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Fossils improve phylogenetic analyses of morphological characters

View ORCID ProfileNicolás Mongiardino Koch, View ORCID ProfileRussell J. Garwood, View ORCID ProfileLuke A. Parry
doi: https://doi.org/10.1101/2020.12.03.410068
Nicolás Mongiardino Koch
1Department of Earth and Planetary Sciences, Yale University, New Haven, CT, USA
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  • For correspondence: nicolas.mongiardinokoch@yale.edu
Russell J. Garwood
2Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
3Earth Sciences Department, Natural History Museum, London, UK
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Luke A. Parry
4Department of Earth Sciences, University of Oxford, Oxford, UK
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Abstract

Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help elucidate macroevolutionary patterns and processes, such as ancestral states and diversification dynamics. However, the effect fossils have on phylogenetic inference from morphological data remains controversial. Previous studies have highlighted their strong impact on topologies inferred from empirical data, but have not demonstrated that they improve accuracy. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here we employ a simulation approach to explore how fossil sampling and missing data affect tree reconstruction across a range of inference methods. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses which simultaneously infer tree topology and divergence times outperform all other methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their unique morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.

Competing Interest Statement

The authors have declared no competing interest.

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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-NC-ND 4.0 International license.
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Posted December 03, 2020.
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Fossils improve phylogenetic analyses of morphological characters
Nicolás Mongiardino Koch, Russell J. Garwood, Luke A. Parry
bioRxiv 2020.12.03.410068; doi: https://doi.org/10.1101/2020.12.03.410068
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Fossils improve phylogenetic analyses of morphological characters
Nicolás Mongiardino Koch, Russell J. Garwood, Luke A. Parry
bioRxiv 2020.12.03.410068; doi: https://doi.org/10.1101/2020.12.03.410068

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