Analysis on crop remains at Los Castillejos (Granada), dated between 4000 and 2500 BCE, have shown that the levels of nitrogen dropped dramatically through the occupation, as well as the corresponding yields (c. 30-40% for all parameters) . While the article does not dwell in the possible reasons behind this, it seems to me that failure to rotate cereals and legumes, as done in later periods, may have been the cause. Another possibility I'm considering could be lack of fertilizer, caused by scarcity of cattle.
Other findings are that, while wheat is found in association with cereal-specialist weeds, barley is found instead related to common weeds. This suggests that barley was cultivated in marginal lands with less labouring. The research was lead by Mónica Aguilera from the University of Barcelona.