ArticleSystematic biology2022
Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 52 citations in OpenAlex.
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- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
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- Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes.Nature communications · 2023Article
- The tree of blobs of a species network: identifiability under the coalescent.Journal of mathematical biology · 2022Article
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- Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests.BMC plant biology · 2022Article
- MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R.Bioinformatics (Oxford, England) · 2021Article
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
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 are 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. [Gene tree discordance; hypothesis test; multispecies coalescent model; quartet concordance factor; simplex plot; species tree].
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.