On the character of and distance between states in a binary switching net

Behavioral examination of binary switching net models has typically concerned itself with an examination of their cyclical character. This article considers two less frequently discussed behavioral variables-the density of 1's in net states and the (Hamming) distance between net states. These variables are studied under fully random nets and under nets controlled at levels of internal homogeneity, forcibility or threshold. A collection of theoretical and simulated results is presented.     

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.     

Logical basis for morphological characters in phylogenetics

Systematists have questioned the distinction between characters and character states and their alignment with the traditional concept of homology. Previous definitions for character and character state show surprising variation. Here it is concluded that characters are simply features expressed as independent variables and character states the mutually exclusive conditions of a character. Together, characters and character states compose what are here termed character statements. Character statements are composed of only four fundamental functional components here identified as locator, variable, variable qualifier, and character state, and these components exist in only two patterns, neomorphic and transformational. Several controversies in character coding and the use of “absent” as a character state are understood here as a consequence of incomplete character statements and the inappropriate mixing of neomorphic and transformational character statements. Only a few logically complete patterns for morphological character data exist; their adoption promises to greatly reduce current variability in character data between analyses. © The Willi Hennig Society 2007.     

Evolution of mouthbrooding and life-history correlates in the fighting fish genus Betta

The origin of and evolutionary transitions among the extraordinary diverse forms of parental care in teleost fish remain largely unknown. The "safe harbor" hypothesis predicts that the evolution from a "guarding" to a "brooding" form of care in teleost fish is associated with shifts in reproductive and life-history features such as reduced fecundity, and increased egg volume with higher parental investment. Robust phylogenetic hypotheses may help to identify evolutionary changes in key traits associated with differences in the form of parental care. Here, we used reconstruction of ancestral character states to study the evolution of the two forms of parental care, bubble nesting and mouthbrooding in the fighting fish genus Betta. We also applied a comparative analysis using the phylogenetic generalized least-squares method to test the "safe harbor" hypothesis by evaluating differences between the two forms of parental care in standard length, life-history traits, and three habitat variables. Evolutionary hypotheses were derived from the first molecular phylogeny (nuclear and mitochondrial DNA sequence data; 4448 bp) of this speciose group. Ancestral character state reconstructions of the evolution of the form of parental care in the genus Betta, using the methods of unweighted parsimony and maximum likelihood, are uncertain and further indicate a high rate of evolutionary transitions. Applying different weights for the suspected directionality of changes, based on the consistent phenotypic and behavioral differences found between bubble nesters and mouthbrooders, recurrent origin of mouthbrooding in the genus Betta is favored using parsimony. Our comparative analyses further demonstrate that bubble nesters and mouthbrooders do not have a consistent set of life-history correlates. The form of parental care in Betta is correlated only with offspring size, with mouthbrooders having significantly bigger offspring than bubble nesters, but is not correlated with egg volume, clutch size, and broodcare duration, nor with any of the three habitat variables tested. Our results thus challenge the general predictions of the "safe harbor" hypothesis for the evolution of alternative brood care forms in the fighting fish genus Betta.     

Floral character states of the Northeast and Tropical East African Swertia species (Gentianaceae)

The floral gross morphological and anatomical character states of 23 African Swertia species are described. Colleters are frequent in Swertia, especially at the lower rim of calyx lobes and are usually placed in a single row except in S. crassiuscula (they are not "typical" colleters). The aestivation of corolla lobes is found to be uniform except in S. engleri var. engieri. Each corolla lobe is beset with either one or two foveae. Foveae are naked or either partly or wholly fimbriated along their margins. No vascular tissue was observed entering the foveae. The taxonomic importance of the the floral character states is discussed.     

Phylogeny of Higher Taxa in Insecta: Finding Synapomorphies in the Extant Fauna and Separating Them from Homoplasies

Most currently applied systematic methods use post-groundplan character states to reconstruct phylogenies in modern higher Insecta/Arthropoda taxa. But, this approach is unable to separate synapomorphies from frequently occurring homoplasies. Conflicting, unresolved and unrealistic higher-level phylogenies result. The reasons are analyzed. A contrasting “groundplan” method, long used in Vertebrata and found to be superior in resolving higher-level phylogenies, is described. This method, as used for insects, uses a highly diversified morphological organ system (such as limb/wing), identifies its homologues in all subphyla and classes, records the full history of its character transformation series in all lineages from the shared Paleozoic ancestor to modern times, pursues the full homologization of its character states in all modern orders, and verifies these data with evidence from other fields of biology. Only such an extremely broad dataset provides the complex information needed to identify and homologize the groundplan character states in modern orders and other higher taxa in the insect/arthropod fauna. After this is accomplished, the gate to recognizing higher-level synapomorphies is open. Only groundplan-level character states include distinct synapomorphies, since homoplasies are either absent or easily detectable. Examples are given. The interpretations of higher phylogenies and evolutionary processes in Hexapoda, based on the unpredictable and often misleading post-groundplan character states found in extant, Tertiary and Mesozoic fauna, are critically compared with those based on the evolution of organ systems, by using the groundplan method.     

