Is it possible to infer demography with a clonal species? SFS based methods leverage on independent loci and programs like SMC++ and other markov coalescent derivatives use recombination. Skyline plots assume no recombination but also no natural selection. This assumption may hold for mitochondria but I'm currently looking at the demography of a parasite where selection has most likely affected the observed variation.
I'm not aware of methods capable of modeling selection, assuming i have found loci under selection, and demography with non-independence of loci. Any suggestions will be greatly appreciated.
There are some coalescent simulators available that include specific modes of selection, recombination and demography. These are the four recently listed in
Article Efficient Coalescent Simulation and Genealogical Analysis fo...
, please find them (without any ranking) below:
Article MSMS: A Coalescent Simulation Program Including Recombinatio...
Article Mbs: Modifying Hudson's ms software to generate samples of D...
Article Cosi2 : An efficient simulator of exact and approximate coal...
Article SELSIM: a program to simulate population genetic data with n...
Personally, I only worked with MSMS so far, so I cannot judge which one is the most appropriate for your specific question.
Forwards in time, there are also solutions available, e.g. Article SLiM: Simulating Evolution with Selection and Linkage
From coalescent simulations, there are many ways to infer demography, e.g. by Approximate Bayesian Computation.
Even with a single locus/few loci, but high enough sample sizes and mutation rates, there can be some success to infer at least some points about demography (from my experience). Of course, this will be not as precise as if there are many unlinked loci available.
What kind of selection do you expect? There could be also other coalescent approaches if selection is acting rapidly in certain fashion, see e.g. the reviews Article On the importance of skewed offspring distributions and back...
Article Coalescence 2.0: A multiple branching of recent theoretical ...
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