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The degree of starshape of a genealogy is readily detectable using summary statistics and can be taken as a surrogate for the effect of past demography and other non-neutral forces. Summary statistics such as Tajima's D and related measures are commonly used for this. However, it is well known that because of their neglect of the genealogy underlying a sample such neutrality tests are far from ideal. Here, we investigate the properties of two types of summary statistics that are derived by considering the genealogy: (i) genealogical ratios based on the number of mutations on the rootward branches, which can be inferred from sequence data using a simple algorithm and (ii) summary statistics that use properties of a perfectly star-shaped genealogy. The power of these measures to detect a history of exponential growth is compared with that of standard summary statistics and a likelihood method for the single and multi-locus case. Statistics that depend on pairwise measures such as Tajima's D have comparatively low power, being sensitive to the random topology of the underlying genealogy. When analysing multi-locus data, we find that the genealogical measures are most powerful. Provided reliable outgroup information is available they may constitute a useful alternative to full likelihood estimation and standard tests of neutrality.

Original publication

DOI

10.1017/s0016672309990139

Type

Journal article

Journal

Genetics research

Publication Date

08/2009

Volume

91

Pages

281 - 292

Addresses

Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. K.R.Lohse@sms.ed.ac.uk

Keywords

Animals, Likelihood Functions, Genetics, Population, Evolution, Molecular, Phylogeny, Linkage Disequilibrium, Mutation, Algorithms, Models, Genetic, Computer Simulation, Genetic Variation