This may be a stupid question but how do we know what sequence is the oldest even if we know the mutation rate? If we examine for example two mDNA samples using 3,000 base pairs and they show a difference how do we know that one is from an older vs a newer lineage? I mean they still both have the same number of base pairs. Furthermore, how do we know what the oldest lineage is from which to compare the differences and construct the tree?

Does this makes sense?

Does this makes sense?

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