In a food web, there are a number of food chains and each organism is part of multiple energy transfer chains. If one organism is removed from the food web, there would be instability for a while and then a new equilibrium would be achieved.
In the present case, if eagles are removed from the food web (say by a disease or infection specific to eagles), their prey (snakes) will suddenly have one less major predator. This will cause an increase in the population of snakes. This increase in the snake population will last for a while. There are other predators of snakes as well and they will suddenly find an increase in food levels. This will cause an increase in their population. The prey of snakes, such as mice, will see a decrease in numbers. Ultimately an equilibrium will be reached between the predator and prey population and snake numbers will stabilize.
Thus, food webs are much more stable systems as compared to food chains, which would have been severely impacted by the loss of organisms at one trophic level. For food webs, the initial effect is much larger than the long term effect.
Hope this helps.
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