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Gene tree discord, simplex plots, and statistical tests under the coalescent

Citation

Rhodes, John; Allman, Elizabeth; Mitchell, Jonathan; Rhodes, John (2021), Gene tree discord, simplex plots, and statistical tests under the coalescent, Dryad, Dataset, https://doi.org/10.5061/dryad.34tmpg4hq

Abstract

A simple graphical device, the simplex plot of quartet concordance factors, is introduced to aid in the exploration of a collection of gene trees on a common set of taxa. A single plot summarizes all gene tree discord, and allows for visual comparison to the expected discord from the multispecies coalescent model (MSC) of incomplete lineage sorting on a species tree. A formal statistical procedure is described that can quantify the deviation from expectation for each subset of four taxa, suggesting when the data is not in accord with the MSC, and thus that either gene tree inference error is substantial or a more complex model such as that on a network may be required. If the collection of gene trees is in accord with the MSC, the plots reveal when substantial incomplete lineage sorting is present. Applications to both simulated and empirical multilocus data sets illustrate the insights provided.

Methods

This is a supplement to a research article. No data is provided.

Usage Notes

The supplement contains a complete description of the simulation procedure.

Funding

National Institutes of Health, Award: R01 GM117590

National Institutes of Health, Award: 2P20 GM103395