Phylogenetic analysis of Russian Permian dicynodonts (Therapsida: Anomodontia): implications for Permian biostratigraphy and Pangaean biogeography

Dicynodont therapsids have been known from the Upper Permian of Eastern Europe since the beginning of the twentieth century, but the phylogenetic relationships of these taxa have not been examined cladistically. Here we present the results of a phylogenetic analysis that includes eight Permian dicynodonts from Russia as well as 18 taxa best known from southern Africa. Our results do not conflict with much of the established picture of Permian dicynodont phylogeny, but are consistent with several novel hypotheses. Most importantly, our analysis suggests that the genus Dicynodon is paraphyletic, and we question its use in correlating widely separated basins. However, we cannot strongly reject a monophyletic Dicynodon . Our results also indicate that the closest Permian relatives of Kannemeyeria lived in Russia, suggesting a Laurasian origin for the lineage that includes this important Triassic taxon. The phylogeny presented here also suggests a Laurasian origin for several other dicynodont clades, but a Gondwanan origin is equally likely given the data at hand. Regardless of where these groups originated, there appears to be some endemism among Late Permian dicynodont faunas. Although our understanding of dicynodont phylogeny is improving, this study emphasizes the disparity in sampling of the dicynodont record between Gondwana and Laurasia and the need for a large scale phylogenetic analysis of Permian and Triassic dicynodonts.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 139 , 157−212.     

The basicranium of dicynodonts (Synapsida) and its use in phylogenetic analysis

Current phylogenetic hypotheses for the dicynodonts conflict, probably because the characters used, especially those of the jaws and facial region, show considerable convergence. Characters of the braincase and basipterygoid articulation of the Late Permian–Middle Triassic dicynodonts Diictodon , Dicynodon , Kingoria, Lystrosaurus , Rechnisaurus , and 14 other genera, may have phylogenetic value. Parsimony analysis and the character compatability permutation test suggest, at the highest possible confidence level, that the data set contains significant hierarchical structure, interpreted as a result of phylogeny. The most parsimonious tree broadly agrees with all recent hypotheses on the relationships among dicynodonts. However, it conflicts with the recent suggestion that Lystrosaurus is part of a clade of Middle–Late Triassic dicynodonts, but supports the basal position of Kingoria . The use of Eodicynodon as an outgroup does not perturb the parsimonious relationship of the included taxa. Topological constraints reveal that phylogenetic hypotheses based only on basicranial characters are not robust. Characters of the basipterygoid articulation and inner braincase have high consistency and retention indices, which suggests that the main evolutionary transformations in the dicynodont basicranium occurred within these structures.     

The jaw function and adaptive radiation of the dicynodont mammal-like reptiles of the Karoo basin of South Africa

The structure and functioning of the dicynodont jaw system are described. A pivoting action of the lower jaw around the palate posteromedian to the caniniform processes is as basic to the jaw movement as is the well-known double-convex jaw articulation. The sequence of origin of the characteristic features of the dicynodonts is analysed cladistically; this demonstrates the patterns of association of these characters into functional character-complexes. The structures of the palate and lower jaw, and their functional integration in feeding, are described and illustrated in standard format. Five different lineages of dicynodont can be identified: Eodicynodon; the robertoids (including Diictodon ); the dicynodontoids (including Dicynodon and the majority of the large dicynodont genera of the Permian and Triassic); the endothiodontoids (including Prodicynodon [='Chelydontops'] and Pristerodon ), and the emydopoids (including Cistecephalus, Myosaurus and Kingoria ). Eodicynodon or a similar form could have been ancestral to the other four lineages. The robertoids probably fed upon the stems and rhizomes of equisetaleans, while the varied dicynodontoids probably fed upon the varied glossopterid seed-ferns. The endothiodontoids, too, were probably herbivorous, but many, perhaps all, of the small emydopoids were burrowing and may have been omnivorous. The dicynodonts were probably ectothermal, and the dicynodontoids may have migrated to warmer latitudes in the winter. Only c. 20 genera of Karoo dicynodont are now recognized as valid, and it is suggested that this fauna is now almost completely known. Their distribution in the Karoo biozones is reviewed and correlated with environmental changes. The Permian ancestors of the Triassic dicynodonts, including Lystrosaurus , probably lived on higher, drier ground, and were therefore already adapted to the more fibrous food that spread into the basins as the climate became drier in the Triassic.     

