Power of the concentrated changes test for correlated evolution

The concentrated changes test (CCT) calculates the probability that changes in a binary character are distributed randomly on the branches of a cladogram. This test is used to examine hypotheses of correlated evolution, especially cases where changes in the state of one character influence changes in the state of another character. The test may be sensitive to the addition of branches that lack either trait of interest (white branches). To examine the effects of the proportion of white branches and of tree topology on the CCT probability, we conducted a simulation analysis using a series of randomly generated 100-taxon trees, in addition to a nearly perfectly balanced (symmetrical) and a completely imbalanced (asymmetrical) 100-taxon tree. Using two models of evolution (gains only, or gains and losses), we evolved character pairs randomly onto these trees to simulate cases where (1) characters evolve independently (i.e., no correlation among the traits) or (2) all changes in the dependent character occur on branches containing the independent trait (i.e., a strong correlation among the traits). This allowed us to evaluate the sensitivity of the CCT to type I and type II errors, respectively. In the simulations, the CCT did not appear to be overly sensitive to the inclusion of white branches (low likelihood of type I error with both CCT probabilities < 0.05 and < 0.01). However, the CCT was susceptible to type II error when the proportion of white branches was < 20%. The test was also sensitive to tree shape and was positively correlated to Colless's tree imbalance statistic I. Finally, the CCT responded differently for simulations where only gains were allowed and those where both gains and losses were permitted. These results indicate that the CCT is unlikely to detect a correlation between characters when no such correlation exists. However, when a trait can be gained but not lost, the CCT is conservative and may fail to detect true correlations among traits (increased type II error). Determination of the sampling universe (the taxa included in the comparative analysis) can strongly influence the probability of making such type II errors. We suggest guidelines to circumvent these limitations.     

ON CONSENSUS, COLLAPSIBILITY, AND CLADE CONCORDANCE

Abstract — Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter-cladogram character conflict for all characters among a set of cladograms.     

Two Requirements for Obtaining Valid Common Patterns under Different Assumptions in Vicariance Biogeography

In vicariance biogeography, widespread or sympatric taxa can be dealt with under assumptions 0, 1, and 2. Data from cladogenetic relationships among taxa of a monophyletic group and their distribution over areas are assumed, in the order 0 → 1 → 2, to represent decreasing information about vicariance events. A less strict assumption carries a larger solution set, i.e., the number of possible area cladograms increases with the decrease in strictness of the assumption applied. We formulate two requirements for obtaining valid general area cladograms from data of several monophyletic groups of taxa. First, the assumptions, and with them the sets of area cladograms derived under these assumptions, should be inclusive. Second, sets of single group area cladograms should be compared for different monophyletic groups under a single assumption. When these two requirements are met, area cladograms become consistent with respect to the processes (vicariance, extinction, and dispersal) that are a priori assumed. The explanatory power increases for any particular monophyletic group of taxa when the set of valid general area cladograms contains a subset of area cladograms derived under a more strict assumption. We discuss examples from literature of how violation of these two requirements affects the results.     

Necessary and sufficient conditions for the existence of certain quadratic invariants under a phylogenetic tree.

Invariants are functions of the probabilities of state configurations among lineages, with expected values equal to zero under certain phylogenies. For two-state sequences, the existence of certain quadratic invariants requires a symmetric substitution model. For sequences with more than two states, the necessary condition for the existence of certain quadratic invariants in terms of independent events is much stronger than symmetry. For DNA sequences, only three parameters are allowed in the substitution model, which includes Kimura's two-parameter model as a special case.     

Using a nonrecursive formula to determine cladogram probabilities

Three properties of bifurcating branching diagrams that are used for representing a specific number of taxa are (1) the number of possible arrangements, (2) the number of possible topologies, and (3) the probabilities of formation according to particular models of cladogenesis. Of these, the probabilities have received the least attention in the literature. Indeed, many biologists would be astonished by the observation that the probability of a commonly cited cladogram containing 35 phyla of the animal kingdom is < 0.0072% of the value of the average probability taken over all possible cladograms! We reviewed works on cladogram arrangements and topologies and developed a computer-generated table of enumerations that extends and corrects such tables in the literature. We also developed a nonrecursive formula for the determination of cladogram probabilities. This formula facilitates calculation and thereby should promote use of cladogram probabilities, which might provide more accurate null hypotheses for tests of cladogenic events than do considerations of cladogram arrangements or topologies.     

