The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste.

BACKGROUND: Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste. RESULTS: The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication. CONCLUSIONS: The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.

Occurrence and Origin of Supernumerary Chromosomes in Partamona (Hymenoptera: Apidae: Meliponini).

Samples from 861 colonies of 12 Partamona species from 125 Brazilian localities were analysed for a SCAR marker specific to the B chromosomes of P. helleri. We identified the SCAR marker in 6 of the 12 species analysed, including 2 (P. gregaria and P. chapadicola) from the pearsoni clade. This is the first report on the presence of this marker in Partamona species that are not included in the cupira clade, which indicates that the B chromosomes probably are more widespread in this genus than previously thought. The analysis revealed a high frequency of the SCAR marker in the samples of P. helleri (0.47), P. cupira (0.46), and P. rustica (0.29), and a low frequency in P. aff. helleri (0.06). The frequency of the marker in P. helleri was correlated with the latitude of the sampling locality, decreasing from north to south. Sequence data on the SCAR marker from 50 individuals of the 6 species in which the presence of this marker was shown revealed a new scenario for the origin of the B chromosomes in Partamona.

Cytochrome-b variation in Apis mellifera samples and its association with COI-COII patterns.

Five Mbo I (Mbo-A, Mbo-M, Mbo-C(1), Mbo-C(2) and Mbo-C(3)) and Hinf I (Hinf-1 to Hinf-5) patterns were observed in Apis mellifera samples after restriction of a 485 bp fragment of the mitochondrial cytochrome-b (cyt-b) gene. Associating the cyt-b Restriction fragment length polymorphism (RFLP) pattern of each sample to its respective previously established COI-COII (Dra I sites) pattern, five restriction patterns (Mbo-C(1), Mbo-C(2), Mbo-C(3), Hinf-1 and Hinf-4) were observed in samples of maternal origin associated to the evolutionary branch C. No deletions or insertions were observed and the nucleotide substitution rate was estimated at 5.4%. Higher nucleotide diversity was observed among the branch C-haplotypes when compared with A and M lineages. Further studies are needed to confirm if the cyt-b + COI-COII haplotypes help to assign certain phylogeographic patterns to the branch C and to clarify phylogenetic relationships among A. mellifera subspecies.

The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps.

Phylogeographic studies have sought to explain the genetic imprints of historical climatic changes and geographic barriers within the Brazilian Atlantic Forest (AF) biota, and consequently two processes of diversification (refugia and barriers) have been proposed. Additionally, there is evidence that eustatic changes influenced the biogeographic history of the AF. Here we evaluate these contrasting diversification processes using two AF social wasp species - the mid-montane Synoeca cyanea and the lowland Synoeca aff. septentrionalis. We analyzed several sources of data including multilocus DNA sequence, climatic niche models and chromosomal features. We find support for idiosyncratic phylogeographic patterns between these wasps, involving different levels of population structure and genetic diversity, contrary suitable climatic conditions during the last glaciation, and contrasting historical movements along the AF. Our data indicate that neotectonics and refugia played distinct roles in shaping the genetic structure of these wasps. However, we argue that eustatic changes influenced the demographic expansion but not population structure in AF biota. Notably, these wasps exhibited chromosomal clines, involving chromosome number and decreasing of GC content, latitudinally oriented along the AF. Together, these results reinforce the need to consider individual organismal histories and indicate that barriers and refugia are significant factors in understanding AF evolution.

Reproductive concessions between related and unrelated members promote eusociality in bees.

Animal societies exhibit remarkable variation in their breeding strategies. Individuals can maximize their fitness by either reproducing or by helping relatives. Social hymenopterans have been key taxa for the study of Hamilton's inclusive fitness theory because the haplodiploid sex-determination system results in asymmetric relatedness among breeders producing conflict over the partitioning of reproduction. In small cooperative groups of insects, totipotent individuals may maximize their inclusive fitness by controlling reproduction despotically rather than helping their relatives. Here, we demonstrate that the dominant females of the primitively eusocial bee Euglossa melanotricha (Apidae: Euglossini) control reproduction, but concede part of the reproductive output with their related and unrelated subordinates. As expected, a dominant female capitalizes on the direct reproduction of related subordinates, according to her interests. We found that reproductive skew was positively correlated with relatedness. The concessions were highly reduced in mother-daughter and sibling nests (relatedness r ± s.d. = 0.54 ± 0.02 and 0.79 ± 0.02, respectively) but much more egalitarian in unrelated associations (r = -0.10 ± 0.01). We concluded that reproductive skew in these primitively eusocial bees is strongly related to the genetic structure of associations, and also that females are able to assess pairwise relatedness, either directly or indirectly, and use this information to mediate social contracts.

Conservation genetics of neotropical pollinators revisited: microsatellite analysis suggests that diploid males are rare in orchid bees.

Allozyme analyses have suggested that Neotropical orchid bee (Euglossini) pollinators are vulnerable because of putative high frequencies of diploid males, a result of loss of sex allele diversity in small hymenopteran populations with single locus complementary sex determination. Our analysis of 1010 males from 27 species of euglossine bees sampled across the Neotropics at 2­11 polymorphic microsatellite loci revealed only five diploid males at an overall frequency of 0.005 (95% CIs 0.002­0.010); errors through genetic nondetection of diploid males were likely small. In contrast to allozyme-based studies, we detected very weak or insignificant population genetic structure, even for a pair of populations >500 km apart, possibly accounting for low diploid male frequencies. Technical flaws in previous allozyme-based analyses have probably led to considerable overestimation of diploid male production in orchid bees. Other factors may have a more immediate impact on population persistence than the genetic load imposed by diploid males on these important Neotropical pollinators.

