The concept of weediness—with its numerous characteristics contributing to complex and variable phenotypes—is difficult to define. Weediness is not an inherent property of certain plant species, but rather is a judgment based on the time and circumstances in which the plant is growing in light of human preferences at that time and place. Thus the simplistic definition of a weed is "a plant in a place where you don't want it." In cultivated fields, a GM crop may become an agricultural pest (weed) by showing up as a "volunteer" in subsequent planting seasons. If engineered for tolerance to a particular herbicide, the "weeds" would be more difficult to control, requiring application of a different herbicide or use of alternative weed control measures. True weediness, however, results from the action of many, many genes. Most crop varieties have been domesticated sufficiently to be nearly incapable of surviving outside of managed agricultural fields; it is unlikely that any single gene transfer would enable them to become pernicious weeds.

Some single-gene traits introduced by genetic engineering may confer a weed-like characteristic that enhances fitness. For example, if a crop's ability to grow in areas outside a cultivated field is held in check by a single limiting factor such as a fungal disease, engineering resistance to the fungus may give the crop an increased ability to spread into adjacent areas. Thus the GM crop, no longer susceptible to the limiting factor, may gain a selective advantage in the local environment by exhibiting the weed-like behavior of invasiveness. Therefore, it may threaten to displace native species. This presents an environmental concern if (and on ly if) the crop has sufficient genetic capacity to become established and persist in those new unmanaged areas.

Of greater concern is the potential for less domesticated self-seeding crops (alfalfa) and commercial tree varieties (pine, poplar, eucalyptus) to become problems. These plants already have a capacity to survive on their own; transgenes could enhance their fitness in the wild. Pine trees, for example, engineered for resistance to seed-feeding insects might gain a significant advantage through decreased seed destruction, potentially allowing them to out compete other indigenous species. If that happened, forest communities could be disrupted.

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