Journal
THEORETICAL POPULATION BIOLOGY
Volume 79, Issue 4, Pages 155-173Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.tpb.2011.01.005
Keywords
Lambda-coalescent; Infinitely many sites model; Likelihood estimation; Importance sampling; Population genetics
Funding
- DFG IRTG [1339]
- NIH [R00-GM080099]
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We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavare (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents. (C) 2011 Elsevier Inc. All rights reserved.
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