Cladistics molecular

Cladistic analysis of molecular sequence characters differs from that described by Hennig17 for organismal characters in several important ways. Molecules do not leave fossils, thus there is no hard record of which character state (i.e., amino acid residue) is ancestral and which is derived at any position in a sequence. The 20 common amino acids are found in all living forms and therefore have nothing inherently ancestral or derived about them. Furthermore, amino acid replacements have no intrinsic directionality, even though some replacements are more likely to occur than others. In other words, amino add replacements are not inherently polarized. In addition, amino acid replacements and nucleotide substitutions are reversible. For these reasons, the character state(s) of the outgroup molecule(s) cannot be assumed to be ancestral. 

Reeves, P. A. and Olmstead, R. G. (2003). Evolution of the TCP gene family in Asteridae cladistic network approaches to understanding regulatory gene family diversification and its impact on morphological evolution. Molecular Biology and Evolution, H, 1997-2009. 

Cladistic analyses suggest that vertebrates evolved from a common ancestor of chordates through a stepwise increase in complexity of the body plan. This process involved the appearance of a number of vertebrate innovations both at an anatomical and a molecular level (Shimeld and Holland, 2000). Morphologically... 

Macromolecules, especially sequences, have surpassed morphological and other organismal characters as the most popular form of data for phylogenetic or cladistic analysis. It is this molecular phylogenetic analysis that we will introduce here. 

Mishler, B.D., Cladistic analysis of molecular and morphological data. Am. J. Phys. Anthropol, 94, 143-156, 1994. 

Paleontology of the past is revived in molecular systematics of the present, in its search for ancestors and centers of origin. The revival ignores, or retreats from, the cladistic reform of paleontology of the 1970s, with historical roots in the work of Louis Dollo (1857-1931) and fossil Inngfishes. The subsequent development of cladistics has been arrested, too, by compnter implementations of character optimization and the ideology of total evidence, which reflects a phenetic rather than cladistic objective the overall similarity of synapomorphy. 

Andersen, N.M., Quantitative cladistics and the reconciliation of morphological and molecular systematics, in Phylogenetik und Molekiile, Schmitt, M., Ed., Edition Archaea, pp. 121-144. 

The subclass Dilleniidae was introduced into angiosperm macrosystematics by Takhtajan (1964) largely influenced by the occiurence of centrifugal stamen initiation in polymerous androecia, which was supposed to be a fundamentally important pattern in macrosystematics. However, the subclass was later dismantled, first by structural cladistic studies (Hufford, 1992) and then also by molecular studies (Chase et al., 1993) (see also Endress et al., 2000). From the present perspective, the feature is not stable at very high systematic levels, however, often it is still at family level. 

P. K. (1998). A combined cladistic analysis of angiosperms using rbcL and non-molecular data sets. Annals of the Missouri Botanical Garden, 85,137-212. 

The systematic relationships of glucosinolate-producing plants and related famihes a cladistic investigation based on morphological and molecular characters. Botanical Journal of die Linnean Society, 151,453-494. 

A cladistic analysis and systematic revision of Charianthus (Miconieae Melastomataceae) using morphological and molecular characters. Systematic Botany, 30,559-584. 

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