Meta-analysis of character utility and phylogenetic information content in cladistic studies of ammonoids

While previous workers have argued persuasively that ammonoid workers should use cladistic approaches to reconstruct phylogeny, relatively few cladistic studies have been published to date. An essential yet challenging part of cladistic analysis is the selection of characters. Are certain types of characters more likely to show homoplasy? Are certain aspects of shell anatomy more likely to contain phylogenetically informative characters? Are datasets with more characters inherently better? To answer these questions, a meta-analysis of character data from published ammonoid phylogenies was performed. I compiled 14 datasets, published between 1989 and 2007, representing parsimony-based phylogenetic analyses of ammonoids. These studies defined a combined total of 323 characters, which were grouped into categories reflecting different aspects of anatomy: shell size and shape, ornament, suture, early ontogeny, body chamber and apertural modifications. Tree searches were re-run to determine overall tree statistics, parsimony permutation tail probability (PTP) tests were calculated to assess the phylogenetic information content of the matrices, and retention and rescaled consistency indices for each character were calculated. My analyses revealed that studies with higher character/taxon ratios did not necessarily produce trees with more information content and less homoplasy, as measured by retention or rescaled consistency indices, because additional characters were often parsimony-uninformative. Rather, studies with relatively few characters could produce high-quality trees if the characters were well-chosen and character states carefully defined. Characters related to the body chamber and adult aperture typically had retention indices of either 0 or 1, rarely in between, indicating that they either worked perfectly or not at all. Suture characters tended to have higher indices than shell shape or ornament characters, suggesting more phylogenetic information and less homoplasy in the suture line than in shell traits. These results should aid in the selection of characters for future cladistic studies of ammonoids.     

HOMOPLASY AND THE CHOICE AMONG CLADOGRAMS

Abstract Cladistic data are more decisive when the possible trees differ more in tree length. When all the possible dichotomous trees have the same length, no one tree is better supported than the others, and the data are completely undecisive . From a rule for recursively generating undecisive matrices for different numbers of taxa, formulas to calculate consistency, rescaled consistency and retention indices in undecisive matrices are derived. The least decisive matrices are not the matrices with the lowest possible consistency, rescaled consistency or retention indices (on the most parsimonious trees); those statistics do not directly vary with decisiveness. Decisiveness can be measured with a newly proposed statistic, DD = − S )/( − S ) (where S = length of the most parsimonious cladogram, = mean length of all the possible cladograms for the data set and M = observed variation). For any data set, can be calculated exactly with simple formulas; it depends on the types of characters present, and not on their congruence. Despite some recent assertions to the contrary, the consistency index is an appropriate measure of homoplasy (= deviation from hierarchy). The retention index seems more appropriate for comparing the fit of different trees for the same data set.     

Morphological, palaeontological and molecular aspects of ichneumonoid phylogeny (Hymenoptera, Insecta)

Ichneumonoid phylogeny is revised on the basis of morphological, palaeontological and molecular evidence. The only previous formal cladistic study of the phylogeny of the families of the superfamily Ichneumonoidea made many assumptions about what families lower taxa belonged to and was based on a very limited set of characters, nearly all of which were uninformative at family level. We have subdivided both Ichneumonidae and Braconidae into major groups, investigated several new character systems, reinterpreted some characters, scored several character states for extinct taxa by examining impression fossils using environment chamber scanning electron microscopy, and included data for a significant new subfamily of Braconidae from Cretaceous amber of New Jersey. Sixteen different variants of the data set were each subjected to parsimony analysis without weighting and with successive approximations weighting employing both maximum and minimum values of both the retention and rescaled consistency indices. Each analysis resulted in one of seven different strict consensus trees. Consensus trees based on subsets of these trees, selected on the basis of the optimal character compatibility index (OCCI), resulted in an eighth distinct tree. All trees had the Braconidae monophyletic with the Trachypetinae as the basal clade, and also had a clade comprising various arrangements of Apozyginae, the Rhyssalinae group, Aphidiinae and 'other cyclostomes', but relationships among the remaining braconid groups varied between trees. Only one of the consensus trees had the Ichneumonidae (including Tanychorella ) monophyletic. The Eoichneumonidae + Tanychora are the sister group the Braconidae in two of the consensus trees. Paxylommatinae were basal in the clade comprising the Eoichneumonidae + Tanychora and the Braconidae. The preferred tree, based on the highest OCCI was used for interpreting character state transitions.     

