Journal
EVOLUTION
Volume 54, Issue 1, Pages 44-50Publisher
SOC STUDY EVOLUTION
DOI: 10.1111/j.0014-3820.2000.tb00006.x
Keywords
coalescence theory; gene flow; likelihood ratio tests; maximum likelihood; population subdivision; single nucleotide polymorphisms
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Funding
- NIGMS NIH HHS [GM40282] Funding Source: Medline
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We develop a Monte Carlo-based likelihood method for estimating migration rates and population divergence times from data at unlinked loci at which mutation rates are sufficiently low that, in the recent past, the effects of mutation can be ignored. The method is applicable to restriction fragment length polymorphisms (RFLPs) and single nucleotide polymorphisms (SNPs) sampled from a subdivided population. The method produces joint maximum-likelihood estimates of the migration rate and the time of population divergence, both scaled by population size, and provides a framework in which to test either for no ongoing gene flow or for population divergence in the distant past. We show the method performs well and provides reasonably accurate estimates of parameters even when the assumptions under which those estimates are obtained are not completely satisfied. Furthermore, we show that, provided that the number of polymorphic loci is sufficiently large, there is some power to distinguish between ongoing gene how and historical association as causes of genetic similarity between pairs of populations.
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