Review of morphological evidence on the phylogeny of basal Hymenoptera (Insecta), with a discussion of the ordering of characters

In a previous study of the phylogeny of basal Hymenoptera, Vilhelmsen (2001; Zool. J. Linn. Soc . 131 : 393–442) compiled an extensive morphological data matrix for a phylogenetic analysis of basal Hymenoptera, comprising 38 hymenopteran genera. In this study, his characters are revised. This results in a cladogram whose relationships largely agree with those proposed by Vilhelmsen, except that the relationships at the base of the Hymenoptera are unresolved. The revised data matrix is expanded by 17 sawfly and three apocritan taxa. Moreover, 112 new morphological characters from different parts of the larval and adult morphology are also added to the data matrix, including 82 from a recent study of the terminal abdominal segments of male Hymenoptera. The addition of the new characters leads to Xyelidae, again, being the sister-group of all other Hymenoptera. The relationships among the sawfly families as proposed by Vilhelmsen are confirmed, except that the relationships among Syntexis , Siricidae and Xiphydriidae + Vespina are unresolved and that the monophyly of Apocrita is not convincingly supported. A separate analysis is performed which includes all extant genera of Xyelidae. The internal phylogeny of Xyelidae is determined as (( Macroxyela Megaxyela ) Xyelecia ( Xyela Pleroneura )).  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 209–243.     

The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences,mitochondrial COI sequence,and morphological characters

Background  

Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae) have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera) using 69 species.     

Phylogenetic analyses of marine sponges within the order Verongida: a comparison of morphological and molecular data

Abstract. Because the taxonomy of marine sponges is based primarily on morphological characters that can display a high degree of phenotypic plasticity, current classifications may not always reflect evolutionary relationships. To assess phylogenetic relationships among sponges in the order Verongida, we examined 11 verongid species, representing six genera and four families. We compared the utility of morphological and molecular data in verongid sponge systematics by comparing a phylogeny constructed from a morphological character matrix with a phylogeny based on nuclear ribosomal DNA sequences. The morphological phylogeny was not well resolved below the ordinal level, likely hindered by the paucity of characters available for analysis, and the potential plasticity of these characters. The molecular phylogeny was well resolved and robust from the ordinal to the species level. We also examined the morphology of spongin fibers to assess their reliability in verongid sponge taxonomy. Fiber diameter and pith content were highly variable within and among species. Despite this variability, spongin fiber comparisons were useful at lower taxonomic levels (i.e., among congeneric species); however, these characters are potentially homoplasic at higher taxonomic levels (i.e., between families). Our molecular data provide good support for the current classification of verongid sponges, but suggest a re-examination and potential reclassification of the genera Aiolochroia and Pseudoceratina . The placements of these genera highlight two current issues in morphology-based sponge taxonomy: intermediate character states and undetermined character polarity.     

Molecular and morphological phylogeny of Diplazontinae (Hymenoptera,Ichneumonidae)

Klopfstein, S., Quicke, D. L. J., Kropf, C. & Frick, H. (2011) Molecular and morphological phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae). —Zoologica Scripta, 40, 379–402. Parasitoid wasps are among the most species rich and at the same time most understudied of all metazoan taxa. To understand their diversification and test hypotheses about their evolution, we need robust phylogenetic hypotheses. Here, we reconstruct the phylogeny of the subfamily Diplazontinae using four genes and 66 morphological characters both in separate analyses and in a total evidence approach. The resulting phylogeny is highly resolved, with most clades supported by multiple independent data partitions. It contains three highly supported genus groups, for which we suggest morphological and behavioural synapomorphies. The placement of some of the genera, especially Xestopelta Dasch, is unexpected, but also supported by morphology. Most of the genera are retrieved as monophyletic, with the exception of the morphologically diverse genus Syrphoctonus Förster. We split this genus into three genera, including Fossatyloides gen. n., to restore the phylogeny–classification link. Conflict between the morphological and the molecular topology was mostly resolved in favour of the molecular partition in the total evidence approach. We discuss reasons for this finding, and suggest strategies for future taxon and character sampling in Diplazontinae.     

