Chloroplast DNA-based studies in molecular ecology may be compromised by nuclear-encoded plastid sequence

Ongoing genetic transfer from mitochondria and plastids into the nucleus is a well-documented fact. While in metazoan molecular ecology the need for surveillance against pseudogene-mediated artefacts when analysing mtDNA sequences is commonly accepted, no comparable measurements have been established for plastid-based studies. We highlight the impact and management of nuclear mitochondrial insertions, argue that nuclear plastid sequences represent an underestimated but major factor in plant molecular ecology, and discuss potential avenues of remedy in chloroplast studies.