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I came across the following in an article about dove hunting:

...the study recorded the hits and misses of 5,094 shots with size 6 and 7 steel shot and 7 1/2 lead shot, killing a total of 1,146 doves, 1,100 of which were necropsied.

After looking this up it seems necropsy is another way of saying that an autopsy was performed; the body was examined after death.

When should we prefer one to the other?

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You'll notice that your quote is about dead birds. That's why the verbal form of "necropsy" was used. An autopsy is performed on human remains; a necropsy, on non-human animal remains. This veterinarian site explains in detail.

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    I love that @deadrat is answering a question about necropsy. – Yuck Jul 8 '15 at 2:24
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    Your username fits in to that sentence quite nicely too... – GetzelR Jul 8 '15 at 3:08
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    If we ever get a question about taxidermy, maybe StuffedDeadRat will answer. – Brian Hitchcock Jul 8 '15 at 5:52

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