A Model of Cell Cleavage

A model is presented which describes, at least to a first approximation, the oserved changes in cell shape and the movement of surface markers associated with cleavage in some types of cells. The model postulates that the constraints governing cell cleavage are minimum surface area and constancy of cell volume. Equations are derived both for the case of symmetric as well as the case of asymmetric cleavage. It is pointed out that the generally symmetric character of cell cleavage is explicable if there is a positive correlation between internal cell pressure and the radii of curvature.     

The Relationship between Corvis ST Tonometry Measured Corneal Parameters and Intraocular Pressure,Corneal Thickness and Corneal Curvature

The purpose of the study was to investigate the correlation between Corneal Visualization Scheimpflug Technology (Corvis ST tonometry: CST) parameters and various other ocular parameters, including intraocular pressure (IOP) with Goldmann applanation tonometry. IOP with Goldmann applanation tonometry (IOP-G), central corneal thickness (CCT), axial length (AL), corneal curvature, and CST parameters were measured in 94 eyes of 94 normal subjects. The relationship between ten CST parameters against age, gender, IOP-G, AL, CST-determined CCT and average corneal curvature was investigated using linear modeling. In addition, the relationship between IOP-G versus CST-determined CCT, AL, and other CST parameters was also investigated using linear modeling. Linear modeling showed that the CST measurement ‘A time-1’ is dependent on IOP-G, age, AL, and average corneal curvature; ‘A length-1’ depends on age and average corneal curvature; ‘A velocity-1’ depends on IOP-G and AL; ‘A time-2’ depends on IOP-G, age, and AL; ‘A length-2’ depends on CCT; ‘A velocity-2’ depends on IOP-G, age, AL, CCT, and average corneal curvature; ‘peak distance’ depends on gender; ‘maximum deformation amplitude’ depends on IOP-G, age, and AL. In the optimal model for IOP-G, A time-1, A velocity-1, and highest concavity curvature, but not CCT, were selected as the most important explanatory variables. In conclusion, many CST parameters were not significantly related to CCT, but IOP usually was a significant predictor, suggesting that an adjustment should be made to improve their usefulness for clinical investigations. It was also suggested CST parameters were more influential for IOP-G than CCT and average corneal curvature.     

Comparative and phylogenetic analysis of developmental sequences

Event pairing has been proposed for the optimization of developmental sequences (event sequences) on a given phylogenetic hypothesis (cladogram) to determine instances of sequence heterochrony. Here, we show that event pairing is faulty, leading to the optimization of impossible hypothetical ancestors, the underestimation of the lengths of the developmental sequences on the tree, and the proposition of synapomorphies that are not supported by the data. When used for phylogenetic analysis, event pairing can even produce cladograms that are inconsistent with the data. These errors are caused by the fact that event pairing treats dependent features as if they were independent. We present a new method for comparative and phylogenetic analysis of developmental sequences that does not exhibit these errors. Our method applies Search-based character optimization and treats the entire developmental sequence as a single character that is then analyzed by using an edit cost function, which specifies the transformation cost between pairs of observed and unobserved character states, and dynamic programming. In other words, the developmental sequence is directly optimized on the tree. We used event pairing as an edit cost function, but others are possible.     

CHARACTER DEFINITIONS AND CHARACTER STATE DELINEATION: THE BETE NOIRE OF PHYLOGENETIC INFERENCE

Abstract— Currently characters are static concepts whose definition and state delineations seldom undergo any scrutiny. Common systematic practice tends to synthesize character slates by combining or dividing observed conditions, a situation most likely due to current theoretical limitations in phylogenetic inference, which tends to ignore problems of multistate characters. This process we refer to as the “synthetic” method for character definition. Character definitions derived for the genera of North American Cochylini (Lepidoptera: Tortricidae) using “synthetic” character states postulated that the cochylines were not monophyletic. The use of cladogram characters and nearest neighbor matrices in uncovering potential flaws in character state delineation is demonstrated. The “synthetic” set of character definitions proved deficient upon such analysis, principally due to its attempt to force highly variable features into a few states. The set of character definitions produced from this analysis is referred to as “reflective” because it does not ignore observed variation. It produces characters with many states and presents problems of setting up transformation series. Three means lor deriving transformations are applied to produce transformation series for the reflective set of character definitions: the unordered outgroup method, morphocline analysis and Transformation Series Analysis (TSA). All three data sets postulated the Cochylini as monophyletic. The three sets of phylogenies were compared. Consensus trees are ambiguous when analysing changes in hierarchy. In order to summarize these results in a manner which does not destroy the phylogenetic structure, positional subtrees, a new means for summarizing multiple solution cladograms, are introduced. It was found that all three sets of transformations produced very different cladograms which in turn were very different from the tree produced by the original, synthetic definitions. The results of each of these methods were assessed for their internal consistency. TSA gave the least contradictory results.     

