Full TextCladistic Analysis and Anthropoid Origins
Response: R. F. Kay, C. Ross, B. A. Williams, D. Johnson

Supplemental Data


About Kay et al. matrix

The accompanying matrix (see also the character list) is a TEXT file in NEXUS format. This data set accompanies the technical response by Kay et al. (1) to a comment by Bloch, et al. (2). It also serves as an archival data set for the original report by Kay et al. published in Science (3).

To replicate the results of our analysis, please follow the following steps.

  1. Import the data set into PAUP (4). It is probably easiest to bring it into MacClade first and then open the file from PAUP.
  2. Under Data, Set character weights, select All and Scale for equal character weighting regardless of the number of states. We set the scale to 100, although this is immaterial to the analysis.
  3. Designate as ordered those characters in the character list that have an asterisk.
  4. It was necessary to constrain the analysis to generate a monophyletic Primates. Because PAUP will not run a Heuristic search with Stepwise Addition that Enforces Topological Constraints, you must add characters to the matrix to do this. Make the outgroups = 0 and all the primates = 1 for these characters. We added 50 of these characters.
  5. Under Search, select Heuristic. Under Heuristic Search Options select Stepwise Addition, Random addition sequence and run about 1000 replications. We have run over 5000 replications of this data set.
  6. By experimenting with the settings you can investigate the effects of different assumptions on the data set. A longer paper for has been submitted to the Journal of Human Evolution that includes more postcranial characters and more in-depth analyses. This data set will be made available when the paper is in press. Feel free to contact us if you have any questions or suggestions.

References

  1. R. F. Kay, C. F. Ross, B. A. Williams, D. Johnson, Science 278, 2135 (1997).
  2. J. I. Bloch et al., ibid., p. 2134.
  3. R. F. Kay, C. F. Ross, B. A. Williams, ibid. 275, 797 (1997).
  4. D. L. Swofford, PAUP Phylogenetic Analysis Using Parsimony, Version 3.1.1 and accompanying manual (Illinois Natural History Survey, Champaign, IL, ed. 3.0, 1993).


See also C. F. Ross' homepage for background and ongoing developments.