I am having trouble finding non-coding cpDNA regions that will provide enough variation and clean reads for for phylogentic analysis. As a result I only have three D4 introns to use. Usually I would have some intergenic spacers or introns from other areas of the chloroplast genome as well.

Is it viable to combine and analyse sequences from the D4 set alone? Or does that result in a high risk for some sort of evolutionary linkage due to their close proximity to one another?