Patterns of gene family evolution and selection across Daphnia

Abstract

Gene family expansion underlies a host of biological innovations across the tree of life. Understanding why specific gene families expand or contract requires comparative genomic investigations clarifying further how species adapt in the wild. This study investigates the gene family change dynamics within several species of Daphnia, a group of freshwater microcrustaceans that are useful model systems for evolutionary genetics. We employ comparative genomics approaches to understand the forces driving gene evolution and draw upon candidate gene families that change gene numbers across Daphnia. Our results suggest that genes related to stress responses and glycoproteins generally expand across taxa, and we investigate evolutionary hypotheses of adaptation that may underpin expansions. Through these analyses, we shed light on the interplay between gene expansions and selection within other ecologically relevant stress response gene families. While we show generalities in gene family turnover in genes related to stress response (i.e., DNA repair mechanisms), most gene family evolution is driven in a species-specific manner. Additionally, while we show general trends towards positive selection within some expanding gene families, many genes are not undergoing selection, highlighting the complex nature of diversification and evolution within Daphnia. Our research enhances the understanding of individual gene family evolution within Daphnia and provides a case study of ecologically relevant genes prone to change.