Probable causes of these extremely different genetic structures

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There are many possible reasons why we are seeing such a large difference in genetic structures in our orchid populations.  One reason could be the geography and other physical characteristics of each wetland.  If there is less water and moisture in one wetland than in another, there could be reason for one orchid to change its characteristics (alleles) to better adapt to less water.  This could be the case for many other variables that fluctuate in each wetland.  What we could discover is that we have some very diverse wetlands in a small area and could be the reason for more orchids that are genetically diverse.  Pollution and human interaction with each wetland and the orchids could play a major role in the orchids' diversity.  Pollution can kill off many types of an orchid because its alleles cannot tolerate high levels of pollution.  Human interaction can do the same, when there is a lot of human activity in an area where orchids grow, this habitat can be disturbed and even destroyed, taking the orchids down with them.