A host driven parasitoid syndrome: Convergent evolution of multiple traits associated with woodboring hosts in Ichneumonidae (Hymenoptera, Ichneumonoidea)

The evolution of convergent phenotypes is of major interest in biology because of their omnipresence and ability to inform the study of evolutionary novelty and constraint. Convergent phenotypes can be combinations of traits that evolve concertedly, called syndromes, and these can be shaped by a common environmental pressure. Parasitoid wasps which use a wide variety of arthropod hosts have also repeatedly and convergently switched host use across their evolutionary history. They thus represent a natural laboratory for the evolution of trait syndromes that are associated with parasitism of specific hosts and host substrates. In this study, we tested the evolution of co-evolving characters in the highly diverse family Ichneumonidae associated with ovipositing in a specific and well-defined substrate: wood. Using a newly constructed phylogeny and an existing morphological dataset, we identified six traits correlated with the wood-boring lifestyle that demonstrate convergent evolution. At least one trait, the presence of teeth on the ovipositor, typically preceded the evolution of other traits and possibly the switch to parasitism of wood-boring hosts. For each trait, we provide a historical review of their associations with wood-boring parasitoids, reevaluate the function of some characters, and suggest future coding improvements. Overall, we demonstrate the convergent evolution of multiple traits associated with parasitism of woodboring hosts and propose a syndrome in a hyper diverse lineage of parasitoid wasps.

A unified view of homology

As it spread through time and into distinct areas of science-from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology-the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of 'concepts of homology'; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 'concepts of homology' in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller's five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.

Against unifying homology concepts: Redirecting the debate

The term "homology" is persistently polysemous, defying the expectation that extensive scientific research should yield semantic stability. A common response has been to seek a unification of various prominent definitions. This paper proposes an alternative strategy, based on the insight that scientific concepts function as tools for research: When analyzing various conceptualizations of homology, we should preserve those distinguishing features that support particular research goals. We illustrate the fruitfulness of our strategy by application to two cases. First, we revisit Lankester's celebrated evolutionary reappraisal of homology and argue that his analysis has been distorted by assimilation to modern agendas. His "homogeny" does not mean the same thing as modern evolutionary "homology," and his "homoplasy" is no mere antonym. Instead, Lankester uses both new terms to pose a question that remains strikingly relevant-how do mechanistic and historical causes of morphological resemblance interact? Second, we examine the puzzle of avian digit homology, which exemplifies disciplinary differences in homology conceptualization and assessment. Recent progress has been fueled by the development of new tools within the relevant disciplines (paleontology and developmental biology) and especially by increasing interdisciplinary cooperation. Conceptual unification has played very little role in this work, which instead seeks concrete evolutionary scenarios that integrate all the available evidence. Together these cases indicate the complex relationship between concepts and other tools in homology research.

Homologues and homology and their related terms in phylogenetic systematics

In the field of phylogenetic systematics, the terms homology and homologue and their relationship to cladistic terms such as character, character state, synapomorphy and symplesiomorphy, as well as their relationships to each other, have been and are still discussed frequently. A recent re-emergence of concepts of homology/homologue free of any reference to explanatory hypotheses prompted us to explore these concepts and their relationships to each other as well as to the concept of morpheme, as introduced recently. All concepts are examined with regard to their ontological status and their bearing in the epistemological process in morphology and phylogenetic systematics. To us, morphemes, homologues and in partem character states refer to things (concrete objects in the ontological sense). However, although morphemes are exclusively descriptive, the latter two represent objects of causal explanations. Homologue always refers to the things themselves, yet a character state also can be a property or the absence of a thing. In this context, a character as a transformation series of character states does not represent a thing but a natural kind. Character states of one character are connected by homology relationships, i.e. common descent. Synapomorphy and symplesiomorphy represent different states of a single transformation series. A nonexplanatory, purely descriptive, concept of homologues is contradictory to its original as well as the post-Darwinian, evolutionary, concept which refers to causal relationships between parts of organisms and their correspondences in the archetype or ancestor, respectively. Character states, homologues and synapomorphies/symplesiomorphies can only be approximated in the form of hypotheses. We argue that the high value of the concept of homology and its related concepts for evolutionary biology should be maintained by acknowledging their explanatory nature and that dilution with nonexplanatory (even idealistic) definitions should be avoided.

