The chloroplast genome has provided sequence data for inferring plant phylogenies for more than a decade. General operational assumptions regarding chloroplast gene sequences are that they are single-copy, under strong functional constraint, and uniparentally inherited. However, studies have demonstrated the transfer of large segments of the chloroplast genome into the nuclear or mitochondrial genomes. Additionally, heteroplasmy and haplotype polymorphism of plastid genomes within and among individuals have been documented. Random sampling of nucleotide sequences from different plastid haplotypes or from paralogous sequences through the course of a systematic investigation may affect the resulting gene tree topology and the inferences drawn from it.