Transcriptome profiling in conservation physiology and ecotoxicology: mechanistic insights into organism–environment interactions to both test and generate hypotheses

A key challenge in conservation biology is to identify natural populations with compromised health and identify causative agents. However, wildlife are exposed to a complex matrix of natural and anthropogenic stressors such that identifying particular agents of distress is difficult. Yet, establishing cause and effect between human-induced environmental changes and adverse health is necessary to guide conservation planning. Transcriptome profiling, with thoughtful experimental design and appropriate metadata, is useful for establishing cause and effect between exposures to environmental stressors and adverse health outcomes. Here we describe transcriptome profiling and associated paradigms that are useful for wildlife health assessment and conservation planning, with particular emphasis on pollution. We emphasize that these tools are important for testing hypotheses about causative agents of distress, but also for generating new hypotheses about causes and consequences. We outline two case studies that highlight attributes of transcriptomics tools and approaches that add value for conservation practitioners.