It is time to move on from homology in comparative biology

The continued use of the idea of homology is questionable on philosophical and scientific grounds. It is based on the widespread idea that a "homologue" in extant taxa can be "traced back" to a feature in common ancestor. In contrast, Richard Owen, who first used the term in 1846, saw homology (homologue) differently, as "sameness": "the same organ in different animals under every variety of form and function." At that point in time, he was not influenced by evolutionary thinking, and more focused on the details and approaches to biological comparison and description. His was a perceptive approach to comparison. This paper argues that the concept of homology no longer plays a useful role in comparative biology. It is a conceptual idea with little or no empirical implications for modern comparisons among phenotypes. Comparative biology now uses formal phylogenetic analysis in which similar features in individuals of two or more taxa are treated as characters on a tree and tested for historical "sameness" in terms of the concept of synapomorphy. If we are to understand the complexities of phenotypic evolution, applying this method to detailed comparative data will be essential. At the same time, a deep understanding of the phenotype and its history will emerge only through the use of multidisciplinary approaches that address historical changes at different hierarchical levels.

Comparative morphological study of the gnathochilarium of millipedes of the suborder Cambalidea (Juliformia: Spirostreptida) assessed by discrete and morphometric character approaches

Phylogenetic relationships of the suborder Cambalidea have been a well-known focus of discussion over the past 100 years. The most recent approach to the suborder is based on the morphology of the sexual structure of males and of the gnathochilarium. The phylogenetic interpretation of the gnathochilarium has been especially criticized due to the poorly understood evolution of its components since no hypothesis of homology has been put forward. This work provides a comparative study of characters of the gnathochilarium. Twenty-one characters are proposed and optimized for 34 terminals from the orders Julida and Spirostreptida. Two datasets were analysed on the basis of whether the sclerite duplomentum corresponds to a mentum fused to a promentum or only to an elongated mentum (promentum being absent). Concatenated analyses were performed with both discrete and morphometric characters to verify the variation in shape of the mentum. In all topologies obtained, Cambalidea were recovered as paraphyletic in terms of the suborder Spirostreptidea. Through constrained searches, Cambalidae, Cambalopsidae and Iulomorphidae were not recovered, while Pseudonannolenidae were recovered only when Physiostreptinae were excluded. The morphological evidence indicates the convergence of the gnathochilarium in Spirostreptidea and in some members of Cambalidea, with independent reversions of the promentum.

Convergence, divergence, and macroevolutionary constraint as revealed by anatomical network analysis of the squamate skull, with an emphasis on snakes

Traditionally considered the earliest-diverging group of snakes, scolecophidians are central to major evolutionary paradigms regarding squamate feeding mechanisms and the ecological origins of snakes. However, quantitative analyses of these phenomena remain scarce. Herein, we therefore assess skull modularity in squamates via anatomical network analysis, focusing on the interplay between 'microstomy' (small-gaped feeding), fossoriality, and miniaturization in scolecophidians. Our analyses reveal distinctive patterns of jaw connectivity across purported 'microstomatans', thus supporting a more complex scenario of jaw evolution than traditionally portrayed. We also find that fossoriality and miniaturization each define a similar region of topospace (i.e., connectivity-based morphospace), with their combined influence imposing further evolutionary constraint on skull architecture. These results ultimately indicate convergence among scolecophidians, refuting widespread perspectives of these snakes as fundamentally plesiomorphic and morphologically homogeneous. This network-based examination of skull modularity-the first of its kind for snakes, and one of the first to analyze squamates-thus provides key insights into macroevolutionary trends among squamates, with particular implications for snake origins and evolution.

Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting

BACKGROUND

Plesiosaurs, diapsid crown-group Sauropterygia, inhabited the oceans from the Late Triassic to the Late Cretaceous. Their most exceptional characteristic are four hydrofoil-like flippers. The question whether plesiosaurs employed their four flippers in underwater flight, rowing flight, or rowing has not been settled yet. Plesiosaur locomotory muscles have been reconstructed in the past, but neither the pelvic muscles nor the distal fore- and hindflipper musculature have been reconstructed entirely.

