Derived Character States Research Articles

Cladistic analysis of the Paleozoic bryozoan families Monticuliporidae and Mesotrypidae

A set of 127 binary and multistate characters, weighted by the number of derived character states, degree of covariation, and level of homoplasy, was used in a cladistic analysis of type species representing 12 genera previously assigned to families Monticuliporidae and Mesotrypidae. The most parsimonious tree consisted of a 10-genus monophyletic crown group with the remaining two genera forming a basal paraphyletic stem group. The composition of the monticuliporid crown group is broadly similar to two earlier classifications while stem group membership matches the family Mesotrypidae. Phenetic groupings, based on overall morphological similarity, have memberships that are similar to those of clades but provide no means of determining the polarity of evolutionary relationships either within or between them. Finally, only the observed stratigraphic ranges of the type species of genera provide a statistically significant match with cladistic branching sequence, perhaps because current composite generic ranges reflect the mixing of species belonging to different genera. Based on cladogram topology, we propose the placement of all 12 genera into a single family Monticuliporidae.

Morphological and genetic differentiation of Bufo toads: two cryptic species in Western Europe (Anura, Bufonidae)

The Common toad Bufo bufo sensu lato is a widespread, morphologically conserved taxon. Recent studies have uncovered deep genetic differentiation between population groups, highlighting the need to revise the current taxonomy of the group and recognize additional species. Here we investigate patterns of variation in molecular (a mitochondrial DNA restriction enzyme assay and sequence data for two nuclear DNA fragments totalling 979 bp) and 17 morphological variables in Northern France where two of these groups meet (B. bufo sensu stricto and B. spinosus), in order to delineate their contact zone and uncover characters that would allow discrimination of the two taxa. Mitochondrial DNA data show an abrupt transition from areas where B. bufo is present to those inhabited by B. spinosus, with a narrow area of overlap east of the city of Caen. Morphometric characters, particularly those related to the positioning of the parotoid glands and metatarsal tubercle shape and size, proved useful in discriminating between species (AUC ≥ 0.97, kappa ≥ 0.79). We then used the differentiating character states to allocate over 300 museum specimens from Western Europe to either species with consistent results, including comparable values of AUC and kappa of the identification models, indicating that models could successfully be applied across datasets. We summarize available evidence relevant to the delineation of the distribution of B. bufo and B. spinosus in France and discuss the characters differentiating both species in an evolutionary context. In view of the observed morphological and genetic differentiation and the absence of unequivocal evidence for widespread hybridization we support the view that B. bufo and B. spinosus are best considered different species. Finally, we propose that ‘parotoids in parallel position’ and a thin and smooth skin are derived character states for B. bufo over the northern part of its range.

Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information

Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary.

North American members of the reticulata-like species group of the water mite genus Kongsbergia (Acari: Hydrachnidiae: Aturidae)

Fifteen North American species of the water mite genus Kongsbergia, 11 of which are new to science, are described andallocated to the newly proposed reticulata-like species group. This group is characterized by synapomorphic contours ofthe dorsal shield in males in the form of symmetrical ridges, an elevated hump anteromedially and a marked depressionposteromedially that bears a medial ridge with the excretory pore at its posterior end. These species are further assigned to six subgroups diagnosed by various shared derived character states of males. Adults of K. reticulata Habeeb, 1956, K.reticulata labyrintha Habeeb, 1957, and K. cyanea Habeeb, 1981 are redescribed based on examination of types and ad-ditional specimens, and all are recognized as full species. The description of adults of K. robisoni Radwell and Smith,2011, is revised slightly based on observations on specimens from recently discovered populations. Adults of 11 new spe-cies are described including K. appalachiana sp. nov., K. atkinsonae sp. nov., K. cooki sp. nov., K.crista sp. nov., K. crum-pae sp. nov., K. humeralis sp. nov., K. floridana sp. nov., K. laurentiana sp. nov., K. setosa sp. nov., K. texana sp. nov., and K. transversa sp. nov.. Distributional data and a key to males for these species are presented.