The skull and the palaeoecological significance of Labidosaurus hamatus, a captorhinid reptile from the Lower Permian of Texas

The cranial skeleton of the large captorhinid reptile Labidosaurus hamatus , known only from the Lower Permian of Texas, is described on the basis of new, undescribed specimens. Labidosaurus is distinguished from other captorhinids by the more extreme sloping of the ventral (alveolar) margin of the premaxilla, a low dorsum sellae of the parabasisphenoid, a reduced prootic, a narrow stapes, and a relatively small foramen intermandibularis medius. Despite the presence of a single row of teeth in each jaw, the skull of Labidosaurus resembles most closely those of moradisaurines, the large multiple-tooth-rowed captorhinids of the latest Early and Middle Permian. A phylogenetic analysis confirms that the single-tooth-rowed L. hamatus is related most closely to moradisaurines within Captorhinidae, a relationship that supports the hypothesis of a diphyletic origin for multiple rows of marginal teeth in captorhinids (in the genus Captorhinus and in the clade Moradisaurinae). In view of the close relationship between L. hamatus and moradisaurines, which are regarded to have been herbivorous, L. hamatus is a critical taxon for studies of the evolution of herbivory in early tetrapods. L. hamatus shares several trademark features of herbivorous adaptation with moradisaurines, which suggest that this captorhinid species was omnivorous. As such, it represents a transitional taxon between faunivorous basal reptiles and the herbivorous moradisaurines.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 237–262.     

Revisiting the contribution of larval characters to an analysis of phylogenetic relationships of basal anurans

The higher-level relationships of anurans have been explored by numerous studies, producing a variety of hypotheses. The relationships of the basal anurans ('archaeobatrachians') are, however, poorly known . In part, this may be because the adult morphology of basal anurans is derived and therefore may not provide suitable phylogenetic signal. Recently, several authors have shown the phylogenetic utility of information derived from anuran larvae. In this paper we conduct separate and combined analyses of anuran relationships based on adult and larval morphology. Our combined results suggest that anurans form two major clades − the pipoids and all other frogs. Evidence also suggests that, taken together, Neobatrachia and Pelobatoidea form a monophyletic group. We discuss support for various groupings as shown by the different data sets. We also comment on the consequences of our phylogenetic hypothesis for the interpretation of reduction of vertebral elements and evolution of Orton's tadpole types in anurans.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 139 , 129−155.     

Ecological diversification and phylogeny of emydid turtles

Ecological diversification is a central topic in ecology and evolutionary biology. We undertook the first comprehensive species-level phylogenetic analysis of Emydidae (an ecologically diverse group of turtles), and used the resulting phylogeny to test four general hypotheses about ecological diversification. Phylogenetic analyses were based on data from morphology (237 parsimony-informative characters) and mitochondrial DNA sequences (547 parsimony-informative characters) and included 39 of the 40 currently recognized emydid species. Combined analyses of all data provide a well-supported hypothesis for intergeneric relationships, and support monophyly of the two subfamilies (Emydinae and Deirochelyinae) and most genera (with the notable exception of Clemmys and Trachemys ). Habitat and diet were mapped onto the combined-data tree to test fundamental hypotheses about ecological diversification. Using continuous coding of ecological characters showed that lineages changed in habitat before diet, ecological change was most frequently from generalist to specialist, and habitat and diet rarely changed on the same branch of the phylogeny. However, we also demonstrate that the results of ancestral trait reconstructions can be highly sensitive to character coding method (i.e. continuous vs. discrete). Finally, we propose a simple model to describe the pattern of ecological diversification in emydid turtles and other lineages, which may reconcile the (seemingly) conflicting conclusions of our study and two recent reviews of ecological diversification.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 577–610.     

