at these times of year, and therefore, there is an increased risk that queens would fall below the ke > 7 threshold. We found that 33.8% of Autumn-produced queens did not meet the threshold, whereas 93.8% of Spring queens were adequately mated. The number of colonies contributing drones to the mating pool was similarly high in both seasons, suggesting that although many colonies have drones, their numbers may be decreased in Autumn and management strategies may be required to boost drone numbers at this time. Finally, queens had similar levels of homozygosity to workers, and inbreeding coefficients were very low, suggesting that inbreeding is not a problem.

Queen Longevity and Fecundity Affect Conflict with Workers over Resource Inheritance in a Social Insect

Resource inheritance is a major source of conflict in animal societies. However, the assumptions and predictions of models of conflict over resource inheritance have not been systematically tested within a single system. We developed an inclusive fitness model for annual eusocial Hymenoptera that predicts a zone of conflict in which future reproductive workers are selected to enforce nest inheritance before the queen is selected to cede the nest. We experimentally tested key elements of this model in the bumblebee Bombus terrestris. In colonies from which queens were sequentially removed, queen tenure was significantly negatively associated with worker male production, confirming that workers gain direct fitness by usurping the queen. In unmanipulated colonies, queen fecundity decreased significantly over the latter part of the colony cycle, confirming that workers' indirect fitness from maintaining queens declines over time. Finally, in an experiment simulating loss of queen fecundity by removal of queens' eggs, worker-to-queen aggression increased significantly and aggressive workers were significantly more likely to become egg layers, consistent with workers monitoring queen fecundity to assess the net benefit of future reproduction. Overall, by upholding key assumptions and predictions of the model, our results provide novel empirical support for kin-selected conflict over resource inheritance.

Viable Triploid Honey Bees (Apis mellifera capensis) Are Reliably Produced in the Progeny of CO2 Narcotised Queens

The haplodiploid system of sex determination of Hymenoptera acts as an exaptation for species to evolve novel forms of asexual reproduction including thelytoky (clonal offspring of the mother). During normal reproduction in Hymenoptera, three of the four products of meiosis that are present in newly-laid eggs are lost as polar bodies, while the remaining pronucleus either develops as a haploid male or fuses with a sperm nucleus to produce a diploid zygote. In contrast, in thelytokous reproduction, which is uncommon but taxonomically widespread, two of the four products of meiosis fuse, as if one acted as a sperm. Queenless workers of Apis mellifera capensis, a subspecies of honey bee from South Africa, routinely reproduce thelytokously. Unmated A. m. capensis queens can also be induced to lay thelytokously by narcosis with carbon dioxide, but mated queens are never thelytokous. We artificially inseminated A. m. capensis queens using CO₂ narcosis. Up to 1/3 of offspring workers carried two maternal alleles and an allele of one father whereas no three-allele progeny were seen in control queens of the arrhenotokous (unfertilized eggs result in males) subspecies A. m. scutellata. Flow cytometry of three-allele individuals revealed that they were triploid and arose from the fertilization of a thelytokous fusion nucleus. We then reared six queens from a narcotized A. m. capensis queen and determined the ploidy of the offspring queens based on microsatellites. One of the five daughters was triploid. Following artificial insemination, this queen produced unfertilized thelytokous diploid eggs at high frequency, and unfertilized triploid eggs at much lower frequency. If fertilized, thelytokous diploid eggs were non-viable, even though triploidy in itself does not impede normal development. In contrast, when the rarer triploid eggs were fertilized, a proportion developed into viable tetraploids. Our study highlights the extraordinary developmental flexibility of haplo-diploid systems.