Genetic and morphological data support placement of Myrmotherula gularis (Spix) in the monotypic genus Rhopias Cabanis and Heine (Aves: Passeriformes: Thamnophilidae)

Recent DNA-based phylogenetic analyses of the family Thamnophilidae have shown that the genus Myrmotherula is polyphyletic. Traditional plumage-based taxonomy has been misleading in terms of identifying independently evolving lineages within the complex. Here, we integrate a molecular phylogeny with morphometric information and ancestral reconstruction of syringeal character states of the Musculi vocales ventrales, to investigate the taxonomic position of M. gularis, a species for which phylogenetic affinities have long been uncertain. We show that M. gularis represents a long branch in the tribe Thamnophilini that is not closely related to any other member of the Myrmotherula complex. Its relationships within the tribe remain uncertain because of the lack of phylogenetic resolution at the base of the tribe. M. gularis shares a derived character state of the M. vocalis ventralis with Taraba, Hypoedaleus, and Mackenziaena, which supports a close relationship between M. gularis and the large antshrikes. M. gularis can be diagnosed from Myrmotherula and Epinecrophylla by this condition of its M. vocalis ventralis, and from Isleria by plumage and other morphological traits. The phylogenetic and morphological distinctiveness of M. gularis does not warrant merging it into any other genus. We propose that this species be placed in a monotypic genus, for which the available name Rhopias applies.

Late Jurassic salamandroid from western Liaoning, China.

A Jurassic salamander, Beiyanerpeton jianpingensis (gen. et sp. nov.), from a recently found site in western Liaoning Province, China is the earliest known record of Salamandroidea. As a Late Jurassic record of the group, it extends the range of the clade by ~40 Ma. The Late Jurassic taxon is neotenic and represented by exceptionally preserved specimens, including fully articulated cranial and postcranial skeletons and bony gill structures close to the cheek region. The fossil beds, consisting of dark-brown volcanic ash shales of the Upper Jurassic Tiaojishan (Lanqi) Formation (Oxfordian), underlie trachyandesite rocks that have yielded a SHRIMP zircon U-Pb date of 157 ± 3 Ma. The fossiliferous beds are substantially older than the Jehol Group, including the Yixian Formation ((40)Ar/(39)Ar dates of 122-129 Ma), but slightly younger than the Middle Jurassic Daohugou horizon ((40)Ar/(39)Ar date of 164 ± 4 Ma). The early fossil taxon shares with extant salamandroids derived character states, including: separated nasals lacking a midline contact, angular fused to the prearticular in the lower jaw, and double-headed ribs on the presacral vertebrae. In contrast to extant salamandroids, however, the salamander shows a discrete and tooth-bearing palatine, and unequivocally nonpedicellate and monocuspid marginal teeth in large and presumably mature individuals. The finding provides insights into the evolution of key characters of salamanders, and also provides direct evidence supporting the hypothesis that the split between Cryptobranchoidea and Salamandroidea had taken placed before the Late Jurassic Oxfordian time. In this aspect, both paleontological and molecular data now come to agree.

New craniodental material of Pronothodectes gaoi Fox (Mammalia, “Plesiadapiformes”) and relationships among members of Plesiadapidae