The geography of diversification in the mormoopids (Chiroptera: Mormoopidae)

The traditional explanation of the distribution of the Mormoopidae is that this family originated in southern Central America or northern South America, later expanding its range north to Mexico and the West Indies, and differentiating into eight species. An alternative fossil-based hypothesis argues that the family originated in the northern Neotropics, reached the Caribbean early in its history, and dispersed to South America after the completion of the Isthmus of Panama. The present study analyses new and previously published sequence data from the mitochondrial 12S, tRNA^val, 16S, and cytochrome b , and the nuclear Rag 2, to evaluate species boundaries and infer relationships among extant taxa. Fixed differences in cytochrome b often coincide with published morphological characters and show that the family contains at least 13 species. Two additional, morphologically indistinct, lineages are restricted to Suriname and French Guiana. Phylogeny-based inferences of ancestral area are equivocal on the geographical origin of mormoopids, in part because several internal nodes are not resolved with the available data. Divergences between Middle American and Antillean populations are greater than those between Mexico/Central America and South America. This suggests that mormoopids diversified in northern Neotropics before entering South America. A northern neotropical origin for mormoopids is congruent with both the Tertiary fossil record and recent phylogenetic hypotheses for the sister family to the Mormoopidae, the Phyllostomidae.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 101–118.     

Systematics and biogeography of the New World species of Trichadenotecnum Enderlein (Insecta: Psocodea: 'Psocoptera': Psocidae)

The taxonomy of the New World species of the genus Trichadenotecnum is revised. A total of 44 species, including 29 new species, were treated. These species are classified into 12 monophyletic species groups, eight of them newly proposed here. Two species previously assigned to Trichadenotecnum , T. pichincha New & Thornton and T. sylvaticum Turner, are recognized as not belonging to this genus. Phylogenetic relationships among 16 previously and presently proposed species groups are estimated based on a data matrix of 58 morphological characters. Trees from these analyses support monophyly of Trichadenotecnum and the proposed species groups. The New World species were divided into three major clades. Based on the phylogenetic hypothesis and distributional pattern of the species groups, the biogeographical history of the New World Trichadenotecnum is discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 651–723.     

Cranial anatomy and phylogenetic position of Suminia getmanovi, a basal anomodont (Amniota: Therapsida) from the Late Permian of Eastern Europe

Suminia getmanovi , a recently discovered basal anomodont from the Late Permian of Russia, is characterized by robust, 'leaf-shaped' teeth, and a masticatory architecture that is similar to that of the highly diverse and cosmopolitan group of Permo-Triassic herbivores, Dicynodontia (Anomodontia). Based on new material, the skull is reconstructed in three dimensions and described in detail. A cladistic analysis of the basal anomodonts, Patranomodon, Galeops, Otsheria, Ulemica , and Suminia , using 37 cranial characters, resulted in a single most parsimonious tree, in which Suminia is united with the Russian taxa, Ulemica and Otsheria. This clade, diagnosed by four unambiguous characters, is designated as Venyukovioidea. The South African anomodont, Galeops , appears as the sister taxon to Dicynodontia. Patranomodon is the most basal anomodont. The cladistic analysis suggests that a 'dicynodont-type' masticatory architecture, with an expanded adductor musculature and sliding jaw articulation, may have originated prior to the advent of the (Venyukovioidea + ( Galeops + Dicynodontia)) clade.     