Cryptic "royal" subfamilies in honey bee (Apis mellifera) colonies

During emergency queen rearing, worker honey bees (Apis mellifera) select several otherwise worker-destined larvae to instead rear as candidates to replace their dead or failing queen. This choice is crucial as the queen is the sole reproductive in the colony and her quality is essential to its success. Because honey bee queens mate with and store sperm from multiple drones, emergency queen selection presents workers with an opportunity to increase fitness by selecting full- (0.75 relatedness), rather than half- (0.25 relatedness), sisters as new queen candidates. Through patriline analysis of colonies along with large numbers of emergency queens reared by each we affirm the purported “royal” patriline theory that, instead of competing nepotistically, workers exhibit bias towards selecting individuals from particular “royal” subfamilies during emergency queen rearing events, Further, we show that these “royal” patrilines are cryptic in honey bee colonies; occurring in such low frequency in the overall colony population that they are frequently undetected in traditional tests of queen mating number and colony composition. The identification of these cryptic “royal” subfamilies reveals that honey bee queens, already considered “hyperpolyandrous,” are mating with even more males than has been previously recognized. These results alter our understanding of reproductive behavior in honey bees, raising questions about the evolutionary implications of this phenomenon.

Chemical reproductive traits of diploid Bombus terrestris males: Consequences on bumblebee conservation

The current bumblebee decline leads to inbreeding in populations that fosters a loss of allelic diversity and diploid male production. As diploid males are viable and their offspring are sterile, bumblebee populations can quickly fall in a vortex of extinction. In this article, we investigate for the first time a potential premating mechanism through a major chemical reproductive trait (male cephalic labial gland secretions) that could prevent monandrous virgin queens from mating with diploid males. We focus our study on the cephalic labial gland secretions of diploid and haploid males of Bombus terrestris (L.). Contrary to initial expectations, our results do not show any significant differentiation of cephalic labial gland secretions between diploid and haploid specimens. Queens seem therefore to be unable to avoid mating with diploid males based on their compositions of cephalic labial gland secretions. This suggests that the vortex of extinction of diploid males could not be stopped through premating avoidance based on the cephalic labial gland secretions but other mechanisms could avoid mating between diploid males and queens.

A genome-wide analysis of simple sequence repeats in Apis cerana and its development as polymorphism markers

The Asian honeybee (Apis cerana) is an important indigenous species that play an indispensable role in the ecological balance and biological diversity. Few studies have been conducted to characterize the simple sequence repeats (SSRs) derived from A. cerana, so, in this study, a genome-wide screening for SSRs were firstly performed in the genome of A. cerana by comparison with that in west honeybee (Apis mellifera). There were 20,9991 SSRs distributed throughout the genome of A. cerana (Korea strain) and di-nucleotides were the most frequent SSR type. Both total number and density of SSRs in A. cerana genome were smaller than that in A. mellifera genome. Through comparing length discrepancy of SSRs loci among several isolates based on sequence alignment, 218 potential polymorphic SSRs primers derived from A. cerana were presented. Five among these SSR markers were evaluated for amplification in twenty-eight colonies of Apis cerana cerana (Chinese honeybee), which showed highly polymorphic, with the value of Polymorphism information content (PIC) ranging from 0.47 to 0.61. All these results will contribute to further develop more effective SSRs markers derived from A. cerana, which can be used to study genetic structure and population polymorphism of Asian honeybee.

Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species

Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. We analyzed and compared the number of SSRs, relative abundance, relative density, guanine-cytosine (GC) content and proportion of SSRs in six taxonomically different bovid species: Bos taurus, Bubalus bubalis, Bos mutus, Ovis aries, Capra hircus, and Pantholops hodgsonii. Our analysis revealed that, based on our search criteria, the total number of perfect SSRs found ranged from 663,079 to 806,907 and covered from 0.44% to 0.48% of the bovid genomes. Relative abundance and density of SSRs in these Bovinae genomes were non-significantly correlated with genome size (Pearson, r < 0.420, p > 0.05). Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di- > tri- > penta- > tetra- > hexanucleotide SSRs. Generally, the number of SSRs, relative abundance, and relative density of SSRs decreased as the motif repeat length increased in each species of Bovidae. The most GC-content was in trinucleotide SSRs and the least was in the mononucleotide SSRs in the six bovid genomes. The GC-contents of tri- and pentanucleotide SSRs showed a great deal of similarity among different chromosomes of B. taurus, O. aries, and C. hircus. SSR number of all chromosomes in the B. taurus, O.aries, and C. hircus is closely positively correlated with chromosome sequence size (Pearson, r > 0.980, p < 0.01) and significantly negatively correlated with GC-content (Pearson, r < -0.638, p < 0.01). Relative abundance and density of SSRs in all chromosomes of the three species were significantly negatively correlated with GC-content (Pearson, r < -0.333, P < 0.05) but not significantly correlated with chromosome sequence size (Pearson, r < -0.185, P > 0.05). Relative abundances of the same nucleotide SSR type showed great similarity among different chromosomes of B. taurus, O. aries, and C. hircus.

