I have a general question about admixture dating methods (for SNP data). The available methods like ROLOFF or ALDER model the testing population as being the composite of two source populations (or surrogates for these populations). However, is it also possible to date single ancestry components within a population? Take an admixed population with 3 ancestry components (A,B,C) - is it then possible to date admixture from B by the choice of the surrogate populations alone? However, how should this be done ideally because there are always two of them so do you keep a single surrogate constant and then use another population to date ancestry component A and then B?
Yes, it is possible to estimate admixture dates using only one surrogate population, although this is only implemented in ALDER and not in ROLLOFF.
The main idea is this (from Dienekes Blogspot):
This is a useful application of the idea that you don't need both reference populations to estimate admixture. If a population A experiences gene flow from another B, then A will become more like B over time, and allele frequency differences between A and B will diminish but will continue to reflect differences between the local and introgressing element. This idea was first used by Pickrell et al. (2012), and a new variation of it is used in the current paper.
There is a clear example a explanation of this use in the original paper when they are testing the Japanese sample. Take a look a the suplemental material which is very extensive but worth the while.