Character State Transformations Research Articles

A new classification of the family Ariidae (Osteichthyes: Ostariophysi: Siluriformes) based on combined analyses of morphological and molecular data

AbstractWe present a new classification of the catfish family Ariidae based on a total-evidence hypothesis, which incorporates data from the examination of 249 morphological and 5603 molecular characters from 131 species. The named taxa in the proposed classification represent groups of species found in the Maximum Parsimony, Maximum Likelihood, and Bayesian Inference analyses or, in some cases, two of the three methods. Each named taxon is provided with a diagnosis derived from a comprehensive summary of the morphological characters and their character-state transformations, as interpreted from the most parsimonious version of the total-evidence tree. Taxa newly named herein are: Cathoropsini, new tribe; Genidentini, new tribe; Sciadeini, new tribe; Aceroichthys, new genus (type species Arius dioctes Kailola, 2000); Bleekeriella, new genus (type species Arius leptaspis Bleeker, 1862); Betancurichthys, new genus (type species Arius madagascariensis Vaillant, 1894); Jayaramichthys, new genus (type species Arius leptonotacanthus Bleeker, 1849); Kyataphisa, new genus (type species Pimelodus nenga Hamilton, 1822); Megalosciades, new genus (type species Arius augustus Roberts, 1978); Paracinetodus, new genus (type species Arius carinatus Weber, 1913); Papuarius, new genus (type species Arius latirostris Macleay, 1883); and Pseudosciades, new genus (type species Arius sona Hamilton, 1822). A key to the genera of Ariidae is presented.

Comparative morphology and evolution of the cranial musculature in bees (Hymenoptera: Apoidea)

Comparative morphological studies in bees are mostly restricted to the skeleton, and the musculature of bees has not been explored much from this perspective. Here we investigate the head extrinsic musculature under an evolutionary perspective. The musculature of 34 bee species belonging to six major lineages and 26 tribes plus two apoid wasps is described, illustrated, and compared. A standardized terminology for the extrinsic musculature is proposed and aligned with the Hymenoptera Anatomy Ontology (HAO). A total of 12 characters derived from the analysis were optimized onto a summary phylogenetic tree. The musculature was found to be conserved among the main bee lineages, and most variation was found in the proboscis; no modification was found in antennal muscles. Four characters are interpreted as synapomorphies for bees, one for the long-tongued bees, three for Halictinae, and one for Megachilinae. We also found that the Apinae clade of cleptoparasites is supported by some character state transformations and that stingless bees have a unique posterior fronto-pharyngeal muscle. Both sexes display similar morphology, except for having two fixed attachment points for the anterior cranio-mandibular muscle in the males of Andreninae. This study provides a foundation for future investigations on bee head musculature on various taxonomic levels.

Phylogenetic analysis and evolutionary morphology of wings in the genus Cenophengus LeConte, 1881 (Coleoptera: Phengodidae: Mastinocerinae) based on morphological characters

The genus Cenophengus LeConte (1881) includes 27 species, distributed from southern United States to northern Costa Rica. In order to test the monophyly of Cenophengus, a cladistic analysis based on 81 morphological characters, 28 species of Cenophengus and 27 outgroup species was conducted. A clade supported by three synapomorphies corresponds to Cenophengus as a monophyletic group according to the relationships obtained under both equaland implied weights. The systematic relevance of the coding of the characters from the wing is discussed and the sequence of the character state transformations for the veins (radial twenty [r3], posterior radial twenty [RP] size, and anterior cubital veins [CuA]) is optimized in the cladogram obtained under implied weights. Cenophengus species are distributed in the Nearctic and Neotropical regions, and particularly in the Mexican Transition Zone, where their greatest diversity is found.