Spatial genetic structure and restricted gene flow in bed bugs (Cimex lectularius) populations in France

Bed bugs (Cimex lectularius) are resurgent blood-sucking ectoparasites that are currently increasing at a rapid rate, particularly in industrialized countries, such as France. Despite the rapid spread of bed bugs, there is a lack of knowledge concerning the population structure and gene flow among C. lectularius populations in France. To fill this gap, a genetic study was conducted using 183 C. lectularius from 14 populations of bed bugs collected in a hotel and in individual apartments in the French Riviera and in the Saint Ouen suburb of Paris. The samples were genotyped using an isolated set of six polymorphic microsatellite loci, including five new loci which were newly isolated and chosen based on prior successful amplification, and one previously described loci (bb15b). The low genetic diversity observed in the samples (of one to five alleles) suggested that most of prospected populations were established by only a few individuals, possibly from a single mated female. The overall genetic differentiation was high and statistically significant (FST=0.556, p<0.0001). Pairwise analysis of the populations indicated significant genetic differentiation for 24 out of the 45 (53%) population pairs associated with FST, ranging from 0.0042 to 0.862. No obvious relationship between the level of genetic differentiation and the geographic distance was observed when considering all samples. Analysis with Structure software identified nine distinct genetic clusters within the dataset. These preliminary results help to elucidate the genetic structure and gene flow of C. lectularius populations in France; however, the available information should be expanded in further studies.

Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species

Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949-1955 and 1975-1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline.

Quantitative Trait Loci for Light Sensitivity, Body Weight, Body Size, and Morphological Eye Parameters in the Bumblebee, Bombus terrestris

Bumblebees such as Bombus terrestris are essential pollinators in natural and managed ecosystems. In addition, this species is intensively used in agriculture for its pollination services, for instance in tomato and pepper greenhouses. Here we performed a quantitative trait loci (QTL) analysis on B. terrestris using 136 microsatellite DNA markers to identify genes linked with 20 traits including light sensitivity, body size and mass, and eye and hind leg measures. By composite interval mapping (IM), we found 83 and 34 suggestive QTLs for 19 of the 20 traits at the linkage group wide significance levels of p = 0.05 and 0.01, respectively. Furthermore, we also found five significant QTLs at the genome wide significant level of p = 0.05. Individual QTLs accounted for 7.5-53.3% of the phenotypic variation. For 15 traits, at least one QTL was confirmed with multiple QTL model mapping. Multivariate principal components analysis confirmed 11 univariate suggestive QTLs but revealed three suggestive QTLs not identified by the individual traits. We also identified several candidate genes linked with light sensitivity, in particular the Phosrestin-1-like gene is a primary candidate for its phototransduction function. In conclusion, we believe that the suggestive and significant QTLs, and markers identified here, can be of use in marker-assisted breeding to improve selection towards light sensitive bumblebees, and thus also the pollination service of bumblebees.

Inheritance of thelytoky in the honey bee Apis mellifera capensis

Asexual reproduction via thelytokous parthenogenesis is widespread in the Hymenoptera, but its genetic underpinnings have been described only twice. In the wasp Lysiphlebus fabarum and the Cape honey bee Apis mellifera capensis the origin of thelytoky have each been traced to a single recessive locus. In the Cape honey bee it has been argued that thelytoky (th) controls the thelytoky phenotype and that a deletion of 9 bp in the flanking intron downstream of exon 5 (tae) of the gemini gene switches parthenogenesis from arrhenotoky to thelytoky. To further explore the mode of inheritance of thelytoky, we generated reciprocal backcrosses between thelytokous A. m. capensis and the arrhenotokous A. m. scutellata. Ten genetic markers were used to identify 108 thelytokously produced offspring and 225 arrhenotokously produced offspring from 14 colonies. Patterns of appearance of thelytokous parthenogenesis were inconsistent with a single locus, either th or tae, controlling thelytoky. We further show that the 9 bp deletion is present in the arrhenotokous A. m. scutellata population in South Africa, in A. m. intermissa in Morocco and in Africanized bees from Brazil and Texas, USA, where thelytoky has not been reported. Thus the 9  p deletion cannot be the cause of thelytoky. Further, we found two novel tae alleles. One contains the previously described 9 bp deletion and an additional deletion of 7 bp nearby. The second carries a single base insertion with respect to the wild type. Our data are consistent with the putative th locus increasing reproductive capacity.

