there are different mistletoe species in the reserve and I want to compare the abundance of the species between the edge of the main forest and fragments as a proxy for habitat preference (between main forest edge and fragment). the transect lengths are the same for both habitat types but it cannot go round the forest because it is a really huge forest.
You should try a stratified sampling approach. Then you select which habitats what to include as factors. That will help you in future analyses.
In my experience the landscape at the non-forest side of the edge is what counts for the diversity and quantity of mistletoes. Especially the (distribution of) berry-eating birds may be decisive. See some of my observations on mistletoes in the Q&A.
The above would imply sampling includes transects perpendicular to the edge for some landscape attributes.
There are more factors than edge vs core fragments. However, if you want to compare just these factors, it is OK. However, you must compare different patches in a wide distribution across the landscape to avoid pseudoreplication problems.
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