Similarity

Recent debates concerning conflicting hypotheses of higher-level phylogeny such as the sister-group relationships of tetrapods, turtles, birds and snakes, serve as examples in the analysis of the nature of morphological evidence as it is currently used in phylogeny reconstruction. We note a recent shift of emphasis towards ever-larger data matrices, which may come at the cost of detailed character analysis and argumentation. Because the assessment of morphological characters necessarily entails a conceptual element of abstraction, there is also a threat that preconceived notions of phylogeny influence character analysis. Because the test of congruence does not address character analysis in itself, we argue that character hypotheses, i.e. primary conjectures of homology, need to be testable, and potentially refutable, in their own right. We demonstrate the use of classical criteria of homology (topological relations and/or connectivity, in conjunction with the subsidiary criteria of special similarity and intermediate forms) in the test, and refutation, of morphological characters. Rejection of the classical criteria of homology in the test of morphological character hypotheses requires the formulation of alternative methods of test and potential falsification of morphological characters that have so far not been proposed. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 59–82.     

Character evolution in Hydrozoa (phylum Cnidaria)

The diversity of hydrozoan life cycles, as manifested in the wide range of polyp, colony, and medusa morphologies, has been appreciated for centuries. Unraveling the complex history of characters involved in this diversity is critical for understanding the processes driving hydrozoan evolution. In this study, we use a phylogenetic approach to investigate the evolution of morphological characters in Hydrozoa. A molecular phylogeny is reconstructed using ribosomal DNA sequence data. Several characters involving polyp, colony, and medusa morphology are coded in the terminal taxa. These characters are mapped onto the phylogeny and then the ancestral character states are reconstructed. This study confirms the complex evolutionary history of hydrozoan morphological characters. Many of the characters involving polyp, colony, and medusa morphology appear as synapomorphies for major hydrozoan clades, yet homoplasy is commonplace.     

Dissecting the ancient rapid radiation of microgastrine wasp genera using additional nuclear genes

Previous estimates of a generic level phylogeny for the ubiquitous parasitoid wasp subfamily Microgastrinae (Hymenoptera) have been problematic due to short internal branches deep in the phylogeny. These short branches might be attributed to a rapid radiation among the taxa, the use of genes that are unsuitable for the levels of divergence being examined, or insufficient quantity of data. We added over 1200 nucleotides from four nuclear genes to a dataset derived from three genes to produce a dataset of over 3000 nucleotides per taxon. While the number of well-supported short branches in the phylogeny increased, we still did not obtain strong bootstrap support for every node. Parametric and nonparametric bootstrap simulations projected that an enormous, and likely unobtainable, amount of data would be required to get bootstrap support greater than 50% for every node. However, a marked increase in the number of well-supported nodes was seen when we conducted a Bayesian analysis of a combined dataset generated from morphological characters added to the seven gene dataset. Our results suggest that, in some cases, combining morphological and genetic characters may be the most practical way to increase support for short branches deep in a phylogeny.     

The relevance of the mesosomal internal structures to the phylogeny of Augochlorini bees (Hymenoptera: Halictinae)

The use of internal skeletal structures is valuable to phylogenetic reconstruction within Hymenoptera; however, these structures were not further investigated for Augochlorini. Previous phylogenetic studies of Augochlorini based only on external morphology were poorly resolved. The objectives of this work are to explore the comparative morphology of internal structures of the mesosoma and to evaluate their potential as information sources for the phylogenetic relationships within the tribe. The internal structures of the Pseudaugochlora graminea (Fabricius, 1804) mesosoma are described in detail and compared with 16 other genera. We propose 24 new character statements for the Augochlorini phylogeny based on internal structures of mesosoma. Prosternum, propleuron and meso/metafurca provided a great number of informative characters. On the other hand, the mesophragma, metanotum and propodeum were less variable. The monophyly of Augochlorini and of all genus groups was corroborated in a parsimony analysis of internal and external morphological characters. Characters derived from internal structures provided the first‐known morphological synapomorphies for the clades: Megaloptidia group + others, Neocorynura group + others and Augochlora group + Megalopta group. These characters helped to elucidate the evolution of the group when analysed together with external morphological characters.     

