Parsimonious Solutions Research Articles

Full-information item bi-factor analysis

A plausibles-factor solution for many types of psychological and educational tests is one that exhibits a general factor ands − 1 group or method related factors. The bi-factor solution results from the constraint that each item has a nonzero loading on the primary dimension and at most one of thes − 1 group factors. This paper derives a bi-factor item-response model for binary response data. In marginal maximum likelihood estimation of item parameters, the bi-factor restriction leads to a major simplification of likelihood equations and (a) permits analysis of models with large numbers of group factors; (b) permits conditional dependence within identified subsets of items; and (c) provides more parsimonious factor solutions than an unrestricted full-information item factor analysis in some cases.

PHYLOGENY OF THE SUBFAMILIES OF THE FAMILY BRACONIDAE (HYMENOPTERA: ICHNEUMONOIDEA): A REASSESSMENT.

Abstract- The recently published phylogeny of Braconidae by Quicke and van Achterberg is reassessed. Character-state definitions and character polarities are evaluated, and more rigorous methods are suggested. Our results indicate that there are many more parsimonious solutions to their data set, the consensus of which differs substantially from their results. Based on our reassessment, little can be said about the relationships among braconid subfamilies. Consensus trees show the cyclostomes as a largely unresolved basal grade. The two other major lineages which have been proposed, the helconoids and microgastroids, are somewhat better resolved, but not consistently so. Relationships among the helconoids vary considerably depending on the parameters used for parsimony analysis.

THREE‐TAXON STATEMENTS: A MORE PRECISE USE OF PARSIMONY?

Abstract— Binary characters can be represented in data matrices by the three‐taxon statements they imply. Transforming characters into three‐taxon statements may increase the sensitivity of parsimony to differences in the fit of data to alternative cladograms. Extrapolation of the technique to multistate features allows semi‐additive characters to be coded accurately. In many cases, analysis of the transformed data produces fewer equally parsimonious solutions than does analysis of the raw data. In other cases, additional equally parsimonious solutions, or even different solutions, may be produced; in those cases, the results appear to accommodate information from a larger number of characters than do the results from raw data.

Phylogeny and classification of the Signiphoridae (Hymenoptera: Chalcidoidea)

. A data set consisting of twenty‐eight anatomical characters scored for twenty‐eight terminal taxa representing the world fauna of Signiphoridae was analysed using parsimony and compatibility methods. The Coccophaginae (Aphelinidae) and the Azotinae (Aphelinidae) were used as outgroups to establish polarity of character state changes. Relationships of Signiphoridae to other Chalcidoidea are discussed. Several multistate characters were treated in the parsimony analyses either as unordered or as ordered into transformation series using additive binary coding, which in some cases drastically reduced the number of equally parsimonious solutions. Monophyly of Signiphoridae is supported by seven synapomorphies. Four genera, Chartocerus, Thysanus, Clytina and Signiphora, are recognized within Signiphoridae based on synapomorphies. Rozanoviella syn.n. and Kerrichiella syn.n. are synonymized under Signiphora. Species of Signiphora are further assigned to four species groups, three of which are demonstrably monophyletic. Nine species or subspecies are transferred to Chartocerus from Signiphora (australicus comb.n., australiensis comb.n., australiensis orbiculatus comb.n., beethoveni comb.n., corvinus comb.n., funeralis comb.n., reticulata comb.n., ruskini comb.n., thusanoides comb.n.), one species to Thysanus from Signiphora (melancholicus comb.n.), and one species to Signiphora from Kerrichiella (coleoptratus comb.n.). A key to genera of Signiphoridae and species groups of Signiphora is presented. A diagnosis, relevant nomenclatural history, and a list of included species are given for each genus and species group, and the biology and distribution of each is summarized.

THE NATURE OF CLADISTIC DATA

Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non‐additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.

AN EMPIRICAL COMPARISON OF MICROCOMPUTER PARSIMONY PROGRAMS.

