3.3. Numts, nuclear copies of mitochondrial sequences

In recent years, a wealth of nuclear mitochondrial-like sequences (numts) in both vertebrates and invertebrates have been reported in the literature. Although found in many organisms, numts seem to be especially common in some avian taxa (Anser; Quinn 1992; Aythyini; Sorenson & Fleischer 1996). Numts present a challenge for phylogenetic and population genetic studies due to unwitting inclusion of paralogous nuclear sequences instead of mitochondrial sequences (Zhang & Hewitt 1996; Sorenson & Quinn 1998). Nuclear insertions are under different mutation constraints compared to the mitochondrial counterparts and therefore the nucleotide substitutions in nuclear copies occur more randomly. In non-coding areas, such as mitochondrial control region, the identification of a nuclear copy is more difficult due to a lack of codon structure compared to a coding area.

The first attempts to amplify the mitochondrial control region from Anser geese (II) resulted in amplification of a nuclear copy. Subsequently, mtDNA enriched isolates were used (Jones et al. 1988) as templates, an approximately 10 kb mitochondrial fragment spanning from cytochrome oxidase I to tRNAphe was amplified and comparison of sequences obtained by using different tissues (with differing ratio of nuclear DNA to mtDNA) as templates as well as comparison of sequences obtained with different primer pairs were used to assure the mitochondrial origin of the sequences. The mtDNA specific primers were designed by comparing the sequences of the nuclear copy and the mitochondrial DNA.