Cranial shape and correlated characters in crocodilian evolution

Crocodilians show a high degree of cranial variation and convergence throughout their 80 million-year fossil record that complicates their phylogenetic reconstruction. Conflicting phylogenetic results from different data partitions and character homoplasies typify crocodilian phylogeny, and differences between molecular and morphological phylogenetic hypotheses are believed to be associated with the slender-snout skull shape of Gavialis gangeticus and Tomistoma schlegelii. Slender-snout skulls are one of five identified eusuchian cranial ecomorph shape categories (ESCs) thought to reflect functional or ecological specialization. This paper tested the effect of transitions among general, blunt and slender ESCs on cranial character-state distributions in phylogeny using the concentrated changes test. In addition, 'tree-free' character compatibility analysis of character independence was conducted on the morphological character matrix to determine if character correlations are observed independent of specific tree topologies. Results suggest cranial ESCs do affect cranial character-state gains in phylogeny. Concentrated changes identify a broad suite of character-state changes that significantly correlate with transitions to slender, general and blunt ESCs on morphological, molecular and combined-data tree topologies, but numbers of correlated characters for each category differ according to topology. Character compatibility analysis results do not mirror the concentrated changes test results and reflect hierarchically distributed support throughout the data. As cranial ESCs affect character-state transitions, it is possible that nonphylogenetic variables could affect inferences of crocodilian phylogeny by affecting cranial morphology.     

An application of dynamic homology to morphological characters: direct optimization of setae sequences and phylogeny of the family Odontellidae (Poduromorpha, Collembola)

The concept of character and the definition of the attribute are two major theoretical issues of phylogenetics. Lately, great progress has been made in the conceptual development of attributes as historical individuals undergoing series of transformations. While operational application of this ideographic concept of character has been possible since the publication of the direct optimization algorithm and POY software, it has been restricted to molecular characters only. The present paper proposes the first application of direct optimization to morphological characters, in the case study of the phylogeny of Odontellidae. This new homology regime is compared to the traditional homology scheme. The theoretical and operational limitations of the application of direct optimization to morphological characters are discussed. Some thoughts on the basics of its generalization to all morphological characters analyzed in a dynamic homology phylogenetic framework are given.
© The Willi Hennig Society 2009;.     

Giant taxon‐character matrices: quality of character constructions remains critical regardless of size

Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate phylogeny, reporting numbers of characters never seen or expected before. However, the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Therefore, the question of whether quantity parallels quality for such influential works remains open. Here, we provide the largest compilation known to us of character construction methods and criteria, as derived from previous studies, and from our own de novo conceptualizations. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures. Upon a revision of two of the currently largest morphological datasets used to test squamate phylogeny, more than one‐third of the almost 1000 characters analysed were classified within at least one of our categories of “types” of characters that should be avoided in cladistic investigations. These characters were removed or recoded, and the data matrices re‐analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies. Our results urge caution against certain types of character choices and constructions, also providing a methodological basis upon which problematic characters might be avoided.     

Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates

Rate distributions are important considerations when testing hypotheses about morphological evolution or phylogeny. They also have implications about general processes underlying character evolution. Molecular systematists often assume that rates are Poisson processes with gamma distributions. However, morphological change is the product of multiple probabilistic processes and should theoretically be affected by hierarchical integration of characters. Both factors predict lognormal rate distributions. Here, a simple inverse modelling approach assesses the best single-rate, gamma and lognormal models given observed character compatibility for 115 invertebrate groups. Tests reject the single-rate model for nearly all cases. Moreover, the lognormal outperforms the gamma for character change rates and (especially) state derivation rates. The latter in particular is consistent with integration affecting morphological character evolution.     

Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: multiple origins of bioluminescence and extreme sexual dimorphism

Evolutionists often use phylogeny to examine independent evolutionary events in search of generality. Therefore, groups of organisms rich in such independent character transitions are particularly valuable for the study of evolution. With respect to eyes, vision, and light-related characters, one such group is Ostracoda (Crustacea). Phylogenies of ostracods, derived from DNA sequence data and morphological characters, are presented. These inferred relationships largely agree with previous assessments of ostracod phylogeny, with the exception of paraphyletic Philomedidae. Based on methods of character reconstruction using these inferred relationships, different groups of ostracods probably evolved both bioluminescence and extreme sexual dimorphism (females lack eyes, males have large eyes) multiple times. Furthermore, myodocopid ostracods may have evolved compound eyes independently of other arthropods. For these and other reasons, it is proposed that the Ostracoda are an exceptionally important group for studying the evolution of vision- and light-related characters.     

How the worm got its pharynx: phylogeny, classification and Bayesian assessment of character evolution in Acoela

Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensive phylogenetic study of Acoela and the taxonomy of the 380 species is chaotic. Here we use two nuclear ribosomal genes and one mitochondrial gene in combination with 37 morphological characters in an analysis of 126 acoel terminals (about one-third of the described species) to estimate the phylogeny and character evolution of Acoela. We present an estimate of posterior probabilities for ancestral character states at 31 control nodes in the phylogeny. The overall reconstruction signal based on the shape of the posterior distribution of character states was computed for all morphological characters and control nodes to assess how well these were reconstructed. The body-wall musculature appears more clearly reconstructed than the reproductive organs. Posterior similarity to the root was calculated by averaging the divergence between the posterior distributions at the nodes and the root over all morphological characters. Diopisthoporidae is the sister group to all other acoels and has the highest posterior similarity to the root. Convolutidae, including several "model" acoels, is most divergent. Finally, we present a phylogenetic classification of Acoela down to the family level where six previous family level taxa are synonymized.     

Per arborem ad astra: morphological adaptations to exploiting the woody habitat in the early evolution of Hymenoptera

We survey morphological features of larval and adult wasps that undergo their entire larval development inside wood and interpret them in view of the lifestyle. The evolution of some of the characters is explored by mapping them on a recently published phylogeny of Hymenoptera. Based on this phylogeny, it is reasonable to assume that wood-living wasps evolved from a xylophagous/mycetophagous stage as displayed by woodwasps to a carnivorous/parasitoid lifestyle, preying on woodboring insect larvae. The latter mode of life is probably ancestral to the Apocrita which comprise the majority of the order; they share this lifestyle with their sister group, the Orussidae. However, most apocritan wasps have radiated into other habitats, the Orussidae and Stephanidae apparently being the only taxa that have retained the ancestral lifestyle of carnivorous wasps. Other apocritan lineages associated with wood (e.g., Aulacidae, Megalyridae, basal Cynipoidea and some Ichneumonoidea and Chalcidoidea) possibly entered this habitat secondarily and independently acquired morphological traits associated with it. The woody habitat was occupied by Hymenoptera during a crucial stage in their evolution where the transition from the phytophagous to carnivorous lifestyle took place. The anatomy of both larva and adults was extensively transformed in the process.     

Inferring and testing hypotheses of cladistic character dependence by using character compatibility

