Last week we discussed the concept of trophic cascades - the effects of one trophic level on not only the trophic level below it (a direct interaction) but on levels one or even more below it (indirect interactions). There are many interesting papers on this topic, but one I mentioned was about the impacts of a top carnivore (coyote) on native bird fauna (via effects on meso-predators such as cats) in California chaparral. That reference is here (and link to the article):
Crooks, Kevin R., and Michael E. Soulé. "Mesopredator release and avifaunal extinctions in a fragmented system." Nature 400.6744 (1999): 563-566.
The other one I mentioned was about the impacts of removing top predators in many different systems. The has been called "trophic downgrading" and a very nice recent paper was published in Science by the ecologist who revealed the interesting food chain dynamics related to sea otters and kelp forests - James Estes. The paper I cited is here:
Estes, James A., et al. "Trophic downgrading of planet earth." Science 333.6040 (2011): 301-306.