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Botanists have long wondered how certain plants can not only thrive in harsh conditions – such as in the searing heat of a desert or the bitter cold of the upper reaches of the Alps – but also wither away as soon as they are shifted to a more agreeable environment, such as in the temperate regions.

A) can not only thrive in harsh conditions – such as in the searing heat of a desert or the bitter cold of the upper reaches of the Alps – but also wither -> 1) "Not only X but also Y", X (thrive in...) and Y (wither away...) are in parallel structure. 2) Such as used for examples of harsh conditions. Now, Meaning wise, "Not only X But also Y" doesn't make sense, because, in later part plants are "withered away". It is a contrasting view. Incorrect.

B) can not only thrive in harsh conditions – for example, in the searing heat of a desert or the bitter cold of the upper reaches of the Alps – but they also wither -> "Not only X but they also Y" is incorrect idiom form.

C) thriving in harsh conditions – such as in the searing heat of a desert or the bitter cold of the upper reaches of the Alps – but they wither -> we don't have verb here. Incorrect.

D) can thrive not only in harsh conditions – namely in the searing heat of a desert or the bitter cold of the upper reaches of the Alps – but also wither -> "Not only X but also Y", X (in harsh conditions...) and Y (wither away...) are not parallel structure.

E) can thrive in harsh conditions – such as in the searing heat of a desert or the bitter cold of the upper reaches of the Alps – but wither -> It is better than A. "But" gives a contrast to meaning, "thrive in harsh conditions...but wither away ...in more agreeable environment".

So, I think E. :)
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IMO A

Not only X but also Y

Botanists have long wondered how certain plants can not only thrive in harsh conditions – such as in the searing heat of a desert or the bitter cold of the upper reaches of the Alps – but also wither away as soon as they are shifted to a more agreeable environment, such as in the temperate regions.

Additionally, parallelism thrive and wither
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