Plesiadapidae are a family of Paleogene mammals thought to have phylogenetic affinities with modern Primates. We describe previously unpublished dentitions and the first skull and isolated petrosals of the plesiadapid Pronothodectes gaoi, collected from middle Tiffanian localities of the Paskapoo Formation in Alberta. Other species of Pronothodectes, traditionally considered the most basal members of the Plesiadapidae, occur at earlier, Torrejonian horizons in Montana, Wyoming, and Alberta. Classification of P. gaoi as a species of Pronothodectes has proved controversial; accordingly, we use the newly available samples and the more extensively preserved specimens to re-evaluate the generic affinities of this species. Included in our study are comparisons with craniodental material known for other plesiadapids and plesiadapiforms. Cladistic analysis of craniodental characters is used to assess the hypothesis that P. gaoi and other species in this genus are basal members of the Plesiadapidae. The new dental evidence confirms that P. gaoi lacks derived character states of other plesiadapids except for a variably present fissuring of the m3 hypoconulid. Moreover, several aspects of the cranium seem to be more primitive in P. gaoi (i.e., more like nonplesiadapid plesiadapiforms) than in later occurring plesiadapids, such as Plesiadapis tricuspidens and Plesiadapis cookei. Cladistic analysis of craniodental morphology supports a basal position of P. gaoi among species of Plesiadapidae, with the exception of other species of Pronothodectes. The basicranium of P. gaoi preserves a laterally placed bony canal for the internal carotid neurovascular system, suggesting that this was the ancestral condition for the family.

A Short-Armed Troodontid Dinosaur from the Upper Cretaceous of Inner Mongolia and Its Implications for Troodontid Evolution

BackgroundThe Troodontidae represents one of the most bird-like theropod groups and plays an important role in our understanding of avian origins. Although troodontids have been known for over 150 years, few known derived troodontid specimens preserve significant portions of both the forelimb and the hindlimb.Methodology/Principal FindingsHere, we report a new troodontid taxon, Linhevenator tani gen. et sp. nov., based on a partial, semi-articulated skeleton recovered from the Upper Cretaceous Wulansuhai Formation of Wulatehouqi, Inner Mongolia, China. L. tani has an unusual combination of primitive and derived character states, though our phylogenetic analysis places it in a derived clade within the Troodontidae. As a derived taxon, L. tani has a dromaeosaurid-like pedal digit II, and this species also possesses a humerus that is proportionally much shorter and more robust than those of most other troodontids.Conclusion/SignificanceThe combination of features present in Linhevenator indicates a complex pattern of character evolution within the Troodontidae. In particular, the discovery of Linhevenator suggests that derived troodontids have independently evolved a highly specialized pedal digit II and have significantly shortened the forelimb over the course of their evolution.

Variation, Variability, and the Origin of the Avian Endocranium: Insights from the Anatomy of Alioramus altai (Theropoda: Tyrannosauroidea)

The internal braincase anatomy of the holotype of Alioramus altai, a relatively small-bodied tyrannosauroid from the Late Cretaceous of Mongolia, was studied using high-resolution computed tomography. A number of derived characters strengthen the diagnosis of this taxon as both a tyrannosauroid and a unique, new species (e.g., endocranial position of the gasserian ganglion, internal ramification of the facial nerve). Also present are features intermediate between the basal theropod and avialan conditions that optimize as the ancestral condition for Coelurosauria—a diverse group of derived theropods that includes modern birds. The expression of several primitive theropod features as derived character states within Tyrannosauroidea establishes previously unrecognized evolutionary complexity and morphological plasticity at the base of Coelurosauria. It also demonstrates the critical role heterochrony may have played in driving patterns of endocranial variability within the group and potentially reveals stages in the evolution of neuroanatomical development that could not be inferred based solely on developmental observations of the major archosaurian crown clades. We discuss the integration of paleontology with variability studies, especially as applied to the nature of morphological transformations along the phylogenetically long branches that tend to separate the crown clades of major vertebrate groups.

Mitochondrial genome sequence of Unionicola parkeri (Acari: Trombidiformes: Unionicolidae): molecular synapomorphies between closely-related Unionicola gill mites

The mitochondrial genome of Unionicola parkeri is a 14,734 bp circular DNA molecule. The sequence and annotation revealed a unique gene order, related to but distinct from the gene order in the closely related species U. foili. Mitochondrial tRNA sequences annotated in this genome predict non-canonical secondary structures for these molecules. The continuing patterns of unique gene orders and unusual tRNA structures in the Trombidiformes in general and Unionicola in particular support the use of phylogenetic approaches that use these types of molecular features as shared, derived character states. Further progress in using these molecular character states to reconstruct phylogeny will depend on careful annotation, especially of tRNA genes.