The threefold parallelism of Agassiz and Haeckel,and polarity determination in phylogenetic systematics

A parallel exists between the threefold parallelism of Agassiz and Haeckel and the three valid methods of polarity determination in phylogenetic systematics. The structural gradation among taxa within a linear hierarchy, ontogenetic recapitulation, and geological succession of the threefold parallelism resemble outgroup comparison, the ontogenetic method, and the paleontological method, respectively, which are methods of polarity determination in phylogenetic systematics. The parallel involves expected congruence among similar components of the distribution of character states among organisms. The threefold parallelism is a manifestation of a world view based on linear hierarchies, whereas polarity determination is part of the methodology of phylogenetic systematics which assumes that organisms are grouped into a nested hierarchy. The threefold parallelism facilitated the ranking of previously established taxa into linear hierarchies consisting mostly of paraphyletic groups. In contrast, methods of polarity determination identify apomorphies that determine and diagnose monophyletic taxa (clades) in the nested genealogical hierarchy. Taxa in linear hierarchies are defined by sets of character states, whereas clades are defined by common ancestry. Although the threefold parallelism was ostensibly abandoned with the rejection of Haeckel's biogenetic law, some of its components continue to facilitate the progressive scenarios that are common in evolutionary thought. Although a general view of progression in organismal history may be invalid, the progressive or directional sequence of character state changes that results in the characterization of a particular clade has considerable heuristic value. Agassiz's ostensibly nested hierarchy and other pre-Darwinian classifications do not provide support for the view that the natural system can be discovered without recourse to the principle of common descent.     

Morphological diversity of the skeletal structures of fleas (Siphonaptera). Part 4: The general characteristic and features of the abdomen

Characters of 25 abdominal structures were analyzed in the fleas of 96 genera representing over 90% of the world fauna. It was shown that different flea taxa could be described based on 16 universal and 12 specific characters, whose 108 states reflect the entire known diversity of the flea abdominal morphology. Of them, 16 characters with 39 states are formulated based on universal terms. Five universal characters with 13 states describe the proportions of various structures, and also the proportions and shapes of their sclerites; 17 specific characters with 69 states describe the structure of the skeletal elements and the patterns of their junctions. Judging by the number of characters (14) and their states (69), the most evolutionarily flexible structures in fleas are the inner sclerites and anchoring structures of the aedeagus, sternite IX in males, and also the spermatheca and tergite I in females. The character states reflecting the possible phylogenetic closeness of taxa comprise 39%, while 61% of the abdominal character states are homoplasies.     

On phylogenetic tests of irreversible evolution

"Dollo's law" states that, following loss, a complex trait cannot reevolve in an identical manner. Although the law has previously fallen into disrepute, it has only recently been challenged with statistical phylogenetic methods. We employ simulation studies of an irreversible binary character to show that rejections of Dollo's law based on likelihood-ratio tests of transition rate constraints or on reconstructions of ancestral states are frequently incorrect. We identify two major causes of errors: incorrect assignment of root state frequencies, and neglect of the effect of the character state on rates of speciation and extinction. Our findings do not necessarily overturn the conclusions of phylogenetic studies claiming reversals, but we demonstrate devastating flaws in the methods that are the foundation of all such studies. Furthermore, we show that false rejections of Dollo's law can be reduced by the use of appropriate existing models and model selection procedures. More powerful tests of irreversibility require data beyond phylogenies and character states of extant taxa, and we highlight empirical work that incorporates additional information.     

Morphological diversity of the skeletal structures of fleas (Siphonaptera). Part 2: The general characteristic and features of the thorax

Analysis of a considerable amount of data on the anatomy of 27 structures of the thorax in 96 genera of fleas (over 90% of the genera in the world fauna) shows that different flea taxa can be described based on 48 universal and specific characters, whose 203 states reflect the entire known diversity of the flea morphology. Of them, 26 characters with 96 states can be formulated based on universal terms; 22 universal characters with 88 states describe the proportions of the segments and their parts, and also proportions and shapes of their sclerites; 23 specific characters with 107 states describe the structure of the thoracic sclerites and ridges as well as the patterns of their junctions. Judging by the number of characters and their states, the most evolutionarily flexible structures in fleas are the mesosternite and its apodeme together with the upper part of the mesopleural rod. Homoplasies at various levels comprise less than half (40%) of all the character states in the thorax structure. The character states reflecting the phylogenetic closeness of taxa make up about 15%.     

