Cladogram

Abstract: Amino acid sequence data are available for ribulose biphosphate carboxylase, plastocyanin, cytochrome c, and ferredoxin for a number of angiosperm families. Cladistic analysis of the data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated. In one analysis of nine angiosperm families and 40 variable amino acid positions from three proteins, the most parsimonious cladograms were 151 steps long and contained 63 parallelisms and reversals (consistency index = 0.583). In another analysis of six families and 53 variable amino acid positions from four proteins, the most parsimonious cladogram was 161 steps long and contained 50 parallelisms and reversals (consistency index = 0.689). Single changes in both data matrices could yield most parsimonious cladograms with quite different topologies and without common monophyletic groups. Presently, amino acid sequence data are not comprehensive enough for phylogenetic reconstruction among angiosperms. More informative positions are needed, either from sequencing longer parts of the proteins or from sequencing more proteins from the same taxa.

Abstract: -Character congruence, the principle of using all the relevant data, and character independence are important concepts in phylogenetic inference, because they relate directly to the evidence on which hypotheses are based. Taxonomic congruence, which is agreement among patterns of taxonomic relationships, is less important, because its connection to the underlying character evidence is indirect and often imperfect. Also, taxonomic congruence is difficult to justify, because of the arbitrariness involved in choosing a consensus method and index with which to estimate agreement. High levels of character congruence were observed among 89 biochemical and morphological synapomorphies scored on 10 species of Epicrates. Such agreement is consistent with the phylogenetic interpretation attached to the resulting hypothesis, which is a consensus of two equally parsimonious cladograms: (cenchria (angulifer (striatus ((chrysogaster, exsul) (inornatus, subflavus) (gracilis (fordii, monensis)))))). Relatively little (11.4%) of the character incongruence was due to the disparity between the biochemical and morphological data sets. Each of the clades in the consensus cladogram was confirmed by two or more unique and unreversed novelties, and six of the eight clades were corroborated by biochemical and morphological evidence. Such combinations of characters add confidence to the phylogenetic hypothesis, assuming the qualitatively different kinds of data are more likely to count as independent than are observations drawn from the same character system. Most of the incongruence occurred in the skeletal subset of characters, and much of that independent evolution seemed to be the result of paedomorphosis. [Biochemical data; character congruence; character independence; Epicrates; evidence; morphological data; paedomorphosis; phylogenetic systematics; taxonomic congruence; total evidence.] The goals of cladistics and phenetics are different. The former estimates phylogeny (Hennig, 1966), the latter seeks stability and convenience in classification (Sokal, 1986:424). Unfortunately, these objectives have become confused, especially where stability is concerned. For example, Hillis (1987:35) stated that "[c]lassifications are best based on information in common among multiple data sets (i.e., consensus trees), whereas the best estimate of phylogeny and best estimate of character evolution are represented in the analysis of the combined data sets." The importance of a conservative information storage-retrieval system is undeniable (e.g., International Code of Zoological Nomenclature, 1985:3), and pheneticists sought justification for their methods in this simple truth (Sokal and Sneath, 1963). Even cladists attributed some significance to stability per se, because the lack of it confounds attempts to discover the single historical pattern (Schuh and Farris, 1981). Not unexpectedly, cladists responded (e.g., Farris, 1971) to the proposition that phenetic methods produce more stable classifications (e.g., Sokal and Sneath, 1963: 264). Analytical precision was demanded by the contestants, and an incredible array of consensus methods and indexes were developed (see lists below). It is important to bear in mind that only information on taxonomic grouping can be used to evaluate the pheneticists' claims, because character congruence is difficult to judge in phenetic analyses. Eventually, the controversy over stability became a relative issue, with cladists arguing greater stability for classifications produced by their methods, as if stability was a goal of phylogenetic systematics. Further, Nelson and Platnick (1981:219; see also Nelson, 1979) attempted to justify cla-

Abstract: -Methods that use outgroups in the reconstruction of phylogeny are described and evaluated by the criterion of parsimony. By considering the character states and relationships of outgroups, one can estimate the states ancestral for a study group or ingroup, even when several character states are found among the outgroups. Algorithms and rules are presented that find the most parsimonious estimates of ancestral states for binary and multistate characters when outgroup relationships are well resolved. Other rules indicate the extent to which uincertainty about outgroup relationships leads to uncertainty about the ancestral states. The algorithms and rules are based on "simple parsimony" in that convergences and reversals are counted equally. After parsimony is measured locally among the outgroups to estimate ancestral states, parsimony is measured locally within the ingroup, given the ancestral states, to find the ingroup cladogram. This two-step procedure is shown to find the ingroup cladograms that are most parsimonious globally; that is, most parsimonious when parsimony is measured simultaneously over the ingroup and outgroups. However, the two-step procedure is guaranteed to achieve global parsimony only when: (a) outgroup relationships are sufficiently resolved beforehand; (b) outgroup analysis is taken to indicate the state not in the most recent common ancestor of the ingroup, but in a more distant ancestor; and (c) ancestral states are considered while the ingroup is being resolved, not merely added afterward to root an unrooted network. The criterion of global parsimony is then applied to evaluate procedures used when outgroup relationships are poorly resolved. The procedure that chooses as ancestral the state occurring most commonly among the outgroups can sometimes yield cladograms that are not globally parsimonious. By the criterion of global parsimony, the best procedure is one that simultaneously resolves the outgroups and ingroup with the data at hand. Finally, simple parsimony can choose among competing hypotheses, but it often fails to indicate how much confidence can be placed in that choice. [Phylogeny reconstruction; cladistic methods; outgroup analysis; character polarity; parsimony.] This paper explores the use of outgroup analysis in phylogeny reconstruction. When reconstructing a phylogeny, a systematist asks: Given a group of organisms (the ingroup), what are the monophyletic subgroups? If the members of a subgroup share a character state that is derived within the group, the monophyly of this subgroup is corroborated (Hennig, 1966; Wiley, 1975). Hence, systematists attempting to infer phylogenies have sought methods for determining whether a given character state is derived (apomorphic) or ancestral (plesiomorphic). Many methods for assessing the evolutionary polarity of characters have been proposed, including outgroup analysis, ingroup analysis, the ontogenetic method, and the paleontological method. These approaches have been reviewed recently by Crisci and Stuessy (1980), de Jong (1980), Stevens (1980), Arnold (1981), Nelson and Platnick (1981), and others. The methods perhaps most widely accepted today are outgroup analysis and the ontogenetic method, the relative merits of which are still being debated (contrast Nelson [1978] and Patterson [1982] with Lundberg [1973], Wheeler [1981] and Voorzanger and van der Steen [1982]). In its simplest form, outgroup analysis can be summarized by the following rule (Watrous and Wheeler, 1981): For a given character with two or more states within a group, the state occurring in related groups is assumed to be the plesiomorphic state. This rule is inadequate, however, when characters vary among the related groups (the outgroups). Arnold (1981) and Farris (1982) have dealt with some cases of