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

Abstract

Premise Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species 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. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. Methods We used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies 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 and BAMM) and semiparametric (DR). Results We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated 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 missingmore » taxa. Conclusions We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.« less

Authors:

Sun, Miao  ^[1];

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Folk, Ryan A.  ^[2];

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• Search DOE PAGES for ORCID "0000-0002-5333-9273"

Gitzendanner, Matthew A.  ^[3];

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Soltis, Pamela S.  ^[4];

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Chen, Zhiduan  ^[5];

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Soltis, Douglas E.  ^[6];

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• Search DOE PAGES for ORCID "0000-0001-8638-4137"

Guralnick, Robert P.  ^[7]

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• Search DOE PAGES for ORCID "0000-0001-6682-1504"

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1. Florida Museum of Natural History University of Florida Gainesville Florida 32611 USA, State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China, Department of Bioscience Aarhus University Aarhus 8000 Denmark
2. Department of Biological Sciences Mississippi State University Mississippi State Mississippi 39762 USA
3. Department of Biology University of Florida Gainesville Florida 32611 USA, Biodiversity Institute University of Florida Gainesville Florida 32611 USA
4. Florida Museum of Natural History University of Florida Gainesville Florida 32611 USA, Biodiversity Institute University of Florida Gainesville Florida 32611 USA, Genetics Institute University of Florida Gainesville Florida 32608 USA
5. State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences Beijing 100093 China
6. Florida Museum of Natural History University of Florida Gainesville Florida 32611 USA, Department of Biology University of Florida Gainesville Florida 32611 USA, Biodiversity Institute University of Florida Gainesville Florida 32611 USA, Genetics Institute University of Florida Gainesville Florida 32608 USA
7. Florida Museum of Natural History University of Florida Gainesville Florida 32611 USA, Biodiversity Institute University of Florida Gainesville Florida 32611 USA

Publication Date:

Tue Jun 09 00:00:00 EDT 2020

Research Org.:

Univ. of Florida, Gainesville, FL (United States)

Sponsoring Org.:

USDOE Office of Science (SC); National Science Foundation (NSF); Chinese Academy of Sciences; National Natural Science Foundation of China (NSFC)

OSTI Identifier:

1632777

Alternate Identifier(s):

OSTI ID: 1632778; OSTI ID: 1803330

Grant/Contract Number:  

DE‐SC0018247; SC0018247; DEB-1208809; DEB-1442280; DBI-1523667; DEB-1916632; XDA19050103; XDB31000000; 31590822

Resource Type:

Published Article

Journal Name:

American Journal of Botany

Additional Journal Information:

Journal Name: American Journal of Botany Journal Volume: 107 Journal Issue: 6; Journal ID: ISSN 0002-9122

Publisher:

Wiley Blackwell (John Wiley & Sons)

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; plant sciences; diversification; mega-phylogeny; modeling; rosids; sampling bias