Screening and characterization of RAPD markers in viscerotropic Leishmania parasites

Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5′ end transversions, and presence of inter– and intra– taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop molecular diagnostics assays to characterize and differentiate VL causing agents.

Aspectos bioecológicos e genético-comportamentais envolvidos na conservação da abelha Jandaíra, Melipona subnitida Ducke (Apidae, Meliponini), e o uso de ferramentas moleculares nos estudos de diversidade

A abelha sem ferrão Melipona subnitida atualmente está presente em quase toda a região nordeste, em função da boa adaptabilidade ao semiárido nordestino e do potencial econômico-ecológico proporcionado pela produção de mel e pela polinização de cultivos em condições de confinamento. Apesar disso, é uma espécie ameaçada devido a processos de degradação ambiental, dentre os quais estão o desmatamento, o uso indiscriminado de agrotóxicos e o extrativismo. Tais interferências tendem a isolar as populações de Jandaíra, provocando uma queda na variabilidade genética e, consequentemente, uma redução na capacidade adaptativa da espécie. Porém, técnicas de biologia molecular estão sendo implementadas, possibilitando que populações desse tipo sejam avaliadas quanto ao seu grau de variabilidade genética. Marcadores moleculares do tipo microssatélites de DNA vêm sendo bastante usados, porém, em função do alto custo exigido para seu desenvolvimento, diversos estudos vêm empregando microssatélites transferidos de táxons próximos com amplo sucesso em estudos voltados à caracterização e à diversidade genética. Dessa forma, a presente revisão objetivou avaliar os mais relevantes aspectos bioecológicos e genético-comportamentais envolvidos na conservação da abelha Jandaíra, a fim de auxiliar na avaliação do grau de diversidade genética da espécie, bem como da sua distribuição entre indivíduos e populações da abelha sem ferrão M. subnitida.

The invasion of southern South America by imported bumblebees and associated parasites

The Palaearctic Bombus ruderatus (in 1982/1983) and Bombus terrestris (1998) have both been introduced into South America (Chile) for pollination purposes. We here report on the results of sampling campaigns in 2004, and 2010-2012 showing that both species have established and massively expanded their range. Bombus terrestris, in particular, has spread by some 200 km year(-1) and had reached the Atlantic coast in Argentina by the end of 2011. Both species, and especially B. terrestris, are infected by protozoan parasites that seem to spread along with the imported hosts and spillover to native species. Genetic analyses by polymorphic microsatellite loci suggest that the host population of B. terrestris is genetically diverse, as expected from a large invading founder population, and structured through isolation by distance. Genetically, the populations of the trypanosomatid parasite, Crithidia bombi, sampled in 2004 are less diverse, and distinct from the ones sampled later. Current C. bombi populations are highly heterozygous and also structured through isolation by distance correlating with the genetic distances of B. terrestris, suggesting the latter's expansion to be a main structuring factor for the parasite. Remarkably, wherever B. terrestris spreads, the native Bombus dahlbomii disappears although the reasons remain unclear. Our ecological and genetic data suggest a major invasion event that is currently unfolding in southern South America with disastrous consequences for the native bumblebee species.

Microsatellites, from molecules to populations and back

Population genetics studies using microsatellites, and data on their molecular dynamics, are on the increase. But, so far, no consensus has emerged on which mutation model should be used, though this is of paramount importance for analysis of population genetic structure. However, this is not surprising given the variety of microsatellite molecular motifs. Null alleles may be disturbing for population studies, even though their presence can be detected through careful population analyses, while homoplasy seems of little concern, at least over short evolutionary scales. Interspecific studies show that microsatellites are poor markers for phylogenetic inference. However, these studies are fuelling discussions on directional mutation and the role of selection and recombination in their evolution. Nonetheless, it remains true that microsatellites may be considered as good, neutral mendelian markers.