The use of plant ontologies in comparative and evolutionary studies should be flexible

The use of plant ontologies in comparative and evolutionary studies should be flexible

Cladistics analysis of Calycanthaceae on the basis of morphological and anatomical characters

Cladistics analysis was carried out to find the correct phylogenetic relationship of the four genera of Calycanthaceae. Morphological and anatomical information from all aspect of the data were considered for the analysis. Siparuna guianensis (Siparunaceae) and Cinnamomum malabatrum (Lauraceae) were considered as out-group. Characters were selected mainly for reasonable argument of the similarity. Character-state transformation and discrimination of the genera were decided based upon the out-group comparison method. PAUP* (ver. 4.0) program was used for the dataset analysis and to make phylogenetic tree. The genera split into two separate genera Idiospermum + Chimonanthus and Sinocalycanthus + Calycanthus. Chimonanthus + Idiospermum are supported strict consensus tree with f-value calculation. Furthermore, Sinocalycanthus and Calycanthus are separated genera. Therefore, Calycanthaceae be redefined wide circumscriptions of the characters. The detailed investigation of the cladistics analysis revealed that the Sinocalycanthus and Calycanthus are the sole genus. DOI: http://dx.doi.org/10.5281/zenodo.3908965 Keywords: Calycanthaceae, Characters and characters state, Cladistics, Out-group, Phylogeny

A revision of the early neotheropod genusSarcosaurusfrom the Early Jurassic (Hettangian–Sinemurian) of central England

AbstractNeotheropoda represents the main evolutionary radiation of predatory dinosaurs and its oldest records come from Upper Triassic rocks (c. 219 Mya). The Early Jurassic record of Neotheropoda is taxonomically richer and geographically more widespread than that of the Late Triassic. The Lower Jurassic (upper Hettangian–lower Sinemurian) rocks of central England have yielded three neotheropod specimens that have been assigned to two species within the genus Sarcosaurus, S. woodi (type species) and S. andrewsi. These species have received little attention in discussions of the early evolution of Neotheropoda and recently have been considered as nomina dubia. Here, we provide a detailed redescription of one of these specimens (WARMS G667–690) and reassess the taxonomy and phylogenetic relationships of the genus Sarcosaurus. We propose that the three neotheropod specimens from the Early Jurassic of central England represent a single valid species, S. woodi. The second species of the genus, ‘S. andrewsi’, is a subjective junior synonym of the former. A quantitative phylogenetic analysis of early theropods recovered S. woodi as one of the closest sister-taxa to Averostra and provides new information on the sequence of character state transformations in the lead up to the phylogenetic split between Ceratosauria and Tetanurae.

No background in biology is assumed

No background in biology is assumed

Outgroup sampling in phylogenetics: Severity of test and successive outgroup expansion

Outgroup sampling is a fundamental step in the design of phylogenetic analyses, independent of optimality criterion, taxonomic group, or source of evidence. Studies have demonstrated the efficient analysis of many thousands of terminals, all of which could be included in any empirical investigation, yet outgroup samples typically include only a small number of terminals. Most discussion of outgroup sampling centers on employing “correct” or “appropriate” outgroup terminals to increase “accuracy” or “reliability” by preventing “errors” such as long branch attraction and “incorrect” ingroup rooting. As an alternative, I develop a theory of outgroup sampling grounded in the logic of scientific discovery, whereby the objective is to test nested hypotheses of ingroup topology and character-state transformation as severely as possible by incorporating outgroup terminals in unconstrained, simultaneous analysis, using background knowledge to select the terminals that have the greatest chance of refuting those hypotheses. This framework provides a logical basis for selecting outgroup taxa but does not provide grounds for limiting the outgroup sample, given that, ceteris paribus, testability and explanatory power increase with the inclusion of additional terminals. Therefore, I propose the ancillary procedure of successively expanding the outgroup sample until ingroup hypotheses become stable (insensitive) to increased sampling, with each expansion guided by the scientific objectives of outgroup sampling. This is a heuristic procedure that does not prevent more outgroup terminals from being sampled or guarantee that ingroup hypotheses will remain insensitive to further outgroup expansion, and it has no bearing on the objective support of a given hypothesis. Nevertheless, it provides an objective, empirical basis for limiting outgroup sampling in a given research cycle. I illustrate this procedure by examining the effect of successive outgroup expansion on the relationships among the poison frog genera Adelphobates, Dendrobates, and Oophaga.

