The combined use of mitochondrial DNA markers and polymerase chain rea
ction (PCR) techniques has greatly enhanced evolutionary studies. Thes
e techniques have also promoted the discovery of mitochondrial-like se
quences in the nuclear genomes of many animals. While the nuclear sequ
ences themselves are interesting, and capable of serving as valuable m
olecular tools, they can also confound phylogenetic and population gen
etic studies. Clearly, a better understanding of these phenomena and v
igilance towards misleading data are needed.