Extended implied weighting

Several extensions to implied weighting, recently implemented in TNT, allow a better treatment of data sets combining morphological and molecular data sets, as well as those comprising large numbers of missing entries (e.g. palaeontological matrices, or combined matrices with some genes sequenced for few taxa). As there have been recent suggestions that molecular matrices may be better analysed using equal weights (rather than implied weighting), a simple way to apply implied weighting to only some characters (e.g. morphology), leaving other characters with a constant weight (e.g. molecules), is proposed. The new methods also allow weighting entire partitions according to their average homoplasy, giving each of the characters in the partition the same weight (this can be used for dynamically weighting, e.g. entire genes, or first, second, and third positions collectively). Such an approach is easily implemented in schemes like successive weighting, but in the case of implied weighting poses some particular problems. The approach has the peculiar implication that the inclusion of uninformative characters influences the results (by influencing the implied weights for the partitions). Last, the concern that characters with many missing entries may receive artificially inflated weights (because they necessarily display less homoplasy) can be solved by allowing the use of different weighting functions for different characters, in such a way that the cost of additional transformations decreases more rapidly for characters with more missing entries (thus effectively assuming that the unobserved entries are likely to also display some unobserved homoplasy). The conceptual and practical aspects of all these problems, as well as details of the implementation in TNT, are discussed.     

Phylogeny of the parasitic wasp subfamily Charipinae (Hymenoptera, Cynipoidea, Figitidae)

The Charipinae are a major group of hyperparasitoids of Hemiptera. Here, we present the first cladistic analysis of this subfamily's internal relationships, based on 96 morphological characters of adults. The data matrix was analysed using uniformly weighted parsimony. The effects of using alternative weighting schemes were explored by performing additional searches employing implied weights criteria. One of the caveats of implied weights analysis is that it lacks an objective criterion for selecting the value of the concavity function. In the present study, differential weighting was used to explore the sensitivity of our results to the alternative assumptions made in the analysis and to select one of the most parsimonious trees under equal weights, which we regard as being the hypothesis that minimizes the amount of ad hoc assumptions. The validity of the two existing tribes and the monophyly of all the genera of Charipinae were tested, in particular the cosmopolitan and highly species-rich Alloxysta and Phaenoglyphis , which appear repeatedly in ecological and biochemical studies of host–parasitoid associations. The evolution of several major characters and the relationships between genera are discussed. On the basis of the phylogenetic results, we discuss a number of taxonomic issues. A new classification of the subfamily is proposed in which no tribes are maintained, Carvercharips is synonymyzed with Alloxysta , and the creation of a new genus from Nepal is justified. Our analysis points to the need for a world revision of the basal genus Phaenoglyphis , which is shown as paraphyletic.     

Testing and weighting characters

Published justifications for weighting characters in parsimony analyses vary tremendously. Some authors argue for weighting a posteriori, some for a priori, and especially those authors that rely on a falsificationist approach to systematics argue for non-weighting. To find a decision, while following the falsificationist approach, one first has to investigate the necessary conditions for the possibility of phylogenetic research to establish an empirical science sensu Popper. A concept of phylogenetic homology together with the criterion of identity is proposed, which refers to the genealogical relations between individual organisms. From this concept a differentiation of the terms character and character state is proposed, defining each character as a single epistemological argument for the reconstruction of a unique transformation event. Synapomorphy is distinguished from homology by referring to the relationship between species instead of individual organisms, thus the set of all synapomorphies constitutes a subset of the set of all homologies. By examining the structure of characteristics during character analysis and hypothesizing specific types of transformations responsible for having caused them, a specific degree of severity is assigned to each identity test. It thus provides a specific degree of corroboration for every hypothesis that successfully passed this test. Since the congruence criterion tests hypotheses of synapomorphy against each other on grounds of their degree of corroboration gained from the identity test, these different degrees of corroboration determine the specific weights given to characters and character state transformations before the cladistic analysis. This provides a reasonable justification for an a priori weighting scheme within a falsificationist approach to phylogeny. It also demonstrates the indispensable necessity of its application.     

Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices

Implied weighting, a method for phylogenetic inference that actively seeks to downweight supposed homoplasy, has in recent years begun to be widely utilized in palaeontological datasets. Given the method's purported ability at handling widespread homoplasy/convergence, we investigate the effects of implied weighting on modelled phylogenetic data. We generated 100 character matrices consisting of 55 characters each using a Markov Chain morphology model of evolution based on a known phylogenetic tree. Rates of character evolution in these datasets were variable and generated by pulling from a gamma distribution for each character in the matrix. These matrices were then analysed under equal weighting and four settings of implied weights (k = 1, 3, 5, and 10). Our results show that implied weighting is inconsistent in its ability to retrieve a known phylogenetic tree. Equally weighted analyses are found to generally be more conservative, retrieving higher frequency of polytomies but being less likely to generate erroneous topologies. Implied weighting is found to generally resolve polytomies while also propagating errors, resulting in an increase in both correctly and incorrectly resolved nodes with a tendency towards higher rates of error compared to equal weighting. Our results suggest that equal weights may be a preferable method for parsimony analysis.     

Parallel tion in the context of character analysis

For the establishment of polarity of character transformation prior to phylogenetic analysis, various logical and biological criteria are discussed; some are rejected on grounds of liability to systematic error, circularity or unwarranted assumptions aboutParallel tion is used as a non-polar term, with forward and reverse to indicate polarity. A computer program for the detection of parallel tion is described which takes taxa in groups of four. The characters, with two derived: two primitive states or three derived: one primitive state, are listed according to the distribution of states over the four taxa. To each of the 15 phylogenies there corresponds a compatible pair of character patterns. Discordant 2: 2 patterns are unconditionally incompatible (Le Quesne test failure), discordant 3: 1 patterns are incompatible conditional upon correct scoring of polarity. For any putative phylogeny the concordant and discordant characters are identified. In cases of competing alternatives these character sets have to be weighed against one another. Character weighting is discussed; it is argued that it is the individual character transformation which should be weighted, in each direction separately.     

A Morphological Basis for Assessing the Phylogeny of the "Tenrecoidea" (Mammalia, Lipotyphla)

A phylogenetic analysis of 35 mammalian taxa focusing on the lipotyphlan family Tenrecidae, based on 193 morphological character states across 71 characters, is undertaken to test several hypotheses of lipotyphlan relationships, including monophyly of the Lipotyphla, Tenrecidae, Malagasy Tenrecidae, and Caribbean Lipotyphla. Explicit tests of these hypotheses are central to understanding larger issues concerning Malagasy and Caribbean biogeography, in addition to mammalian phylogeny. Methodologically, several different parameters are created with which to determine the sensitivity of resulting clades to initial assumptions about a posteriori character weighting, missing data, and multistate character ordering. Clades produced by this data set that appear despite perturbations in these parameters and that are supported by other confidence-assessment techniques contradict Malagasy tenrecid monophyly and the association of soricids with the Caribbean taxon Solenodon. Results regarding tenrecid and lipotyphlan monophyly are more ambiguous and depend on certain assumptions regarding treatment of character ordering, weighting, and missing data. An alternative phylogeny supporting an African mammal clade receives no support from the data set discussed herein.     

Cladistic analysis and osteological descriptions of the frog species in the Leptodactylus fuscus species group (Anura, Leptodactylidae)

The genus Leptodactylus is predominantly Neotropical (a few species have colonized the southern Neartic region) and is distributed from Texas to Argentina and on certain Caribbean islands. Leptodactylus was divided into five groups of species: Leptodactylus melanonotus , Leptodactylus ocellatus, Leptodactylus fuscus , Leptodactylus pentadactylus and Leptodactylus marmoratus . Among these, the L. fuscus group is the one with most species, with 27 taxa. Characters unverified in most of the species are used to define the L. fuscus group. However, the monophyly of the group has never been tested rigorously in a quantitative phylogenetic context. Thus, the main goal of this study was to test such monophyly and to construct a phylogeny of the L. fuscus group. A matrix of 114 characters scored across 43 taxa was constructed, with 31 characters taken from external morphology, 58 from adult skeletons, 16 from larval chondrocranium, 5 from ethology and 4 from morphometric data were included. Out of all the species examined, 23 belonged to the ingroup and 20 to the outgroup. The data set was analysed with implied weights, by using TNT software. The monophyly of the group was strongly supported in the fittest cladogram obtained. The optimizations of some characters on this hypothesis support traditional evolutionary hypotheses. The optimizations also suggest the presence of paedomorphic character states in some species, which is also discussed.     