METHODS

All plesiosaur locomotory muscles were reconstructed in order to find out whether it is possible to identify muscles that are necessary for underwater flight including those that enable flipper rotation and twisting. Flipper twisting has been proven by hydrodynamic studies to be necessary for efficient underwater flight. So, Cryptoclidus eurymerus fore- and hindflipper muscles and ligaments were reconstructed using the extant phylogenetic bracket (Testudines, Crocodylia, and Lepidosauria) and correlated with osteological features and checked for their functionality. Muscle functions were geometrically derived in relation to the glenoid and acetabulum position. Additionally, myology of functionally analogous Chelonioidea, Spheniscidae, Otariinae, and Cetacea is used to extract general myological adaptations of secondary aquatic tetrapods to inform the phylogenetically inferred muscle reconstructions.

RESULTS

A total of 52 plesiosaur fore- and hindflipper muscles were reconstructed. Amongst these are flipper depressors, elevators, retractors, protractors, and rotators. These muscles enable a fore- and hindflipper downstroke and upstroke, the two sequences that represent an underwater flight flipper beat cycle. Additionally, other muscles were capable of twisting fore- and hindflippers along their length axis during down- and upstroke accordingly. A combination of these muscles that actively aid in flipper twisting and intermetacarpal/intermetatarsal and metacarpodigital/metatarsodigital ligament systems, that passively engage the successive digits, could have accomplished fore-and hindflipper length axis twisting in plesiosaurs that is essential for underwater flight. Furthermore, five muscles that could possibly actively adjust the flipper profiles for efficient underwater flight were found, too.

Multiple Origins of Extracellular DNA Traps

Extracellular DNA traps (ETs) are evolutionarily conserved antimicrobial mechanisms present in protozoa, plants, and animals. In this review, we compare their similarities in species of different taxa, and put forward the hypothesis that ETs have multiple origins. Our results are consistent with a process of evolutionary convergence in multicellular organisms through the application of a congruency test. Furthermore, we discuss why multicellularity is related to the presence of a mechanism initiating the formation of ETs.

Morphological similarity and dental homologies in two sigmodontine rodents (Mammalia, Cricetidae) from different tribes: A topological analysis to explore convergence

We present a topological analysis of the third upper molars (M3) using the recently developed ICAMER nomenclatural system as a way to understand the dental morphological similarity in sigmodontine rodents, the most speciose subfamily of cricetids. The method is explored in Scapteromys aquaticus and Abrothrix olivacea, taxa belonging to two diverse tribes, Akodontini and Abrotrichini, respectively, which exhibit high similarity regarding several craniodental traits as well as external anatomy. Both species show morphologically similar M3 in adults characterized by cylindrification and the isolation of a large central fossette arising from the marginal fusion of the anterior and posterior lobes. The results indicate that, before the wear, these rodents have a strongly different topological pattern at the cuspal level, mostly involving production of the connection between the main cusps. The central fossette derives from the isolation of part of the metaflexus in Scapteromys, while in Abrothrix it originates from the hypoflexus. The topological analysis provides a new approach to sigmodontine systematics, including the ability to detect diagnostic characters of both tribes. More important, it constitutes a new step toward an integrative phylogeny of fossil and living cricetids.

Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

BACKGROUND

The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored.

RESULTS

Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group.

CONCLUSIONS

We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

Multiplicity of Research Programs in the Biological Systematics: A Case for Scientific Pluralism

Biological diversity (BD) explored by biological systematics is a complex yet organized natural phenomenon and can be partitioned into several aspects, defined naturally with reference to various causal factors structuring biota. These BD aspects are studied by particular research programs based on specific taxonomic theories (TTs). They provide, in total, a framework for comprehending the structure of biological systematics and its multi-aspect relations to other fields of biology. General principles of individualizing BD aspects and construing TTs as quasi-axiomatics are briefly considered. It is stressed that each TT is characterized by a specific combination of interrelated ontological and epistemological premises most adequate to the BD aspect a TT deals with. The following contemporary research programs in systematics are recognized and characterized in brief: phenetic, rational (with several subprograms), numerical, typological (with several subprograms), biosystematic, biomorphic, phylogenetic (with several subprograms), and evo-devo. From a scientific pluralism perspective, all of these research programs, if related to naturally defined particular BD aspects, are of the same biological and scientific significance. They elaborate “locally” natural classifications that can be united by a generalized faceted classification.

