Single-cell transcriptomics reveals rapid divergence of genes guiding meiosis and spermiogenesis in two passerine birds.

Spermatogenesis is a complex process in which spermatogonia differentiate into haploid sperm cells. Genes guiding this process are subject to an evolutionary trade-off between purifying selection preserving basic functions and positive selection favoring fast gamete production and innovative sperm traits. The outcome of this trade-off varies across the spermatogenesis stages in mammals but remains unexplored for species with ZW sex chromosomes, such as birds. Here, we identify 20 cell clusters comprising somatic and germline cells across stages of spermatogenesis by using single-cell RNA sequencing of collared and pied flycatcher testis. Based on an ortholog comparison with mammals and analyses of differential gene expression between two closely related flycatcher species and lineage-specific protein sequence evolution, we find evidence for rapid divergence of genes expressed during the second and last major stages of spermatogenesis (meiosis and spermiogenesis). The genes that are differentially expressed between the two flycatcher species are enriched for Gene Ontology biological processes that are fundamental for sperm function. Although genes expressed during spermiogenesis are known to evolve fast in mammals, our results imply that gene expression at meiosis is subject to stronger positive selection or is less constrained by purifying selection and/or by intralocus sexual conflict in birds compared with mammals. We also find signals of fast-evolving Z-linked genes expressed during meiosis, consistent with the lack of sex chromosome silencing during meiosis (i.e., meiotic sex chromosome inactivation [MSCI]) in birds.