Abstract- The effectiveness and efficiency of two microcomputer parsimony programs (Felsenstein's PHYLIP and Swofford's PAUP), and a prototype version of a third (SHEN, to be incorporated in Farris' HENNIG-86), are evaluated with reference to 35 data sets, including those previously used by Luckow and Pimentel (1985) to benchmark mainframe programs. Both PHYLIP and PAUP can be used effectively; with careful selection of options, their accuracy can equal or surpass that of older mainframe programs. PHYLIP is relatively inefficient (in use of computer time); its usefulness is also limited by the inability of its heuristic algorithms to detect multiple equally parsimonious solutions in a single run. PHYLIP's exact algorithm (branch-and-bound) and PAUP's heuristic and exact algorithms do not share the latter drawback but require users to spend unreasonable amounts of time coping with redundant output. The remarkable effectiveness of these programs offers hope that (particularly with the advent of multitasking microcomputers) exact and cost-effective solutions will be obtainable in many, if not all, cladistic analyses.

MAJOR CLADES OF THE ANGIOSPERMS.

Abstract- Our knowledge of fundamental angiosperm interrelationships is still very incomplete. The absence of a narrowly circumscribed gymnosperm outgroup, ideally the sister group, makes character evaluation, necessary for a cladistic analysis, difficult. According to current views the superorder Magnoliiflorae with a number of other groups, for example the monocotyledons, may represent a complex of families near the base of the angiosperms. Interrelationships of groups within the monocotyledons are much better understood than those between groups within the dicotyledons. A cladogram of monocotyledon orders based on earlier work by R. Dahlgren, H. T. Clifford, and F. N. Rasmussen is presented. A data matrix for a sample of the angiosperms with 61 characters for 49 taxa, mostly magnoliifloran and related families, is presented. The characters are polarized mainly according to the current view that the primitive angiosperm morphotype is a woody dicotyledon with strobiloid flowers. As an alternative the matrix is adjusted following W. C. Burger's conjecture that the primitive angiosperm was a herbaceous monocotyledon with trimerous flowers. Both matrices were run in a computerized parsimony analysis, resulting in numerous equally parsimonious solutions. This result is illustrative of the great homoplasy in the available character information, and also of how little actually is known about fundamental angiosperm interrelationships or phylogeny.

Correction: Wagner Networks and Wagner Trees: A Presentation of Methods for Estimating Most Parsimonious Solutions

Correction: Wagner Networks and Wagner Trees: A Presentation of Methods for Estimating Most Parsimonious Solutions

WAGNER NETWORKS AND WAGNER TREES: A PRESENTATION OF METHODS FOR ESTIMATING MOST PARSIMONIOUS SOLUTIONS

SummaryThe methods of Wagner network and Wagner tree construction are presented. A worked example, based on a set of hypothetical taxa, is examined in detail. Additional examples, representing real and artificial data sets, are also examined. The existence of alternative choices at several stages in the algorithms leads to solutions that may not be most parsimonious estimates. There apparently is no non‐arbitrary method for choosing between the alternatives. The examples presented illustrate that there may be multiple equally parsimonious solutions for a given data set and that neither algorithm can ensure a most parsimonious solution.

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

Fitch, W. M. (Dept. of Physiological Chemistry, Univ. of Wisconsin, Madison, Wisconsin, 53706), 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool., 20:406-416.-A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented. The character states used as examples are the four messenger RNA nucleotides encoding the amino acid sequences of proteins, but the method is general. [Evolution; parsimonious trees.] It has been a goal of those attempting to deduce phylogenetic relationships from information on biological characteristics to find the ancestral relationship(s) that would permit one to account for the descent of those characteristics in a manner requiring a minimum number of evolutionary steps or changes. The result could be called the most parsimonious evolutionary tree and might be expected to have a high degree of correspondence to the true phylogeny (Camin and Sokal, 1965). It's justification lies in the most efficient use of the information available and does not presuppose that evolution follows a most parsimonious course. There are no known algorithms for finding the most parsimonious tree(s) apart from the brute force method of examining nearly every possible tree.' This is impractical for trees involving a dozen or more taxonomic units. Most numerical taxonomic procedures (Sokal and Sneath, 1963; Farris, 1969, 1970; Fitch and Margoliash, 1967) provide dendrograms that would be among the more parsimonious solutions; one just cannot be sure that a more parsimonious tree structure does not exist. Farris (1970) has explicitly considered the parsimony principle as a part of 'An elegant beginning to an attack on the problem has recently been published by Farris (1969) who developed a method which estimates the reliability of various characters and then weights the characters on the basis of that reliability. his method which, like the present method, has its roots in the Wagner tree (Wagner,