Spiders did not repeatedly gain, but repeatedly lost, foraging webs

Much genomic-scale, especially transcriptomic, data on spider phylogeny has accumulated in the last few years. These data have recently been used to investigate the diverse architectures and the origin of spider webs, concluding that the ancestral spider spun no foraging web, that spider webs evolved de novo 10-14 times, and that the orb web evolved at least three times. These findings in fact result from a particular phylogenetic character coding strategy, specifically coding the absence of webs as logically equivalent, and homologous to, 10 other observable (i.e., not absent) web architectures. "Absence" of webs should be regarded as inapplicable data. To be analyzed properly by character optimization algorithms, it should be coded as "?" because these codes-or their equivalent-are handled differently by such algorithms. Additional problems include critical misspellings of taxon names from one analysis to the next (misspellings cause some optimization algorithms to drop terminals, which affects taxon sampling and results), and mistakes in spider natural history. In sum, the method causes character optimization algorithms to produce counter-intuitive results, and does not distinguish absence from secondary loss. Proper treatment of missing entries and corrected data instead imply that foraging webs are primitive for spiders and that webs have been lost ∼5-7 times, not gained 10-14 times. The orb web, specifically, may be homologous (originated only once) although lost 2-6 times.

Giant taxon-character matrices II: a response to Laing et al. (2017)

The trend towards big data analyses in evolutionary biology has been observed in phylogenetics via the assembly of giant datasets composed of genomic and phenotypic data. We recently (Simões et al., 2017. Giant taxon-character matrices: Quality of character constructions remains critical regardless of size. Cladistics 33, 198-219) presented a critique of the phylogenetic character concepts used in current morphological datasets, with the caution that giant datasets did not obviate the empirical requirement of rigor in character construction. Laing et al. (2017. Giant taxon-character matrices: The future of morphological systematics. Cladistics, https://doi.org/10.1111/cla.12197) have since argued that we had 'suggested' that large datasets inherently contain flawed characters, and that we had presented a substandard methodology of phylogenetic analysis. Laing et al. concluded by discussing their approach to phylogenetic signal, total evidence and the inevitability of large datasets. We here reply to Laing et al. by reviewing what we actually wrote regarding dataset size, characters and methodology. We show that Laing et al.'s. central premise is unsupported, thus characterizing a Straw Man argument, and deeply misrepresents our original study. In part two, we discuss total evidence and phylogenetic signal issues raised by Laing et al. that are of major consequence to the appropriate construction of large morphological datasets.

Towards a semantic approach to numerical tree inference in phylogenetics

Conventional approaches to phylogeny reconstruction require a character analysis step prior to and methodologically separated from a numerical tree inference step. The former results in a character matrix that contains the empirical data analysed in the latter. This separation of steps involves various methodological and conceptual problems (e.g. homology assessment independent of tree inference and character optimization, character dependencies, discounting of alternative homology hypotheses). In morphology, the character analysis step covers the stages of morphological comparative studies, homology assessment and the identification and coding of morphological characters. Unfortunately, only the last stage requires some formalism, whereas the preceding stages are commonly regarded to be pre-rational and intuitive, which is why their reproducibility and analytical accessibility is limited. Here, I introduce a rational for a semantic approach to numerical tree inference that uses sets of semantic instance anatomies as data source instead of character matrices, thereby avoiding the above-mentioned problems. A semantic instance anatomy is an ontology-based description of the anatomical organization of a specimen in the form of a semantic graph. The semantic approach to numerical tree inference combines and integrates the steps of character analysis and numerical tree inference and makes both analytically accessible and communicable. Before outlining first steps for a research programme dedicated to the semantic approach to numerical tree inference, I discuss in detail the methodological, conceptual, and computational challenges and requirements that first have to be dealt with before adequate algorithms can be developed.

Novel Approaches for Phylogenetic Inference from Morphological Data and Total-Evidence Dating in Squamate Reptiles (Lizards, Snakes, and Amphisbaenians)

Here, I combine previously underutilized models and priors to perform more biologically realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backward transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for “asymmetric.” The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical data sets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend toward recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across data sets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological data sets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.