Outbreeding and lack of temporal genetic structure in a drone congregation of the neotropical stingless bee Scaptotrigona mexicana

Drone aggregations are a widespread phenomenon in many stingless bee species (Meliponini), but the ultimate and proximate causes for their formation are still not well understood. One adaptive explanation for this phenomenon is the avoidance of inbreeding, which is especially detrimental for stingless bees due to the combined effects of the complementary sex-determining system and the small effective population size caused by eusociality and monandry. We analyzed the temporal genetic dynamics of a drone aggregation of the stingless bee Scaptotrigona mexicana with microsatellite markers over a time window of four weeks. We estimated the drones of the aggregation to originate from a total of 55 colonies using sibship re-construction. There was no detectable temporal genetic differentiation or sub-structuring in the aggregation. Most important, we could exclude all colonies in close proximity of the aggregation as origin of the drones in the aggregation, implicating that they originate from more distant colonies. We conclude that the diverse genetic composition and the distant origin of the drones of the S. mexicana drone congregation provides an effective mechanism to avoid mating among close relatives.

Reproductive conflict in bumblebees and the evolution of worker policing

Worker policing (mutual repression of reproduction) in the eusocial Hymenoptera represents a leading example of how coercion can facilitate cooperation. The occurrence of worker policing in "primitively" eusocial species with low mating frequencies, which lack relatedness differences conducive to policing, suggests that separate factors may underlie the origin and maintenance of worker policing. We tested this hypothesis by investigating conflict over male parentage in the primitively eusocial, monandrous bumblebee, Bombus terrestris. Using observations, experiments, and microsatellite genotyping, we found that: (a) worker- but not queen-laid male eggs are nearly all eaten (by queens, reproductive, and nonreproductive workers) soon after being laid, so accounting for low observed frequencies of larval and adult worker-produced males; (b) queen- and worker-laid male eggs have equal viabilities; (c) workers discriminate between queen- and worker-laid eggs using cues on eggs and egg cells that almost certainly originate from queens. The cooccurrence in B. terrestris of these three key elements of "classical" worker policing as found in the highly eusocial, polyandrous honeybees provides novel support for the hypothesis that worker policing can originate in the absence of relatedness differences maintaining it. Worker policing in B. terrestris almost certainly arose via reproductive competition among workers, that is, as "selfish" policing.

Genetic variability of arrhenotokous and thelytokous Venturia canescens (Hymenoptera)

The ichneumonid wasp Venturia canescens (Hymenoptera) has been studied extensively for foraging behaviour and population dynamics of sexually (arrhenotokous) and parthenogenetically (thelytokous) reproducing individuals. Here we report the development of a set of microsatellite markers for V.canescens and use them to show that arrhenotokous individuals have more genetic variability than thelytokous ones, which are even homozygous for all tested loci. Crosses between arrhenotokous individuals suggested one marker, Vcan071, to be linked with the Complementary Sex Determiner (CSD) locus and one, Vcan109, with the Virus Like Protein (vlp-p40) locus. The genome size of V. canescens was estimated to be 274–279 Mb. We discuss how both reproductive modes can give rise to the observed genetic variability and how the new markers can be used for future genetic studies of V. canescens.

Workers dominate male production in the neotropical bumblebee Bombus wilmattae (Hymenoptera: Apidae)

Background

Cooperation and conflict in social insects are closely linked to the genetic structure of the colony. Kin selection theory predicts conflict over the production of males between the workers and the queen and between the workers themselves, depending on intra-colonial relatedness but also on other factors like colony efficiency, sex ratios, cost of worker reproduction and worker dominance behaviour. In most bumblebee (Bombus) species the queen wins this conflict and often dominates male production. However, most studies in bumblebees have been conducted with only a few selected, mostly single mated species from temperate climate regions. Here we study the genetic colony composition of the facultative polyandrous neotropical bumblebee Bombus wilmattae, to assess the outcome of the queen-worker conflict over male production and to detect potential worker policing.

