A method that allows year-to-year patterns of weather variability to be characterized in the contexts of global warming and cooling trends in applied in a combined analysis of long-term monthly weather records and data from an ecological monitoring project in southern New Mexico. The analysis suggests a cause-effect hypothesis of recent decertification in the North American Southwest. The links between the atmosphere and the biosphere are based on the fundamentally different responses to specific weather regimes of semidesert grasses with a C4 photosynthetic pathway and desert shrubs with a C3 photosynthetic pathway. The hypothesis appears to be of sufficient generality to explain the complex, but well-documented, floristic changes that have occurred in the same region since the last glacial maximum.