Histology of sculptured cranial dermal bones of the stem salamander Kokartus honorarius (Amphibia: Caudata) from the Middle Jurassic of Kyrgyzstan

Kokartus honorarius from the Middle Jurassic (Bathonian) of Kyrgyzstan is one of the oldest and basalmost salamanders in the fossil record, and this taxon is useful for documenting a primitive caudate condition and patterns of character state transformations within Caudata. Here, we provide a histological analysis of its dermal bones based on two thin sections of a fragment of a sculptured dermal skull roof bone (squamosal?). The dermal bone histology of Kokartus is similar to that of basal crown-group tetrapods (e.g. temnospondyls, lepospondyls and seymouriamorphs) in the following features: the presence of basic pattern of organisation of dermal bones (diploë structure); the cancellous middle region occupies larger space than the compact cortices; active remodelling with the formation of numerous erosion bays and secondary osteons; high number of vascular canals with the formation a dense vascular network (= ‘rete vasculosum’); and parallel-fibred bone is a dominant type of primary bone matrix. Crown-group salamanders retained the diploë structure, but demonstrate features of simplification (in comparison with Kokartus): absence of pronounced sculpture, lower degree of vascularisation and lower degree of remodelling. The simplification of the histological structure is a derived feature for the Caudata which appeared during the transition from stem-group to crown-group salamanders.

Ultrastructural study of the female gametophyte and the epistase in Cabombaceae and Nymphaeaceae

Ultrastructural studies on the female gametophyte are restricted to species at relatively derived positions in the angiosperm phylogenetic tree. Therefore, this topic remains mostly unknown for the early-divergent lineages, in which a four-celled megagametophyte is common. Here, ultrastructure of the megagametophyte and micropylar nucellar epidermis was investigated in Cabomba caroliniana A. Gray (Cabombaceae), Nymphaea gardneriana Planch. and Victoria cruziana Orb. (Nymphaeaceae). The micropylar nucellar epidermis of the studied species differentiates into an epistase. These cells have metabolically active cytoplasm and thickened inner tangential walls. Epistase ultrastructure is compatible with a transfer cell specialization. This tissue may play an adaptive role in the secretion of chemotropic substances to direct the pollen tube growth toward the female gametophyte. The cytological characteristics of the female germ unit in members of Cabombaceae and Nymphaeaceae are generally similar to other angiosperms that develop a typical seven-celled, eight-nucleate female gametophyte; however, they differ in some specific points. In V. cruziana and N. gardneriana, the micropylar end of the synergids develops a rudimentary filiform apparatus with slight inward projections. By contrast, the synergids lack a filiform apparatus in C. caroliniana. Unlike most studied angiosperms, the filiform apparatus in the clade Cabombaceae-Nymphaeaceae is underdeveloped or absent, therefore character state transformations have occurred within basal angiosperms. The potential evolutionary shifts of this reproductive feature are highlighted.

Bony ornamentation of the catfish pectoral-fin spine: comparative and developmental anatomy, with an example of fin-spine diversity using the Tribe Brachyplatystomini (Siluriformes, Pimelodidae)