Results

A total of 120 males from five colonies were genotyped with up to nine microsatellite markers to infer their parentage. Four of the five colonies were queen right at point of time of male sampling, while one had an uncertain queen status. The workers clearly dominated production of males with an average of 84.9% +/- 14.3% of males being worker sons. In the two doubly mated colonies 62.5% and 96.7% of the male offspring originated from workers and both patrilines participated in male production. Inferring the mother genotypes from the male offspring, between four to eight workers participated in the production of males.

Conclusions

In this study we show that the workers clearly win the queen-worker conflict over male production in B. wilmattae, which sets them apart from the temperate bumblebee species studied so far. Workers clearly dominated male production in the singly as well the doubly mated colonies, with up to eight workers producing male offspring in a single colony. Moreover no monopolization of reproduction by single workers occurred.

A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae

Background

The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL) mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level.

Results

The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs) and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG.

Conclusions

This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae.

Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

Background

Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms.

Results

Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus) ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (AT)_n, (AG)_n and (CT)_n were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AAT)_n and (ATT)_n being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms.

Conclusions

Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of two closely related Meloidogyne species. 2,245 di- to hexanucleotide loci were identified in the genome of M. incognita, providing adequate material for the future development of a wide range of microsatellite markers in this major plant parasite.

Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX titanium pyrosequencing

Background

Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (Apis mellifera and Danio rerio), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes.

Results

The A. mellifera genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase.

Conclusions

This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.

Genome-wide analysis of tandem repeats in Daphnia pulex--a comparative approach

Background

DNA tandem repeats (TRs) are not just popular molecular markers, but are also important genomic elements from an evolutionary and functional perspective. For various genomes, the densities of short TR types were shown to differ strongly among different taxa and genomic regions. In this study we analysed the TR characteristics in the genomes of Daphnia pulex and 11 other eukaryotic species. Characteristics of TRs in different genomic regions and among different strands are compared in details for D. pulex and the two model insects Apis mellifera and Drosophila melanogaster.

Results

Profound differences in TR characteristics were found among all 12 genomes compared in this study. In D. pulex, the genomic density of TRs was low compared to the arthropod species D. melanogaster and A. mellifera. For these three species, very few common features in repeat type usage, density distribution, and length characteristics were observed in the genomes and in different genomic regions. In introns and coding regions an unexpectedly high strandedness was observed for several repeat motifs. In D. pulex, the density of TRs was highest in introns, a rare feature in animals. In coding regions, the density of TRs with unit sizes 7-50 bp were more than three times as high as for 1-6 bp repeats.

Conclusions

TRs in the genome of D. pulex show several notable features, which distinguish it from the other genomes. Altogether, the highly non-random distribution of TRs among genomes, genomic regions and even among different DNA-stands raises many questions concerning their functional and evolutionary importance. The high density of TRs with a unit size longer than 6 bp found in non-coding and coding regions underpins the importance to include longer TR units in comparative analyses.

Comparative study on the use of specific and heterologous microsatellite primers in the stingless bees Melipona rufiventris and M. mondury (Hymenoptera, Apidae)

Due to their high degree of polymorphism, microsatellites are considered useful tools for studying population genetics. Nevertheless, studies of genetic diversity in stingless bees by means of these primers have revealed a low level of polymorphism, possibly the consequence of the heterologous primers used, since in most cases these were not specifically designed for the species under consideration. Herein we compared the number of polymorphic loci and alleles per locus, as well as observed heterozygosity in Melipona rufiventris and M. mondury populations, using specific and heterologous primers. The use of specific primers placed in evidence the greater frequency of polymorphic loci and alleles per locus, besides an expressive increase in observed heterozygosity in M. rufiventris and M. mondury, thereby reinforcing the idea that populational studies should be undertaken by preferably using species-specific microsatellite primers.

