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Neglecting model selection alters phylogenetic inference

View ORCID ProfileMichael Gerth
doi: https://doi.org/10.1101/849018
Michael Gerth
Department of Biological and Medical Sciences, Oxford Brookes University, Gispy Lane, OX3 0BP, Oxford, United Kingdom,
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  • ORCID record for Michael Gerth
  • For correspondence: mgerth@brookes.ac.uk mgerth@brookes.ac.uk
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ABSTRACT

Molecular phylogenetics is a standard tool in modern biology that informs the evolutionary history of genes, organisms, and traits, and as such is important in a wide range of disciplines from medicine to palaeontology. Maximum likelihood phylogenetic reconstruction involves assumptions about the evolutionary processes that underlie the dataset to be analysed. These assumptions must be specified in forms of an evolutionary model, and a number of criteria may be used to identify the best-fitting from a plethora of available models of DNA evolution. Using many empirical and simulated nucleotide sequence alignments, Abadi et al.1 have recently found that phylogenetic inferences using best models identified by six different model selection criteria are, on average, very similar to each other. They further claimed that using the model GTR+I+G4 without prior model-fitting results in similarly accurate phylogenetic estimates, and consequently that skipping model selection entirely has no negative impact on many phylogenetic applications. Focussing on this claim, I here revisit and re-analyse some of the data put forward by Abadi et al. I argue that while the presented analyses are sound, the results are misrepresented and in fact - in line with previous work - demonstrate that model selection consistently leads to different phylogenetic estimates compared with using fixed models.

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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 4.0 International license.
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Posted November 25, 2019.
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Neglecting model selection alters phylogenetic inference
Michael Gerth
bioRxiv 849018; doi: https://doi.org/10.1101/849018
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Neglecting model selection alters phylogenetic inference
Michael Gerth
bioRxiv 849018; doi: https://doi.org/10.1101/849018

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