The anatomy and development of the siluriform pectoral-fin spine is described, illustrated and a terminology is suggested for its parts. Catfish pectoral-fin spines exhibit considerable diversity of size, shape, robustness, surface texture and, especially, details of the dentated or serrated anterior and posterior margins. This study illustrates the variety, and taxonomic and phylogenetic significance of pectoral-fin spine diversity in the South American goliath catfishes of the tribe Brachyplatystomini, family Pimelodidae, based on examination of spines of post-juvenile and adult specimens representing all eight living species of Brachyplatystoma and Platynematichthys. Unique pectoral-spine characters and character combinations serve to distinguish all eight species. Features of the pectoral-spines that change with growth are also described. Within the current phylogenetic framework of Pimelodidae, brachyplatystomines show character-state transformations and synapomorphies of the pectoral-fin spines that support hypotheses of monophyly for the subgenera Malacobagrus (B. rousseauxii, B. filamentosum, B. capapretum), and Goslinia (new usage) (B. platynemum, B. juruense), and also suggest a close relationship between B. tigrinum and subgenus Goslinia. Platynematichthys notatus and B. vaillantii retain relatively plesiomorphic features of the pectoral-fin spines.

Phylogenetics and evolutionary morphology of the Neotropical true bug genus Epipolops (Hemiptera: Heteroptera: Geocoridae)

AbstractSpecies of Epipolops Herrich‐Schaeffer (Hemiptera: Geocoridae), comprising the largest genus of Pamphantinae, are among the most bizarre true bugs because of their striking morphology. To elucidate evolutionary morphology in Epipolops, a phylogenetic analysis was performed using 17 species and 36 adult morphological characters. Two cladograms were obtained under equal and implied weight analyses, showing slight differences between them. Two new species, E. stridulatus sp.n. and E. univallensis sp.n., are described, and E. meridionalis Pirán is resurrected from synonymy with E. frondosus Herrich‐Schaeffer. A key to the known species of Epipolops is provided. The systematic relevance of the unique characters of the genus is discussed and the sequence of character state transformations for both the anterior and posterior lateral processes of the pronotum are optimized on the cladogram obtained under implied weights. Species of Epipolops are found in the Neotropical region and the Mexican Transition Zone, with some clades and species restricted to certain South American subregions.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:CB72D5DA‐D86B‐4B91‐93A2‐88894F7120C9.

Emended diagnosis and phylogenetic relationships of the Upper Cretaceous fossil snake Najash rionegrina Apesteguía and Zaher, 2006

ABSTRACT—The fossil snake Najash rionegrina, from the Cenomanian–Turonian (Upper Cretaceous) of Argentina, is reinterpreted after examination of the type and referred material. The current diagnosis is emended in the light of important considerations that cast doubt on the attribution of type and referred specimens (a braincase, a quadrate, and two dentary/lower jaw fragments) used to systematize this taxon. Alternative interpretations of the anatomy of the sacrum and hind limbs are proposed. Following the reevaluation of the anatomy of the type specimen and the removal from this taxon of the above-mentioned referred material, the phylogenetic position of N. rionegrina was tested in a series of maximum parsimony analyses that included all groups of extant snakes, all best-known fossil snakes (i.e., Pachyrhachis, Haasiophis, Eupodophis, Madtsoiidae, and Dinilysia), and alternative outgroups. Regardless of the outgroup used to polarize the character-state transformations, our phylogenetic analyses found no support for the hypothesis that Najash rionegrina occupies a position as the most basal snake. Depending on the outgroup, Najash is placed (1) in a position basal to all living snakes, but more derived than other fossil forms (most notably Pachyrhachis, Eupodophis, and Haasiophis); or (2) as the most basal representative of a clade of fossil snakes that is the sister group of living snakes; or (3) as the most basal representative of a clade of fossil snakes that is located between the Scolecophidia and the Alethinophidia. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP

Evolutionary morphology of the hemolymph vascular system in scorpions: A character analysis

Phylogenetically informative characters from the internal anatomy of scorpions were first reported more than 150 years ago, but the subject received little attention after the mid-1920s. Recent investigations, using traditional dissection, illustration and histological sectioning, microscopy, and innovative new methods for investigating complex soft tissue anatomy identified a new wealth of variation. Additionally, these investigations confirmed the phylogenetic significance of previously identified structures. Building on earlier work we present a more detailed description of the hemolymph vascular system (HVS) in scorpions, based on comparison of the vascular structures of the heart and the branching pattern of the prosomal arteries among 45 exemplar species representing most of the major scorpion lineages. Using corrosion-casting, MicroCT in combination with computer-aided 3D-reconstruction, and scanning electron microscopy, we conceptualize a series of phylogenetically informative characters for the anterior aorta system and characters of the heart and associated structures (e.g. arrangement of the ostia) of scorpions. Furthermore, we optimize the possible evolution of these new characters on a previous hypothesis of scorpion phylogeny, and discuss alternative character state transformations, their evolutionary consequences, and possible underlying evolutionary mechanisms acting on the HVS.

