Trees of unusual size: biased inference of early bursts from large molecular phylogenies

PLoS One. 2012;7(9):e43348. doi: 10.1371/journal.pone.0043348. Epub 2012 Sep 5.

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 signature when extinction was low. Under moderate extinction, both the [Formula: see text]-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Biodiversity
  • Biological Evolution
  • Computer Simulation
  • Ecology
  • Extinction, Biological
  • Genetic Speciation
  • Humans
  • Models, Statistical
  • Phylogeny*
  • Reproducibility of Results
  • Species Specificity

Grants and funding

LJH and MWP were funded by National Science Foundation grant DEB-0919499. MWP also received funding from a NSERC-PGS-M award. This material is based in part upon work supported by the National Science Foundation under Cooperative Agreement No. DBI-0939454. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.