Larval Morphology of Meruidae (Coleoptera: Adephaga) and Its Phylogenetic Implications

Abstract Meruidae, or comb-clawed cascade beetles, are a recently discovered monotypic family of Adephaga endemic to Venezuela. The larvae of Meruidae are described for the first time, based on material of Meru phyllisaeSpangler & Steiner, 2005, collected together with adults in southern Venezuela. External morphological features, including chaetotaxy, are reported for the mature larva and an assessment made of the polarity of larval characters of phylogenetic utility in Adephaga. Larvae of Meruidae possess a mixture of primitive and derived character states, and they are unique within the Adephaga in that here the mandibles are asymmetrical, the respiratory system is comprised of only two pairs of spiracles (= oligopneustic), the claws are pectinate, and the abdominal sternite VIII is prolonged overlapping the abdominal sternite IX. A parsimony analysis based on 18 informative larval characteristics was conducted with the program PAUP*. The most parsimonious trees confirm Meruidae as a relatively basal lineage within the Dytiscoidea. Both Meru Spangler & Steiner and Noteridae are hypothesized to have diverged anterior to Amphizoidae, Aspidytidae, Hygrobiidae, and Dytiscidae.

Stick insect on unsafe ground: does a fossil from the early Eocene of France really link Mesozoic taxa with the extant crown group of Phasmatodea?

The recently described Gallophasma longipalpis from Earliest Eocene French amber is considered to be a key fossil taxon that phylogenetically links ‘Mesozoic Phasmatodea’ with extant stick and leaf insects. However, our re‐evaluation of the evidence provided for this placement reveals that Gallophasma does not possess any unambiguous synapomorphies with extant forms, e.g. neither with Euphasmatodea nor with the more inclusive Phasmatodea. The fusion of abdominal segment 1 with the metathoracic segment, a derived character state present in both Gallophasma and Euphasmatodea, shows fundamental structural differences, and cannot be homologized between both taxa. We argue that the presence of a well‐developed, externally visible ovipositor and four‐segmented cerci in Gallophasma can be interpreted only as plesiomorphic with regards to all extant Phasmatodea, or even to Phasmatodea plus its putative sister groups Embioptera or Orthoptera. Gallophasma does not belong to the stem lineage of recent Phasmatodea, and is referred to best as ‘lower Neoptera’ or Polyneoptera incertae sedis. Therefore, this fossil may be central to reconstructing the ground pattern of the aforementioned orthopteroid lineages, and to determining wing character polarity within Polyneoptera.

The anatomy of the basal ornithischian dinosaur Eocursor parvus from the lower Elliot Formation (Late Triassic) of South Africa

Ornithischia is a morphologically and taxonomically diverse clade of dinosaurs that originated during the Late Triassic and were the dominant large-bodied herbivores in many Cretaceous ecosystems. The early evolution of ornithischian dinosaurs is poorly understood, as a result in part of a paucity of fossil specimens, particularly during the Triassic. The most complete Triassic ornithischian dinosaur yet discovered is Eocursor parvus from the lower Elliot Formation (Late Triassic: Norian–Rhaetian) of Free State, South Africa, represented by a partial skull and relatively complete postcranial skeleton. Here, the anatomy of Eocursor is described in detail for the first time, and detailed comparisons are provided to other basal ornithischian taxa. Eocursor is a small-bodied taxon (approximately 1 m in length) that possesses a plesiomorphic dentition consisting of unworn leaf-shaped crowns, a proportionally large manus with similarities to heterodontosaurids, a pelvis that contains an intriguing mix of plesiomorphic and derived character states, and elongate distal hindlimbs suggesting well-developed cursorial ability. The ontogenetic status of the holotype material is uncertain. Eocursor may represent the sister taxon to Genasauria, the clade that includes most of ornithischian diversity, although this phylogenetic position is partially dependent upon the uncertain phylogenetic position of the enigmatic and controversial clade Heterodontosauridae.

