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Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

View ORCID ProfileJoseph F. Walker, View ORCID ProfileXing-Xing Shen, View ORCID ProfileAntonis Rokas, View ORCID ProfileStephen A. Smith, View ORCID ProfileEdwige Moyroud
doi: https://doi.org/10.1101/2020.04.20.049999
Joseph F. Walker
1The Sainsbury Laboratory, University of Cambridge, Bateman Street, CB2 1LR, Cambridge, UK
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  • For correspondence: edwige.moyroud@slcu.cam.ac.uk joseph.walker@slcu.cam.ac.uk
Xing-Xing Shen
2Institute of Insect Sciences, Agro-Complex A239, 866 Yuhangtang Road, Hangzhou 310058, Zhejiang University, China
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Antonis Rokas
3Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Stephen A. Smith
4Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103, USA
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Edwige Moyroud
1The Sainsbury Laboratory, University of Cambridge, Bateman Street, CB2 1LR, Cambridge, UK
5Department of Genetics, University of Cambridge, Downing place, CB2 3EJ, Cambridge, UK
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  • For correspondence: edwige.moyroud@slcu.cam.ac.uk joseph.walker@slcu.cam.ac.uk
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Abstract

The genomic data revolution has enabled biologists to develop innovative ways to infer key episodes in the history of life. Whether genome-scale data will eventually resolve all branches of the Tree of Life remains uncertain. However, through novel means of interrogating data, some explanations for why evolutionary relationships remain recalcitrant are emerging. Here, we provide four biological and analytical factors that explain why certain genes may exhibit “outlier” behavior, namely, rate of molecular evolution, alignment length, misidentified orthology, and errors in modeling. Using empirical and simulated data we show how excluding genes based on their likelihood or inferring processes from the topology they support in a supermatrix can mislead biological inference of conflict. We next show alignment length accounts for the high influence of two genes reported in empirical datasets. Finally, we also reiterate the impact misidentified orthology and short alignments have on likelihoods in large scale phylogenetics. We suggest that researchers should systematically investigate and describe the source of influential genes, as opposed to discarding them as outliers. Disentangling whether analytical or biological factors are the source of outliers will help uncover new patterns and processes that are shaping the Tree of Life.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/jfwalker/AnalyzingOutliers

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 21, 2020.
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Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices
Joseph F. Walker, Xing-Xing Shen, Antonis Rokas, Stephen A. Smith, Edwige Moyroud
bioRxiv 2020.04.20.049999; doi: https://doi.org/10.1101/2020.04.20.049999
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Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices
Joseph F. Walker, Xing-Xing Shen, Antonis Rokas, Stephen A. Smith, Edwige Moyroud
bioRxiv 2020.04.20.049999; doi: https://doi.org/10.1101/2020.04.20.049999

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