A Hypothesis-Independent Method of Character Weighting for Cladistic Analysis

Abstract— A hypothesis-independent method of weighting cladistir characters, based on character compatibility, is proposed. The method is used in two fashions, to generate cladograms, and to select from multiple minimum length cladograms. To illustrate the techniques, published data on Hoplinema (Coleoptera) are reanalysed. The method is contrasted with other weighting techniques which arc generally found to be hypothesis dependent.     

Asymmetric facilitation can reduce size inequality in plant populations resulting in delayed density‐dependent mortality

Size inequality in plant populations is a ubiquitous feature that has received much attention due to ecological and evolutionary implications. The mechanisms driving size inequality were mainly attributed to different modes of competition (symmetric versus asymmetric), while the potential effects of different modes of facilitation (symmetric versus asymmetric) to this pattern have not yet been fully explored. We employed an individual‐based model to explore the relative roles of both competition and facilitation simultaneously along an environmental stress gradient. Special emphasis was given to the assessment of symmetric facilitation (plants receive benefit from each other equally or proportionally to benefactors’ sizes) and asymmetric facilitation (beneficiary plants receive benefits from benefactor plants that are higher than proportional to the benefactors’ size) in altering plant size inequality. We found that independent of the particular mode of competition, symmetric facilitation generally increased size inequality, whereas asymmetric facilitation decreased it. This pattern was consistent along the stress gradient. Because of their different effects on size inequality, symmetric facilitation accelerated self‐thinning, whereas asymmetric facilitation delayed the onset of density‐dependent mortality, promoting survival under intermediate stress conditions. We compared our model predictions with both 1) a previous modelling study focusing on the effect of (symmetric) facilitation on the size inequality, and 2) re‐analysed data from a published experiment generating asymmetric facilitation of plants against enhanced ultraviolet‐B (UV‐B). Whereas our model predictions and the results of the empirical experiment were consistent, we found that previous theoretical results that solely relied on symmetric facilitation need to be re‐adjusted. Our study showed that combinations of different modes of competition and facilitation can alter size inequality in different ways and with important consequences for the onset of density‐dependent mortality during population development. Explicitly considering different modes and mechanisms of interactions (both facilitation and competition) will improve mechanistic understanding in plant ecology.     

Hydroxycinnamoyltransferases Involved in the Accumulation of Caffeic Acid Esters in Gametophytes and Sporophytes of Equisetum arvense

Four hydroxycinnamoyltransferases from Equisetum arvense L. were studied that catalyze the formation of mono-O-caffeoyl-meso-tartrate, di-O-caffeoyl-meso-tartrate, 5-O-caffeoylshikimate (dactylifrate), and 5-O-caffeoylquinate (chlorogenate). The enzymes were classified as coenzyme A (CoA)-ester-dependent acyltransferases (EC 2.3.1), i.e. hydroxycinnamoyl-CoA:meso-tartrate hydroxycinnamoyltransferase (CTT), hydroxycinnamoyl-CoA:caf-feoyl-meso-tartrate hydroxycinnamoyltransferase (CCT), hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (CST), and hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase. The CTT, CCT, and CST were partially purified and separated from E. arvense gametophytes by hydrophobic interaction chromatography on Fractogel TSK Butyl-650 followed by molecular exclusion on fast protein liquid chromatography-Superdex-75 with 87-, 62-, and 130- fold enrichments and 12, 8, and 11% yields, respectively. The enzyme activities obtained with caffeoyl-CoA were 95 (CTT), 74 (CCT), and 200 [mu]kat (CST) kg-1 protein. The apparent native relative molecular weight values were found to be approximately 45,000 (CTT), 52,000 (CCT), and 50,000 (CST). Each enzyme showed highest activities at pH 7.5, the CCT and CST in Tris-HCl (1.2 and 1.0 M) and the CTT in imidazole-HCl (1.25 M). Enzyme activities were stimulated more than 3-fold by 100 mM ascorbate. The apparent energies of activation (kilojoules mol-1) were calculated to be 56 (CTT), 69 (CST), and 76 (CCT). The enzymes accepted cinnamoyl-CoA and various hydroxycinnamoyl-CoAs. The time course of the transferase activities along with that of a fourth one, hydroxycinnamoyl-CoA:quinate hydroxycinnamoyltransferase, and the pattern of product accumulation were determined during a 1-year growth period of the E. arvense sporophytes.     

Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis

Chaperonins use ATPase cycling to promote conformational changes leading to protein folding. The prokaryotic chaperonin GroEL requires a cofactor, GroES, which serves as a "lid" enclosing substrates in the central cavity and confers an asymmetry on GroEL required for cooperative transitions driving the reaction. The eukaryotic chaperonin TRiC/CCT does not have such a cofactor but appears to have a "built-in" lid. Whether this seemingly symmetric chaperonin also operates through an asymmetric cycle is unclear. We show that unlike GroEL, TRiC does not close its lid upon nucleotide binding, but instead responds to the trigonal-bipyramidal transition state of ATP hydrolysis. Further, nucleotide analogs inducing this transition state confer an asymmetric conformation on TRiC. Similar to GroEL, lid closure in TRiC confines the substrates in the cavity and is essential for folding. Understanding the distinct mechanisms governing eukaryotic and bacterial chaperonin function may reveal how TRiC has evolved to fold specific eukaryotic proteins.     

When does the incongruence length difference test fail?

This paper examines the efficiency of the incongruence length difference test (ILD) proposed by Farris et al. (1994) for assessing the incongruence between sets of characters. DNA sequences were simulated under various evolutionary conditions: (1) following symmetric or asymmetric trees, (2) with various mutation rates, (3) with constant or variable evolutionary rates along the branches, and (4) with different among-site substitution rates. We first compared two sets of sequences generated along the same tree and under the same evolutionary conditions. The probability of a Type-I error (wrongly rejecting the true hypothesis of congruence) was substantially below the standard 5% level of significance given by the ILD test; this finding indicates that the choice of the 5% level is rather conservative in this case. We then compared two data sets, still generated along the same tree, but under different evolutionary conditions (constant vs. variable evolutionary rate, homogeneity vs. heterogeneity rate of substitution). Under these conditions, the probability of rejecting the true hypothesis of congruence was greater than the 5% given by the ILD test and increased with the number of sites and the degree to which the tree was asymmetric. Finally, the comparison of the two data sets, simulated under contrasting tree structures (symmetric vs. asymmetric) but under the same evolutionary conditions, led us to reject the hypothesis of congruence, albeit weakly, particularly when the number of informative sites was low and among-site substitution rate heterogeneous. We conclude that the ILD test has only limited power to detect incongruence caused by differences in the evolutionary conditions or in the tree topology, except when numerous characters are present and the substitution rate is homogeneous from site to site.     

The unfalsifiability of cladograms and its consequences

Popper's falsificationism provides the normative reference system in recent discussions regarding theory and methodology of systematics. According to Popper, the falsifiability of a hypothesis represents a necessary precondition for its corroborability. It is shown that cladograms, independent of “strict”, “methodological” or “sophisticated” falsification, are not falsifiable in principle. No present observation is prohibited by any tree hypothesis and, thus, no Popperian test of cladograms exists. It is shown that the congruence test, which is commonly said to represent a Popperian test of cladograms, instead tests sets of apomorphy hypotheses. Three different strategies that have been proposed to circumvent this problem are discussed and refuted: (1) referring to Popper's convention to renounce ad hoc maneuvers; (2) referring to Popper's treatment of probability hypotheses; and (3) decoupling corroboration from falsification. As a consequence, within a Popperian framework the unfalsifiability of cladograms implies that cladograms cannot explain any present day observation and, thus, represent metaphysical hypotheses. However, Popper's falsificationism has been criticized and questioned by many philosophers before and it seems to be about time that phylogeneticists develop their own philosophy of phylogenetics that meets their specific requirements of a historical science that is not seeking for universal laws and regularities, but instead reconstructing particular historical events. © The Willi Hennig Society 2007.     

A model of leg coordination in the stick insect,Carausius morosus

Mechanisms dependent upon leg position coordinate the alternate stepping of adjacent ipsilateral and contralateral legs in the stick insect. In this insect, swing duration and step amplitude are independent of walking speed. A simple geometrical model of the leg controller is used here to test different mechanisms for compatibility with these two invariant features. Leg position is the state variable of a relaxation oscillator and position thresholds determine the transitions between swing and stance. The coordination mechanisms alter these thresholds. The position-dependent mechanisms considered differ either in the form or the speed-dependence of the function relating the shift in the posterior threshold of the receiving leg to the position of the sending leg. The results identify parameter combinations leading to alternate stepping with symmetric or asymmetric phase distributions, to shifts in the posterior extreme position as a function of speed, to double stepping or to in-phase stepping. An optimal position-dependent excitatory mechanism is described. Finally the consequences of adding either inhibitory influences or time-dependent excitatory influences are analyzed.     

