Although numerous studies have surveyed the frequency with which different plant characters are associated with polyploidy, few statistical tools are available to identify the factors that potentially facilitate polyploidy. We describe a new probabilistic model, BiChroM, designed to associate the frequency of polyploidy and chromosomal change with a binary phenotypic character in a phylogeny. BiChroM provides a robust statistical framework for testing differences in rates of polyploidy associated with phenotypic characters along a phylogeny while simultaneously allowing for evolutionary transitions between character states. We used BiChroM to test whether polyploidy is more frequent in woody or herbaceous plants, based on tree with 4711 eudicot species. Although polyploidy occurs in woody species, rates of chromosome doubling were over six times higher in herbaceous species. Rates of single chromosome increases or decreases were also far higher in herbaceous than woody species. Simulation experiments indicate that BiChroM performs well with little to no bias and relatively little variance at a wide range of tree depths when trees have at least 500 taxa. Thus, BiChroM provides a first step toward a rigorous statistical framework for assessing the traits that facilitate polyploidy.
Bibliographical noteFunding Information:
R. Zenil-Ferguson designed research, wrote article, organized data, performed statistical analyses, and programmed R package chromploid. J.M. Ponciano performed statistical analyses, and wrote article. J.G. Burleigh designed research, organized data, and wrote article. The authors thank Dr. Jeremy Beaulieu for helpful advice in the implementation of pruning algorithm, Dr. Nick Matzke for suggestions about the use of large matrices and Drs. Luke Harmon and Fran?ois Michonneau who offered advice about chromploid R package implementation. We also thank Dr. Scott A. McKinley for the suggestion of exploring the performance of matrix exponentials, and Lauren Suarez for scoring many of the woody and herbaceous character states. This manuscript was greatly improved thanks to the critical comments of associate editor Dr. C?cile An? and two anonymous reviewers. Support for R. Zenil-Ferguson provided by NSF DDIG DEB-1501547 and NSF DEB-1208912. The doi for our data is 10.5061/dryad.6g2c7.
© 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.
- Chromosome number