After another look I kind of agree with Doug. Better still, a rebuild of the sentence might have worked. It's one of those things that wouldn't matter much if you said it but which looks awkward in print.

The cultivated apple-tree was first introduced into this country by the earliest settlers, and it is thought to do as well or better here than anywhere else.

"The cultivated apple tree, first introduced into this country by the earliest settlers, is thought to do at least as well here as anywhere else."

I left it in, but I'm not keen on "is thought..." as it's tantamount to weasel words (thought by who?) but hey ho, and "apple tree" does not need a hyphen.