PHYLOGENY OF THE NEMERTEAN SUBCLASS PALAEONEMERTEA (ANOPLA, NEMERTEA)

Abstract— A cladistic analysis based on 50 morphological characters was performed for 49 of the 98 species currently assigned to the subclass Palaeonemertea (phylum Nemertea), and six additional undescribed species. Thirty-five species were excluded from the parsimony analysis because of the high number of unknowns in the character matrix, and one species since it was considered a nomen nudum . An initial analysis suggested that the subclass Hoplonemertea is the sistergroup to the clade Palaeo- and Heteronemertea and the ingroup cladograms are rooted using a paraphyletic outgroup based on this information. Seventy-two equally most parsimonious cladograms were found; the consistency index was low but tree-length distribution for the character set is skewed to the left, and the cladograms are invariably shorter than trees based on random data. These cladograms suggested a character transformation series for the cerebral organ where this complex character reappeared several times after being absent. We considered this biologically implausible and the final discussion is based on three cladograms, one step longer than the most parsimonious, where the evolution of this character appears to be more realistic. The cladistic analysis indicates that many previously recognized genera (e.g. Cephalothrix, Procephalothrix and Cephalotrichella ), and higher taxa, are paraphyletic. It furthermore indicates that the previously suggested hypothesis of the Archinemertea as a monophyletic sistertaxon to Palaeonemertea is unsupported.     

PHYLOGENIES AND THE ANALYSIS OF EVOLUTIONARY SEQUENCES,WITH EXAMPLES FROM SEED PLANTS

Studies of character evolution have frequently relied on ahistorical correlations rather than on phylogenies. However, correlations do not estimate the number of times that a trait evolved, and they are insensitive to the direction or the temporal sequence of character transformation. In contrast, cladograms can provide this information. A cladistic test of the hypothesis that the evolution of dioecy is favored in animal-dispersed plants indicates that dioecy may have originated somewhat more often in such lineages. Nevertheless, differences in rates of speciation or extinction must largely account for the observed species-level correlation between dispersal and breeding system. In considering the evolution of individual traits, cladograms help identify the context in which a feature evolved and specify which organisms should be compared in evaluating the causes of character change. Determining whether a feature and a performance advantage were strictly historically correlated or followed one another in sequence helps to distinguish whether the trait is an adaptation or an exaptation for the function. For example, cladograms of seed plants suggest that double fertilization arose incidentally prior to the origin of angiosperms and that the resulting product was later co-opted and elaborated as a nutritive tissue for the developing embryo. The order of character assembly in a lineage also bears on the evolution of functional and developmental interdependencies. In particular, it may be possible to trace the evolution of a character's “burden” from an initial period, during which change is more likely, through later stages, wherein successful modification is less likely owing to the evolution of dependent characters. The evolution of vessels and of floral phyllotaxis in angiosperms may exemplify this pattern. Recognition that the likelihood of character transformation may change during the evolution of a group warns against character weighting in phylogenetic analysis.     

Coding polymorphism for phylogeny reconstruction

The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yielding signals that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recommended. This holds for coding polymorphism in species as well as in supraspecific taxa. In this light we remark on methods proposed by previous authors.     

Something for nothing? Reconstruction of ancestral character states in asterinid sea star development

SUMMARY Traits from early development mapped onto phylogenetic trees can potentially offer insight into the evolutionary history of development by inferring the states of those characters among ancestors at nodes in the phylogeny. A key and often-overlooked aspect of such mapping is the underlying model of character evolution. Without a well-supported and realistic model ("nothing"), character mapping of ancestral traits onto phylogenetic trees might often return results ("something") that lack a sound basis. Here we reconsider a challenging case study in this area of evolutionary developmental biology: the inference of ancestral states for ecological and morphological characters in the reproduction and larval development of asterinid sea stars. We apply improved analytical methods to an expanded set of asterinid phylogenetic data and developmental character states. This analysis shows that the new methods might generally offer some independent insight into choice of a model of character evolution, but that in the specific case of asterinid sea stars the quantitative features of the model (especially the relative probabilities of different directions of change) have an important effect on the results. We suggest caution in applying ancestral state reconstructions in the absence of an independently corroborated model of character evolution, and highlight the need for such modeling in evolutionary developmental biology.