Environmental risk assessment is a critical tool for protecting biodiversity and its effectiveness is predicated on predicting how natural populations respond to environmental stressors. Yet, routine toxicity testing typically examines only one genotype, which may render risk assessments inaccurate at the population scale. To determine the importance of intraspecific variation in the translation of toxicity testing to populations, we quantified the magnitude of genetic variation within 20Daphnia magnaclones derived from one lake using whole genome sequencing and phenotypic assays. We repeated these assays across two exposure levels ofMicrocystis aeruginosa, a cosmopolitan freshwater contaminant. We found considerable intraspecific genetic variation in survival, growth, and reproduction. Exposure toMicrocystisamplified the degree of intraspecific variation. Simulations demonstrate assays employing one clone failed to produce an estimate within the 95% confidence interval over half of the time. These results illuminate the importance of incorporating intraspecific genetic variation, but not necessarily genome sequences, into toxicity testing to reliably predict how natural populations will respond to environmental stressors.

Rainbow trout (Oncorhynchus mykiss) are a partially migratory species wherein some individuals undergo long-distance anadromous migrations, and others stay as residents in their native freshwater streams. The decision to migrate is known to be highly heritable, and yet, the underlying genes and alleles associated with migration are not fully characterized. Here we used a pooled approach of whole-genome sequence data from migratory and resident trout of two native populations-Sashin Creek, Alaska and Little Sheep Creek, Oregon-to obtain a genome-wide perspective of the genetic architecture of resident and migratory life history. We calculated estimates of genetic differentiation, genetic diversity, and selection between the two phenotypes to locate regions of interest and then compared these associations between populations.We identified numerous genes and alleles associated with life history development in the Sashin Creek population with a notable area on chromosome 8 that may play a critical role in the development of the migratory phenotype. However, very few alleles appeared to be associated with life history development in the Little Sheep Creek system, suggesting population-specific genetic effects are likely important in the development of anadromy. Our results indicate that a migratory life history is not controlled by a singular gene or region but supports the idea that there are many independent ways for a migratory phenotype to emerge in a population. Therefore, conserving and promoting genetic diversity in migratory individuals is paramount to conserving these populations. Ultimately, our data add to a growing body of literature that suggests that population-specific genetic effects, likely mediated through environmental variation, contribute to life history development in rainbow trout.