The eyes of Tullimonstrum reveal a vertebrate affinity

Tullimonstrum gregarium is an iconic soft-bodied fossil from the Carboniferous Mazon Creek Lagerstätte (Illinois, USA). Despite a large number of specimens and distinct anatomy, various analyses over the past five decades have failed to determine the phylogenetic affinities of the 'Tully monster', and although it has been allied to such disparate phyla as the Mollusca, Annelida or Chordata, it remains enigmatic. The nature and phylogenetic affinities of Tullimonstrum have defied confident systematic placement because none of its preserved anatomy provides unequivocal evidence of homology, without which comparative analysis fails. Here we show that the eyes of Tullimonstrum possess ultrastructural details indicating homology with vertebrate eyes. Anatomical analysis using scanning electron microscopy reveals that the eyes of Tullimonstrum preserve a retina defined by a thick sheet comprising distinct layers of spheroidal and cylindrical melanosomes. Time-of-flight secondary ion mass spectrometry and multivariate statistics provide further evidence that these microbodies are melanosomes. A range of animals have melanin in their eyes, but the possession of melanosomes of two distinct morphologies arranged in layers, forming retinal pigment epithelium, is a synapomorphy of vertebrates. Our analysis indicates that in addition to evidence of colour patterning, ecology and thermoregulation, fossil melanosomes can also carry a phylogenetic signal. Identification in Tullimonstrum of spheroidal and cylindrical melanosomes forming the remains of retinal pigment epithelium indicates that it is a vertebrate; considering its body parts in this new light suggests it was an anatomically unusual member of total group Vertebrata.

Morphological cladistic analysis resolves the generic limits of the Neotropical potter wasp genera Minixi Giordani Soika and Pachyminixi Giordani Soika (Hymenoptera : Vespidae : Eumeninae)

The generic classification of Neotropical Eumeninae has been termed chaotic, and synonymisation of taxa has become constant in recent years. Recognition of some generic limits are problematic due to features showing a great deal of variation, such as the length of the first metasomal tergum. This applies to the Neotropical Alphamenes van der Vecht, Minixi Giordani Soika and Pachyminixi Giordani Soika. Minixi has already been demonstrated to be paraphyletic in regards to Pachyminixi. These taxa are the focus of the present study, which used morphological data to infer the phylogenetic relationships among their constituent species. A total of 14 taxa and 34 characters were subjected to cladistic analysis under implied weighting. A single most-parsimonious cladogram was obtained, recovering Pachyminixi as monophyletic. Minixi, however, was paraphyletic relative to Pachyminixi and they are thus synonymised, with the former name having priority. A new species from Mexico, Minixi mariachii, sp. nov., is described. Minixi joergenseni bicingulatus (Zavattari, 1912) is synonymised under M. joergenseni (Schrottky, 1909), comb. nov. Additional new combinations are: Minixi arechavaletae (Brèthes, 1903), comb. nov., M. bifasciatum (von Schulthess, 1904), comb. nov., M. brethesi (Bertoni, 1927), comb. nov., M. sumichrasti (de Saussure, 1875), comb. nov., and M. uruguyense (de Saussure, 1855), comb. nov. Illustrations and a new key to species of Minixi are provided. The present study enhances our knowledge on Neotropical potter wasp systematics, providing one further step into a natural classification for a group whose taxonomy has suffered from irrational splitting of genera in the past century.

Evolution of Metapostnotum in Flat Wasps (Hymenoptera, Bethylidae): Implications for Homology Assessments in Chrysidoidea

Some authors in the past based their conclusions about the limits of the metapostnotum of Chrysidoidea based on the position of the mesophragmo-metaphragmal muscle, rather than aspects of the skeleton and musculature associated with the metapectal-propodeal complex. The latter character system suggests another interpretation of the metapostnotum delimitation. Given this scenario, the main goal of this work is to present a new perspective on the metapostnotum in Chrysidoidea, especially Bethylidae, helping to resolve questions related to the evolution of the metapostnotum. This is based on homologies established by associating of insertion points of ph2-ph3 and ph3-T2 muscles with the delimitation of the respective sclerite the muscles insert into. Our results indicate that, according the position of the metaphragmal muscles, the metapostnotum in Bethylidae is medially expanded in the propodeal disc and has different forms of configuration. Internally, the limits of the metapostnotum can be tracked by the shape of the mesopostnotum, and vice versa. Thus, the anteromedian area of the propodeal disc sensu Evans was reinterpreted in the current study as the metapostnotum. In conjunction with associated structures, we provide evidence to clarify the relationships between the families within Chrysidoidea, although certain families like Embolemidae, Dryinidae and Chrysididae exhibit extreme modifications of the condition found in Aculeata, as observed in Bethylidae. We review the terminology used to describe anatomical features on the metapectal-propodeal complex in Bethylidae in general, and provide a list of recommended terms in accordance with the online Hymenoptera Anatomy Ontology. The morphology of the studied subfamilies are illustrated. Studies that focus on a single structure, across a larger number of taxa, are more insightful and present specific questions that can contribute to broader issues, thus providing a better understanding of the morphology and evolution of insects.

