Recombination and the properties of Tajima's D in the context of approximate-likelihood calculation.
I show that Tajima's D, a commonly used summary of the site-frequency spectrum for single-nucleotide polymorphism data, is a biased summary of the site-frequency spectrum. Under neutral models, this bias depends on the population recombination rate. This bias of D in summarizing the data makes inference of demographic parameters sensitive to assumptions about recombination rates.
Thornton
Kevin
K
Cornell University, 227 Biotechnology Building, Ithaca, NY 14853, USA. kt234@cornell.edu
D015982:Bias; D003198:Computer Simulation; D003710:Demography; D005828:Genetics, Population; D016013:Likelihood Functions; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*