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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Coherent and incoherent inference in phylogeography and human evolution
1Department of Biology, Washington University, St Louis, MO 63130, USA. temple_a@wustl.edu
Summary
Statistical measures of hypothesis fit must be logically consistent. Incoherent methods, like approximate Bayesian computation (ABC), can produce illogical results, as seen in human evolution studies. Coherent methods offer valid statistical inference.
Area of Science:
- Statistical modeling
- Evolutionary biology
- Phylogenetics
Background:
- Nested and overlapping composite hypotheses are common in statistical modeling.
- Coherent measures of fit ensure logical consistency, where special cases do not have higher probability than general models.
- Incoherence in statistical inference leads to mathematically incorrect and illogical conclusions.
Purpose of the Study:
- To define and illustrate statistical incoherence in hypothesis testing.
- To identify causes of incoherence in methods like approximate Bayesian computation (ABC).
- To propose corrections for coherence and highlight coherent alternatives.
Main Methods:
- Defining coherence in statistical measures of fit for nested and composite hypotheses.
- Analyzing the approximate Bayesian computation (ABC) method for statistical incoherence.
- Comparing ABC with nested clade phylogeographic analysis for coherence and hypothesis testing capabilities.
Main Results:
- The approximate Bayesian computation (ABC) method demonstrated incoherence, assigning a vastly higher probability to a nested human evolution model than a more general one.
- Incoherent inferences, particularly in human evolution studies favoring the out-of-Africa replacement hypothesis, lack statistical and logical validity.
- Nested clade phylogeographic analysis was identified as a coherent alternative, capable of testing individual hypothesis components.
Conclusions:
- Incoherence in statistical inference is a critical flaw rendering results invalid.
- Approximate Bayesian computation (ABC) requires corrections to ensure logical consistency.
- Coherent methods like nested clade phylogeographic analysis provide statistically sound approaches for evolutionary hypothesis testing.
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