A priori assumptions about characters as a cause of incongruence between molecular and morphological hypotheses of primate interrelationships

When molecules and morphology produce incongruent hypotheses of primate interrelationships, the data are typically viewed as incompatible, and molecular hypotheses are often considered to be better indicators of phylogenetic history. However, it has been demonstrated that the choice of which taxa to include in cladistic analysis as well as assumptions about character weighting, character state transformation order, and outgroup choice all influence hypotheses of relationships and may positively influence tree topology, so that relationships between extant taxa are consistent with those found using molecular data. Thus, the source of incongruence between morphological and molecular trees may lie not in the morphological data themselves but in assumptions surrounding the ways characters evolve and their impact on cladistic analysis. In this study, we investigate the role that assumptions about character polarity and transformation order play in creating incongruence between primate phylogenies based on morphological data and those supported by multiple lines of molecular data. By releasing constraints imposed on published morphological analyses of primates from disparate clades and subjecting those data to parsimony analysis, we test the hypothesis that incongruence between morphology and molecules results from inherent flaws in morphological data. To quantify the difference between incongruent trees, we introduce a new method called branch slide distance (BSD). BSD mitigates many of the limitations attributed to other tree comparison methods, thus allowing for a more accurate measure of topological similarity. We find that releasing a priori constraints on character behavior often produces trees that are consistent with molecular trees. Case studies are presented that illustrate how congruence between molecules and unconstrained morphological data may provide insight into issues of polarity, transformation order, homology, and homoplasy.

Species-level phylogenetic analysis of pterocephaliids (Trilobita, Cambrian) from the Great Basin, western USA

Considerable systematic work devoted to late Cambrian trilobites includes very little species-level phylogenetic analysis. This paper presents the phylogenetic analysis of 36 species representing eight genera assigned to the Family Pterocephaliidae that occur in the Great Basin of the western United States during the Steptoean stage (Furongian). Continuous characters are treated in four different ways: discretization using finite mixture coding, discretization using gap-weighting, “as such” using ranges of values as implemented in the phylogeny program TNT, and exclusion altogether. Results indicate that even the inclusion of only a few continuous characters dramatically increases the resolution of nodes. Despite the different treatments of continuous characters, major features of the trees are shared across all results. The subfamily Pterocephaliinae is restricted to genera which possess a concave anterior border. Relative stratigraphic placement was estimated using a composite section built in CONOP and used to scale the tree topologies and to assess stratigraphic consistency. Although previously hypothesized multispecies evolutionary series are not supported by the results, tree topology, stratigraphic distribution, and optimized character state transformation support the interpretation of several sister taxa as direct ancestor-descendent pairs.

Slippery when wet: Phylogeny and character evolution in the gelatinous cyanobacterial lichens (Peltigerales, Ascomycetes)

