Radojicic J.M., Krizmanic I., Kasapidis P., Zouros E. Extensive mitochondrial heteroplasmy in hybrid water frog (Pelophylax spp.) populations from Southeast Europe // Ecology and Evolution, 2015. doi: 10.1002/ece3.1692
There are several examples of heteroplasmy. In fact there are many cases in humans that relate to late onset health issues. However, since most mitochondrial genes are prone to purifying selection mutations do not often persist for very long and thus usually examples of heteroplasmy relate to single point mutations or indel in organisms with uniparental inheritance. There are cases of biparental inheritance in which case you can get to copies of mitochondrion that are vastly different from one another.
i.e. Sex-Biased Mitochondrial DNA Heteroplasmy in the Marine Mussel Mytilus http://rspb.royalsocietypublishing.org/content/242/1305/149
In uniparental inheriting organisms if you see the presence of several mutations (heterogeneous sites) or if a mutation leads to a substantial change in the amino acid sequence then it is probably an indication of a numt or contamination. However, if you get an occasional point mutation when screening large numbers of samples that is not too uncommon.
Hope this answers your question and if you are looking for more examples of heteroplasmy there are several in many diverse array of taxa from plants, to vertebrates, to invertebrates.
Also here is a recent Nature Review on the topic as it relates to human health.
Regaring the frequence, it is hard to answer, Shokralla et al. 2014 found 10% of ambiguities in a large dataset of DNA barcodes (possibly numts or heteroplasmy). For numts, there seem to be no phylogenetic congruence with their presence/frequence, indeed, when examing two close congeneric species of beetles, we found one free of numts while the other was mush affected. (https://www.researchgate.net/publication/272359549_Ghost_mtDNA_haplotypes_generated_by_fortuitous_NUMTs_can_deeply_disturb_infra-specific_genetic_diversity_and_phylogeographic_pattern)
I hope this helps
Julien
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