A New Nonmammalian Eucynodont (Synapsida: Therapsida) from the Triassic of Northern Gansu Province, China, and its Biostratigraphic and Biogeographic Implications

Abstract A new trirachodontid eucynodont, Beishanodon youngi, is named and described based on a well-preserved skull from Triassic lacustrine deposits exposed in the Beishan Hills, northern Gansu Province, China. The new discovery documents the second record of trirachodontid eucynodonts known from China, along with Sinognathus gracilis from the Middle Triassic Ermaying Formation exposed in Shanxi Province. Cladistic analysis supports the placement of the new taxon as the sister group of Sinognathus, and the two together can be classified in Sinognathinae, a new subfamily differentiated from other trirachodontids by possession of several derived character states, including extremely short snout and strongly expanded temporal region. In addition, the stratigraphic and biogeographic significance of the new discovery are discussed. Because trirachodontids have a restricted stratigraphic range in the Triassic, as best documented by the Cynognathus Assemblage Zone of South Africa, discovery of the new fossil o...

The first diplodocid from Asia and its implications for the evolutionary history of sauropod dinosaurs

Abstract: An isolated anterior caudal vertebra from the Qingshan (= Ch'ing shan) Formation (Early Cretaceous) of Shandong Province, China, is redescribed and shown to be an advanced diplodocid sauropod. This specimen possesses several derived character states that are typically observed in advanced diplodocoids or diplodocids, including the following: a mildly procoelous centrum; a deep pit‐like pneumatic fossa immediately below the caudal rib; wing‐ or fan‐shaped caudal ribs; and complex lamination of the neural spine. The neural spine is apomorphically short and the centrum is short relative to its height compared to those of other diplodocids, which, when coupled with the specimen’s unique geographical location and stratigraphical age, suggests that it probably represents a new taxon. This caudal vertebra provides the first convincing evidence that diplodocids were present in Asia, perhaps as a result of the dispersal of neosauropod lineages from Europe and/or North America during the Early Cretaceous. The discovery of a member of the Diplodocidae in the Early Cretaceous also indicates that this clade did not become extinct at the Jurassic/Cretaceous boundary as previously supposed.

The morphology of the larval head of Tipulidae (Diptera, Insecta) – The dipteran groundplan and evolutionary trends

External and internal head structures of the larva of Tipula montium are described in detail. The results are compared to conditions found in other representatives of Tipuloidea and other dipteran and antliophoran lineages. Despite of the conceivably basal position of Tipulomorpha within Diptera, the larvae are mainly characterised by derived features. The partially retracted head, the specific hemicephalic condition and several other derived character states support the monophyly of Tipuloidea. A clade comprising Tipuloidea excluding Pediciidae is suggested by the strongly retracted head, by deep dorsolateral incisions of the head capsule, by a distinctly toothed anterior premental margin, by the loss of the second extrinsic maxillary muscle, and possibly by the loss of the pharyngeal filter. Eriopterinae and Hexatominae are characterised by a tendency towards an extreme reduction of the head capsule. Limoniinae, Cylindrotomidae, and Tipulidae form a clade supported by the presence of a premaxillary suture. This implies the non-monophyly of Limoniidae. A feature shared by Cylindrotomidae and Tipulidae is the presence of a movable lacinia mobilis. However, this is arguably a plesiomorphic feature, as it also occurs in Nannochoristidae. Features of the larval head of Trichoceridae, which were included in Tipulomorpha, do not show affinities with those of Tipuloidea. Trichocerid larvae share a specialised subdivided mandible with larvae of psychodomorph groups. Tipuloidea are a highly specialised group. The characters examined did not reveal plesiomorphic features supporting a basal position, and features suggesting closer affinities with Brachycera are vague. The evolution of dipteran larval head structures was apparently strongly affected by the loss of legs and the tendency to live in cryptic habitats. Diptera are the group of Endopterygota with the highest number of apomorphic features of the larval head. The appendages are generally simplified and the muscular apparatus is strongly reduced. Specialised features evolving within dipteran lineages include specifically arranged brushes of hairs on the labrum and epipharynx, movable messores, subdivided mandibles, different mandibular brushes, and a far-reaching reduction of labial parts.

Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull

The fossil record is a unique source of evidence for important evolutionary phenomena such as transitions between major clades. Frustratingly, relevant fossils are still comparatively rare, most transitions have yet to be documented in detail and the mechanisms that underpin such events, typified by rapid large scale changes and for which microevolutionary processes seem insufficient, are still unclear. A new pterosaur (Mesozoic flying reptile) from the Middle Jurassic of China, Darwinopterus modularis gen. et sp. nov., provides the first insights into a prominent, but poorly understood transition between basal, predominantly long-tailed pterosaurs and the more derived, exclusively short-tailed pterodactyloids. Darwinopterus exhibits a remarkable 'modular' combination of characters: the skull and neck are typically pterodactyloid, exhibiting numerous derived character states, while the remainder of the skeleton is almost completely plesiomorphic and identical to that of basal pterosaurs. This pattern supports the idea that modules, tightly integrated complexes of characters with discrete, semi-independent and temporally persistent histories, were the principal focus of natural selection and played a leading role in evolutionary transitions.

Dynamic Modification of Oral Innervation During Metamorphosis in Branchiostoma belcheri, the Oriental Lancelet

The oral apparatus in lancelets undergoes a remarkable modification during larval development, especially during metamorphosis, when the oral innervation is radically altered. The larval mouth opens on the left side at the early larval stage, and a peripheral nerve network, the oral nerve ring (ONR), develops around it. The ONR enlarges as the mouth expands caudally, eventually receiving fibers from nerves as far back as the tenth on the left side. The mouth shrinks during metamorphosis, and with this change the ONR regresses; the posterior sixth to tenth nerves become freed from the connection with the ONR, whereas the fourth and fifth nerves retain their connections. This modification is the basis for the asymmetric innervation to the velum. There is no mesodermal or mesenchymal restriction for guiding nerve patterning as typically found in vertebrate cranial nerves. Rather, it seems to be the ONR, which has no counterpart in vertebrates, that plays pivotal roles for patterning the nervous system in the oral region. The oral innervation pattern in lancelets represents a derived character state that may be related to the asymmetry of the ancestral body and head.

Persisting stemma neuropils in Chaoborus crystallinus (Diptera: Chaoboridae): Development and evolution of a bipartite visual system

Stemmata or "larval" eyes are of crucial importance for the understanding of the evolution and ontogeny of the hexapod's main visual organs, the compound eyes. Using classical neuroanatomical techniques, I showed that the persisting stemmata of Chaoborus imagos are connected to persisting stemma neuropils neighboring the first and second order neuropils of the compound eyes, and therefore also the imago possesses a stemma lamina and medulla closely associated with the architecture and the developmental pattern of those of the compound eyes. The findings are compared with other arthropods, e.g. accessory lateral eyes in Amandibulata and Myriapoda, suggesting some ancestral rather than derived character states.

Genome Desertification in Eutherians: Can Gene Deserts Explain the Uneven Distribution of Genes in Placental Mammalian Genomes?

The evolution of genome size as well as structure and organization of genomes belongs among the key questions of genome biology. Here we show, based on a comparative analysis of 30 genomes, that there is generally a tight correlation between the number of genes per chromosome and the length of the respective chromosome in eukaryotic genomes. The surprising exceptions to this pattern are placental mammalian genomes. We identify the number and, more importantly, the uneven distribution of gene deserts among chromosomes, i.e., long (>500 kb) stretches of DNA that do not encode for genes, as the main contributing factor for the observed anomaly of eutherian genomes. Gene-rich placental mammalian chromosomes have smaller proportions of gene deserts and vice versa. We show that the uneven distribution of gene deserts is a derived character state of eutherians. The functional and evolutionary significance of this particular feature of eutherian genomes remains to be explained.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-009-9251-4) contains supplementary material, which is available to authorized users.