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Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies

  • Matthew W. Pennell ,

    mwpennell@gmail.com

    Affiliations Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, United States of America, Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America, BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, United States of America

  • Brice A. J. Sarver,

    Affiliations Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, United States of America, Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America, BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, United States of America

  • Luke J. Harmon

    Affiliations Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, United States of America, Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America, BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, United States of America

Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies

  • Matthew W. Pennell, 
  • Brice A. J. Sarver, 
  • Luke J. Harmon
PLOS
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Abstract

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signat