Following on from the previous example discussing gene introgression the possible consequences that can be considered include assessing how the novel gene will impact the population and whether or not this impact will affect an organism that is within the framework of the previously set protection goals.

Also using an example where gene flow and introgression could lead to a potential adverse effect, what impact the presence of a transgene will have on biodiversity will depend on its effect on individual fitness as well as on the importance of that species relative to the protection goals. For instance, if a sexually compatible species, present in the receiving environment, is directly relevant to a biodiversity protection goal (e.g. it is a protected species) then the impact on biodiversity can be assessed by looking directly at the impact of the transgene on the population. If the sexually compatible species is not directly related to a biodiversity management goal, then the impact of the expression of the transgene will be dependent on indirect interactions. Indirect effects may be challenging to assess (see section 5.1), and are dependent on the ecological importance of the species.