Many lichen fungi form symbioses with filamentous Nostoc cyanobacteria, which cause the lichen to swell and become extremely gelatinous when moist. Within the Lecanoromycetes, such gelatinous lichens are today mainly classified in the Collemataceae (Peltigerales, Ascomycota). We performed Bayesian MCMC, maximum likelihood, and maximum parsimony analyses of three independent markers (mtSSU rDNA, nuLSU rDNA, and RPB1), to improve our understanding of the phylogeny and classification in the Peltigerales, as well as the evolution of morphological characters that have been used for classification purposes in this group. The Collemataceae and the non-gelatinous Pannariaceae are paraphyletic but can be re-circumscribed as monophyletic if Leciophysma, Physma, Ramalodium and Staurolemma are transferred to the Pannariaceae. The gelatinous taxa transferred to the Pannariaceae deviate from other Collemataceae in having simple ascospores, and several also have a ring-shaped exciple as in other Pannariaceae, rather than the disc-shaped exciple found in the typical Collemataceae. Both Collema and Leptogium are non-monophyletic. The re-circumscribed Collemataceae shares a distinct ascus type with the sister group Placynthiaceae and the Coccocarpiaceae, whereas Pannariaceae includes a variety of structures. All Pannariaceae have one-celled ascospores, whereas all Collemataceae have two- or multi-celled spores. Reconstructions of the number of character state transformations in exciple structure, thallus gelatinosity, and ascus apex structure indicate that the number of transformations is distinctly higher than the minimum possible. Most state transformations in the exciple took place from a ring-shaped to a disc-shaped exciple. Depending on the reconstruction method, most or all transformations in thallus structure took place from a non-gelatinous to a gelatinous thallus. Gains and losses of internal structures in the ascus apex account for all or a vast majority of the number of transformations in the ascus, whereas direct transformations between asci with internal structures appear to have been rare.

LEAF SHAPE EVOLUTION IN THE SOUTH AFRICAN GENUSPELARGONIUML’ HÉR. (GERANIACEAE)

Leaf shapes reflect complex assemblages of shape-determining elements, yet evolutionary studies tend to treat leaf shape as a single attribute, for example cordate or linear. As with all complex structures, individual elements of a leaf could theoretically evolve independently and at different rates to the extent permitted by genetic and functional limitations. We examined relative evolutionary lability of shape-determining elements in the highly diverse South African plant genus Pelargonium (Geraniaceae). We used SIMMAP to calculate Bayesian posterior probabilities for ancestral states of leaf-shape characters for major nodes across multiple phylogenetic trees. Trees were derived from a Bayesian analysis of DNA sequence data from four partitions. We found that shape elements differed in rates of character-state transformations across the tree. Leaf base, apex, and overall outline had low rates. Transformations in venation occurred at slightly higher rates and were associated with shifts in venation among major clades. Leaf margin type and overall leaf size showed intermediate rates, whereas high rates were observed in the extent of lamina lobing and functional leaf size. The results indicate that suites of elements characteristic of the recently evolved xerophytic lineage, for example pinnate venation, dissected lamina, and entire margins, were acquired piecemeal over nested levels of the phylogeny.

How to identify (as opposed to define) a homoplasy: Examples from fossil and living great apes

There is much debate on the definitions of homoplasy and homology, and on how to spot them among character states used in a phylogenetic analysis. Many advocate what I call a “processual approach,” in which information on genetics, development, function, or other criteria help a priori in identifying two character states as homologous or homoplastic. I argue that the processes represented by these criteria are insufficiently known for most organisms and most characters to be reliably used to identify homoplasies and homologies. Instead, while not foolproof, phylogeny should be the ultimate test for homology. Character states are assumed to be homologous a priori because this is falsifiable and because their initial inclusion in the character-state analysis is based on the assumption that they may be phylogenetically informative. If they fall out as symplesiomorphies or synapomorphies in a phylogenetic analysis, their status as homologies remains unfalsified. If they fall out as homoplasies, having evolved independently in more than one clade, their status as homologous is falsified, and a homoplasy is identified. The character-state transformation series, functional morphology, finer levels of morphological comparison, and the distribution and correlation of characters all help to explain the presence of homoplasies in a given phylogeny. Explaining these homoplasies, and not ignoring them as “noise,” should be as much a goal of phylogenetic analysis as the production of a phylogeny. Examples from the fossil record of Miocene hominoids are given to illustrate the advantages of a process-informs-pattern-recognition-after-the-fact approach to understanding the evolution of character states.

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

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