Modes of natural selection on maternal and zygotic gene expression in Drosophila melanogaster embryos

Early embryonic development involves the coordination of gene expression from two distinct genomes, as mothers load eggs with gene products prior to the beginning of zygotic transcription. Because the maternal transcriptome is controlled by the mothers regulatory genotype rather than that of the embryo, these two sequential developmental programs may experience distinct evolutionary constraints and selection pressures despite both existing within the embryo. To infer modes of selection on gene expression at maternal and zygotic developmental stages, we used single-embryo RNA-sequencing and conducted variance tests of selection on transcriptomes of parents and F2 segregants of tropical and temperate Drosophila melanogaster embryos. We found that approximately 10% of maternal transcripts and 5% of zygotic transcripts showed signals of selection. Genome-wide, directional selection was more common than stabilizing selection. However, among core early developmental genes and transcription factors, maternal transcription showed patterns of both stabilizing and directional selection, whereas zygotic transcription was predominantly under stabilizing selection. Many heat shock genes showed patterns of directional selection between tropical and temperate embryos, consistent with local adaptation. Additionally, directional selection in piRNA-pathway genes suggests a role for germline defense during embryogenesis. Overall, while our data support the canonical view that core developmental networks are constrained by stabilizing selection, the genome-wide prevalence of directional selection highlights a substantial and previously underappreciated contribution of diversifying selection to the evolution of early development. Article SummaryThe evolution of embryonic gene expression remains poorly characterized on microevolutionary timescales. We conducted genetic crosses between tropical and temperate Drosophila melanogaster, combining single-embryo RNA sequencing with variance tests of selection, to infer patterns of adaptive evolution in gene expression. We found pervasive signals of selection. While core developmental genes were largely under stabilizing selection, directional selection was the predominant mode of selection genome-wide. These findings challenge the paradigm that early embryogenesis is evolutionarily inflexible, suggesting that diversifying selection and local adaptation play key roles in the evolution of development on short evolutionary timescales.