Extensions and improvements to the chordal graph approach to the multistate perfect phylogeny problem

The multistate perfect phylogeny problem is a classic problem in computational biology. When no perfect phylogeny exists, it is of interest to find a set of characters to remove in order to obtain a perfect phylogeny in the remaining data. This is known as the character removal problem. We show how to use chordal graphs and triangulations to solve the character removal problem for an arbitrary number of states, which was previously unsolved. We outline a preprocessing technique that speeds up the computation of the minimal separators of a graph. Minimal separators are used in our solution to the missing data character removal problem and to Gusfield's solution of the perfect phylogeny problem with missing data.     

景观特征评估—LCA体系与HLC体系比较研究与启示

发端于英国的LCA和HLC这2套体系日益成为景观特征评估的重要方法和工具。从发展历程、方法步骤及其在不同尺度上的实践与应用等方面比较分析,发现LCA体系在跨国区域、国家尺度上的景观特征类型识别与区划具有明显优势,评估结果能包容更多的景观特征,但公众参与评估的深度和对景观历史维度的关注存在局限;HLC专注于历史景观的特征识别,在地方行政和场地尺度上对景观演变和历史景观特征类型识别优于LCA体系,但评估结果不及后者全面,二者存在互补性。合理借鉴和融合2套体系,进行景观特征类型识别和区划,将有助于指导中国国土景观、乡村景观的合理管护和利用。     

Character compatibility of molecular markers to distinguish asexual and sexual reproduction

Particularly in polyploids, the potential of the high variability of dominant markers such as random amplified polymorphic DNA fragments (RAPDs) and amplified fragment length polymorphisms (AFLPs) in population genetic studies and analysis of breeding systems is reduced due to their dominant nature. In contrast, the criterion of character compatibility is hindered neither by dominance nor by polyploidy as allelic interpretation is not necessary. Character compatibility, which can be used to detect events of genetic exchange (or recombination), is particularly informative if these events are expected to be rare such as in taxa with extensive vegetative reproduction or apomixis. Binary unordered characters such as presence and absence of anonymous DNA markers are incompatible if all four pairwise combinations of character states are present among the individuals studied. Because incompatible character state distributions defy any progenitor–derivative relationship among individuals, they provide strong evidence for genetic exchange. Both the absolute number of incompatible character combinations and the probability of compatibility can be used as a measure of incompatibility. Although these measures may not directly relate to the frequency of genetic exchange, they provide a useful tool to heuristically explore data sets. The most commonly used input for multivariate analyses and analysis of molecular variance in population genetic studies of (dis)similarity of marker distributions are amalgamates of mutation and recombination. Character compatibility can be used to complement these traditional methods of analysis. Advantages and disadvantages of character incompatibility relative to multilocus analysis of modes of reproduction and population genetics are demonstrated with data from RAPDs, isozymes, and restriction fragment length polymorphisms (RFLPs) of the nuclear ribosomal and chloroplast genome.     

Trends in the evolution of dicotyledonous seeds based on character associations, with special reference to pachychalazy and recalcitrance

VON TEICHMAN, I. & VAN WYK, A. E., 1991. Trends in the evolution of dicotyledonous seeds based on character associations, with special reference to pachychalazy and recalcitrance. The possible evolutionary status of the endothelium, hypostase, pachychalaza and the recalcitrant viability behaviour of seeds is considered in relation to bitegmy/unitegmy, crassinucellate/tenuinucellate ovules, nuclear/cellular endosperm development, large/small seed size, woody/herbaceous habit and tropical/temperate habitat. The presence of the endothelium, hypostase, pachychalaza and recalcitrance in dicotyledonous families is plotted against Dahlgren's system of classification. Results are compared with Sporne's advancement index for the various families. An endothelium is considered derived since it occurs more often in highly evolved superorders and is significantly associated with derived ovule and endosperm character states as well as with smaller seed size. A hypostase appears to be relatively ancestral and is significantly associated with pachychalazy and recalcitrance. The endothelium and hypostase have developed independently in many taxa and could be interpreted as being structurally and functionally analogous. Pachychalazy and recalcitrance are significantly associated with ancestral ovule character states and, at the species level, with large seed size (overgrown seed), woody habit and tropical habitat. The presence of pachychalazy, recalcitrance and associated large seed size are therefore regarded as ancestral character states of the dicotyledons. Consideration of currently accepted dicta on seed character state polarity, suggests a reversal in the evolutionary status of pachychalazy and large seed size.     