The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complementary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny and therefore assume that nonphylogenetic correlation has a negligible effect on initial tree construction. This paper develops "tree-free" methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis before phylogeny reconstruction, or can be used simply to test for correlated evolution. We first develop an approach for visualizing suites of correlated characters by using character compatibility. Two characters are compatible if they can be used to construct a tree without homoplasy. The approach is based on the examination of mutual compatibilities between characters. The number of times two characters i and j share compatibility with a third character is calculated, and a pairwise shared compatibility matrix is constructed. From this matrix, an association matrix analogous to a dissimilarity matrix is derived. Eigenvector analyses of this association matrix reveal suites of characters with similar compatibility patterns. A priori character subsets can be tested for significant correlation on these axes. Monte Carlo tests are performed to determine the expected distribution of mutual compatibilities, given various criteria from the original data set. These simulated distributions are then used to test whether the observed amounts of nonphylogenetic correlation in character suites can be attributed to chance alone. We have applied these methods to published morphological data for caecilian amphibians. The analyses corroborate instances of dependent evolution hypothesized by previous workers and also identify novel partitions. Phylogenetic analysis is performed after reducing correlated suites to single characters. The resulting cladogram has greater topological resolution and implies appreciably less change among the remaining characters than does a tree derived from the raw data matrix.     

A morphological supermatrix‐based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny,missing data and homoplasy

Although 11 studies have addressed the systematics of the four families and 281 fish species of the ecomorphologically diverse Anostomoidea, none has proposed a global hypothesis of relationships. We synthesized these studies to yield a supermatrix with 463 morphological characters among 174 ingroup species, and inferred phylogeny with parsimony and Bayesian optimization. We evaluated the applicability of the supermatrix approach to morphological datasets, tested its sensitivity to missing data, determined the impact of homoplastic characters on phylogenetic resolution, and determined the distribution of homologies and homoplasies on the topology. Despite more than 60% missing data, analyses supported the monophyly of all families, and phylogenetic structure degraded only with inclusion of species with high percentages of missing data and in analyses limited to homoplasies. The latter differs modestly from the full matrix indicating phylogenetic signal in homoplastic characters. Character distributions differ across the phylogeny, with a greater prevalence of homologies at deeper nodes and homoplasies nearer the tips than expected by chance. This may suggest early diversification into distinct bauplans with subsequent diversification of faster evolving character systems. The morphological supermatrix approach is powerful and allows integration of classical data with modern methods to examine the evolution of multiple character systems.     

Why do morphological phylogenies vary in quality? An investigation based on the comparative history of lizard clades

Phylogenies based on morphology vary considerably in their quality: some are robust and explicit with little conflict in the data set, whereas others are far more tenuous, with much conflict and many possible alternatives. The main primary reasons for untrue or inexplicit morphological phylogenies are: not enough characters developed between branching points, uncertain character polarity, poorly differentiated character states, homoplasy caused by parallelism or reversal, and extinction, which may remove species entirely from consideration and can make originally conflicting data sets misleadingly compatible, increasing congruence at the expense of truth. Extinction differs from other confounding factors in not being apparent either in the data set or in subsequent analysis. One possibility is that variation in the quality of morphological phylogenies has resulted from exposure to different ecological situations. To investigate this, it is necessary to compare the histories of the clades concerned. In the case of explicit morphological phylogenies, ecological and behavioural data can be integrated with them and it may then be possible to decide whether morphological characters are likely to have been elicited by the environments through which the clade has passed. The credibility of such results depends not only on the phylogeny being robust but also on its detailed topology: a pectinate phylogeny will often allow more certain and more explicit statements to be made about historical events. In the case of poor phylogenies, it is not possible to produce detailed histories, but they can be compared with robust phylogenies in the range of ecological situations occupied, and whether they occupy novel situations in comparison with their outgroups. LeQuesne testing can give information about niche homoplasy, and it may also be possible to see if morphological features are functionally associated with ecological parameters, even if the direction of change is unknown. Examination of the robust and explicit phylogeny of the semaphore geckoes (Pristurus) suggests that its quality does stem from a variety of environmental factors. The group has progressed along an ecological continuum, passing through a series of increasingly severe niches that appear to have elicited many morphological changes. The fact that niches are progressively filled reduces the likelihood of species reinvading a previous one with related character reversal. Because the niches of advanced Pristurus are virtually unique within the Gekkonidae the morphological changes produced are also very rare and therefore easy to polarize. Ecological changes on the main stem of the phylogeny are abrupt and associated character states consequently well differentiated.(ABSTRACT TRUNCATED AT 400 WORDS)