A new basal sauropodiform from South Africa and the phylogenetic relationships of basal sauropodomorphs

We present a new medium‐sized basal sauropodomorph, S efapanosaurus zastronensis gen. et sp. nov. , from the Upper Triassic?Lower Jurassic Elliot Formation of South Africa. It is represented by parts of the postcranial skeleton of at least four individuals, including: cervical, dorsal, sacral and caudal vertebrae, most of the forelimb, and part of the hindlimb. Sefapanosaurus bears several autapomorphies of the astragalus, and referred material also shows autapomorphic features. The inclusion of Sefapanosaurus in a phylogenetic analysis places it within the group of sauropodomorphs more closely related to sauropods than to Massospondylus (i.e. Sauropodiformes), increasing the currently known diversity of the so‐called ‘transitional forms’ leading to Sauropoda. Character optimization revealed the presence of several features that are common for taxa placed within the transitional branches basal to Sauropoda. Sefapanosaurus, together with other transitional sauropodomorphs reported during the last decade, highlights the importance of Gondwanan taxa for understanding the palaeobiodiversity, global distribution, and macroevolutionary changes in the group related to the rise of sauropods. © 2015 The Linnean Society of London     

The influence of caudofemoral musculature on the titanosaurian (Saurischia: Sauropoda) tail skeleton: morphological and phylogenetic implications

Due to their abundance, taxonomic and morphological diversity, wide range of body sizes and broad geographical distribution, titanosaurian sauropods were one of the most important Cretaceous herbivorous dinosaur groups. Consequently, titanosaurs constitute one of the best samples in which to evaluate the relationship between bony structures and unpreserved soft-tissues within Sauropoda. We reconstruct the morphology and interpret the implications of selected soft-tissues associated with the titanosaurian caudal skeleton. These tissues, especially the M. caudofemoralis longus (CFL), exerted a considerable influence on the anatomy of the caudal vertebrae and haemal arches. In all studied titanosaurian taxa, the reconstructed caudofemoral musculature corresponds to one of three principal morphotypes that accord with previously recognised phylogenetic patterns within the clade. Basal titanosaurians had an elongate M. CFL that extended for much of the proximal half of the tail; in saltasaurines, this muscle was much shorter. Non-saltasaurine lithostrotians exhibited an intermediate condition. Furthermore, the differing position of the fourth trochanter, and therefore, the insertion of the caudofemoral muscles, among various titanosaurian taxa suggests distinctions in the locomotor function of these animals.     

Leaf anatomy of Bruniaceae: ecological, systematic and phylogenetic aspects

CARLQUIST, S., 1991. Leaf anatomy of Bruniaceae: ecological, systematic and phylogenetic aspects. Quantitative and qualitative data are given for 60 species of the 12 genera of Bruniaceae; most data are based on liquid-preserved material. Leaves of Bruniaceae are basically linear (broader forms are probably derived) with an apicula that contains phellogen activity. Most bruniaceous leaves have some degree of isolateral construction, with transition to normal bifacial construction in a few species, but more commonly transition to 'inverse' bifacial structure (stomata on adaxial face, palisade on abaxial face). The latter type is correlated with the tendency for leaves to be appressed to stems. Tannins and very likely other dark-staining materials are very characteristic of mesophyll cells. Six genera have a large strand of fibres on the midvein and rhomboidal crystals in bundle sheath cells. The other six genera have few or no fibres on veins and have druses in mesophyll cells (but not in bundle sheath cells). These distinctions may relate to intrafamilial taxonomy, but they also support the primitive position usually accorded to Audouinia, Thamnea and Tittmannia. A key to genera based on leaf antomy is offered. Details of epidermal cell shape, cuticular relief and trichome form and structure based on scanning electron microscopy are given. Leaf anatomy, combined with other features, favours a relationship between Bruniaceae and Grubbiaceae in particular and in broader contexts allies Bruniaceae to rosalean and possibly hamamelidalean families.     

A new phylogenetic classification for the gymnophthalmid genera Cercosaura , Pantodactylus and Prionodactylus (Reptilia: Squamata)

Because of the poor state of knowledge of many of the gymnophthalmid genera, systematic revision is necessary to render the classification consistent with evolutionary history. To that end, I conducted a review of the species of three genera of the Cercosaurinae which appear to form a monophyletic group: Cercosaura , Pantodactylus , and Prionodactylus . Phylogenetic analysis of 61 morphological characters was conducted after specimens of all species were examined to evaluate the composition of each taxon. The phylogenetic reconstruction suggested that the genus Prionodactylus was paraphyletic. A new phylogenetic classification is proposed that synonymizes Pantodactylus and Prionodactylus with Cercosaura. Cercosaura is redefined to include 11 species and seven subspecies. A key is provided to distinguish among species.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 101−115.     

