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Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini).

Brand P, Ramírez SR, Leese F, Quezada-Euan JJ, Tollrian R, Eltz T - BMC Evol. Biol. (2015)

Bottom Line: To identify whether shifts in pheromone composition among related lineages of orchid bees are associated with divergence in chemosensory genes of the olfactory periphery, we searched for patterns of divergent selection across the antennal transcriptomes of two recently diverged sibling species Euglossa dilemma and E. viridissima.Our results revealed that orthologs with signatures of divergent selection between E. dilemma and E. viridissima were significantly enriched for chemosensory genes.Our results suggest that rapid changes in the chemosensory gene family occurred among closely related species of orchid bees.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitätsstrasse 150, D-44801, Bochum, Germany. pbrand@ucdavis.edu.

ABSTRACT

Background: Insects rely more on chemical signals (semiochemicals) than on any other sensory modality to find, identify, and choose mates. In most insects, pheromone production is typically regulated through biosynthetic pathways, whereas pheromone sensory detection is controlled by the olfactory system. Orchid bees are exceptional in that their semiochemicals are not produced metabolically, but instead male bees collect odoriferous compounds (perfumes) from the environment and store them in specialized hind-leg pockets to subsequently expose during courtship display. Thus, the olfactory sensory system of orchid bees simultaneously controls male perfume traits (sender components) and female preferences (receiver components). This functional linkage increases the opportunities for parallel evolution of male traits and female preferences, particularly in response to genetic changes of chemosensory detection (e.g. Odorant Receptor genes). To identify whether shifts in pheromone composition among related lineages of orchid bees are associated with divergence in chemosensory genes of the olfactory periphery, we searched for patterns of divergent selection across the antennal transcriptomes of two recently diverged sibling species Euglossa dilemma and E. viridissima.

Results: We identified 3185 orthologous genes including 94 chemosensory loci from five different gene families (Odorant Receptors, Ionotropic Receptors, Gustatory Receptors, Odorant Binding Proteins, and Chemosensory Proteins). Our results revealed that orthologs with signatures of divergent selection between E. dilemma and E. viridissima were significantly enriched for chemosensory genes. Notably, elevated signals of divergent selection were almost exclusively observed among chemosensory receptors (i.e. Odorant Receptors).

Conclusions: Our results suggest that rapid changes in the chemosensory gene family occurred among closely related species of orchid bees. These findings are consistent with the hypothesis that strong divergent selection acting on chemosensory receptor genes plays an important role in the evolution and diversification of insect pheromone systems.

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Distribution of non-synonymous amino acid substitutions across Odorant Receptor (OR) domains. a The white bars represent the sum of all non-synonymous substitutions detected in the respective domain over all ORs. OR12, OR41 and OR45 are highlighted because they showed the most non-synonymous substitutions between E. dilemma and E. viridissima. IN: Intracellular N-terminus, TM: Transmembrane domain, EL: External loop, IL: Internal loop, EC: Extracellular C-terminus. b Predicted membrane topology for OR41. Fixed non-synonymous substitutions between E. dilemma and E. viridissima are highlighted in black
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Fig3: Distribution of non-synonymous amino acid substitutions across Odorant Receptor (OR) domains. a The white bars represent the sum of all non-synonymous substitutions detected in the respective domain over all ORs. OR12, OR41 and OR45 are highlighted because they showed the most non-synonymous substitutions between E. dilemma and E. viridissima. IN: Intracellular N-terminus, TM: Transmembrane domain, EL: External loop, IL: Internal loop, EC: Extracellular C-terminus. b Predicted membrane topology for OR41. Fixed non-synonymous substitutions between E. dilemma and E. viridissima are highlighted in black