Wing base structural data support the sister relationship of megaloptera and neuroptera (insecta: neuropterida)

The phylogenetic status and the monophyly of the holometabolous insect order Megaloptera has been an often disputed and long unresolved problem. The present study attempts to infer phylogenetic relationships among three orders, Megaloptera, Neuroptera, and Raphidioptera, within the superorder Neuropterida, based on wing base structure. Cladistic analyses were carried out based on morphological data from both the fore- and hindwing base. A sister relationship between Megaloptera and Neuroptera was recovered, and the monophyly of Megaloptera was corroborated. The division of the order Megaloptera, the traditional higher classification, into Corydalidae (Corydalinae + Chauliodinae) and Sialidae, was also supported by our wing base data analyses.

The higher-level phylogenetic relationships of the Eumeninae (Insecta, Hymenoptera, Vespidae), with emphasis on Eumenes sensu lato

Cladistic analyses were carried out to infer the phylogenetic relationships among taxa that were originally part of the large genus Eumenes. Terminals belonging to other eumenine lineages were also included, as well as terminals from other vespid subfamilies. Analyses under equal weights and implied weights were carried out, and better results were obtained with the latter. The results corroborated the monophyly of Eumeninae, and recovered Zethini sensu lato as the sister-lineage to the remaining eumenines. Eumenes sensu lato as originally recognized is paraphyletic relative to Odynerus sensu lato. A natural classification at the tribal level congruent with the phylogenetic results may be proposed, and the names Zethini, Odynerini, and Eumenini are already available. This is the most comprehensive phylogeny of the Eumeninae to date. A new generic synonymy is Alfieria Giordani Soika, 1934 = Delta de Saussure, 1855.

Wing pattern diversity in Brassolini butterflies (Nymphalidae, Satyrinae)

This study describes and compares the diverse dorsal and ventral wing color patterns of Brassolini butterflies. Thirty-three species are illustrated, where pattern elements of the nymphalid ground plan are labeled in color. In general, a larger number of pattern elements can be identified on the ventral than on the dorsal surface of both wings, and the forewing has a larger number of discernible pattern elements than the hind wing. The dorsal elements are broad, diffuse, and more difficult to identify against the typically brown brassoline wing background color. Species with a light colored dorsal background served as a guide for our proposal that fewer pattern elements are present dorsally, particularly on the hind wing. Colorful bands or markings generally present on the dorsal surface seem to be associated with specific pattern elements and have correspondence to the ventral pattern. We refer to these as trailing bands, and they constitute a predominant feature of the brassoline dorsal coloration. We propose a subordinate groundplan for brassolines and interpret some of the ventral pattern variation in light of their phylogeny. Dorsal color pattern variation that leads to sexual dimorphism and mimetic resemblance are also discussed.

When can clades be potentially resolved with morphology?

Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of character information leads to a lack of 'intrinsic' resolution, an issue that cannot be solved with additional morphological data. It is unclear how often we should expect clades to be intrinsically resolvable in realistic circumstances, as intrinsic resolution must increase as taxonomic sampling decreases. Using branching simulations, I quantify intrinsic resolution across several models of morphological differentiation and taxonomic sampling. Intrinsically unresolvable clades are found to be relatively frequent in simulations of both extinct and living taxa under realistic sampling scenarios, implying that intrinsic resolution is an issue for morphology-based analyses of phylogeny. Simulations which vary the rates of sampling and differentiation were tested for their agreement to observed distributions of durations from well-sampled fossil records and also having high intrinsic resolution. This combination only occurs in those datasets when differentiation and sampling rates are both unrealistically high relative to branching and extinction rates. Thus, the poor phylogenetic resolution occasionally observed in morphological phylogenetics may result from a lack of intrinsic resolvability within groups.

