Some mitochondrial DNA samples consistently show sequence heteroplasmy indicating that both types of sequences occur within the population. People usually tend to discard heteroplasmic samples from analyses and only use 'clean' sequences. However, discarding such sequences also means ignoring important population processes/information. One option to deal with heteroplasmic sequences could be using both the sequence variants as two different samples but I am not sure how acceptable is this approach among population geneticists and evolutionary biologists. I would appreciate any thoughts. Thanks.
I might think of it in terms of different haplotypes....
If individuals consistently display two types of sequence (when you only expect one), then there could be several causes e.g. duplication, heteroplasmy etc..
In which case, you might have three different haplotypes:
1. AAA
2. BBB
3. AAA and BBB
If you are able to consistently detect the same individual(s) with haplotype 3 then that is very interesting. Even more interesting is if there are several individuals within a population with haplotype 3.
For subsequent pop gen analysis, this is how I might consider coding up the data you describe. Good luck!
This is interesting. I am sure that there is only limited number of cases where people dealt with heteroplasmy. First, you must be sure that it is not contamination. Then, other possibility is that you have pseudogene and if you try to separate mitochondrials prior to DNA extraction one of the signals will be gone. Finally, if it is real heteroplasmy, you should report it in your organism (if it was not known before). Finally, you should treat both of your haplotypes separately, but if you did not find them in pure state, you will have a problem of phasing. Anyway, if you are building phylogeny based on your sequences, all tree-building methods will not be adequate way of representing genealogy. Phangorn package in R calculates distance file with more accurate mutation scheme. (ALASTAIR J. POTTS1,∗, TERRY A. HEDDERSON1, AND GUIDO W. GRIMM2 Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron Syst. Biol. 63(1):1–16, 2014) Output file (Distnex.nex) could be processed in SplitsTree4 – Distance_network.
It could be analogous to 2N nuclear genome (although more than two parental mitochondria could be in one single individual. Cummulative heteroplasmy). But if you assume just two mitochondrial DNA for your heteroplasmic individuals, you can try Phase to infer and split individual ¨alelles¨.
I appreciate all suggestions. My study system is appearing to be an interesting case. I am trying to see how widespread it is. Thanks again.