During phylogenetic analysis of the Nepenthaceae cpDNA trnK intron, it became 
apparent that a second non-functional copy of the locus was present in most of 
the investigated taxa. The translocation event was older than the radiation of 
all recent Nepenthaceae, and the translocated pseudogenized copy was conserved 
in nearly all members of the plant family. Using single chloroplast PCR and 
inverse PCR, we could exclude a plastom location for the second copy. Although 
translocation into the nucleus is possible, mitochondrial localization seems 
more likely based on these data. In total, the translocated sequence contained 
at least 3525 base pairs (bp) that were homologous to the Spinacia oleracea 
chloroplast genome. Comparative phylogenetic analysis of the non-functional copy 
revealed a high amount of homoplasies compared to topologies from the cpDNA trnK 
intron phylogenetic reconstruction. Therefore, this copy proved to be 
insufficient for phylogenetic reconstruction of the family. Since two different 
paralogs of the non-functional copy were found in one species, it is feasible 
that different paralogs were conserved in different groups and that paralogous 
sequences were included in the data matrix. These data demonstrate that 
phylogenetic analyses of pseudogenized copies of phylogenetically relevant loci 
should be performed with great caution. In addition, pseudogenized copies can 
exist in nearly every member of a plant family, and can be PCR-amplified at 
levels comparable to the specific copy. In this case, the inclusion of such 
copies can easily remain unnoticed, thus leading to faulty hypotheses.