Molecular identification of species of the genus Euglossa Latreille (Hymenoptera: Apidae, Euglossini).

Euglossine bees interact with more than 60 plant families of the Neotropical region. The richness and abundance of these bees have been intensively studied in different ecosystems using the methodology of capturing males with chemical baits. Females are poorly known for most of the species and morphological characters for their taxonomic classification have not yet been described. The purpose of this study was to use allozymes and restriction patterns of the mitochondrial regions 16S and Cyt b to identify species of Euglossa Latreille. Bees were collected while visiting Thevetia peruviana (Apocynaceae) flowers in five cities of the state of São Paulo, Brazil. Three Euglossa species were identified among the 305 individuals collected. Euglossa cordata (L.) was the only species found in all cities, while E. securigera Dressler and E. townsendi Cockerell were restricted to two and one cities respectively. EST-3 was a diagnostic marker, whereas ICD, MDH, ME and PGM were informative for species identification when used in combination. Restriction by VspI of the amplified 16S fragment differentiated the three species and showed intraspecific polymorphism for E. cordata and E. securigera. The Cyt b region showed distinctive patterns for E. townsendi but it was not possible to differentiate the other two species. Our results describe potentially useful genetic markers for the identification of Euglossa spp. at the species and group level.

Genetic variability and level of differentiation among Brazilian pantanal wood stork populations.

The Wood Stork (Mycteria americana) is a colonial wading bird of the tropical and lower subtropical zones. We assessed genetic structure within and among five stork colonies from the Brazilian Pantanal and compared our data with those from North American populations. Samples of 234 individuals were studied using protein electrophoresis to evaluate genetic variability and interpopulation differentiation. Of 22 loci examined, 7 were polymorphic (mean heterozygosity = 0.068). The low Fst value (0.005) indicated little intraspecific variation among breeding colonies. Estimated number of migrants per generation based on private alleles (Nm = 11.3) and on Fst (48.8) suggests high gene flow Nei's genetic distance values among Pantanal colonies ranged from 0.0001 to 0.0034, demonstrating low genetic divergence among populations. Our data can be explained by supposing high gene flow levels among Pantanal colonies, and between North and South American populations, intermediated by a probable interbreeding population in Central America.

Differentiation of Melipona quadrifasciata L. (Hymenoptera, Apidae, Meliponini) subspecies using cytochrome b PCR-RFLP patterns

Melipona quadrifasciata quadrifasciata and M. quadrifasciata anthidioides are subspecies of M. quadrifasciata, a stingless bee species common in coastal Brazil. These subspecies are discriminated by the yellow stripe pattern of the abdominal tergites. We found Vsp I restriction patterns in the cytochrome b region closely associated to each subspecies in 155 M. quadrifasciata colonies of different geographical origin. This mitochondrial DNA molecular marker facilitates diagnosis of M. quadrifasciata subspecies matrilines and can be used to establish their natural distribution and identify hybrid colonies.

Molecular identification of species of the Genus Euglossa Latreille (Hymenoptera: Apidae, Euglossini)

Euglossine bees interact with more than 60 plant families of the Neotropical region. The richness and abundance of these bees have been intensively studied in different ecosystems using the methodology of capturing males with chemical baits. Females are poorly known for most of the species and morphological characters for their taxonomic classification have not yet been described. The purpose of this study was to use allozymes and restriction patterns of the mitochondrial regions 16S and Cyt b to identify species of Euglossa Latreille. Bees were collected while visiting Thevetia peruviana (Apocynaceae) flowers in five cities of the state of São Paulo, Brazil. Three Euglossa species were identified among the 305 individuals collected. Euglossa cordata (L.) was the only species found in all cities, while E. securigera Dressler and E. townsendi Cockerell were restricted to two and one cities respectively. EST-3 was a diagnostic marker, whereas ICD, MDH, ME and PGM were informative for species identification when used in combination. Restriction by VspI of the amplified 16S fragment differentiated the three species and showed intraspecific polymorphism for E. cordata and E. securigera. The Cyt b region showed distinctive patterns for E. townsendi but it was not possible to differentiate the other two species. Our results describe potentially useful genetic markers for the identification of Euglossa spp. at the species and group level.

As abelhas euglossíneas interagem com mais de 60 famílias de plantas da Região Neotropical. Sua riqueza e abundância têm sido intensamente estudadas em diferentes ecossistemas utilizando-se a metodologia de captura de machos em iscas-armadilhas. As fêmeas, entretanto, são pouco conhecidas para a maioria das espécies, e caracteres morfológicos que permitam sua identificação taxonômica não têm sido descritos. O propósito deste trabalho foi utilizar alozimas e padrões de restrição das regiões mitocondriais 16S e Cit b para identificar espécies do gênero Euglossa Latreille. As abelhas foram coletadas enquanto visitavam flores de Thevetia peruviana (Apocynaceae) em cinco cidades do estado de São Paulo. Foram identificadas três espécies de Euglossa entre os 305 indivíduos coletados. Euglossa cordata (L.) foi a única espécie presente em todas as cidades, enquanto E. securigera Dressler e E. townsendi Cockerell foram encontradas em duas e uma cidade, respectivamente. EST-3 mostrou-se ser marcador diagnóstico, enquanto ICD, MDH, ME e PGM foram locos informativos para a identificação de espécies quando considerados conjuntamente. A restrição com VspI da região 16S amplificada, além de diferenciar as três espécies, apresentou polimorfismo intraespecífico para E. cordata e E. securigera. A região Cit b apresentou padrões característicos para E. townsendi, mas não permitiu diferenciar as outras duas espécies. Os resultados descrevem marcadores genéticos potencialmente úteis para a identificação de Euglossa spp. ao nível de espécie e grupo de espécies.