Ancestral inference from haplotypes and mutations. (English) Zbl 1405.92174
Summary: We consider inference about the history of a sample of DNA sequences, conditional upon the haplotype counts and the number of segregating sites observed at the present time. After deriving some theoretical results in the coalescent setting, we implement rejection sampling and importance sampling schemes to perform the inference. The importance sampling scheme addresses an extension of the Ewens sampling formula for a configuration of haplotypes and the number of segregating sites in the sample. The implementations include both constant and variable population size models. The methods are illustrated by two human Y chromosome datasets.
MSC:
| 92D10 | Genetics and epigenetics |
| 92D20 | Protein sequences, DNA sequences |
| 92D15 | Problems related to evolution |
Keywords:
ancestral inference; coalescent inference; Ewens sampling formula; ancestral lineages; standing variationReferences:
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