Strategies for increasing production of goods from working and natural systems have raised concerns that the diversity of species on which these services depend may be eroding. This loss of natural capital threatens to homogenize global food supplies and compromise the stability of human welfare. We assess the trade-off between artificial augmentation of biomass and degradation of biodiversity underlying a populations' ability to adapt to shocks. Our application involves the augmentation of wild stocks of Central Valley Chinook salmon in California. Hatchery practices that may be leading to homogenization of the stocks in this system have generated warnings that genetic erosion may cause a loss of the `portfolio effect'. Furthermore, the value of this loss is not accounted for in decision-making. Loss of the portfolio effect is expected to leave stocks poorly equipped to weather shocks to their survivorship, leading to decline and greater variability in population levels. We construct an integrated bioeconomic model of biomass and genetic diversity. Our results show how practices that homogenize natural systems can still generate positive economic returns in the fishery. However, such a system can become only weakly sustainable---the substitution of more physical capital and labor for natural capital must be maintained for gains to persist. Artificial augmentation also weakens the capacity for adaptation should this investment cease and can cause substantial loss of population wildness. We also introduce an optimization method novel to resource economics---forward dynamic programming---to solve the model without simplifying restrictions imposed previously.