Isolation and characterization of microsatellite markers from the Mediterranean fruit fly, Ceratitis capitata: cross-species amplification in other Tephritidae species reveals a varying degree of transferability

The Mediterranean fruit fly, Ceratitis capitata, is a pest of major economic importance and has become a model for the development of SIT control programs for insect pests. Significant information has been accumulated on classical and population genetics of this species during the past 2 decades. However, the availability of molecular markers is limited. Here, we present the isolation and characterization of 159 microsatellite clones and the development of 108 polymorphic microsatellite markers for this insect pest. Mapping by in situ hybridization to polytene chromosomes of 21 microsatellite clones enriched the cytogenetic map that was previously constructed by our group. The enriched map provides a large number of STSs for future genome mapping projects. Cross-species amplification of these microsatellite loci in 12 Tephritidae species and sequence analysis of several amplification products indicated a varying degree of transferability and their possible usefulness as molecular and genetic markers in these species where genetic and molecular tools are limited.

Novel microsatellite DNA loci for Bombus terrestris (Linnaeus, 1758)

We present details and characteristics of 123 novel polymorphic microsatellite DNA loci for Bombus terrestris. Thirty-four of these loci have been tested in nine other Bombus species and 25 of them showed polymorphisms in at least one species. These microsatellite DNA loci together with the already established 60 loci will be useful for characterizing wild and managed populations of B. terrestris and other Bombus species as well as for detailed genetic studies in including mapping studies and genome annotations.

Isolation and characterization of microsatellite markers from the olive fly, Bactrocera oleae, and their cross-species amplification in the Tephritidae family

Background

The Tephritidae family of insects includes the most important agricultural pests of fruits and vegetables, belonging mainly to four genera (Bactrocera, Ceratitis, Anastrepha and Rhagoletis). The olive fruit fly, Bactrocera oleae, is the major pest of the olive fruit. Currently, its control is based on chemical insecticides. Environmentally friendlier methods have been attempted in the past (Sterile Insect Technique), albeit with limited success. This was mainly attributed to the lack of knowledge on the insect's behaviour, ecology and genetic structure of natural populations. The development of molecular markers could facilitate the access in the genome and contribute to the solution of the aforementioned problems. We chose to focus on microsatellite markers due to their abundance in the genome, high degree of polymorphism and easiness of isolation.

Results

Fifty-eight microsatellite-containing clones were isolated from the olive fly, Bactrocera oleae, bearing a total of sixty-two discrete microsatellite motifs. Forty-two primer pairs were designed on the unique sequences flanking the microsatellite motif and thirty-one of them amplified a PCR product of the expected size. The level of polymorphism was evaluated against wild and laboratory flies and the majority of the markers (93.5%) proved highly polymorphic. Thirteen of them presented a unique position on the olive fly polytene chromosomes by in situ hybridization, which can serve as anchors to correlate future genetic and cytological maps of the species, as well as entry points to the genome. Cross-species amplification of these markers to eleven Tephritidae species and sequencing of thirty-one of the amplified products revealed a varying degree of conservation that declines outside the Bactrocera genus.

Conclusion

Microsatellite markers are very powerful tools for genetic and population analyses, particularly in species deprived of any other means of genetic analysis. The presented set of microsatellite markers possesses all features that would render them useful in such analyses. This could also prove helpful for species where SIT is a desired outcome, since the development of effective SIT can be aided by detailed knowledge at the genetic and molecular level. Furthermore, their presented efficacy in several other species of the Tephritidae family not only makes them useful for their analysis but also provides tools for phylogenetic comparisons among them.

Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis

The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.

Microsatellite markers from the Chagas disease vector, Rhodnius prolixus (Hemiptera, Reduviidae), and their applicability to Rhodnius species

Ten microsatellites were isolated and characterized from a partial genomic library of Rhodnius prolixus, the principal Chagas disease vector in Venezuela, Colombia and Central America. These polymorphic molecular markers could be particularly useful in Chagas disease control initiatives. A wider applicability of the primer-pairs isolated was shown, from 6 to 10 loci being amplifiable in five out of the ten Rhodnius species tested, namely R. domesticus, R. nasutus, R. neglectus, R. neivai and R. robustus. Interestingly, all the loci were amplified in the latter. These markers may be of interest to trace the colonization of human dwellings from triatomine sylvatic populations in order to better define epidemiological risk patterns.