The evolution of pelvic osteology and soft tissues on the line to extant birds (Neornithes)

Substantial differences in pelvic osteology and soft tissues separate crown group crocodylians (Crocodylia) and birds (Neornithes). A phylogenetic perspective including fossils reveals that these disparities arose in a stepwise pattern along the line to extant birds, with major changes occurring both within and outside Aves. Some character states that preceded the origin of Neornithes are only observable or inferable in extinct taxa. These transitional states are important for recognizing the derived traits of neornithines. Palaeontological and neontological data are vital for reconstructing the sequence of pelvic changes along the line to Neornithes. Soft tissue correlation with osteological structures allows changes in soft tissue anatomy to be traced along a phylogenetic framework, and adds anatomical significance to systematic characters from osteology. Explicitly addressing homologies of bone surfaces reveals many subtleties in pelvic evolution that were previously unrecognized or implicit. I advocate that many anatomical features often treated as independent characters should be interpreted as different character states of the same character. Relatively few pelvic character states are unique to Neornithes. Indeed, many features evolved quite early along the line to Neornithes, blurring the distinction between 'avian' and 'non-avian' anatomy.     

Quantitative genetic variability maintained by mutation-stabilizing selection balance: sampling variation and response to subsequent directional selection

A model of genetic variation of a quantitative character subject to the simultaneous effects of mutation, selection and drift is investigated. Predictions are obtained for the variance of the genetic variance among independent lines at equilibrium with stabilizing selection. These indicate that the coefficient of variation of the genetic variance among lines is relatively insensitive to the strength of stabilizing selection on the character. The effects on the genetic variance of a change of mode of selection from stabilizing to directional selection are investigated. This is intended to model directional selection of a character in a sample of individuals from a natural or long-established cage population. The pattern of change of variance from directional selection is strongly influenced by the strengths of selection at individual loci in relation to effective population size before and after the change of regime. Patterns of change of variance and selection responses from Monte Carlo simulation are compared to selection responses observed in experiments. These indicate that changes in variance with directional selection are not very different from those due to drift alone in the experiments, and do not necessarily give information on the presence of stabilizing selection or its strength.     

On the Three-Taxon Approach to Parsimony Analysis

The following three basic defects for which three-taxon analysis has been rejected as a method for biological systematics are reviewed: (1) character evolution is a priori assumed to be irreversible; (2) basic statements that are not logically independent are treated as if they are; (3) three-taxon statements that are considered as independent support for a given tree may be mutually exclusive on that tree. It is argued that these criticisms only relate to the particular way the three-taxon approach was originally implemented. Four-taxon analysis, an alternative implementation that circumvents these problems, is derived. Four-taxon analysis is identical to standard parsimony analysis except for an unnatural restriction on the maximum amount of homoplasy that may be concentrated in a single character state. This restriction follows directly from the basic tenet of the three-taxon approach, that character state distributions should be decomposed into basic statements that are, in themselves, still informative with respect to relationships. A reconsideration of what constitutes an elementary relevant statement in systematics leads to a reformulation of standard parsimony as two-taxon analysis and to a rejection of four-taxon analysis as a method for biological systematics.     