Morphometric variation in the hominoid orbital aperture: a case study with implications for the use of variable characters in Miocene catarrhine systematics

Variable characters are ubiquitous in hominoid systematics and present a number of unique problems for phylogenetic analyses that include extinct taxa. As yet, however, few studies have quantified ranges of variation in complex morphometric characters within extant taxa and then used those data to assess the consistency with which discrete character states can be applied to poorly represented fossil species. In this study, ranges of intrageneric morphometric variation in the shape of the hominoid orbital aperture are estimated using exact randomization of average pairwise taxonomic distances (ATDs) derived from size-adjusted centroid, height-width, and elliptic Fourier (EF) variables. Using both centroid and height-width variables, 19 of the 21 possible ATDs between individuals representing seven extinct catarrhine taxa (Aegyptopithecus, Afropithecus, Ankarapithecus, Ouranopithecus, Paranthropus, Sivapithecus and Turkanapithecus) can be observed within a single extant hominoid subspecies, although generally with low probabilities. A resampling study is employed as a means for gauging the effect that this intrataxonomic variation may have on the consistency with which discrete orbital shape character states can be delimited given the small sample sizes available for most Miocene catarrhine taxa preserving this feature (i.e., n=1). For each type of morphometric variable, 100 cluster (UPGMA) analyses of pairwise ATDs are performed in which a single individual is randomly selected from each hominoid genus and analyzed alongside known extinct taxa; consensus trees are computed in order to obtain the frequencies with which different shape clusters appeared in each of the three analyses. The two major clusters appearing most frequently in all three consensus trees are found in only 57% (centroid variables), 49% (height-width variables), and 36% (EF variables) of these trees. If ranges of variation within represented extinct taxa could also be estimated, these frequencies would certainly be far lower. Hominoids clearly exhibit considerable intrageneric, intraspecific, and even intrasubspecific variation in orbit shape, and substantial morphometric overlap exists between taxa; consequently, discrete character states delimiting these patterns of continuous variation are likely to be highly unreliable in phylogenetic analyses of living and extinct species, particularly as the number of terminal taxa increases. Morphological phylogenetic studies of extant catarrhines that assess the effect of different methods (e.g., use of objective a priori weighting or frequency coding of variable characters, inclusion vs. exclusion of variable characters, use of specific vs. supraspecific terminal taxa) on phylogenetic accuracy may help to improve the techniques that systematists employ to make phylogenetic inferences about extinct taxa.     

Geometric and traditional morphometrics for the assessment of character state identity: multivariate statistical analyses of character variation in the genus Arrenurus (Acari,Hydrachnidia, Arrenuridae)

Geometric and traditional morphometric approaches are tested to describe and reveal taxonomic characters and character states in variation of shape and size of idiosoma morphology in the Arrenuridae. Patterns of variation of idiosoma and glandularia features of males from 11 Mexican species of Arrenurus (Megaluracarus) and two species of subgenus Dadayella were explored with five landmark configurations and three sets of interlandmark distances. Separate principal component analyses (PCA) and canonical variate analyses (CVA) were performed for each data set. The eight multivariate analyses of variance among 13 a priori groups (species) detected significantly different morphometric variants, which were interpreted as different taxonomic character states. Patterns of character state similarity among species were examined with unweighted‐pair grouping method using averages (UPGMA) cluster analyses on Mahalanobis distances. Analyses of five landmark configurations revealed important taxonomical variation in the anterior idiosoma outline (10 character states), the outline of the posterior region or cauda (13 states), the distribution of postocularia, and the second and third pairs of dorsoglandularia (nine states), the fourth pair of dorsoglandularia (three states), and ventroglandularia on the posterior side of idiosoma (nine character states). Multivariate analyses of three sets of distance measurements also resulted in the detection of potential taxonomic characters related to idiosoma size (12 character states), postocularia and dorsoglandularia (13 states), and ventroglandularia (nine character states). Morphometric analyses of distances and shapes provide a formal basis for the interpretation of taxonomic characters, and for the discovery of character states. These characters should be investigated further in a wider sample of species for the phylogenetic systematics of these water mites. In the meantime, idiosoma regions and structures were tested for congruence in a phylogenetic analysis, and were proposed as homologous among the species sampled.     

A cladistic analysis of Hydrophis subgenus Chitulia (McDowell, 1972) (Serpentes, Hydrophiidae)

The Hydrophis subgenus Chitulia was analysed using the computer program Hennig86 (version 1.5). The character data set comprises 22 two-state characters, giving a minimum of 22 steps. Four trees with a length of 37 steps and a consistency index of 0.59 were found using the "ie*" option. The results indicate that the subgenus Chitulia is paraphyletic, and that the group has been based solely on plesiomorphic character states. The order of taxa input, the display of the root, and the effect of unknown character states using Hennig86 are commented on.     

Generalization of the Lotka-Volterra equation]

A complete qualitative study of Lotka--Volterra model with cooperative interactions in the system predator-prey is carried out. The model is as follows: (see abstract). The character of all possible stationary states is investigated in the first quadrant of the phase plane of the model variables depending on the system parameters. It is shown that for the generalized model considered unstable and stable limit cycles only of the infinite amplitude are possible in the first quadrant.