Reflecting the clonal replication of maternal mtDNA, all copies of mtDNA genomes are identical (homoplasmic) as a rule. Due to the high copy number of mtDNA, however, a mutation in some of the mtDNA results in a mixture of variant mtDNA genomes, a condition known as heteroplasmy (Holt et al., 1990). Heteroplasmy is operationally defined as the presence of two or more subpopulations (types) of mtDNA genomes within a mitochondrion, cell, tissue, organ or individual, and may be observed in several ways, such as two or more mtDNA types in one tissue sample, and one mtDNA type in one tissue sample and a different mtDNA type in another sample (Budowle et al., 2003). On occasion, children of a heteroplasmic mother may be homoplasmic. This occurs through the inheritance of the mother's predominant mtDNA type (or one of the predominant types) due to a 'bottleneck' mechanism that segregates minor mtDNA types (Holland and Parsons, 1999).

Heteroplasmy is most often observed in hair samples because genetic drift is allowed to operate and bottlenecks are created due to a hair follicle's semiclonal nature (Budowle et al., 2003). One disadvantage of using mtDNA for forensic individual identification is the possibility that the occurrence of heteroplasmy will confuse the interpretation of the results and potentially lead to an erroneous exclusion rather than a match. However, the presence of heteroplasmy can also increase the power of the match when it is present in both the unknown and reference samples.

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