Decline and conservation of bumble bees

Declines in bumble bee species in the past 60 years are well documented in Europe, where they are driven primarily by habitat loss and declines in floral abundance and diversity resulting from agricultural intensification. Impacts of habitat degradation and fragmentation are likely to be compounded by the social nature of bumble bees and their largely monogamous breeding system, which renders their effective population size low. Hence, populations are susceptible to stochastic extinction events and inbreeding. In North America, catastrophic declines of some bumble bee species since the 1990s are probably attributable to the accidental introduction of a nonnative parasite from Europe, a result of global trade in domesticated bumble bee colonies used for pollination of greenhouse crops. Given the importance of bumble bees as pollinators of crops and wildflowers, steps must be taken to prevent further declines. Suggested measures include tight regulation of commercial bumble bee use and targeted use of environmentally comparable schemes to enhance floristic diversity in agricultural landscapes.

Invasion success of the bumblebee, Bombus terrestris, despite a drastic genetic bottleneck

In early 1992, the European bumblebee, Bombus terrestris, was first seen in Tasmania and currently has spread to most of the island. Here, we report on the genetic structure, using micro-satellites, of the invading population from samples collected in the years 1998-2000, a few years after the first sighting of the species in its new area. The data show that the Tasmanian population has a very low genetic diversity, with less than half of the allelic richness (Richness=2.89 alleles; H(exp)=0.591) and lower levels of heterozygosity as compared to populations in New Zealand (4.24 alleles; H(exp)=0.729) and Europe (5.08 alleles; H(exp)=0.826). In addition, the genetic data suggest that the invasion must have happened once, probably around late 1991, and was the result of very few, perhaps only two, individuals arriving in Tasmania. Furthermore, these founders came from the New Zealand population. Today, the population in the south of Tasmania seems to act as a source population from which individuals migrate into other parts of the state. A similar source-sink structure seems also the case for New Zealand. The data show that B. terrestris is a highly invasive species capable of establishing itself even after a dramatic genetic bottleneck. B. terrestris may be an invasive species due to the haplo-diploid sex determination system, which exposes recessive, deleterious mutations to selection. Offspring of such purged lines may then be able to tolerate high levels of inbreeding.

Non-destructive genotyping and genetic variation of fanning in a honey bee colony

The relationship between workers from different patrilines in a naturally mated queen honey bee colony is very complex due to queen polyandry, and still poorly characterized. Here, we report a means of determining the genotype of living workers in a natural honey bee colony by a new non-destructive method, which makes it possible to observe the relationship between behaviours and genotypes. DNA was extracted from the exuvia, found at the bottom of each brood cell, and confirmed to be identical to the DNA extracted from the thorax muscle of the bee emerging from that particular cell. The genotypes were thus determined using DNA from the exuviae without having to hurt or kill the organisms. The emerging workers were marked with coloured, numbered tags to enable behavioural observations over their entire life. Using this new method, we determined 20 patrilines in a naturally mated queen colony, and discovered that the patriline composition of bees exhibiting fanning behaviour was significantly different from the patriline composition of the whole colony. Our results confirm that the genetic structure of a natural insect society plays a fundamental role in the division of labour. The new non-destructive method reveals a novel avenue for the determination of relationships between the behaviours and genes of social insects.

Genetic Differentiation of the Giant Honey Bee (Apis dorsata) in Thailand Analyzed by Mitochondrial Genes and Microsatellites

Genetic diversity and population differentiation of the giant honey bee (Apis dorsata) in Thailand were examined. Six PCR-RFLP mitotypes were generated from digestion of the COI-COII, Cytb-tRNA(ser), ATPase6-8, and lrRNA genes with Dra I and Hin fI. Low genetic diversity (h=0.074, pi=0.032%) and a lack of genetic population differentiation between A. dorsata originating from geographically different regions were observed from mtDNA polymorphisms (P > 0.05). In contrast, microsatellite (A14, A24, and A88) polymorphisms revealed a relatively high level of genetic diversity in A. dorsata (H (o)=0.68-0.74, average number of alleles per locus=6.0-9.0). Both A24 and A88 indicated significant population differentiation between bees from the north-to-central region (north, northeast, and central regions), peninsular Thailand, and Samui Island.