Mentions: Non-synonymous changes in ligand binding domains of receptor proteins can alter affinities towards ligands, modifying ligand interaction patterns [12, 63–67]. We determined the spatial distribution of non-synonymous substitutions along OR and IR protein sequences with dN/dS > 1 to examine potential effects on ligand binding domains. Therefore, we predicted transmembrane domains (Additional file 1: Table S6; Additional file 2: Figure S6), the regions of OR proteins most sensitive to non-synonymous substitutions with regard to ligand binding [12, 64, 66]. Moreover, we used homology to known Drosophila IRs and the closely related ionotropic glutamate receptors (iGluRs) to infer ligand-binding domains (see Methods). In total, 24 (51 %) of the 47 non-synonymous substitutions fixed in the 10 ORs having dN/dS > 1 between E. dilemma and E. viridissima were located in one of the seven transmembrane domains (Table 3; Fig. 3) which covered between 19.3 % and 35.8 % of the OR amino acid sequence (Mean: 30.5 %; Additional file 1: Table S6). Additionally, 3 (38 %) of 8 replacement substitutions were located in the IR ligand binding domains that covered 16.5 % and 14.7 % of the IR03 and IR11 amino acid sequence, respectively (Mean: 15.6). Interestingly, only three of the 12 chemosensory receptors (two ORs and one IR) did not reveal any change in the amino acid sequence of respective ligand binding domains. In order to test whether fixed non-synonymous substitutions are randomly distributed among ORs and IRs, we applied a goodness-of-fit test on the observed number of substitutions by estimating the mean proportion of receptor proteins that span ligand-binding domains. These tests revealed that the observed number of fixed non-synonymous substitutions were non-randomly distributed among ORs and were significantly enriched for transmembrane domains (Goodness-of-fit χ2 = 9.38; p < 0.01; IRs: χ2 = 2.91; p < 0.1). Furthermore, non-synonymous substitutions in ligand-binding domains were positively correlated with the number of non-synonymous substitutions (Pearson’s correlation coefficient; r = 0.91; p < 0.001). Concomitantly, the four chemosensory receptors that exhibited at least five fixed substitutions had the most replacement substitutions in ligand binding domains (up to 9 in OR41; Table 3), thus increasing the likelihood that such non-synonymous substitutions lead to changes in ligand-binding affinities.Fig. 3


Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini).

Brand P, Ramírez SR, Leese F, Quezada-Euan JJ, Tollrian R, Eltz T - BMC Evol. Biol. (2015)

Distribution of non-synonymous amino acid substitutions across Odorant Receptor (OR) domains. a The white bars represent the sum of all non-synonymous substitutions detected in the respective domain over all ORs. OR12, OR41 and OR45 are highlighted because they showed the most non-synonymous substitutions between E. dilemma and E. viridissima. IN: Intracellular N-terminus, TM: Transmembrane domain, EL: External loop, IL: Internal loop, EC: Extracellular C-terminus. b Predicted membrane topology for OR41. Fixed non-synonymous substitutions between E. dilemma and E. viridissima are highlighted in black
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Related In: Results  -  Collection

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Fig3: Distribution of non-synonymous amino acid substitutions across Odorant Receptor (OR) domains. a The white bars represent the sum of all non-synonymous substitutions detected in the respective domain over all ORs. OR12, OR41 and OR45 are highlighted because they showed the most non-synonymous substitutions between E. dilemma and E. viridissima. IN: Intracellular N-terminus, TM: Transmembrane domain, EL: External loop, IL: Internal loop, EC: Extracellular C-terminus. b Predicted membrane topology for OR41. Fixed non-synonymous substitutions between E. dilemma and E. viridissima are highlighted in black
Mentions: Non-synonymous changes in ligand binding domains of receptor proteins can alter affinities towards ligands, modifying ligand interaction patterns [12, 63–67]. We determined the spatial distribution of non-synonymous substitutions along OR and IR protein sequences with dN/dS > 1 to examine potential effects on ligand binding domains. Therefore, we predicted transmembrane domains (Additional file 1: Table S6; Additional file 2: Figure S6), the regions of OR proteins most sensitive to non-synonymous substitutions with regard to ligand binding [12, 64, 66]. Moreover, we used homology to known Drosophila IRs and the closely related ionotropic glutamate receptors (iGluRs) to infer ligand-binding domains (see Methods). In total, 24 (51 %) of the 47 non-synonymous substitutions fixed in the 10 ORs having dN/dS > 1 between E. dilemma and E. viridissima were located in one of the seven transmembrane domains (Table 3; Fig. 3) which covered between 19.3 % and 35.8 % of the OR amino acid sequence (Mean: 30.5 %; Additional file 1: Table S6). Additionally, 3 (38 %) of 8 replacement substitutions were located in the IR ligand binding domains that covered 16.5 % and 14.7 % of the IR03 and IR11 amino acid sequence, respectively (Mean: 15.6). Interestingly, only three of the 12 chemosensory receptors (two ORs and one IR) did not reveal any change in the amino acid sequence of respective ligand binding domains. In order to test whether fixed non-synonymous substitutions are randomly distributed among ORs and IRs, we applied a goodness-of-fit test on the observed number of substitutions by estimating the mean proportion of receptor proteins that span ligand-binding domains. These tests revealed that the observed number of fixed non-synonymous substitutions were non-randomly distributed among ORs and were significantly enriched for transmembrane domains (Goodness-of-fit χ2 = 9.38; p < 0.01; IRs: χ2 = 2.91; p < 0.1). Furthermore, non-synonymous substitutions in ligand-binding domains were positively correlated with the number of non-synonymous substitutions (Pearson’s correlation coefficient; r = 0.91; p < 0.001). Concomitantly, the four chemosensory receptors that exhibited at least five fixed substitutions had the most replacement substitutions in ligand binding domains (up to 9 in OR41; Table 3), thus increasing the likelihood that such non-synonymous substitutions lead to changes in ligand-binding affinities.Fig. 3

Bottom Line: To identify whether shifts in pheromone composition among related lineages of orchid bees are associated with divergence in chemosensory genes of the olfactory periphery, we searched for patterns of divergent selection across the antennal transcriptomes of two recently diverged sibling species Euglossa dilemma and E. viridissima.Our results revealed that orthologs with signatures of divergent selection between E. dilemma and E. viridissima were significantly enriched for chemosensory genes.Our results suggest that rapid changes in the chemosensory gene family occurred among closely related species of orchid bees.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Universitätsstrasse 150, D-44801, Bochum, Germany. pbrand@ucdavis.edu.

ABSTRACT

Background: Insects rely more on chemical signals (semiochemicals) than on any other sensory modality to find, identify, and choose mates. In most insects, pheromone production is typically regulated through biosynthetic pathways, whereas pheromone sensory detection is controlled by the olfactory system. Orchid bees are exceptional in that their semiochemicals are not produced metabolically, but instead male bees collect odoriferous compounds (perfumes) from the environment and store them in specialized hind-leg pockets to subsequently expose during courtship display. Thus, the olfactory sensory system of orchid bees simultaneously controls male perfume traits (sender components) and female preferences (receiver components). This functional linkage increases the opportunities for parallel evolution of male traits and female preferences, particularly in response to genetic changes of chemosensory detection (e.g. Odorant Receptor genes). To identify whether shifts in pheromone composition among related lineages of orchid bees are associated with divergence in chemosensory genes of the olfactory periphery, we searched for patterns of divergent selection across the antennal transcriptomes of two recently diverged sibling species Euglossa dilemma and E. viridissima.

Results: We identified 3185 orthologous genes including 94 chemosensory loci from five different gene families (Odorant Receptors, Ionotropic Receptors, Gustatory Receptors, Odorant Binding Proteins, and Chemosensory Proteins). Our results revealed that orthologs with signatures of divergent selection between E. dilemma and E. viridissima were significantly enriched for chemosensory genes. Notably, elevated signals of divergent selection were almost exclusively observed among chemosensory receptors (i.e. Odorant Receptors).

Conclusions: Our results suggest that rapid changes in the chemosensory gene family occurred among closely related species of orchid bees. These findings are consistent with the hypothesis that strong divergent selection acting on chemosensory receptor genes plays an important role in the evolution and diversification of insect pheromone systems.

Show MeSH