摘要:

Abstract —A priori differential weighting of molecular characters is a common methodological practice in molecular phylogenetics and evolution. This has been a largely subjective exercise with few criteria for deciding which characters to down‐weight and how much to do so. A priori differential weighting is conducted to remove heterogeneity from the data sets and to improve the congruence among the informative, and usually more conservative characters. Herein, we test whether congruence is improved with a priori differential weighting by using the incongruence length difference test on a linked genetic data set consisting of 14 mammalian taxa and the 13 protein coding genes of the mitochondrial genome. Weighting by omitting the third codon position did not improve congruence with respect to the equally weighted data, while weighting transversions did improve the congruence between the 13 protein coding genes. Nonetheless, the most parsimonious tree found from transversion weighting did not differ from one using all of the data equally weigh

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00008.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract —Several algorithms to speed up branch swapping searches for most parsimonious trees are described. The method for indirect tree length calculation when moving a clipped clade, based on final states for the divided tree, is expanded to take into account polymorphic characters, and to include the possibility of rejecting several locations as suboptimal by checking just one node. Three different algorithms for faster estimation of final state assignments for the divided tree based on calculations for the whole tree are presented. The first of these is approximate; it uses information from the final state sets for the whole tree. The second is exact, but it is slower than the first, and requires more memory; it is based on the union of the state sets of the descendants for each node. The third is also exact; it requires more memory and programming effort than the other two but it is faster, it is based on final and preliminary state sets for the whole tree (“incremental two‐pass optimization”). Efficient ways to derive state assignments for collapsing trees, based on final states for the divided tree, are described. The recently proposed method of “incremental optimization” is discussed. It is likely that searches using that method will be no faster than searches using indirect calculation as originally described, and will be quite slower than the modified indirect calculation described here. Searches using that method will probably be significantly slowed down when zero‐length branches are to be collapsed, since shortcuts for faster collapsing are not direct

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00009.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract —Arguments for and against combined analysis of multiple data sets in phylogenetic inference are reviewed. Simultaneous analysis of combined data better maximizes cladistic parsimony than separate analyses, hence is to be preferred. Simultaneous analysis can allow “secondary signals” to emerge because it measures strength of evidence supporting disparate results. Separate analyses are useful and of interest to understanding the differences among data sets, but simultaneous analysis provides the greatest possible explanatory power, and should always be evaluated when possible. The mechanics of simultaneous analysis are disc

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00010.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract —The three‐taxon approach to phylogenetic analysis separates the universe of cladograms into a larger number of classes of solutions showing decreasing degrees of fit to data than does conventional Farris optimization. The three‐taxon approach applies to character analysis Nelson and Platnick's interpretation 2 of multiple branching in clado

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00011.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract —Commonly used permutation tail probability (PTP) and topology dependent permutation tail probability (T‐PTP) tests incorporate an inappropriate treatment of designated outgroup taxa, and for that reason are biased either for (PTP) or for or against (T‐PTP) rejection of the null hypothesis. A modified test is proposed, in which this source of bias is elimi

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00012.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract —Contrary to the impression given by Trueman (1996), Bremer (1988) introduced what is now called Bremer support; Faith (1991) did not. Neither did Mishler and Donoghue (1991). Attaching Faith and Cranston's (1991) acronym PTP to Archie's (1989) test does not help make the authorship clear, and the same applies to Källersjö et al.'s (1992) total support t

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00013.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract —In 1991 de Pinna (Cladistics 7: 367–394) coined the term primary homology as the putative homology statements prior to tree reconstruction. However, some confusion still exists regarding the conjectural nature of homology and to the analysis of DNA sequences. By dividing de Pinna's term primary homology into topographical identity and character state identity, we emphasize the sequential refinement of putative homology statements. We discuss the problem of transformational versus taxic homology and explain the application of our terms to DNA sequence d

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00014.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY