Access

You are not currently logged in.

Access JSTOR through your library or other institution:

login

Log in through your institution.

Journal Article

A Phylogenetic Analysis of the Caminalcules. II. Estimating the True Cladogram

Robert R. Sokal
Systematic Zoology
Vol. 32, No. 2 (Jun., 1983), pp. 185-201
DOI: 10.2307/2413280
Stable URL: http://www.jstor.org/stable/2413280
Page Count: 17
Were these topics helpful?
See something inaccurate? Let us know!

Select the topics that are inaccurate.

Cancel
  • Download ($42.00)
  • Add to My Lists
  • Cite this Item
A Phylogenetic Analysis of the Caminalcules. II. Estimating the True Cladogram
Preview not available

Abstract

The ability of numerical methods to estimate the true cladogram is examined, using the Caminalcules as an example. This group of "organisms" was generated artificially according to principles believed to resemble those operating in real organisms. Estimated cladograms obtained by numerical methods are only moderately good estimates of the true cladogeny. Of the various models applied in numerical cladistics, the closeness of approximation to the true cladogeny is in the following order: best-Wagner parsimony and Camin-Sokal parsimony; second-polymorphism parsimony; third-character compatibility and Fitch's nonsequential method; fourth-UPGMA phenograms; worst-Dollo parsimony. Since the data matrix contains NC (no comparison) states, numerical cladistic algorithms that take account of these states give better results than those that do not. For distance Wagner algorithms, there is little difference in the outcome between midpoint rooting and rooting with a zero vector or with the true ancestor. By separate permutations of the order of the OTUs that are input to the numerical algorithm, trees of varying length were obtained from which the shortest could be chosen. Shortest trees, computed globally over all OTUs or separately for each Caminalcule genus, are not necessarily those that best estimate the true cladogeny. Numerical cladistic estimates separately computed for genera are poorer than those based on the entire taxon. The effects of homoplasy and divergence on the results of phenetic and cladistic algorithms are investigated in general and employed to explain in detail the differences among the true cladogram, the phenogram, and the estimated cladogram. The agreements observed are all in cases where given taxa diverge greatly from ancestral stems. Discrepancies are due to (A) parallelisms in the cladogeny affecting phenetic similarities and (B) divergence of cladistically close relatives increasing the relative phenetic similarity of cladistically more distant relatives. These two cases are about equally frequent.

Page Thumbnails

  • Thumbnail: Page 
185
    185
  • Thumbnail: Page 
186
    186
  • Thumbnail: Page 
187
    187
  • Thumbnail: Page 
188
    188
  • Thumbnail: Page 
189
    189
  • Thumbnail: Page 
190
    190
  • Thumbnail: Page 
191
    191
  • Thumbnail: Page 
192
    192
  • Thumbnail: Page 
193
    193
  • Thumbnail: Page 
194
    194
  • Thumbnail: Page 
195
    195
  • Thumbnail: Page 
196
    196
  • Thumbnail: Page 
197
    197
  • Thumbnail: Page 
198
    198
  • Thumbnail: Page 
199
    199
  • Thumbnail: Page 
200
    200
  • Thumbnail: Page 
201
    201