Brain gangliosides in monotremes, marsupials and placentals: phylogenetic and thermoregulatory aspects

The concentration and composition of brain gangliosides of 17 mammalian species belonging to the subclasses of Prototheria (monotremes), Metatheria (marsupials), and Eutheria (placentals) were investigated. The mean concentration of brain gangliosides ranges from 525 to 610 micrograms NeuAc/g wet wt in monotremes, 445-900 micrograms in marsupials and from 630 to 1130 micrograms in the placentals. In the phylogenetic series of mammals, a decrease in the complexity of brain ganglioside composition becomes obvious: a drastic reduction in the number of individual ganglioside fractions particularly those of the c-pathway of biosynthesis, took place from the level of monotremes to that of the marsupials and placentals. In monotremes, marsupials and "lower" placentals (insectivores) the percentage of alkali-labile gangliosides is relatively low (between traces and 5%), whereas in the higher evolved mammals it amounts to about 20% of all gangliosides. The ratio of the contents of the two major mammalian ganglioside fractions GD1a and GT1b is generally in the range of 1.0 and even higher; in the heterothermic platypus from the monotremes and in hibernators among the placental mammals, however, it is much lower (about 0.8). These data support the hypothesis that the brain ganglioside composition not only depends on the phylogenetic level of nervous organization (cephalization) but is additionally correlated with the state of thermal adaptation.     

A new infrageneric classification and phylogenetic trends in the genusRhododendron (Ericaceae)

Recent studies have improved the infrageneric classification ofRhododendron, including my own investigations on flavonoids and anthocyanins as chemosystematic markers. From a synoptical comparison of morphological, anatomical and phytochemical characters a new system for the genus is proposed. Phylogenetic character progressions and relationships among subgenera, sections and subsections are discussed and illustrated. Key positions for subg.Candidastrum between chori subgenerumRhododendron andNomazalea, and for subg.Choniastrum between chori subgenerumHymenanthes andNomazalea are suggested.     

A new superfamily classification of the Caridea (Crustacea: Pleocyemata) based on phylogenetic pattern

Present groupings of Caridea are notoriously unsatisfactory at the superfamily level. Principles of phylogenetic systematics are used to reconstruct 14 monophyletic subgroups of Caridea, based on 19 synaomorphies of adults. The following sequenced phylogenetic classification is provided (main diagnostic character for each superfamily within brackets): 1. Atyoidea (distal lash of Mxp, reduced); Oplophoridae; Atyidae; Pasiphaidae; Agostocarididae; Alvinocarididae; Bresiliidae; Psalidopodidae; Disciadidae; 2. Stylodactyloidea (mandibular palp with 2 segments or absent); Stylodactylidea; Campylonotidae; 3. Eugonatonotoidea (abdominal somite III with dorsal carina bifurcate); Eugonatonotidae; 4. Palaemonoidea (basal segment of antennular peduncle with distolateral tooth); Rhynchocinetidae; Palaemonidae; 5. Nematocarcinoidea (ventral lobe of scaphognathite narrowly triangular); Nematocarcinidae; 6. Pandaloidea (P₁ with chela microscoic or absent); Pandalidae; “Plesionikidae”; Heterocarpidae; Heterocarpoididae; Dorodoteidae; Thalassocarididae; Physetocarididae; 7. Crangonoidea (incisor process of mandible absent); Barbouriidae; Lysmatidae; Merguiidae, fam. n.; Processidae; Glyphocrangonidae; Crangonidae; 8. Alpheoidea (carpus of P₂ with less than 17 segments); Merhippolytidae, fam. n.; Nauticarididae; Alopidae; Bythocarididae; Thoridae; Hippolytidae; Pterocarididae, fam. n.; Ogyrididae; Alpheidae. The monotypic hippolytid taxon Thorellinae, subfam. n., has been formally diagnosed. A survey of the lower Caridea has furnished 276 enera and 2418 species and subspecies. The new superfamily system is simpler, genealogically informative and more precisely diagnosed than previous schemes. These have failed as general reference systems because they were based on the wrong premises that similarities indicate phylogenetic relationships or can be used to construct a single acceptable hierarchy.     

