I've heard of a boy called Jem too...isn't he from Anne of Green Gables?
There are also names that mean flower, like Florian.
Jonquil?
I don't know about gemstones, but for just general natural stones and trees, there are quite a few.
Sterling, Flint, Alder, Willow, Oleander, Thorne, Sage, Rowan, Forrest, Moss, Heath, Leaf/Leif.
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