Paulo Cseri Ricardo

Cleptoparasitism, or brood parasitism, is a striking behavioral strategy observed in approximately 13% of all bee species, yet its genomic underpinnings remain largely unexplored. We present the first high-quality genome assembly of the Neotropical cleptoparasitic bee Coelioxoides waltheriae (Nomadinae), a species that parasitizes the nests of Tetrapedia diversipes . The final assembly comprises 194.8 Mbp across 388 contigs, with an N50 of 1.47 Mbp and 97.4% BUSCO completeness, representing the second smallest genome among cleptoparasitic bees. Repetitive elements constitute only 14.6% of the genome, suggesting that its compact size is primarily driven by repeat reduction rather than gene loss. Comparative genomic analyses across 42 hymenopteran species revealed a pronounced contraction bias in gene family size changes in C. waltheriae (expansion ratio of 13.66%), a pattern also observed in other cleptoparasitic lineages. Expanded orthogroups presented functions associated with cuticle-related genes, transposases (e.g., PiggyBac ) potentially linked to host infiltration and defense, while contracted orthogroups showed significant reductions in sensory perception (e.g., odorant receptors), detoxification (e.g., cytochrome P450), and metabolic genes, reflecting the reduced ecological demands of a parasitic lifestyle. Furthermore, non-target DNA analysis identified associations with Roubikia mites (a known symbiont of its host), as well as fungi and bacteria, providing ecological context for this species. Our findings establish an important genomic reference for cleptoparasitic bees, demonstrating that the evolution of parasitism is associated with targeted gene family contractions alongside expansions, offering new insights into the genomic signatures of behavioral specialization.

Cleptoparasitism, also known as brood parasitism, is a widespread strategy among bee species in which the parasite lays eggs into the nests of the host species. Even though this behavior has significant ecological implications for the dynamics of several species, little is known about the molecular pathways associated with cleptoparasitism. To shed some light on this issue, we used gene expression data to perform a comparative analysis between two solitary neotropical bees: Coelioxoides waltheriae, an obligate parasite, and their specific host Tetrapedia diversipes. We found that ortholog genes involved in signal transduction, sensory perception, learning, and memory formation were differentially expressed between the cleptoparasite and the host. We hypothesize that these genes and their associated molecular pathways are engaged in cleptoparasitism-related processes and, hence, are appealing subjects for further investigation into functional and evolutionary aspects of cleptoparasitism in bees.

Cleptobiosis, the act of raiding other species to obtain food or resources, is widespread among animals but rarely obligatory. The eusocial stingless bee Lestrimelitta limao is one of the few species that depend entirely on cleptobiosis, raiding other stingless bee colonies for survival. To investigate the molecular basis and evolutionary adaptations associated with this specialized lifestyle, we compared the transcriptomes of foraging workers of L. limao and three non-robber stingless bees – Nannotrigona testaceicornis , Scaptotrigona aff. depilis , and Tetragonisca angustula . Our analysis revealed that differentially expressed orthologs were predominantly downregulated in L. limao workers, suggesting reduced transcriptional activity during foraging in this species. These downregulated genes fall into three major functional categories potentially linked to cleptobiotic adaptations: (1) detoxification and chemoreception genes, including cytochrome P450s and odorant receptors, indicating decreased exposure to phytochemicals; (2) neuronal and synaptic genes, such as para and Dys , possibly reflecting neurophysiological modifications; and (3) mitochondrial and carbohydrate metabolism genes, suggesting lower energetic demands. These findings provide novel insights into the molecular mechanisms shaping cleptobiotic behavior in eusocial bees.

Genetics can provide invaluable tools for management and conservation of bee populations, which are declining worldwide. Among these tools, microsatellite are very useful molecular markers for population analyses. The aim of this study was to isolate and characterize microsatellites for Epicharis (Anepicharis) dejeanii and Epicharis (Epicharis) nigrita, two Neotropical species of solitary bees, both exhibiting the habit of nesting in aggregations. Microsatellite loci were identified from two enriched genomic libraries. The characterization and analysis of loci were carried out using 35 females of E. dejeanii and 34 of E. nigrita. In total, we report the development of 12 microsatellite loci for E. dejeanii and 13 for E. nigrita. For E. dejeanii, all loci were polymorphic, the number of alleles per locus ranged from 2 to 12, averaging 8.7 and, observed and expected heterozygosity were 0.485 (range 0.229–0.857) and 0.633 (range 0.288–0.843), respectively. For E. nigrita, only nine out of 13 loci amplified were polymorphic, the number of alleles per locus ranged from 2 to 12, averaging 5.5. For this species, the observed and expected heterozygosity were 0.440 (range 0.118–0.676) and 0.545 (range 0.167–0.814), respectively. Cross-amplification of primers was successful in other Centridini species. The two sets of loci described for E. dejeanii and E. nigrita species are polymorphic and informative and show promising applicability for both population genetic approaches and relatedness on these and other Centridini species.

Here we investigated the consequences of PCR amplification errors in the identification of intraindividual mtDNA variation. The bumblebee Bombus morio was chosen as model for the COI gene amplification tests with two DNA polymerases (Taq and Q5) presenting different error rates. The amplifications using Taq resulted in a significant increase of singleton haplotypes per individual in comparison to Q5. The sequence characteristics indicated that Taq resulted haplotypes are mostly due to amplification errors. Studies focusing on intraindividual variability should address special attention to the DNA polymerase fidelity to avoid overestimation of heteroplasmic haplotypes.

Tetragonula carbonaria, Tetragonula davenporti, Tetragonula hockingsi and Tetragonula mellipes comprise a species complex of Australian stingless bee species known as the ‘Carbonaria’ group. The species are difficult to distinguish morphologically and the major species-defining characters relate to comb architecture and nest entrance ornamentation. The taxonomy of the group is further complicated by likely nuclear mitochondrial pseudogenes (numts) and inter-specific hybrids. Here we demonstrate the existence of COI numts and isolate and characterize the ‘true’ mt-COI gene in T. carbonaria and T. hockingsi. Numts were isolated from enriched-nuclear DNA extraction followed by PCR amplification and Sanger sequencing, and were recognized by the presence of deletions and/or premature stop codons in the translated sequences. The mt-COI sequences were obtained from NGS sequencing using purified mtDNA. In T. carbonaria, two numts (numt1 and numt2) were identified and a third (numt3) was identified in T. hockingsi. Numt2 and numt3 are similar (1.2% sequence divergence), indicating a recent common origin. The genetic distance between the mt-COI of the two Tetragonula species was higher than might be expected for closely related species, 16.5%, corroborating previous studies in which T. carbonaria and T. hockingsi were regarded as separate species. The three numts are more similar to the COI of other stingless bee species, including Australian Austroplebia australis and South American Melipona bicolor (81.7–83.9%) than to the mt-COI of their own species (70–71.4%). This is because the mt-COI of T. carbonaria and T. hockingsi differ greatly from other Meliponinae. Our findings explain some formerly puzzling aspects of Carbonaria biogeography, and misinterpreted amplifications.