Ecological niche differentiation in the Aphelocoma jays: a phylogenetic perspective

The Aphelocoma jays have become an important touchstone in behavioural ecology and biogeography – the corpus of studies of this genus makes it an important point of reference. Aphelocoma evolutionary history, nevertheless, has been the subject of two papers reaching opposite conclusions, even though they were based on the same allozyme data set. Herein, we present a second molecular data set – 500 bases of the ND2 gene – and analyse it cladistically to arrive at a new hypothesis of phylogenetic relationships. Recent hypotheses by other investigators of a hybrid origin of Aphelocoma populations are strongly contradicted. The ecological context within which these evolutionary processes are taking place is characterized using new tools for modelling ecological niches of species along a spectrum from humid tropical to dry temperate habitats. Evolutionary patterns of ecological niches are shown to consist of drastic departures from rate-uniformity and ecological niche conservatism.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 369–383.     

Python phylogenetics: inference from morphology and mitochondrial DNA

We used nucleotide sequences from four mitochondrial genes and structural features of the mitochondrial control region, combined with a revised, previously published, morphological data set to infer phylogenetic relationships among the pythons. We aimed to determine which of two competing hypotheses of relationships of the genera Aspidites and Python best explains the evolutionary and bioegeographical history of the family. All analyses of the combined data recover a set of relationships in which (1) the genus Python is paraphyletic with the two east Asian species, P. reticulatus and P. timoriensis , as the sister lineage to the seven Australo-Papuan python genera. We support recognition of a distinct genus for the P. reticulatus  +  P. timoriensis clade; (2) the remaining species of the genus Python form a clade which is the sister lineage to the remainder of the family; (3) the genus Aspidites is embedded among the Australo-Papuan genera. The seemingly primitive characteristics of Aspidites may be better interpreted as reversals or specializations that have accompanied a switch to burrowing in this genus. Resolution of the relationships among the Australo-Papuan lineages is weak, possibly because of rapid diversification early in the history of the radiation. We assessed the tempo of the Indo-Australian python radiation using a maximum likelihood framework based on the birth–death process. We find strong support for elevated speciation rates during the period when Australia collided with the proto-Indonesian archipelago. The data support an origin for pythons outside Australia, followed by a radiation into Australia during the mid-Tertiary.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 603–619.     

The performance of morphological characters in broad-scale phylogenetic analyses

In view of their propositional content (i.e. they can be right or wrong), character statements (i.e. statements that predicate characters of organisms) are treated as low-level hypotheses. The thesis of the present study is that such character statements, as do more complex scientific theories, come with variable scope. The scope of a hypothesis, or theory, is the domain of discourse over which the hypothesis, or theory, ranges. A character statement is initially introduced within the context of a certain domain of discourse that is defined by the scale of the initial phylogenetic analysis. The doctrine of 'total evidence' requires the inclusion of previously introduced characters in subsequent studies. As a consequence, the initial scope of character statements is widened to the extent that the scale of subsequent analyses is broadened. Scope expansion for character statements may result in incomplete characters, in the subdivision of characters, or in ambiguity of reference (indeterminacy of the extension of anatomical terms). Character statements with a wide scope are desirable because they refer to characters with the potential to resolve deep nodes in phylogenetic analyses. Care must be taken to preserve referential unambiguity of anatomical terms if the originally restricted scope of a character statement is expanded to match a broad-scale phylogenetic analysis.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 297–308.     

A new scanilepiform from the Lower Triassic of northern Gansu Province,China, and phylogenetic relationships of non‐teleostean Actinopterygii

A new scanilepiform, Beishanichthys brevicaudalis gen. et sp. nov. , is named and described based on fossils from the Lower Triassic lake deposits exposed in Beishan area, Gansu Province, China. The discovery documents a new record of this group, which is significantly older than other known scanilepiforms from China, and is slightly younger than Evenkia from the Lowest Triassic of Central Siberia. Although the Beishan beds were previously interpreted as Late Permian in age, based on megaplant fossils, this new discovery supports the reinterpretation of the deposits as Early Triassic in age, based on vertebrate fossils from the same locality and horizon. Phylogenetic analysis was conducted to resolve the relationships of Scanilepiformes with other actinopterygian clades, and the inter‐relationships within Scanilepiformes. Contrary to previous thought that scanilepiforms are closely related to the Amiidae, the phylogenetic results of this study recognize the Scanilepiformes as stem‐group neopterygians. Relationships of the Scanilepiformes and Australosomus with other neopterygians remain unresolved. With a characteristic long‐based dorsal fin, scanilepiforms represent a small group that emerged in Early Triassic freshwater environments, inhabited Eurasia and North America during the Middle–Late Triassic, briefly invaded the marine environment by the Late Triassic in Europe, and became extinct at the end of Triassic. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 595–612.     