Comparative morphology of terminal-instar larvae of Cynipoidea: phylogenetic implications

We describe the external morphology of the terminal-instar larvae of 30 species of Cynipoidea (Hymenoptera), with special reference to the head capsule and mouthparts. Twenty-five of the species belong to the Cynipidae and are gall inducers or phytophagous inquilines (guests) in galls, while five represent different insect-parasitic lineages of the Cynipoidea. Although we find only limited variation in body shape, the head sclerites and mandibles offer many characters of potential phylogenetic value. For instance, the mandibles of the parasitoids have one large pointed tooth, with several smaller dents along the inner margin in core figitids, whereas the phytophagous gall inducers and inquilines have mandibles with two or three blunt teeth of subequal size. The mandibles of inquiline larvae are unique in being covered by vertical striations and in having a dominating, broad second tooth. We summarize the qualitative variation among the studied terminal-instar larvae in terms of 33 morphological characters and one life-history trait and examine the phylogenetic implications of these data by running parsimony analyses under uniform character weights and under implied weights (Goloboff weights). The analysis under uniform weights is poorly resolved but the relationships suggested by the implied-weights analysis are largely congruent with previous analyses of adult morphology and molecular data. The larval data support inclusion of the genus Liposthenes in the Neaylax – Isocolus clade, in agreement with the molecular data but in weak conflict with adult morphology. However, the larval data agree with adult morphology and conflict with the molecular data in supporting monophyly of the inquilines.     

Phylogeny of Callibaetis (Ephemeroptera: Baetidae) based on morphology of nymphs and adults

Callibaetis is considered to be one of the most problematic genera among mayflies by a series of taxonomic inaccuracies that have accumulated over the last two centuries. Despite these taxonomic problems, two independent hypotheses of species groups have been proposed. In the first hypothesis, three species groups for North America were proposed, and in the second, three species groups were proposed for South American. In these hypotheses, the generic delimitation and monophyly of Callibaetis have not been evaluated under a cladistic framework. Taking this into account, the objectives of this study were to verify the monophyly of Callibaetis and whether the groups of species proposed for the genus are corroborated as natural. The matrix included 128 morphological characters and one habitat character, 119 discrete characters were compiled (101 of nymphs and 18 of adults), and six imaginal characters are related to pigmentation pattern. Continuous characters were ratios and were represented by 10 characters (nine for nymphs and one for adults). The data set was analysed under implied weights. Group support was estimated with relative Bremer support and frequency differences. The results corroborated the monophyletic nature of Callibaetis and the generic status of Callibaetoides; however, the groups proposed for North and South American Callibaetis species were not corroborated. Our study indicated four groups of species for the genus, which we proposed as subgenera: Callibaetis, Abaetetuba subgen. n. Aiso subgen. n. and Cunhaporanga subgen. n.     

EXACT INDICES, CRITERIA TO SELECT FROM MINIMUM LENGTH TREES

Abstract— Modifications of the consistency, retention and rescaled consistency indices are introduced. These apply to particular transformations of a character state rather than all of the transformations of a character. For example, if one observes relatively many losses in a character state over a suite of minimum length trees, a low weight is applied to the transformation to a loss; however, these observations infer nothing on the probability of the character state being gained independently. If the same character state shows few or no convergent gains on the suite of minimum length cladograms, then gains receive a relatively high weight. Conversely, if for a particular character state, convergent gains are common and losses rare, the transformation to a loss is given a higher weight than the transformation to a gain. For multistate characters, each possible transformation is weighted independently. Three indices are proposed, i.e. the exact consistently index, the exact retention index and the exact rescaled consistency index. The consistency index is modified to deal with characters with unknown entries.
The methods outlined not only select (or generate) preferred tree topologies but they also choose character optimizations, even for trees of identical topology.     

Phylogeny of the Homalotina (Coleoptera: Staphylinidae: Aleocharinae) based on morphology

The aleocharine subtribe Homalotina Heer represents one of the most diverse lineages of Staphylinidae. Despite its wide distribution and diversity, the phylogenetic relationships of the subtribe remain poorly understood. Here, we present the first cladistic analysis of the Homalotina based on morphological data. The subtribe is hypothesized to be a monophyletic group consisting of seven genera (Anomognathus Solier, Cephaloxynum Bernhauer, Holisomimus Cameron, Homalota Mannerheim, Neomalota Cameron, Stenomastax Cameron, and Thecturota Casey). The dataset for phylogenetic analysis comprised 83 characters representing 245 character states derived from adult morphology. These data were analysed using equal weighting and implied weighting schemes (k = 1–6) and results support the monophyly of the subtribe based on two synapomorphic characters (complete postoccipital sutures on head, posterolateral margin of metacoxae with macrosetae) and three homoplastic characters (medial setae on prementum not extended to apex of ligula, medial setae on labium contiguous, posterolateral angle of elytron slightly sinuate). Generic relationships differ in each analysis within the Homalotina (EW, IW with k = 1, 2–4, 5–6) although there are some identical topologies among the IW trees. Clades A, B, C, D, H, J and G were resolved as monophyletic in all weighting regimes. The monophyly of the genera is relatively well supported except for the genera Homalota and Stenomastax. Homalota species were recovered in four independent clades (clade C, D, I, K) and the Stenomastax species were recovered in two independent lineages. Candidates for the possible new genera are discussed. We herein transfer Homalota flavomaculata Bernhauer to the genus Stenomastax, resulting in the new combination [Stenomastax flavomaculata (Bernhauer)]. Our preliminary character correlation tests using phylogenetic pairwise comparisons did not support the hypothesis of association between flattened body form, and subcortical habitat and anterior shift of antennal insertion in Homalotini.     

