Evidence for Convergent Nucleotide Evolution and High Allelic Turnover Rates at the complementary sex determiner Gene of Western and Asian Honeybees

Abstract

Our understanding of the impact of recombination, mutation, genetic drift, and selection on the evolution of a single gene is still limited. Here we investigate the impact of all these evolutionary forces at the complementary sex determiner (csd) gene that evolves under a balancing mode of selection. Females are heterozygous at the csd gene and males are hemizygous; diploid males are lethal and occur when csd is homozygous. Rare alleles thus have a selective advantage, are seldom lost by the effect of genetic drift, and are maintained over extended periods of time when compared with neutral polymorphisms. Here, we report on the analysis of 17, 19, and 15 csd alleles of Apis cerana, Apis dorsata, and Apis mellifera honeybees, respectively. We observed great heterogeneity of synonymous (piS) and nonsynonymous (piN) polymorphisms across the gene, with a consistent peak in exons 6 and 7. We propose that exons 6 and 7 encode the potential specifying domain (csd-PSD) that has accumulated elevated nucleotide polymorphisms over time by balancing selection. We observed no direct evidence that balancing selection favors the accumulation of nonsynonymous changes at csd-PSD (piN/piS ratios are all <1, ranging from 0.6 to 0.95). We observed an excess of shared nonsynonymous changes, which suggest that strong evolutionary constraints are operating at csd-PSD resulting in the independent accumulation of the same nonsynonymous changes in different alleles across species (convergent evolution). Analysis of csd-PSD genealogy revealed relatively short average coalescence times ( approximately 6 Myr), low average synonymous nucleotide diversity (piS < 0.09), and a lack of trans-specific alleles that substantially contrasts with previously analyzed loci under strong balancing selection. We excluded the possibility of a burst of diversification after population bottlenecking and intragenic recombination as explanatory factors, leaving high turnover rates as the explanation for this observation. By comparing observed allele richness and average coalescence times with a simplified model of csd-coalescence, we found that small long-term population sizes (i.e., N(e) < 10(4)), but not high mutation rates, can explain short maintenance times, implicating a strong historical impact of genetic drift on the molecular evolution of highly social honeybees.

Similar but not the same: insights into the evolutionary history of paralogous sex-determining genes of the dwarf honey bee Apis florea

“…Interestingly, in this previous study, no trans-specific alleles (alleles that are more closely related to an allele from another species than to other alleles from the same species) were detected (Hasselmann et al, 2008b). Trans-species alleles that can be maintained for 430 million years are frequently observed in other systems under balancing selection, such as in two well-studied cases: the major histocompatibility complex of vertebrates (Takahata, 1990) and the selfincompatibility S-locus of plants (Vekemans and Slatkin, 1994).…”

“…The csd gene encodes an SR-type protein, harboring an arginine/serine-rich and a proline-rich domain. In addition to these domains and in contrast to fem, csd is characterized by the hypervariable region (HVR), forming repeated structures of species-specific amino acid motifs that are highly variable in length (Hasselmann et al, 2008b). Heterozygous csd is required to induce the female pathway by interacting with transformer 2 (Nissen et al, 2012), leading to a female-spliced fem transcript; this decision is maintained throughout the development by a positive feedback loop.…”

“…Consequently, rare or newly evolved csd alleles that increase in frequency within a population rarely contribute to the formation of diploid males (Yokoyama and Nei, 1979). This rare-allele advantage or negative frequency-dependent selection as one form of balancing selection results in a prolonged persistence time for csd alleles that segregate in honey bee populations (Hasselmann and Beye, 2004;Hasselmann et al, 2008b).…”

“…The csd alleles of the different Apis species analyzed so far are on an average not older than the corresponding species split, although several csd alleles of Apis dorsata and A. mellifera could have predated speciation, as the divergence of allele pairs exceeds the mean interspecies divergence (d S 40.14; Hasselmann et al, 2008b). Interestingly, in this previous study, no trans-specific alleles (alleles that are more closely related to an allele from another species than to other alleles from the same species) were detected (Hasselmann et al, 2008b).…”

“…In Apis, the relatively short average coalescence time of functional csd alleles (5-7 million years) can be best explained by a high allelic turnover rate, indicating small, long-term effective population sizes. Consequently, a strong historical impact of genetic drift as an evolutionary force might have affected csd allele evolution (Hasselmann et al, 2008b). A recent comprehensive evaluation of the dynamics of csd alleles in A. mellifera subpopulations showed that (i) the evolutionary rate giving rise to a new specificity is high and particularly driven by a HVR and that (ii) only few (4-5) amino acid substitutions are sufficient to give rise to a novel functional heterozygotic csd specificity (Lechner et al, 2014).…”