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Confirmation Biases

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The confirmation bias is the tendency to focus on information that confirms our existing beliefs and ignore information that is inconsistent with our expectations. For example, if you think that your professor is not very nice, you notice all of the instances of rude behavior exhibited by the professor while ignoring the countless pleasant interactions he is involved in on a daily basis. Have you ever fallen prey to the confirmation bias, either as the source or target of such bias?

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Related Experiment Video

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In Situ Transmission Electron Microscopy with Biasing and Fabrication of Asymmetric Crossbars Based on Mixed-Phased a-VOx

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Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method.

¹Department of Biology, University of Ottawa, Ottawa, Canada, K1N 6N5.

|August 23, 2019

Summary

Likelihood phylogenetic methods can exhibit "starless bias" due to conflicting signals, and rate heterogeneity estimation is confounded with tree topology. New R scripts are provided for evaluating phylogenetic trees.

Keywords:

maximum likelihood molecular phylogenetics rate heterogeneity star-tree paradox starless

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Area of Science:

Phylogenetics
Computational Biology
Evolutionary Biology

Background:

Likelihood-based phylogenetic methods are widely used for inferring evolutionary relationships.
Understanding biases in these methods is crucial for accurate evolutionary inference.
Previous studies have identified various sources of bias in phylogenetic analyses.

Purpose of the Study:

To identify sources of starless bias and parameter-estimation bias in likelihood-based phylogenetic methods.
To investigate the confounding effect of rate heterogeneity on tree topology estimation.
To develop and implement likelihood methods for evaluating phylogenetic trees with rate heterogeneity.

Main Methods:

Analysis of site pattern combinations in a 4-Operational Taxonomic Unit (OTU) case.
Investigation of the impact of gamma distribution for modeling rate heterogeneity.
Implementation of likelihood methods in R scripts for phylogenetic tree evaluation.

Main Results:

Identified specific site pattern combinations causing "starless bias" where equidistant sequences do not yield a star tree.
Demonstrated that estimating rate heterogeneity (gamma distribution shape parameter α) is strongly confounded with tree topology.
Showed that "rate heterogeneity" is not sequence-specific and its estimation depends on the imposed tree structure.

Conclusions:

Starless bias can arise from an excess of conflicting phylogenetic signals.
The interpretation of rate heterogeneity parameters requires careful consideration of the inferred tree topology.
Developed R scripts provide tools for teaching and exploring likelihood methods in phylogenetics, particularly for star vs. resolved trees with rate heterogeneity.