Mitonuclear discordance has been widely reported in animal species. In stingless bees, the occurrence of mitonuclear discordance is favoured by the adopted colony-founding strategy [dependent colony foundation (DCF)], with phylopatric females and dispersing males. To address the extent to which the DCF system is reflected in the population structure of Partamona helleri, a stingless bee found in Brazilian Atlantic Forest, we sampled for sequences of maternally heritable mitochondrial DNA (mtDNA) and biparentally inherited nuclear microsatellite markers in workers from 339 colonies, covering its entire distribution range. We found evidence of mitonuclear discordance in P. helleri, which is compatible with the DCF strategy. Genetic structuring of the mtDNA was associated with the occupation of an area by few female lineages, and genetic structuring of the nuclear DNA was associated with isolation by distance. Phylogeographical analysis showed that the origin of P. helleri seems to have been in the region of the state of Bahia 860 000 years ago and that the divergence between the lineages began 520 000 years ago. From this primary centre of dispersal, a main north-to-south migration route occurred, resulting in the occupation of areas in the southern portion of the Atlantic Forest, probably favoured by the dynamics of evergreen forest expansions during the Quaternary.

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.