First report of Apatosaurus (Diplodocidae: Apatosaurinae) from the Cleveland-Lloyd Quarry in the Upper Jurassic Morrison Formation of Utah: Abundance,distribution, paleoecology,and taphonomy of an endemic North American sauropod clade

A cervical vertebra preserved at the famous and productive Cleveland-Lloyd Dinosaur Quarry in the Upper Jurassic Morrison Formation of Utah is that of an Apatosaurus, a sauropod dinosaur genus not previously recognized at the site and the first new dinosaur taxon identified at the site in years. The presence of Apatosaurus at a mudstone site dominated by other taxa, both theropod and sauropod, suggests a pattern of preservation within the Morrison Formation in which sites in fine-grained sediments yield dramatically uneven relative abundances of dinosaurs, with variable dominant taxa by site, compared with more time-averaged and attritional coarse-grained channel sandstone deposits. In addition, the continued demonstration of the wide-spread occurrence and abundance of Apatosaurus within the Morrison Formation, and the absence of its clade among diplodocid faunas on other continents, suggest that this group may have been endemic to North America during the Late Jurassic and that it may have originated there, though this is far from clear.     

Molecular cloning, sequencing, and phylogenetic relationships of a new potyvirus: sugarcane streak mosaic virus, and a reevaluation of the classification of the potyviridae

The nucleic acid of a serologically distinct potyvirus, originally isolated out of sugar cane from Pakistan, was reverse transcribed and the 3' terminal 2000 bp was PCR amplified, cloned, and sequenced. Phylogenetic comparisons of viruses representing each genus of the Potyviridae show that the Pakistani isolate is most closely related to the rymoviruses wheat streak mosaic virus (WSMV) and brome streak mosaic virus. We therefore propose that this new virus species be named sugar cane streak mosaic virus to reflect its similarity to WSMV. The phylogenetic data also show that the genus Rymovirus contains at least two unique evolutionary lineages. Thus the current taxonomy, based on transmission vector, is paraphyletic. We present an analysis of the taxonomic relationships among members of the family and propose a classification that both resolves the paraphyly and more accurately represents the evolutionary history of the Potyviridae.     

Autopodial skeletal diversity in hystricognath rodents: Functional and phylogenetic aspects

Metapodials and phalanges of the second to fourth digital ray were measured for the hands and feet of 214 specimens belonging to 45 extant species of hystricognath rodents, encompassing members of all major clades of the radiation. Principal components analysis (PCA), the phalangeal index of the third digital ray in the hands and feet, and the relationship between second and fourth digital ray were used to investigate intrinsic autopodial proportions as well as to provide a base for comparisons between hands and feet. PCA separated cursorial Hystricognathi from arboreal ones, but lead to little distinction in other locomotory modes. Cursors have longer metapodials and shorter phalanges, particularly in their hind limb, while arboreal species have relatively longer manual and pedal phalanges. Terrestrial, scansorial, fossorial, and semi-aquatic species were not clearly distinguished, but there is a tendency towards elongated manual digits and relatively short feet in most fossorial species. Closely related species with similar locomotory habits tend to group together in PCA morphospace, and also have similar phalangeal indices. The results are in agreement with current hypotheses on locomotory adaptations of the hand and foot, and concur with many previous findings on autopodial proportions in arboreal, cursorial, and fossorial species. They also highlight the limited use of autopodial proportions for inferring systematic affinities. The lack of distinction in the majority of species is likely related to the lack of highly specialized locomotory types in Hystricognathi.     

A phylogenetic study of the neotropical catfish family Cetopsidae (Osteichthyes, Ostariophysi, Siluriformes), with a new classification

A hypothesis on the phylogenetic relationships of the neotropical catfish family Cetopsidae is proposed on the basis of the parsimony analysis of 127 morphological characters and most of the species currently recognized. The family and its two recognized subfamilies, the Cetopsinae and Helogeninae, are corroborated as monophyletic, in agreement with recent studies. Previously proposed classifications of the Cetopsinae, however, were found to be poorly representative of the phylogenetic relationships within the subfamily. Major generic rearrangements are implemented in order that the classification of the Cetopsinae reflects the phylogenetic hypothesis. Pseudocetopsis Bleeker (1862) was found to be polyphyletic and to include several disjunct lineages. One of these lineages, recently named as the genus Cetopsidium Vari, Ferraris, and de Pinna (2005), is the sister group to the rest of the Cetopsinae. Denticetopsis Ferraris (1996) is the next sister group to the remainder of the Cetopsinae. The remaining species of the Cetopsinae belong to one of two sister genera, Paracetopsis Bleeker (1862) and Cetopsis Spix and Agassiz (1829). The latter genus includes species formerly assigned to Hemicetopsis Bleeker (1862), Bathycetopsis Lundberg and Rapp Py‐Daniel (1994) and Pseudocetopsis Bleeker (1862). Continued recognition of Hemicetopsis and Bathycetopsis would have required the creation of several additional new genera for various species previously in Pseudocetopsis that form a series of sister groups to a clade composed of Cetopsis oliveirai (Lundberg and Rapp Py‐Daniel, 1994), C. coecutiens (Lichtenstein, 1819) and C. candiru (Spix and Agassiz, 1829). Cetopsis oliveirai is a highly paedomorphic species that displays surprising similarities with conditions in juvenile specimens of C. coecutiens, a species that attains a large body size. Such similarities are not evident in adult specimens of the latter species. A new classification is proposed, within which the subfamily Cetopsinae consists of three tribes, the Cetopsidiini, the Cetopsini and the Denticetopsini. The results of the study form the basis for a discussion of the phylogenetic position of the family within the Siluriformes, the phylogenetic biogeography of the Cetopsidae, paedomorphosis and gigantism in the family, and the effect of different semaphoronts on the intrafamilial phylogeny. Journal compilation © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 150 , 755–813. No claim to original US government works.     

