Patterns of DNA Methylation in Development, Division of Labor and Hybridization in an Ant with Genetic Caste Determination

Abstract

BackgroundDNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events.Methodology/Principal FindingsSodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucleotides in P. barbatus. We also found methylation of non-CpG sequences. This validated two bioinformatics methods for predicting gene methylation, the bias in observed to expected ratio of CpG dinucleotides and the density of CpG/TpG single nucleotide polymorphisms (SNP). Frequencies of genomic DNA methylation were determined for different developmental stages and castes using ms-AFLP assays. The genetic caste determination system (GCD) is probably the product of an ancestral hybridization event between P. barbatus and P. rugosus. Two lineages obligately co-occur within a GCD population, and queens are derived from intra-lineage matings whereas workers are produced from inter-lineage matings. Relative DNA methylation levels of queens and workers from GCD lineages (contemporary hybrids) were not significantly different until adulthood. Virgin queens had significantly higher relative levels of DNA methylation compared to workers. Worker DNA methylation did not vary among developmental stages within each lineage, but was significantly different between the currently hybridizing lineages. Finally, workers of the two genetic caste determination lineages had half as many methylated cytosines as workers from the putative parental species, which have environmental caste determination.Conclusions/SignificanceThese results suggest that DNA methylation may be a conserved regulatory mechanism moderating division of labor in both bees and ants. Current and historic hybridization appear to have altered genomic methylation levels suggesting a possible link between changes in overall DNA methylation and the origin and regulation of genetic caste determination in P. barbatus.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

“…We found that high levels of DNA methylation (mCG/CG) correspond well with CpG depletion in exons (Spearman's R = À0.53) ( Fig. 3B; Supplemental Tables 11,12), indicating that some genes in ants are distinguished by DNA methylation, similar to the honeybee (see also Bonasio et al 2012;Smith et al 2012). Functional analysis of genes putatively methylated in all seven ant genomes (low CpG O/E) revealed enrichment for housekeeping functions, including transcription, translation, and cellular metabolic function (FDR < 0.05) (Supplemental Tables 13-15), as reported for the honeybee (Elango et al 2009).…”

“…Given the abundance of conserved regulatory elements in ant genomes, we examined three mechanisms previously implicated in the regulation of social traits or phenotypic plasticity: direct modification of DNA by methylation (Kucharski et al 2008;Bonasio et al 2012;Smith et al 2012), transcriptional and translational regulation by small RNAs (Pauli et al 2011), and transcriptional regulation by transcription factors (TFs) (Rebeiz et al 2011).…”

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

“…The sequencing of more species with different levels of plasticity and multiple phenotypes will be required to confirm this hypothesis (6). However, the available data suggest that these hallmarks contrast with those hallmarks of eusocial insects with low plasticity like the honey bee and most ants, where a large proportion of genes, functionality, and network differentiation are associated with phenotypic differentiation (44,(53)(54)(55)(56)(57)(58), and where phenotypes appear to be regulated by DNA methylation (24,25,30,34,35,37,(59)(60)(61)(62). Comparisons of species with contrasting evolutionary histories, as in our study species, will be especially valuable in revealing the molecular signatures at the origin of social evolution (e.g., in P. canadensis) and in reversions from complex to simple behaviors (e.g., in D. quadriceps).…”

Genome methylation patterns across castes and generations in a parasitoid wasp

“…These modifications exert epigenetic control that suppresses or activates gene expression (Smith et al. 2012). …”

“…DNA methylation is potentially important in shaping phenotypes and adaptations to the environment, such as in caste determination in eusocial species (Smith et al. 2012; ‏Yan et al. 2014; but see Libbrecht et al.…”