The relative sensitivity of different alignment methods and character codings in sensitivity analysis

Sensitivity analysis provides a way to measure robustness of clades in sequence‐based phylogenetic analyses to variation in alignment parameters rather than measuring their branch support. We compared three different approaches to multiple sequence alignment in the context of sensitivity analysis: progressive pairwise alignment, as implemented in MUSCLE; simultaneous multiple alignment of sequence fragments, as implemented in DCA; and direct optimization followed by generation of the implied alignment(s), as implemented in POY. We set out to determine the relative sensitivity of these three alignment methods using rDNA sequences and randomly generated sequences. A total of 36 parameter sets were used to create the alignments, varying the transition, transversion, and gap costs. Tree searches were performed using four different character‐coding and weighting approaches: the cost function used for alignment or equally weighted parsimony with gap positions treated as missing data, separate characters, or as fifth states. POY was found to be as sensitive, or more sensitive, to variation in alignment parameters than DCA and MUSCLE for the three empirical datasets, and POY was found to be more sensitive than MUSCLE, which in turn was found to be as sensitive, or more sensitive, than DCA when applied to the randomly generated sequences when sensitivity was measured using the averaged jackknife values. When significant differences in relative sensitivity were found between the different ways of weighting character‐state changes, equally weighted parsimony, for all three ways of treating gapped positions, was less sensitive than applying the same cost function used in alignment for phylogenetic analysis. When branch support is incorporated into the sensitivity criterion, our results favour the use of simultaneous alignment and progressive pairwise alignment using the similarity criterion over direct optimization followed by using the implied alignment(s) to calculate branch support.     

A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data

The phylogenetic relationships of 22 species of Coelopidae are reconstructed based on a data matrix consisting of morphological and DNA sequence characters (16S rDNA, EF-1alpha). Optimal gap and transversion costs are determined via a sensitivity analysis and both equal weighting and a transversion cost of 2 are found to perform best based on taxonomic congruence, character incongruence, and tree support. The preferred phylogenetic hypothesis is fully resolved and well-supported by jackknife, bootstrap, and Bremer support values, but it is in conflict with the cladogram based on morphological characters alone. Most notably, the Coelopidae and the genus Coelopa are not monophyletic. However, partitioned Bremer Support and an analysis of node stability under different gap and transversion costs reveal that the critical clades rendering these taxa non-monophyletic are poorly supported. Furthermore, the monophyly of Coelopidae and Coelopa is not rejected in analyses using 16S rDNA that was manually aligned. The resolution of the tree based on this reduced data sets is, however, lower than for the tree based on the full data sets. Partitioned Bremer support values reveal that 16S rDNA characters provide the largest amount of tree support, but the support values are heavily dependent on analysis conditions. Problems with direct comparison of branch support values for trees derived using fixed alignments with those obtained under optimization alignment are discussed. Biogeographic history and available behavioral and genetic data are also discussed in light of this first cladogram for Coelopidae based on a quantitative phylogenetic analysis.     

Transition Confidence and Modified Mean Values: Confidence Measures for Hypotheses of Character State Transition between Nodes and Ancestral State Optimizations

A measure is introduced to quantify the reliability of character state transitions and character state stasis (lack of character state change between nodes). The mean value of a character state at an internal node is altered to obtain a measure termed the modified mean. Modified mean values at connecting nodes are employed to determine the support for hypotheses of character state transition/stasis between the nodes. The lowest of the two neighboring modified mean values implied by an hypothesis of character state transition/stasis is used as a direct measure of support for that hypotheses of character state transformation or stasis between the respective nodes.     