A new basal dicynodont from the Upper Permian of South Africa

The skull of a small anomodont therapsid, from the Tapinocephalus Assemblage Zone (Abrahamskraal Formation, Beaufort Group, Upper Permian) in Northern Cape Province, South Africa, represents a new basal dicynodont and is described in detail. Colobodectes cluveri gen. et sp. nov. is distinguished from other dicynodonts by an anteroposteriorly extensive caniniform process, parietals that were broadly overlapped posterolaterally by posterodorsal processes of the postorbitals, diverging anterior palatal ridges, and a dorsoventrally low foramen magnum. A phylogenetic analysis indicates that Colobodectes is the basalmost member of a dicynodont clade that excludes Eodicynodon . This position is not particularly strong, as two additional steps are needed to make Colobodectes and Eodicynodon oosthuizeni exchange places on the most parsimonious tree. Another discovery of the phylogenetic analysis is that there is little basis for recognizing Eodicynodon oelofseni as the closest relative of E. oosthuizeni . The former species is identified as the sister taxon of a clade that includes the latter and all other dicynodonts.     

Anatomically preserved cardiocarpalean ovules in the late Palaeozoic Angara floral province of Russia

A new species of Cardiocarpus from the Sim River Basin in the southern Urals of Russia is the first anatomically preserved cardiocarpalean ovule from the Permian of the Angara floral province. Specimens are preserved in a soft organic limestone with large numbers of juvenile bactritoid protoconchs. Ovules are roughly ellipsoidal in the major plane, up to 6.0–7.5 mm in length and 5.3 mm in width, with a diminutive wing and a rounded chalaza. The outer surface of the ovules is smooth. In longitudinal sections, two vascular tissue channels traverse the sclerotesta at the chalaza, and appear to extend to near the apex within each wing. There is a simple, dome-shaped pollen chamber at the apex, which lies below a narrow micropyle. The sclerotesta consists of one or two layers of longitudinally orientated cells at the interior, and sclereids that are radially elongated towards the periphery. The sarcotesta is incompletely preserved, but displays an outer layer of cells that are somewhat elongated towards the long axis of the ovule. Numerical cladistic analysis reveals little correlation between the structure of cardiocarpalean morphotaxa and the phylogenetic relationships of the plants that produced them, where affinities are known. Cardiocarpus angarensis sp. nov. enriches our understanding of Permian spermatophytes in temperate climates of the Northern Hemisphere, and reveals that ovules similar to those of Euramerican and Cathaysian provinces characterized an Angaran spermatophyte.  Journal compilation © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 297–305. No claim to original US government works.     

Evolution of facial innervation in anomodont therapsids (Synapsida): Insights from X‐ray computerized microtomography