How to identify (as opposed to define) a homoplasy: examples from fossil and living great apes

There is much debate on the definitions of homoplasy and homology, and on how to spot them among character states used in a phylogenetic analysis. Many advocate what I call a "processual approach," in which information on genetics, development, function, or other criteria help a priori in identifying two character states as homologous or homoplastic. I argue that the processes represented by these criteria are insufficiently known for most organisms and most characters to be reliably used to identify homoplasies and homologies. Instead, while not foolproof, phylogeny should be the ultimate test for homology. Character states are assumed to be homologous a priori because this is falsifiable and because their initial inclusion in the character-state analysis is based on the assumption that they may be phylogenetically informative. If they fall out as symplesiomorphies or synapomorphies in a phylogenetic analysis, their status as homologies remains unfalsified. If they fall out as homoplasies, having evolved independently in more than one clade, their status as homologous is falsified, and a homoplasy is identified. The character-state transformation series, functional morphology, finer levels of morphological comparison, and the distribution and correlation of characters all help to explain the presence of homoplasies in a given phylogeny. Explaining these homoplasies, and not ignoring them as "noise," should be as much a goal of phylogenetic analysis as the production of a phylogeny. Examples from the fossil record of Miocene hominoids are given to illustrate the advantages of a process-informs-pattern-recognition-after-the-fact approach to understanding the evolution of character states.     

Burning Straw Men Sheds Little Light: a Reply to Whiting and Kelly

Wilkinson (1991a) developed arguments that the distributions of primitive character states may delimit clades, and proposed a method that exploited the evidence of primitive character state distributions for inferring clades. Whiting and Kelly (1995) presented a critique of these ideas, arguing that they are logically incoherent and that the method does not succeed in its aims. This critique severely misrepresents the original arguments and the method, and amounts to no more than an attack on a straw man.     

Propensity of a circadian clock to adjust to the 24h day-night light cycle and its sensitivity to molecular noise

The circadian clock of Drosophila melanogaster and its tendency to adjust to the day-night light cycle is simulated by deterministic and stochastic methods. The robustness of the locking to the light-cycle with respect to molecular noise is studied. It is found that within the model studied, the molecular noise in the stochastic simulation erases the finer injection-locking structures, stronger injection signals are needed and the locking has the character of prolonged locked time intervals with cycle slips in between. The simulations are compared to a simple injection-locking model with noise that seems to describe the overall behavior well.     

The geometric mean length, a new statistic to describe the distribution of character steps on a tree

The geometric mean length (GML) is proposed as a new statistic aimed at describing the evenness of character changes on a tree for a given set of character optimizations. It is the geometric mean of the number of steps on each branch of the tree, varying between a maximum value when all branch lengths are equal, and a minimum value when all branches but one have only one character step. It can be scaled according to its theoretical maximum value, thus indicating a relative GML that allows a comparison of the evenness of character steps between different tree topologies.     

Phenotypic plasticity to light intensity in Arabidopsis thaliana: invariance of reaction norms and phenotypic integration

Phenotypic plasticity (the pattern of response of organisms to changes in environmental conditions) and phenotypic integration (the pattern of character correlations) are important components of our understanding of the evolution of complex phenotypes. Most studies published so far in this area have been conducted within populations with the express aim of predicting future response to evolutionary forces. However, among-population differentiation for plasticity and trait correlations are important indicators of recent past events that have shaped the currently observable phenotypes. We investigated variation in the reaction norms of several traits in a large number of accessions of Arabidopsis thaliana exposed to different levels of light quantity as well as the environmental lability of the corresponding across-population character variance–covariance matrix. Our results show that there is an astounding degree of inter-population variation for character means and very little variation for plasticity, in agreement with the idea that A. thaliana is a light-specialist often occurring in open, disturbed habitats. However, this plant also shows patterns of plasticity that are predicted to be adaptive based on functional ecological considerations, such as an increase in either specific leaf area or leaf number (but not both) under low light. We also demonstrate that the set of character correlations in A. thaliana is extremely stable to changes in light availability, contrary to previous findings in the same species when different environmental factors were considered. Several processes that might have been responsible for the observed patterns are discussed as a prelude to follow-up research on these problems.     

