Fig. 1. Genetic and phenotypic differentiation of E. dilemma and E. viridissima.

a Bees were collected at 15 sampling sites (Supplementary Table 1) including both allopatric (blue: E. dilemma, green: E. viridissima) and sympatric populations (hatched). Dashed lines indicate the distributions of E. dilemma genetic lineages following the coloring scheme described below. Photograph shows a E. dilemma male perching during perfume display. b E. dilemma (shades of blue) and E. viridissima (green) are genetically differentiated over the first two PC axes (left), which jointly explained <4% of the genetic variation, suggesting low genetic differentiation between lineages. Separation of the two lineages in sympatry suggests that they are reproductively isolated (right; Supplementary Fig. 1). Symbols are identical to legend in a. c Populations within E. dilemma (k = 2) were separated before species (k = 3) in a genetic clustering analysis, supporting population structure within E. dilemma (Supplementary Fig. 2) and low interspecific genetic differentiation. Several individuals drew ancestry from multiple genetic lineages suggesting admixture. d Perfume phenotypes were species-specific (left), independent of geography or co-occurrence (right), mainly due to the relative quantity of the major compounds HNDB and L97 (Supplementary Fig. 9). E. dilemma color scheme: light blue (a, b, c): Ed_north, dark blue (a, b, c): Ed_south, intermediate blue (a, d): E. dilemma (comprising all populations), purple (b): admixed populations Los Tuxtlas and Cordoba.