I've been pondering this post for a while but will just be brief.  A recent study published in the journal Science by Anthony D.M. Smith and his colleagues reports that extensive fishing of low trophic level species (I discuss this in Eating our Way to Civility:  A Dinner Party Guide, but these are species that eat plankton directly such as sardines, mackerel, and krill) may threaten the ecosystems in which they are being harvested unless harvest rates decline.  
Here's the abstract:
Low–trophic level species account for more than 30% of global fisheries  production and contribute substantially to global                         food security. We used a range of ecosystem  models to explore the effects of fishing low–trophic level species on  marine ecosystems,                         including marine mammals and seabirds, and on  other commercially important species. In five well-studied ecosystems,  we found                         that fishing these species at conventional  maximum sustainable yield (MSY) levels can have large impacts on other  parts of                         the ecosystem, particularly when they constitute  a high proportion of the biomass in the ecosystem or are highly  connected                         in the food web. Halving exploitation rates  would result in much lower impacts on marine ecosystems while still  achieving                         80% of MSY.  
Why this is an alarming result is because while we've known that harvesting animals higher on the food chain, which by their very nature are less abundant, puts them at risk of extinction (and indeed has driven some species to economic extinction).  Thus, the suggestion from fisheries experts was that the seas could still provide resources if we ate lower on the food chain.  While, at some level, the Smith et al. result is expected (we really do pull a LOT of energy out of the seas!), it's still shocking because maximum sustainable yield (MSY) is a term that implies that the population will persist when harvested at that level.  The Smith et al. paper makes us consider the effects on other, non-target species in the ecosystem that rely on these low trophic level species.  
As a friend commented today:  farm-raised tilapia anyone?  (Note:  I've got some tilapia recipes in the book!).
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