PARSIMONY AND THE CHOICE BETWEEN DIFFERENT TRANSFORMATIONS FOR THE SAME CHARACTER SET

Abstract— When phylogeneticists choose among alternative hypotheses, they choose the one that requires the fewest ad hoc assumptions, i.e. the one that is the most parsimonious. For some systematists, choosing among alternative transformation series for the same set of taxa is equivalent to attaining trees with shorter length and minimal homoplasy. Homoplasy is shown to be composed of hierarchical discordance and scattering, which are recognized and described for the first time. Neither the consistency nor retention indices can be used in assessing different theories of multistate character transformation because both are affected by the shape of the transformation series rather than the character state distribution on a tree. Fits of transformations to a tree are better assessed by comparing the transformation to the cladogram character and the nearest neighbor network. Nearest neighbor networks are graphical representations of the nearest neighbor matrix. Transformations with the closest greatest number of matches between cladogram characters and the least complexity in the nearest neighbor network are preferred. These transformations are shown to make the fewest number of ad hoc statements and hence to be the most parsimonious. A means for obtaining cladogram characters and nearest neighbor matrices using a widely distributed microcomputer program is presented.     

A COMPUTER ASSISTED ANALYSIS OF THE RELATIONSHIPS OF THE HIGHER CATEGORIES OF TURTLES

Abstract— A character matrix of 39 characters for 14 supregeneric categories of living and extinct turtles was examined using PAUP 2.41 and 3.0L. The Branch and Bound algorithm found a single most parsimonious cladogram of 55 steps, consistency index of 0.709, retention index of 0.848 and a rescaled consistency index of 0.601. The cladogram is identical to that proposed by Gaffney and Meylan (1988). The Pleurodira and Cryptodira are each shown to be monophyletic and are supported by synapomorphies involving complex structures of the basicranium and adductor musculature. These synapomorphies are judged to be relatively well-tested homologies. A paraphyletic Cryptodira occurs in 18% of 38 equally parsimonious trees 57 steps in length, but these trees are based on characters, such as absence of pterygoid teeth, that are susceptible to homoplasy in amniotes. We re-iterate the notion that it is better to choose fewer, well-analysed characters than large numbers of poorly analysed characters.     

Systematics of New World Monkeys (Platyrrhini, Primates) Based on 16S Mitochondrial DNA Sequences: A Comparative Analysis of Different Weighting Methods in Cladistic Analysis

In order to investigate the effects of different weighting methods on a phylogeny reconstruction based on DNA sequences and to evaluate the phylogenetic information content of various secondary structures, a fragment of the large ribosomal mitochondrial gene (16S) was sequenced from 13 species of New World monkeys, three species of catarrhines, and Tarsius. The data were analyzed cladistically without weighting characters or changes, and with different weighting methods: a priori differential weights for transitions and transversions, two variants of dynamic weighting for each kind and direction of change, and successive approximations, using both the character consistency index (CI) and the rescaled consistency index (RC). The results were compared with published trees constructed from nuclear sequences of ε-globins and morphological characters by different authors. The result of the analysis of the mtDNA data set with successive approximations, using the RC as weighting function, was the closest to the topology on which all molecular and morphological trees concur. Other relationships were unique to this tree. "Loops" were the type of secondary structure that showed maximum variation in sequence length and sites with the lowest character CI and RC. A large number of sites within loops showed high values for these indices, however, which suggests that uniform downweighting of these regions represents a large loss of phylogenetic information. Successive weighting, which assigns a weight for each particular character, seems to be a desirable alternative to this practice. We propose a new variant of dynamic weighting, which we call homoplasy-correcting dynamic weighting, that like dynamic weighting, is applicable to any kind of sequence, coding or noncoding.     

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.     

Phylogeny of the mayfly family Leptohyphidae (Insecta: Ephemeroptera) in South America

Abstract.  A cladistic analysis of the South American members of the Ephemeropteran family Leptohyphidae is presented. A matrix of 73 taxa and 124 morphological characters was analysed under two distinct weighting criteria (implied weighting, which weights characters as a whole, and self-weighted optimization, which differentially weights character state transformations). To assess the monophyly of the Leptohyphidae, representatives of Ephemerellidae, Ephemerythidae, Machadorythidae, Teloganodidae, Tricorythidae, Coryphoridae and Melanemerellidae were also included. Trees were rooted in Ephemerellidae. Conspicuous differences in consensus topology occur when transformation costs among character states are weighted (including asymmetries). The differences in the assessments of character reliability in the two weighting criteria used are discussed. In many cases, self-weighting, in allowing for asymmetries in transformation costs, considered many of the character state transformations as more reliable (= informative) than implied weights (which needlessly down-weighted the whole character). The results confirm the monophyly of Leptohyphidae and support its sister-group relationship with Coryphoridae. The shortest trees do not support the recently proposed division of Leptohyphidae into two subfamilies. Ephemerelloidea higher classification is discussed briefly.     