The composition and physicochemical properties of the blood lipoproteins in rats exposed to external gamma irradiation]

Content of lipids, character of chemiluminescence of blood plasma and certain classes of lipoproteins have been studied. Geometrical parameters, nature and quantity of charged groups of lipoprotein particles accessible for titration have been determined 1 and 30 days after a single external gamma irradiation of rats in a dose of 3 Gy. The used irradiation dose exerts an expressed hyperlipidemic effect retained for one month after irradiation. The disturbances in the spectrum of blood lipids and lipoproteins are of hyper-beta and hyper-prebeta lipoproteinemia character. Considerable disturbances of physicochemical properties of different classes of lipoproteins have been detected. They are exhibited in changes of the pattern of free-radical processes, state of the charge of surface ionogenic groups and geometrical parameters of lipoprotein particles. Changes registered by the methods of potentiometric titration and correlation spectroscopy are most expressed in lipoproteins of very low density and those of low density.     

A comparative study of the diagnostic value of polyclonal and monoclonal antibodies to human IgM in immunoenzyme diagnostic agents]

Monoclonal antibodies (McAb) to human IgM, capable of recognizing antigenic determinants of different character, have been obtained. Three type-specific McAb have been used in diagnostic systems for the determination of specific IgM antibodies in the sera of patients with hepatitides A and B. The affinity constant and high specificity of McAb have made it possible to change affinity-purified polyclonal antibodies to heavy chains of IgM for the gamma fraction of hybridoma-induced ascitic fluids without decreasing the sensitivity and specificity of test systems. The main advantages of McAb are the standard character of the reagent and reproducibility of its properties.     

Problematic character coding methods in morphology and their effects

The effects of different coding practices in morphological phylogenetic analysis are well documented. In many cases, we can determine that certain practices can be regarded as undesirable and should be avoided. Certain coding practices do not correctly translate the expected information to the cladistic algorithm. It may go unnoticed that expressions of character information in character lists, which may be entirely logical to any reader, do not necessarily reflect the mathematics employed by a phylogenetic algorithm. Despite a wealth of literature on coding procedures and documentation of these issues, problematic character coding practices are still common. A review is provided of different coding and character formulation practices, particularly relating to multistate character information that may either: (1) lead to a failure to capture grouping information implied in the character list; (2) cause problematic weighting or spuriously high certainty in particular optimizations; and (3) impose congruence artificially, by linking more than one variable character to a particular state. Each of these is reviewed and presented with a hypothetical example. Recommendations for avoiding these pitfalls are described in light of how parsimony algorithms work with character data. Character lists must be drawn up not only to present character variation logically, but also with consideration for how computer algorithms implement cladistic logic. The widespread use of problematic character coding procedures may account for some of the perceived problems with morphological data. Therefore, an exploration of the effects of these methods and standardization of methods should be a goal for the very near future. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 489–498.     

Are Polyphaga (Coleoptera) really a basal neopteran lineage – a reply to Kazantsev

In a study on the mandible and mandibular articulation of larvae of the lycid genus Platerodrilus Kazantsev proposes a phylogenetic scheme with Polyphaga as a basal group of Neoptera and Lycidae as a basal group within Polyphaga. Here we point out different problems with his interpretation. The taxon sampling was not sufficient. The characters of endopterygote larvae cannot be compared to characters of adults in a phylogenetic context. The neotenic characters of female and adult male Lycidae are not sufficiently taken into account. A phylogenetic hypothesis should be based on multiple character systems and all available data must be considered. Kazantsev based his conclusions on a single isolated character complex. His hypothesis is in deep conflict with a phylogeny based on the molecular data, which clearly show that Lycidae are nested within Elateroidea. The molecular and morphological evidence also implies that females are aberrant neotenic forms and by no means ‘primitive’. Kazantsev's hypothesis is problematic because the presented data are insufficient and the character evaluation is not based on a numerical analysis.