A web-based histology atlas for the freshwater Cladocera species Daphnia magna

Daphnia are keystone species of freshwater habitats used as model organisms in ecology and evolution. They are also routinely used as environmental sentinels in regulatory toxicology and are increasingly contributing to new approach methodologies (NAM) for chemical risk assessments Yet, it is challenging to establish causal links between biomolecular (omics) responses to chemical exposure and their toxicity phenotypes without a baseline knowledge of tissue- and cell-morphology of healthy individuals. Here, we introduce the Daphnia Histology Reference Atlas (DaHRA, ), which provides a baseline of wildtype anatomical and microanatomical structures of female and male Daphnia magna . This interactive web-based resource features overlaid vectorized demarcation of anatomical structures that compliant with an anatomical ontology created for this atlas. Since sex is environmentally induced in Daphnia , DaHRA is a map of sexual dimorphism by phenotypic plasticity. We also benchmark this tool for mechanistic toxicology by exposing Daphnia to acetaminophen and use the atlas to document its effects in organs, tissues, and cell-types. DaHRA represents an essential step towards correlating phenotypes with the discovery power of hypothesis-free, molecular backdrop against which pathology can be interpreted, thereby offering a platform to elucidate how genetic variation and external perturbations cascade through multiple biological scales to influence phenotype. Synopsis Whole-organism Daphnia atlas as foundation for unbiased phenotyping, and its utility in characterizing sexual dimorphism and effects of chemical toxicity. ### Competing Interest Statement The authors have declared no competing interest.