EVOLUTIONARY CHARACTER ANALYSIS: TRACING CHARACTER CHANGE ON A CLADOGRAM

Abstract— There has been little formal discussion concerning character analysis in cladistics, even though characters and their character state trees are central to phylogenetic analyses. We refer to this field as Evolutionary Character Analysis. This paper defines the components of evolutionary character analysis: character state trees, transmodal characters, cladogram characters, attribute and character phylogenies; and the use of these components in phylogenetic inference and evolutionary studies. Character state trees and their effect on cladogram construction are discussed. A new method for numerically coding complex character state trees is described that further reduces the number of variables required to describe them. This method, ordinal coding, reduces the size of data matrices, and facilitates retrieval of state codes. This paper advocates the use of both biological evidence and evidence internal to the cladogram itself to construct character state trees (CSTs). We discuss general models of character evolution (morphocline analysis, Fitch minimum mutation model, etc.) and their role in forming CSTs. Character state trees formed with theories of character evolution are referred to as transmodal characters. These transmodal characters are contrasted with cladogram characters (Mickevich, 1982), and the place of each in a phylogenetic analysis is discussed. The method for determining cladogram characters is detailed with more complicated examples than found in previous publications. We advocate testing transmodal characters by comparing them with the resultant cladogram characters. This comparison involves transformation series analysis (TSA; Mickevich, 1982) which is viewed as an extension of reciprocal illumination. The TSA procedure and its place in hypothesis testing are reviewed. Tracing the evolution of characters interests both systematists and non-systematists alike. When character state trees (transmodal characters) are optimized on pre-existing phylogenies, character phylogenies and attribute phylogenies result. Attributes are defined as a feature that may or may not be homologous (i.e., ecological categories, plant hosts, etc.). We provide two illustrations of this approach, one involving the evolution of the anuran ear and another involving the coevolution of the butterfly Heliconius and its hostplants. Finally, the components of phylogenetic character analysis can be used to test more general evolutionary theories such as the biogenetic law and vicariance biogeography.     

Phylogenetic analysis of the Rhabdocoela (Platyhelminthes) with emphasis on the Neodermata and relatives

Phylogenetic systematic analysis of 24 taxa representing the rhabdocoel platyhelminths, based on a suite of 89 morphological characters, produced two equally parsimonious trees, 181 steps long, with a consistency index (CI) of 0.69 and a rescaled consistency index (RCI) of 0.56, differing only with respect to that portion of the tree containing Umagillidae, Acholadidae, Graffillinae, Pseudograffillinae, Pterastericolidae and Hypoblepharinidae. Our results accommodate all previously proposed sister taxa to the Neodermata in a single clade in which ((Dalyelliidae + Temnocephalida) Typhloplanidae) is the sister group of ((Fecampiidae +  Urastoma ) ( Udonella ((Aspidogastrea + Digenea) (Monogenea (Gyrocotylidea (Amphilinidea + Eucestoda)))))). Bootstrap and jackknife analyses indicate that the groupings of ((Dalyelliidae + Temnocephalida) Typhloplanidae) and of ((Fecampiidae +  Urastoma ) ( Udonella ((Aspidogastrea + Digenea) (Monogenea (Gyrocotylidea (Amphilinidea + Eucestoda)))))) are highly robust, with the latter clade having a CI of 90% and RCI of 82%. Disagreements among previous analyses of these taxa have been due to the influence of missing data for critical characters in key taxa and differences in the taxa analysed, rather than any inherent weakness in the morphological data. Non-phylogenetic systematic approaches to homology assessment and misconceptions regarding phylogenetic systematic methodology are discussed. Recent analyses combining sequence data with a subset of approximately 60% of the morphological characters should be re-assessed using the entire morphological database. Even if Udonella is a monogenean, it is most parsimonious to suggest that the common ancestor of the Neodermata had a vertebrate–arthropod two-host life cycle.     

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.     

Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three‐item statements

The cladistic literature does not always specify the kind of multistate character treatment that is applied for an analysis. Characters can be treated either as unordered transformation series or as rooted [three‐item analysis (3ia)] or unrooted state trees (ordered characters). We aimed to measure the impact of these character treatments on phylogenetic inference. Discrete characters can be represented either as rows or columns in matrices (e.g. for parsimony) or as hierarchies for 3ia. In the present study, we use simulated and empirical examples to assess the relative merits of each method considering both the character treatment and representation. We measure two parameters (resolving power and artefactual resolution) using a new tree comparison metric, ITRI (inter‐tree retention index). Our results suggest that the hierarchical character representation not only results (with our simulation settings) in the greatest resolving power, but also in the highest artefactual resolution. Our empirical examples provide equivocal results. Parsimony unordered states yield less resolving power and more artefactual resolutions than parsimony ordered states, both with our simulated and empirical data. Relationships between three operational taxonomic units (OTUs), irrespective of their relationships with other OTUs, are called three‐item statements (3is). We compare the intersection tree (which reconstructs a single tree from all of the common 3is of source trees) with the traditional strict consensus and show that the intersection tree retains more of the information contained in the source trees. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 914–930.     

Reconstructing ancestral character states: a critical reappraisal

Using parsimony to reconstruct ancestral character states on a phylogenetic tree has become a popular method for testing ecological and evolutionary hypotheses. Despite its popularity, the assumptions and uncertainties of reconstructing the ancestral states of a single character have received less attention than the much less challenging endeavor of reconstructing phylogenetic trees from many characters. Recent research suggests that parsimony reconstructions are often sensitive to violations of the almost universal assumption of equal probabilities of gains and losses. In addition, maximum likelihood has been developed as an alternative to parsimony reconstruction, and has also revealed a surprising amount of uncertainty in ancestral reconstructions.     

What does morphology tell us about orchid relationships?—a cladistic analysis

A cladistic analysis of Orchidaceae was undertaken for 98 genera using 71 morphological apomorphies based on a reconsideration of previous character analyses and newly discovered variation. The equally weighted analysis found 60 000 most parsimonious trees with low consistency (CI = 0.29) but high retention (RI = 0.83). The strict consensus reveals a significant amount of structure, and most traditionally recognized subfamilies are supported as monophyletic, including the Apostasioideae, Cypripedioideae, Spiranthoideae, and Epidendroideae. Orchidoideae in the broad sense are paraphyletic, giving rise to spiranthoids. Vanilloids are sister to epidendroids, although exhibiting several states otherwise found only in clearly basal groups, such as Apostasioideae. The nonvandoid epidendroids are poorly resolved, due to a high degree of homoplasy. The vandoids appear to be monophyletic, contrary to recent molecular evidence, possibly due to repeated parallel development of the vandoid character suite. The importance of vegetative characters as evidence putatively independent from floral features is demonstrated in the placement of Tropidia. Implied weighting analysis of these data resulted in similar patterns at high levels, although the Orchidoideae and Spiranthoideae may each be monophyletic and the nonvandoid epidendroids are more resolved. The high degree of structure implied in previous orchid classifications must be reconsidered, given the poor resolution at lower levels in the present trees.     

Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs

A method to assess the cost of character state transformations based on their congruence is proposed. Measuring the distortion of different transformations with a convex increasing function of the number of transformations, and choosing those reconstructions which minimize the distortion for all transformations, may provide a better optimality criterion than the linear functions implemented in currently used methods for optimization. If trees are optimized using such a measure, transformation costs are dynamically determined during reconstructions; this leads to selecting trees implying that the possible state transformations are as reliable as possible. The present method is not iterative (thus avoiding the concern of different final results for different starting points), and it has an explicit optimality criterion. It has a high computational cost; algorithms to lessen the computations required for optimizations and searches are described.     

Evaluation of some methods for hybrid analysis, exemplified by hybridization in Argyrantheimim (Asteraceae)

A grouping of transformations is proposed: 1) "Element transformations", aimed at changing relations between elements within a single character vector; and 2) "vector transformations", aimed at changing relations between different character vectors. Logarithmic element transformation seemed suitable for revealing variation in size characters.
Principal coordinate analysis (PCO) was appropriate for determination of dimensionality and structural extremes (parentage). Due to polynomial distortions, however, variation in extreme populations was underestimated and variation in intermediate populations exaggerated.
A "character index", the mean of a specimen's ranged characters, is suggested to replace Anderson's hybrid index. Knowledge of parentage and parental maxima, but not of variation in pure parental populations, is required. The character index combined with modified Gay triangles was found suitable for revealing the structure of the material, which showed mainly one-dimensional variation. The material analysed comprised Argyranthemum broussonetü, A. frutescens , a hybrid swarm and experimental F₁ hybrids between these species; and A. sundingü , which was found to be a stabilized hybrid derivative, probably evolved by hybrid speciation with external barriers.     