The Late Triassic dinosauromorph Sacisaurus agudoensis (Caturrita Formation; Rio Grande do Sul, Brazil): anatomy and affinities

Silesauridae is an exclusively Triassic group of dinosauromorphs, knowledge on the diversity of which has increased dramatically in the last few years. Silesaurid relationships are still contentious, as a result in part of different homology statements, particularly regarding the typical edentulous mandible tip of these animals. One of the most complete silesaurids yet discovered is Sacisaurus agudoensis from the Caturrita Formation (Late Triassic: Norian) of Rio Grande do Sul, Brazil, represented by numerous isolated bones recovered from a single site. The anatomy of S. agudoensis is fully described for the first time here, and comparisons are provided to other basal dinosauromorphs. S. agudoensis is a small-bodied animal (less than 1 m in length) that possesses a dentition consisting of leaf-shaped crowns with large denticles in the carinae, a plesiomorphic propubic pelvis with an almost fully closed acetabulum, elongate distal hindlimbs suggesting well-developed cursorial ability, and a laterally projected outer malleolus in the tibia. All previous numerical phylogenies supported a non-dinosaur dinosauromorph affinity for Silesauridae, but the reanalysis of one of those studies suggests that a position within Dinosauria is not unlikely, with silesaurids forming the basal branch of the ornithischian lineage.

Understanding phylogenetic incongruence: lessons from phyllostomid bats

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.

Ontogeny and homology of the skeletal elements that form the sucking disc of remoras (Teleostei, Echeneoidei, Echeneidae)

The sucking disc of the sharksuckers of the family Echeneidae is one of the most remarkable and most highly modified skeletal structures among vertebrates. We studied the development of the sucking disc based on a series of larval, juvenile, and adult echeneids ranging from 9.3 mm to 175 mm standard length. We revisited the question of the homology of the different skeletal parts that form the disc using an ontogenetic approach. We compared the initial stages of development of the disc with early developmental stages of the spinous dorsal fin in a representative of the morphologically basal percomorph Morone. We demonstrate that the "interneural rays" of echeneids are homologous with the proximal-middle radials of Morone and other teleosts and that the "intercalary bones" of sharksuckers are homologous with the distal radials of Morone and other teleosts. The "intercalary bones" or distal radials develop a pair of large wing-like lateral extensions in echeneids, not present in this form in any other teleost. Finally the "pectinated lamellae" are homologous with the fin spines of Morone and other acanthomorphs. The main part of each pectinated lamella is formed by bilateral extensions of the base of the fin spine just above its proximal tip, each of which develops a row of spinous projections, or spinules, along its posterior margin. The number of rows and the number of spinules increase with size, and they become autogenous from the body of the lamellae. We also provide a historical review of previous studies on the homology of the echeneid sucking disc and demonstrate that the most recent hypotheses, published in 2002, 2005 and 2006, are erroneous.

A challenge to categories: “What, if anything, is a mosasaur?”

The concept of “mosasaur” is explored from the perspective of its historical origins, and tested empirically and phylogenetically in order to examine the concept in its modern application. Historical analysis of the origins of the concept of “mosasaur” makes it clear that the term bears significant historical burden (comparative anatomic, empirical, phylogenetic, paleontological, etc.). In order to address the flaws in the concept of mosasaur properly, this treatise critically assesses Camp’s [1923] diagnostic characters for Anguimorpha, Platynota, Varanoidea, and Mosasauroidea, concluding that Camp’s data permit mosasaurs to be viewed only as anguimorphans, not platynotans nor varanoids. A similar critical assessment is given for the characters used to diagnose anguimorphans and varanoids in Estes et al. [1988], concluding here that not a single character out of twenty-two is shared between varanoids and mosasaurs. The character concept developed by Romer [1956] for the “posteriorly retracted nares” of varanoids, and then later mosasaurs, is critically examined and found to be insufficient as a test of similarity of the intended primary homologs. The recent work of Rieppel et al. [2007], Conrad [2008] and Conrad et al. [2010] is critically reviewed as these authors revive the use, and subdivision, of the “posteriorly retracted nares” as a character in anguimorph phylogenetic analysis. Based on these criticisms, it is concluded here that there is no character-based evidence to support phylogenetic hypotheses that mosasaurs are derived aquatic varanoid lizards. A key recommendation of this treatise is that the hypothesis conceiving of mosasaurs as derived aquatic varanoids be abandoned. The final critical review presented in this treatise examines the taxonomic implications, relating to the concept of “mosasaur”, arising from the hypothesis of convergent paddle-like limb evolution in mosasaurs as presented by Bell and Polcyn [2005]. In conclusion, it is recognized that the concept and term “mosasaur” has ceased to exist in any biologically meaningful way, and that the future requires the construction of a new suite of terms and concepts to convey what we now think we know about these animals.