RT Journal Article
SR Electronic
T1 Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 042044
DO 10.1101/042044
A1 Luca Ferretti
A1 Alice Ledda
A1 Thomas Wiehe
A1 Guillaume Achaz
A1 Sebastian E. Ramos-Onsins
YR 2017
UL http://biorxiv.org/content/early/2017/01/12/042044.abstract
AB We investigate the dependence of the site frequency spectrum (SFS) on the topological structure of genealogical trees. We show that basic population genetic statistics – for instance estimators of θ or neutrality tests such as Tajima’s D – can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima’s D and Fay and Wu’s H depend in a direct way on a peculiar measure of tree balance which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu’s H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulae for these extreme values as a function of sample size and number of segregating sites.