A METHOD FOR TESTING THE CORRELATED EVOLUTION OF TWO BINARY CHARACTERS: ARE GAINS OR LOSSES CONCENTRATED ON CERTAIN BRANCHES OF A PHYLOGENETIC TREE?

A method is presented for assessing whether changes in a binary character are more concentrated than expected by chance on certain branches of a phylogenetic tree. It can be used to test for correlated evolution of two characters by asking whether changes in the first character are significantly concentrated on those branches on which the second character has a specified state. Thus, one could test whether this specified state is associated with, and thus might enable or select, gains or losses in the first character. The probability of achieving a concentration as or more extreme than that observed under the null hypotheses that changes are distributed randomly on the cladogram is obtained by calculating (a) the number of ways that n gains and m losses can be distributed on the cladogram and (b) the number of ways that p gains q losses can be distributed on the branches of interest given n gains and m losses in the cladogram overall. Summing (b) for appropriate p and q then dividing by (a) yields the desired probability. Simulations suggest that biases resulting from errors in parsimony reconstructions of ancestral states are not extreme.     

A new balance index for phylogenetic trees

Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over all pairs of different leaves, of the depth of their lowest common ancestor. This index makes sense for arbitrary trees, can be computed in linear time and it has a larger range of values and a greater resolution power than other indices like Colless’ or Sackin’s. We compute its maximum and minimum values for arbitrary and binary trees, as well as exact formulas for its expected value for binary trees under the Yule and the uniform models of evolution. As a byproduct of this study, we obtain an exact formula for the expected value of the Sackin index under the uniform model, a result that seems to be new in the literature.     

Evolution of myrmecophytism in western Malesian Macaranga (Euphorbiaceae)

Plants inhabited by ants (myrmecophytes) have evolved in a diversity of tropical plant lineages. Macaranga includes approximately 300 paleotropical tree species; in western Malesia there are 26 myrmecophytic species that vary in morphological specializations for ant association. The origin and diversification of myrmecophytism in Macaranga was investigated using phylogenetic analyses of morphological and nuclear ITS DNA characters and studies of character evolution. Despite low ITS variation, the combined analysis resulted in a well-supported hypothesis of relationships. Mapping myrmecophytism on all most parsimonious trees resulting from the combined analysis indicated that the trait evolved independently between two and four times and was lost between one and three times (five changes). This hypothesis was robust when tested against trees constrained to have three or fewer evolutionary transformations, although increased taxon sampling for the ITS analysis is required to confirm this. Mapping morphological traits on the phylogeny indicated that myrmecophytism was not homologous among lineages; each independent origin involved a suite of different specializations for ant-plant association. There was no evidence that myrmecophytic traits underwent sequential change through evolution; self-hollowing domatia evolved independently from ant-excavated domatia, and different food-body production types evolved in different lineages. The multiple origins of myrmecophytism in Macaranga were restricted to one small, exclusively western Malesian lineage of an otherwise large and nonmyrmecophytic genus. Although the evolution of aggregated food-body production and the formation of domatia coincided with the evolution of myrmecophytism in all cases, several morphological, ecological, and biogeographic factors appear to have facilitated and constrained this radiation of ant-plants.     

Character-state space versus rate of evolution in phylogenetic inference

With only four alternative character states, parallelisms and reversals are expected to occur frequently when using nucleotide characters for phylogenetic inference. Greater available character‐state space has been described as one of the advantages of third codon positions relative to first and second codon positions, as well as amino acids relative to nucleotides. We used simulations to quantify how character‐state space and rate of evolution relate to one another, and how this relationship is affected by differences in: tree topology, branch lengths, rate heterogeneity among sites, probability of change among states, and frequency of character states. Specifically, we examined how inferred tree lengths, consistency and retention indices, and accuracy of phylogenetic inference are affected. Our results indicate that the relatively small increases in the character‐state space evident in empirical data matrices can provide enormous benefits for the accuracy of phylogenetic inference. This advantage may become more pronounced with unequal probabilities of change among states. Although increased character‐state space greatly improved the accuracy of topology inference, improvements in the estimation of the correct tree length were less apparent. Accuracy and inferred tree length improved most when character‐state space increased initially; further increases provided more modest improvements. © The Willi Hennig Society 2004.