摘要:

Abstract—A method is described to assess directly the number of DNA sequence transformations, evolutionary events, required by a phylogenetic topology without the use of multiple sequence alignment. This is accomplished through a generalization of existing character optimization procedures to include insertion and deletion events (indels) in addition to base substitutions. The crux of the model is the treatment of indels as processes as opposed to the patterns implied by multiple sequence alignment. The results of this procedure are directly compatible with parsimony‐based tree lengths. In addition to the simplicity of the method, it appears to generate more efficient (simpler) explanations of sequence variation than does multiple alignm

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00189.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00190.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract—The Rubiaceae are one of the largest of the families of angiosperms, with over 10000 species. The tribal and subfamilial classification is provisional due to the lack of phylogenetic hypotheses. The present study of the Rubiaceae is based on 33 genera and three data sets, one morphological and two molecular from chloroplast DNA, restriction sites andrbcL sequences. There is much congruence between the morphological and the molecular data sets, but also conflict. For parsimony reasons, the best phylogenetic hypothesis is a tree based on an analysis of the combined data sets. The so‐called “total evidence” criterion for the combined analysis is simply a reiteration of the principle of parsimony. In this particular study, the classification would be almost the same even if based on the separate analyses instead of the combined. Despite the inapplicability of consensus trees or trees from separate analyses for phylogenetic hypotheses and classification, separate analyses may provide important information. It is the best way to reveal conflicts between different data sets. Knowledge of the conflicts can promote further detailed investigation in order to improve understanding of characters and phylogenetic hypotheses. In this study, the tribe Vanguerieae provides such an example; morphological data support a position in the subfamily Cinchonoideae, but DNA and a tree based on the combined data support a position in subfamily Ixoroideae. The tribe's position in the morphological tree is probably due to missing information concerning the correct pollen presentation system. Bootstrap fractions and K. Bremer's branch support values are used to evaluate the stability of particular nodes in the trees. Interestingly these values are not always correlated, e.g. in the morphological tree, the node with the highest branch support value has very low bootstrap fraction. The reasons for these differences are unclear, but large differences are presumably more likely to occur on short b

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00191.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract—A matrix of 41 Embiid taxa (representing the 8 formally recognized families of the Order) and 36 characters were cladistically analysed as a first attempt for understanding the higher classification of the Order Embioptera. The resulting trees were rooted with Clothodidae as the sister group of the other Embioptera. The results suggest that the current classification contains several artificial groups. With the rooting used, only Anisembiidae and Australembiidae are monophyletic. Embiidae is polyphyletic, as Australembiidae+ Notoligotomidae,Enveja(incertae sedis) and Oligotomidae+Teratembiidae appear within Embiidae, and the “embiid”Microembiaappears within Notoligotomidae. Oligotomidae is paraphyletic in terms of Teratembiidae. Four of the genera included in the analysis are paraphyletic:Mesembia, Chelicerca(in terms ofDactylocercaandPelorembia),Aposthonia(in terms ofOligotoma), andMetoligotoma(in terms ofAustralembia).PelorembiaandDactylocercaare synonymized withCheli

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00192.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract—Amino acid encoding genes contain character state information that may be useful for phylogenetic analysis on at least two levels. The nucleotide sequence and the translated amino acid sequences have both been employed separately as character states for cladistic studies of various taxa, including studies of the genealogy of genes in multigene families. In essence, amino acid sequences and nucleic acid sequences are two different ways of character coding the information in a gene. Silent positions in the nucleotide sequence (first or third positions in codons that can accrue change without changing the identity of the amino acid that the triplet codes for) may accrue change relatively rapidly and become saturated, losing the pattern of historical divergence. On the other hand, non‐silent nucleotide alterations and their accompanying amino acid changes may evolve too slowly to reveal relationships among closely related taxa. In general, the dynamics of sequence change in silent and non‐silent positions in protein coding genes result in homoplasy and lack of resolution, respectively. We suggest that the combination of nucleic acid and the translated amino acid coded character states into the same data matrix for phylogenetic analysis addresses some of the problems caused by the rapid change of silent nucleotide positions and overall slow rate of change of non‐silent nucleotide positions and slowly changing amino acid positions. One major theoretical problem with this approach is the apparent non‐independence of the two sources of characters. However, there are at least three possible outcomes when comparing protein coding nucleic acid sequences with their translated amino acids in a phylogenetic context on a codon by codon basis. First, the two character sets for a codon may be entirely congruent with respect to the information they convey about the relationships of a certain set of taxa. Second, one character set may display no information concerning a phylogenetic hypothesis while the other character set may impart information to a hypothesis. These two possibilities are cases of non‐independence, however, we argue that congruence in such cases can be thought of as increasing the weight of the particular phylogenetic hypothesis that is supported by those characters. In the third case, the two sources of character information for a particular codon may be entirely incongruent with respect to phylogenetic hypotheses concerning the taxa examined. In this last case the two character sets are independent in that information from neither can predict the character states of the other. Examples of these possibilities are discussed and the general applicability of combining these two sources of information for protein coding genes is presented using sequences from the homeobox region of 46 homeobox genes fromDrosophila melanogasterto develop a hypothesis of genealogical relationship of these genes in this large multi

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00193.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00194.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY

摘要:

Abstract—The controversy over whether protist symbionts ofCryptocercusand termites were inherited from a common ancestor or transferred secondarily has been long standing. We present here the first phylogenetic test of these hypotheses and show that the transfer hypothesis is better supporte

ISSN:0748-3007    

DOI:10.1111/j.1096-0031.1996.tb00195.x

出版商:Blackwell Publishing Ltd    

年代:1996

数据来源: WILEY