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Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants


Specialized queens and life-time unmated workers evolved once in the common ancestor of all ants, but whether caste development across ants continues to be at least partly regulated by a single core set of genes remains obscure. We analysed brain transcriptomes from five ant species (three subfamilies) and reconstructed the origins of genes with caste-biased expression. Ancient genes predating the Neoptera were more likely to regulate gyne (virgin queen) phenotypes, while the caste differentiation roles of younger, ant-lineage-specific genes varied. Transcriptome profiling showed that the ancestral network for caste-specific gene regulation has been maintained, but that signatures of common ancestry are obscured by later modifications. Adjusting for such differences, we identified a core gene-set that: (1) consistently displayed similar directions and degrees of caste-differentiated expression; and (2) have mostly not been reported as being involved in caste differentiation. These core regulatory genes exist in the genomes of ant species that secondarily lost the queen caste, but expression differences for reproductive and sterile workers are minor and similar to social paper wasps that lack differentiated castes. Many caste-biased ant genes have caste-differentiated expression in honeybees, but directions of caste bias were uncorrelated, as expected when permanent castes evolved independently in both lineages.

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Fig. 1: Likelihood ratios of genes with caste-biased expression in the brains of five ant species originating at subsequent phylogenetic nodes.
Fig. 2: Gene expression signatures of species identity and caste type, calculated from 6,672 one-to-one orthologues across 7 ant species.
Fig. 3: PCAs for brain transcriptomes calculated from 6,672 one-to-one orthologues across seven ant species, after adjusting for either species- or colony-level variation in the mean and variance of gene expression.
Fig. 4: Expression levels for conserved caste regulatory genes expressed in the brains of gynes and workers across the five ant species with typical queen–worker differentiation.

Data availability

RNA-Seq data have been deposited under BioProject accession number PRJNA427677 (


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This work was supported by grants from the Lundbeck Foundation (R190-2014-2827 to G.Z.), Carlsberg Foundation (CF16-0663 to G.Z.), Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13000000 to G.Z.) and Biodiversity Research Center, Academia Sinica (100-2311-B-001-015-MY3, 103-2311-B-001-018-MY3 and 104-2314-B-001-009-MY5 to J.W.), as well as an Academia Sinica Career Development Grant (to J.W.) and an ERC Advanced Grant (323085 to J.J.B.). We thank C. Guo, H. Yu and Q. Li for coordination of the sequencing at BGI.

Author information




G.Z., J.J.B., J.W. and B.Q. designed the experiments. R.S.L., N.-C.C. and B.Q. reared and isolated the ant colonies in the laboratory. B.Q. and N.-C.C. collected the ants, dissected the ant brains and extracted RNA. B.Q. constructed the cDNA libraries. N.-C.C. and J.W. generated the transcriptome data for S. invicta. B.Q. analysed the data. B.Q., G.Z. and J.J.B. interpreted the data and wrote and revised the manuscript.

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Correspondence to Jacobus J. Boomsma or Guojie Zhang.

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Supplementary Table 2: Number and percentage of genes originated (earliest detected) in each phylogenetic lineage

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Qiu, B., Larsen, R.S., Chang, NC. et al. Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants. Nat Ecol Evol 2, 1782–1791 (2018).

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