Relationships between the evolution of species and their ecosystems can be difficult to accurately assess due to the high number of confounding biological variables (e.g., biotic interactions among community members and the resulting complex relationships between genetic pathways and organism phenotypes). Thus, progress in ecological genomics by making inferences about fundamental ecological patterns and processes is hampered by high biodiversity and subsequent complex biotic interactions. Study systems that are naturally low in biological and ecological complexity, and strongly structured by abiotic drivers, can serve as models for bridging the gap between controlled mesocosm experiments and natural ecosystems. The terrestrial ecosystems of the Antarctic dry valleys have low biodiversity and constrained ecological complexity, primarily because ecological communities are so strongly shaped by physical, rather than biological, factors. The harsh constraints of the physical environment on organismal evolution and the structure of ecological communities make this an optimal natural system for disentangling the influence of specific environmental parameters on genotype/phenotype and gene by environment interactions. This work reviews the biology, evolution, and ecology of an emerging model organism, the free-living nematode Plectus murrayi, in a model ecosystem, the McMurdo Dry Valleys (MDVs) of Antarctica. In the MDVs, habitat suitability, including nutrient availability, has been shown to drive organismal (nematode) life history evolution, including growth and reproduction, primarily by way of changes in the expression of developmental genes. Changes in growth rates and reproductive schedules are accomplished primarily through alterations of nuclear rRNA gene copy number. The predicted and observed responses to natural experiments have been replicated in the laboratory, providing a synthesis of field observations and experimental evolution. Studying such natural model systems as this could fill several persistent knowledge gaps in our understanding of how genetic variation, genomic architecture, and gene regulation drive the genotype-phenotype paradigm, and the consequent effects of these drivers on ecosystem structure and functioning.