Global allele polymorphism indicates a high rate of allele genesis at a locus under balancing selection

Abstract

When selection favours rare alleles over common ones (balancing selection in the form of negative frequency-dependent selection), a locus may maintain a large number of alleles, each at similar frequency. To better understand how allelic richness is generated and maintained at such loci, we assessed 201 sequences of the complementary sex determiner (csd) of the Asian honeybee (Apis cerana), sampled from across its range. Honeybees are haplodiploid; hemizygotes at csd develop as males and heterozygotes as females, while homozygosity is lethal. Thus, csd is under strong negative frequency-dependent selection because rare alleles are less likely to end up in the lethal homozygous form. We find that in A. cerana, as in other Apis, just a few amino acid differences between csd alleles in the hypervariable region are sufficient to trigger female development. We then show that while allelic lineages are spread across geographical regions, allelic differentiation is high between populations, with most csd alleles (86.3%) detected in only one sample location. Furthermore, nucleotide diversity in the hypervariable region indicates an excess of recently arisen alleles, possibly associated with population expansion across Asia since the last glacial maximum. Only the newly invasive populations of the Austral-Pacific share most of their csd alleles. In all, the geographic patterns of csd diversity in A. cerana indicate that high mutation rates and balancing selection act together to produce high rates of allele genesis and turnover at the honeybee sex locus, which in turn leads to its exceptionally high local and global polymorphism.

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Fig. 1: The distribution of analyzed samples of A. cerana across its native range (yellow) and invasive range (red).
Fig. 2: Fragment of the sex locus of the Asian honeybee Apis cerana.
Fig. 3: The genealogy of csd alleles inferred using the maximum likelihood method.
Fig. 4: Allele differentiation between populations.

Data availability

DNA sequences of csd alleles identified in this study have been submitted to GenBank: accession numbers MN334337–MN334481.

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Acknowledgements

Thanks to Gabriele Buchmann for assistance in the lab, and Nadine Chapman, Greg Good, Jurgen Paar, the Queensland Department of Agriculture and Fisheries and the Australian Government Department of Agriculture and Water Resources for collecting samples. We thank Siriwat Wongsiri, Wandee Wattanachaiyingcharoen Pyamas Sopaladawan and Madeleine Beekman for help with collections in Thailand, and M.S. Reddy and Madeleine Beekman for help in India. GD was supported by the National Natural Science Foundation of China (31800463) and the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2015-IAR). RG was supported by a University of Sydney Postdoctoral Fellowship. Research funding came from Australian Research Council DP190101500 and DP150101985 to BPO and RG

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Ding, G., Hasselmann, M., Huang, J. et al. Global allele polymorphism indicates a high rate of allele genesis at a locus under balancing selection. Heredity (2020). https://doi.org/10.1038/s41437-020-00358-w

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