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I'm stuck with a sentence from GRE test.

Researchers analyzing refuse from one Pueblo community found remains of maize — a Peublo crop — in 44 percent of samples from years when the community flourished, but in only 10 percent of samples from years near the time of depopulation, while the remains of wild plants increased significantly.

In the above passage, I confused the meaning of the bold sentence. It means that remains of maize is 44 percent? Or they found them in 44 percent of samples (they don't know the real percentage of remains)?

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    Note, by the way, that a dash (—) should be represented by two hyphens (--), not just one. Or in Questions and Answers you can use the html code —. – StoneyB Mar 1 '17 at 12:06
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You can just leave out the words between the hyphens which gives you

Researchers ...found remains of maize in 44 percent of samples ...

So your second reading is correct. They found them in 44 percent of the samples from the years when the community flourished.

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They have used the - to mark the start and end of a kind of informative note. For example...

The jacket, which she had bought for a considerable amount of money, was now in ruins on the floor.

The note in the example is to give you some relevant information, in this case that the worthless object on the floor was once worth a lot of money. In your example the note works like this

  • Before: one Pueblo community found remains of maize in 44 percent of samples from years when the community flourished
  • After: one Pueblo community found remains of maize (which is a Peublo crop) in 44 percent of samples from years when the community flourished

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