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doi:10.1534/genetics.107.072538
A more recent version of this article appeared on September 1, 2007.
REGULAR RESEARCH PAPERS |
On the Choice of Genetic Distance in Spatial-Genetic Studies
Paul Fearnhead 1*
1 Lancaster University
* To whom correspondence should be addressed. E-mail: p.fearnhead{at}lancaster.ac.uk.
Submitted on February 23, 2007
Revised on April 6, 2007
Accepted on 29 June 2007
We look at how to choose genetic distance so as to maximise the power of detecting spatial structure. We answer this question through analysing two population genetic models that allow for a spatially structured population in a continuous habitat. These models, like most that incorporate spatial structure, can be characterised by a separation of time scales: the history of the sample can be split into a scattering and collecting phase, and it is only during the scattering phase that the spatial locations of the sample affects the coalescence times. Our results suggest that the optimal choice of genetic distance is based upon splitting a DNA sequence into segments, and counting the number of segments at which two sequences differ. The size of these segments depends on the length of the scattering phase for the population genetic model.
Key Words: Isolation by Distance, MLST data, Spatial Autocorrelation