Coherent and incoherent inference in phylogeography and human evolution
- 22 March 2010
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 107 (14), 6376-6381
- https://doi.org/10.1073/pnas.0910647107
Abstract
A hypothesis is nested within a more general hypothesis when it is a special case of the more general hypothesis. Composite hypotheses consist of more than one component, and in many cases different composite hypotheses can share some but not all of these components and hence are overlapping. In statistics, coherent measures of fit of nested and overlapping composite hypotheses are technically those measures that are consistent with the constraints of formal logic. For example, the probability of the nested special case must be less than or equal to the probability of the general model within which the special case is nested. Any statistic that assigns greater probability to the special case is said to be incoherent. An example of incoherence is shown in human evolution, for which the approximate Bayesian computation (ABC) method assigned a probability to a model of human evolution that was a thousand-fold larger than a more general model within which the first model was fully nested. Possible causes of this incoherence are identified, and corrections and restrictions are suggested to make ABC and similar methods coherent. Another coalescent-based method, nested clade phylogeographic analysis, is coherent and also allows the testing of individual components of composite hypotheses, another attribute lacking in ABC and other coalescent-simulation approaches. Incoherence is a highly undesirable property because it means that the inference is mathematically incorrect and formally illogical, and the published incoherent inferences on human evolution that favor the out-of-Africa replacement hypothesis have no statistical or logical validity.Keywords
This publication has 30 references indexed in Scilit:
- Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getulaMolecular Ecology, 2009
- WHY DOES A METHOD THAT FAILS CONTINUE TO BE USED? THE ANSWEREvolution, 2009
- Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographical analysis vs. approximate Bayesian computationMolecular Ecology, 2009
- Bayesian inference of population size history from multiple lociBMC Evolutionary Biology, 2008
- Statistical evaluation of alternative models of human evolutionProceedings of the National Academy of Sciences, 2007
- Combining Phylogeography with Distribution Modeling: Multiple Pleistocene Range Expansions in a Parthenogenetic Gecko from the Australian Arid ZonePLOS ONE, 2007
- GENETICS AND RECENT HUMAN EVOLUTIONEvolution, 2007
- Out of Africa again and againNature, 2002
- Sensitivity in Bayesian Statistics: The Prior and the LikelihoodJournal of the American Statistical Association, 1991
- Estimating the Dimension of a ModelThe Annals of Statistics, 1978