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

American Journal of Botany
Miao SunRobert P Guralnick

Abstract

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. 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). We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schem...Continue Reading

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Citations

Jun 29, 2021·American Journal of Botany·Ryan A Folk, Carolina M Siniscalchi

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Software Mentioned

polytomy resolver
BAMM
treePL
RPANDA
OpenTree
OpenTree PY Toys
TACT
Open Tree of Life
Phyx
PASTIS

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