Anomodontia was the most successful herbivorous clade of the mammalian stem lineage (non‐mammalian synapsids) during the late Permian and Early Triassic. Among anomodonts, Dicynodontia stands apart because of the presence of an osseous beak that shows evidence of the insertion of a cornified sheath, the ramphotheca. In this study, fourteen anomodont specimens were microCT‐scanned and their trigeminal canals reconstructed digitally to understand the origin and evolution of trigeminal nerve innervation of the ramphotheca. We show that the pattern of innervation of the anomodont “beak” is more similar to that in chelonians (the nasopalatine branch is enlarged and innervates the premaxillary part of the ramphotheca) than in birds (where the nasopalatine and maxillary branches play minor roles). The nasopalatine branch is noticeably enlarged in the beak‐less basal anomodont Patranomodon, suggesting that this could be an anomodont or chainosaur synapomorphy. Our analyses suggest that the presence or absence of tusks and postcanine teeth are often accompanied by corresponding variations of the rami innervating the caniniform process and the alveolar region, respectively. The degree of ossification of the canal for the nasal ramus of the ophthalmic branch also appears to correlate with the presence of a nasal boss. The nasopalatine canal is absent from the premaxilla in the Bidentalia as they uniquely show a large plexus formed by the internal nasal branch of the maxillary canal instead. The elongated shape of this plexus in Lystrosaurus supports the hypothesis that the rostrum evolved as an elongation of the subnarial region of the snout. Finally, the atrophied and variable aspect of the trigeminal canals in Myosaurus supports the hypothesis that this genus had a reduced upper ramphotheca.     

Phylogenetic relationships among Acestrorhynchus species (Ostariophysi: Characiformes: Acestrorhynchidae)

A total of 104 osteological and external morphological features were examined in 13 species of Acestrorhynchus and 15 outgroup taxa to advance a hypothesis of relationships within the genus. Two most parsimonious hypotheses corroborate the monophyly of Acestrorhynchus but differ in the hypothesized relationships of Acestrorhynchus heterolepis . Three proposed supraspecific assemblages are at least partially correlated with groups of species previously diagnosed on the basis of colour pattern: (1) Acestrorhynchus britskii , Acestrorhynchus grandoculis , Acestrorhynchus microlepis , and Acestrorhynchus minimus ; (2) Acestrorhynchus falcirostris , Acestrorhynchus isalineae , and A. Acestrorhynchus nasutus ; and (3) Acestrorhynchus abbreviatus , Acestrorhynchus altus , Acestrorhynchus falcatus , Acestrorhynchus lacustris , and Acestrorhynchus pantaneiro . In one hypothesis A. heterolepis is proposed as the closest relative of the clade formed by A. falcirostris , A. isalineae , and A. nasutus , and in the alternative hypothesis it is proposed as a sister species of the clade formed by A. abbreviatus , A. altus , A. falcatus , A. lacustris , and A. pantaneiro . Relationships among species of the latter clade remain unresolved. Two independent episodes of reduction of body size are hypothesized to have occurred within the genus: one associated with the clade formed by A. grandoculis and A. minimus , and the other with the clade formed by A. isalineae and A. nasutus . © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 691–757.     

Simultaneous analysis of basal Hymenoptera (Insecta): introducing robust-choice sensitivity analysis

Molecular characters are analysed on their own and in combination with morphological data to examine the phylogenetic relationships of the basal lineages of Hymenoptera ('Symphyta'). This study covers 47 sawfly genera and nine apocritan families and includes molecular sequences from five genes − 12S, 16S, 18S and 28S ribosomal genes and cytochrome oxidase 1 − as well as 343 morphological characters. A robust-choice sensitivity analysis is performed with the data. First, the simultaneous analysis is repeated three times, each time employing a different step matrix for weighting the transformations of the molecular characters. Then, the results of all three simultaneous analyses are summarized in a strict consensus in order to avoid basing the conclusions on a narrow set of assumptions. This methodology is discussed in the paper. The relationships among superfamilies largely confirm previous hypotheses, being (Xyeloidea (Tenthredinoidea s.l. (Pamphilioidea (Cephoidea (Siricoidea (Xiphydrioidea (Orussoidea Apocrita))))))), where Siricoidea is understood as Siricidae+Anaxyelidae. However, the relationships within Tenthredinoidea s.s. proposed here are novel: ({Argidae Pergidae}[ Athalia {(Diprionidae Cimbicidae) Tenthredinidae minus Athalia }]).  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 79, 245–275.