The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata

Abstract

Understanding the evolution of animal societies, considered to be a major transition in evolution, is a key topic in evolutionary biology. Recently, new gateways for understanding social evolution have opened up due to advances in genomics, allowing for unprecedented opportunities in studying social behavior on a molecular level. In particular, highly eusocial insect species (caste-containing societies with nonreproductives that care for siblings) have taken center stage in studies of the molecular evolution of sociality. Despite advances in genomic studies of both solitary and eusocial insects, we still lack genomic resources for early insect societies. To study the genetic basis of social traits requires comparison of genomes from a diversity of organisms ranging from solitary to complex social forms. Here we present the genome of a subsocial bee, Ceratina calcarata This study begins to address the types of genomic changes associated with the earliest origins of simple sociality using the small carpenter bee. Genes associated with lipid transport and DNA recombination have undergone positive selection in C. calcarata relative to other bee lineages. Furthermore, we provide the first methylome of a noneusocial bee. Ceratina calcarata contains the complete enzymatic toolkit for DNA methylation. As in the honey bee and many other holometabolous insects, DNA methylation is targeted to exons. The addition of this genome allows for new lines of research into the genetic and epigenetic precursors to complex social behaviors.

Keywords: epigenetics; insect genome; maternal care; small carpenter bee; social evolution.

Fig. 1.—

Phylogenetic placement of Ceratina calcarata. Divergence dates taken from Kapheim et al. (2015) and Rehan and Schwarz (2015). Ceratina and Apis diverged approximately 105 Ma. Tree topology was confirmed by an analysis of orthologous 4-fold degenerate sites (supplementary material, Supplementary Material online).

Fig. 2.—

Gene family overlap among four bee lineages. The 11 species were sorted into 4 groups based on taxonomic classification: (1) Ceratina calcarata (subfamily Xylocopinae) versus (2) subfamily Apinae (Apis florae, Apis mellifera, Bombus impatiens, Bombus terrestris, Eufriesea mexicana, Habropoda laboriosa, and Melipona quadrifasciata) versus (3) family Halictidae (Lasioglossum albipes and Dufourea novaeangliae) versus (4) family Megachilidae (Megachile rotundata). Numbers indicate the gene families in each comparison. A total of 5,307 gene families are shared among all 11 bee species.

Fig. 3.—

DNA methylation in Ceratina calcarata. (a) Unrooted neighbor-joining cladogram showing relationships among the DNA methyltransferase proteins DNMT1 (D1), DNMT2 (D2), and DNMT3 (D3) from C. calcarata and 10 other bee species, demonstrating the presence of a fully functional DNA methylation toolkit in C. calcarata. Polytomies are plotted for nodes with less than 75% support among 1,000 bootstrap replicates. (b) Spatial profiles of mean DNA methylation levels in genes with significant methylation from C. calcarata and the honey bee Apis mellifera. Exons are divided into 150 proportional bins and introns are divided into 200 proportional bins. DNA methylation is preferentially targeted to exons 1–3, and levels decay toward the 3′ end of genes in each species (Wilcoxon rank-sum tests between exons 1–3 and 4–n, P < 0.0001). (c) Percent of CG dinucleotides, exons, and introns targeted by DNA methylation in 5,698 shared orthologs suggests more widespread targeting of DNA methylation in C. calcarata versus A. mellifera, whereas (d) mean methylation levels suggest that C. calcarata exhibits lower levels of DNA methylation, where targeted, compared with A. mellifera.