I read a fascinating statistic a few days ago regarding breathing and marathoning: an average marathoner breathes TWO DAYS worth of air during a typical marathon. Remarkable.
Okay, this is interesting, but how does it affect us? First, we are taking in a lot of stuff into our lungs that we really are not prepared for, or at least we are not physically prepared for the amount of stuff. Stuff in this case includes all particulates like dust, pollution, pollen, etc. I suppose this is a greater problem for those toward the back of the pack in a middle-to-large size marathon where the runners ahead have stirred up all kinds of road gunk.
My thought here is that if you take in two days of stuff into your lungs in just a few hours, and this stuff is very different from what you breathe in an office, your lungs are probably not able to self-clean during the marathon. This can reasonably lead to a reduction in VO2 efficiency and consequently reduced performance.
Now I'm not sure what I can do about this during the marathon barring wearing a gas mask and running from the front, neither of which will happen, but it is something to consider if aerobic performance seems to be flagging during the latter stages of a marathon. Possible solutions: core conditioning to provide extra late strength in moving air forcefully through the lungs and running at least in the first 25% of runners.
Otherwise, like you've heard here before, just run.