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The observation of prey dying of sepsis would then be explained by the natural instinct of water buffalos, who are not native to the islands where the Komodo dragon lives, to run into water when attacked. The warm, feces filled water would then cause the infections.

Source: http://en.wikipedia.org/wiki/Komodo_dragon

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The first then refers to some context that you did not quote.

The article first links the sepsis in prey to the Komodo's saliva, but that theory is negated by the fact that there is nothing special about that saliva.

So when the saliva does not explain the sepsis, then it is explained by the water buffaloes.

The second then simply indicates that something happens in sequence after something else: the buffaloes get into the water, infect it, and then the water causes infections.

The would is used to indicate that this explanation is a possibility, not an irrefutable fact. We could rewrite the paragraph more or less as follows:

[The observation of prey dying of sepsis was explained by the Komodo saliva, but it seems that saliva is not the cause. If indeed the saliva is not the reason for the sepsis, t]he observation of prey dying of sepsis could alternatively in that case be explained by the natural instinct of water buffalos, who are not native to the islands where the Komodo dragon lives, to run into water when attacked. The warm, feces filled water could in that scenario subsequently cause the infections.

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