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Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids

View ORCID ProfileMiao Sun, Ryan A. Folk, Matthew A. Gitzendanner, Robert P. Guralnick, Pamela S. Soltis, Zhiduan Chen, Douglas E. Soltis
doi: https://doi.org/10.1101/749325
Miao Sun
1Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
2State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
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Ryan A. Folk
3Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
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Matthew A. Gitzendanner
4Department of Biology, University of Florida, Gainesville, FL 32611, USA
5Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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Robert P. Guralnick
1Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
5Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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Pamela S. Soltis
1Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
5Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
6Genetics Institute, University of Florida, Gainesville, FL 32608, USA
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Zhiduan Chen
2State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
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  • For correspondence: zhiduan@ibcas.ac.cn dsoltis@ufl.edu
Douglas E. Soltis
1Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
4Department of Biology, University of Florida, Gainesville, FL 32611, USA
5Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
6Genetics Institute, University of Florida, Gainesville, FL 32608, USA
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  • For correspondence: zhiduan@ibcas.ac.cn dsoltis@ufl.edu
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Abstract

Premise of the Study Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification rates. These now-common approaches typically (1) are characterized by incomplete coverage without explicit sampling methodologies, and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. Here we use an empirical example to examine effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionists based on those results.

Methods We used a supermatrix for rosids, a large clade of angiosperms, and its well-sampled subclade Cucurbitaceae, as empirical case studies. We compared results using this large phylogeny with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA, BAMM) and semiparametric (DR).

Key Results We find the impact of sampling on diversification estimates is idiosyncratic and often strong. As compared to full empirical sampling, representative and random sampling schemes either depress or exaggerate speciation rates depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.

Conclusions We (1) urge caution in use of summary backbone trees containing only higher-level taxa, (2) caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees, and (3) stress the importance of explicit sampling methodologies in macroevolutionary studies.

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-ND 4.0 International license.
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Posted August 29, 2019.
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Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids
Miao Sun, Ryan A. Folk, Matthew A. Gitzendanner, Robert P. Guralnick, Pamela S. Soltis, Zhiduan Chen, Douglas E. Soltis
bioRxiv 749325; doi: https://doi.org/10.1101/749325
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Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids
Miao Sun, Ryan A. Folk, Matthew A. Gitzendanner, Robert P. Guralnick, Pamela S. Soltis, Zhiduan Chen, Douglas E. Soltis
bioRxiv 749325; doi: https://doi.org/10.1101/749325

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