The genomic footprint of sexual conflict

Abstract

Genes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic ‘tug-of-war’ between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

“…The new C. maculatus genome assembly is a substantial improvement over previous resources for this species (e.g., [38]), with a total size of 1.01 gigabases and N50 of 149 kilobases [67]. Additionally, BUSCO estimates of completeness from sets of preserved proteins are high (75% complete, 10% partially complete).…”

“…We then demultiplexed the Fastq files using custom perl scripts (these scripts are available from Dryad, https://doi.org/10.5061/dryad.3j9kd51dw). We used the mem algorithm from bwa (version 0.7.17-r1188) [81] to align the 936 million, 150 bp DNA sequences from the backcross lines to a recently published, C. maculatus genome assembly [67]. We also aligned the Fastq files from our older beetle datasets (L1, L1R, L2, L2R, L14A, L14B, M) to the recent assembly.…”

“…It has long served as a model system for investigating the evolution of insect-plant interactions [58][59][60], and has been used more recently to examine a variety of questions in evolutionary biology, especially those involving sexual selection and sexual conflict (e.g., [61][62][63][64][65]). Because of current advances in genomic resources, this system is poised as an emerging model system for evolutionary genomics as well [38,66,67].…”

“…In the current study, we build on past work by re-analyzing population-genomic data from the E&R experiments in the context of an improved genome assembly and annotation [67]. We combine this reanalysis with genome-wide association mapping of two performance traits (adult weight and development time) and with gene-expression data.…”

The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae) provides insight into host plant specialization

“…Chrysomelids are a large and highly diverse family of beetles, with approximately 40,000 described species in the world [19], many of which are economically important pests of agricultural crops [20]. To date, genomes have been assembled for three oligophagous species, the Colorado potato beetle, Leptinotarsa decemlineata [21], the cowpea weevil, Callosobruchus maculatus [22] and the ragweed leaf beetle, Ophraella communa [23]. Consequently, the genome for A. viridicyanea will add to our genomic resources for a monophagous member of the Chrysomelidae.…”