First phylogenetic analysis of the family Neriidae (Diptera), with a study on the issue of scaling continuous characters

Neriidae are a small family of acalyptratae flies, mostly distributed in the tropics. Very little is known about their biology, and the evolutionary relationships among species have never been evaluated. We perform the first comprehensive phylogenetic analysis of the family, including 48 species from all biogeographic regions inhabited, as well as five species of Micropezidae and one Cypselosomatidae as outgroups. We build a morphological data matrix of 194 characters, including 72 continuous characters. We first explore ways to deal with the issue of scaling continuous characters, including rescaling ranges to unity and using implied weighting. We find that both strategies result in very different phylogenetic hypotheses, and that implied weighting reduces the problem of scaling, but only partially. Furthermore, using implied weighting after rescaling characters improves the congruence between partitions and results in higher values of group support. With respect to the Neriidae, we confirm the monophyly of the family and of most its genera, although we do not obtain any of the currently accepted suprageneric groups. We propose to restrict the Eoneria and Nerius groups exclusively to the Neotropical fauna, and synonymize Glyphidops subgenus Oncopsia Enderlein with Glyphidops subgenus Glyphidops Enderlein, eliminating the subgeneric divisions. This revised phylogeny presents a striking biogeographic consistency, and shows that previous main divisions of the family were based on events of convergence.     

THE PHYLOGENETIC RELATIONSHIPS AMONG REQUIEM AND HAMMERHEAD SHARKS: INFERRING PHYLOGENY WHEN THOUSANDS OF EQUALLY MOST PARSIMONIOUS TREES RESULT

Abstract— Protein variation among 37 species of carcharhiniform sharks was examined at 17 presumed loci. Evolutionary trees were inferred from these data using both cladistic character and a distance Wagner analysis. Initial cladistic character analysis resulted in more than 30 000 equally parsimonious tree arrangements. Randomization tests designed to evaluate the phylogenetic information content of the data suggest the data are highly significantly different from random in spite of the large number of parsimonious trees produced. Different starting seed trees were found to influence the kind of tree topologies discovered by the heuristic branch swapping algorithm used. The trees generated during the early phases of branch swapping on a single seed tree were found to be topologically similar to those generated throughout the course of branch swapping. Successive weighting increased the frequency and the consistency with which certain clades were found during the course of branch swapping, causing the semi-strict consensus to be more resolved. Successive weighting also appeared resilient to the bias associated with the choice of initial seed tree causing analyses seeded with different trees to converge on identical final character weights and the same semi-strict consensus tree.
The summary cladistic character analysis and the distance Wagner analysis both support the monophyly of two major clades, the genus Rhizoprionodon and the genus Sphyrna. . The distance Wagner analysis also supports the monophyly of the genus Carcharhinus . However, the cladistic analysis suggests that Carcharhinus is a paraphyletic group that includes the blue shark Prionace glauca .     

A morphological phylogeny of Agrotis Ochsenheimer (Lepidoptera,Noctuidae), with emphasis on the South American species

The monophyly of Agrotis Ochsenheimer in addition to the relationships among the South American species of the genus and the relationship between Agrotis and Feltia Walker are examined. A cladistic analysis was performed based on 45 terminals, with 28 ingroup and 17 outgroup taxa, and 126 characters (two continuous and 124 discrete) from adult morphology, including male and female genitalia. Parsimony analyses were performed under equal and implied weighting. Results support Agrotis as a monophyletic group, sister to the South American species of Feltia (Feltia tent.), and the latter being more closely related to Agrotis than to the ‘true’ Feltia. Species of Agrotis that branched off first (including the type species) have characters shared with both Feltia and Agrotis. South American species of Agrotis (with some proviso) form a clade that branched off later, with some weakly supported species groups that had been proposed in previous works. Biogeographical aspects of the group are discussed after optimizing species distributions on the tree. Trees obtained after analyses using implied weights show similar relationships to those under equal weights, particularly regarding Feltia tent., showing Feltia tent. plus Agrotis forming a monophyletic group, sister to the ‘true’ Feltia.     

The Usefulness of the Sting Apparatus in Phylogenetic Reconstructions in Vespids,with Emphasis on the Epiponini: More Support for the Single Origin of Eusociality in the Vespidae

This study aimed at testing the utility of characters derived from chitinous structures of the sting apparatus for elucidating relationships among the genera of Epiponini. The characters were obtained from the spiracular and quadrate plates, gonostylus, and sting. The data matrix was analyzed using parsimony with equal and implied weighting. Sting characters were also optimized on the tree of Wenzel & Carpenter (1994). Consensus of analysis using equal weights parsimony resulted in a tree with low resolution, but the use of implied weighting improved the results and a consensus tree with a better resolution was obtained. Implied weighting analysis showed an interesting result with Vespinae and Epiponini (the taxa that present the highest degree of sociality) together in a clade. The overall uniformity in morphology of sting apparatus and a possible influence of sociality on morphology could explain these results. The evolution of some characters is discussed.