Diagnosis, classification, and phylogenetic relationships of the orphnine scarab beetles (Coleoptera, Scarabaeidae: Orphninae)

Orphnine scarab beetles (Orphninae) are widely distributed in the tropical and subtropical regions of the southern continents except for Australia. The catalogue of nominal taxa of orphnines includes 2 tribes, 15 genera, and 195 species. Diagnosis of the group, based on adult morphological characters, is as follows: antennae 10-segmented with 3-segmented club; mandibles with 2?C4 scissorial teeth and well developed mola; labrum and mandibles protruding past clypeus and visible from above; scutellum well developed in winged species, reduced but distinct in wingless species; wings with distinct anal area; apices of anterior tibia in males without spur but normally with a few robust setae; anterior coxa with longitudinal hollow on anterior surface; tarsi with 2 similar claws; middle and hind tibiae with 2 apical spurs; abdominal sternite 2 with sub-triangular to rounded plectrum; dorsal surface of hind coxae with oval flat stridulatory file; pygidium partly hidden under elytra; parameres symmetrical; bursa copulatrix sacciform, membranous; spermatheca C-shaped, not sclerotized; accessory vaginal glands developed; abdomen with 2 sclerotized tergites (VII?CVIII) and 6 visible sternites (III?CVIII). Preliminary phylogenetic analysis based on 47 characters of adult morphology shows that the tribe Aegidiini Paulian is a natural, monophyletic group. The genus Stenosternus Karsch described from a single specimen from S?o Tomé Island (Gulf of Guinea), is morphologically more similar to the New World taxa than to the Old World ones and is provisionally placed in Aegidiini. The tribe Orphnini Erichson seems non-monophyletic and has no synapomorphies. The genus Orphnus is apparently a polyphyletic group and it needs taxonomic revision. The hypothesis on sister-group relationship of Orphninae and Allidiostomatinae, based on molecular data, is not supported by the morphological characters. The stridulatory organs (the putative synapomorphy of Orphninae + Allidiostomatinae) are not identical in these groups; the mouthparts and female genitalia are essentially different. Orphninae have chewing mouthparts with large scissorial teeth and well developed mola, which is characteristic of generalist saprophagous species. Allidiostomatinae have mandibles with scissorial teeth and mola reduced; they also have sclerotized bursa copulatrix and sclerotized mandibular duct which opens on the dorsal side near condyle. Considering the present day development of alpha-taxonomy of most orphnine taxa, especially the speciose genus Orphnus, it seems premature to propose changes in higher classification of the subfamily. To clarify the phylogenetic position of the Orphninae among scarab beetles it is essential to include representative members of all taxa of orphnine lineage (sensu Browne, Scholtz, 1998) into the analysis.     

Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers

Short interspersed elements (SINEs) are a class of dispersed mobile sequences that use RNA as an intermediate in an amplification process called retroposition. The presence-absence of a SINE at a given locus has been used as a meaningful classification criterion to evaluate phylogenetic relations among species. We review here recent developments in the characterisation of plant SINEs and their use as molecular makers to retrace phylogenetic relations among wild and cultivated Oryza and Brassica species. In Brassicaceae, further use of SINE markers is limited by our partial knowledge of endogenous SINE families (their origin and evolution histories) and by the absence of a clear classification. To solve this problem, phylogenetic relations among all known Brassicaceae SINEs were analyzed and a new classification, grouping SINEs in 15 different families, is proposed. The relative age and size of each Brassicaceae SINE family was evaluated and new phylogenetically supported subfamilies were described. We also present evidence suggesting that new potentially active SINEs recently emerged in Brassica oleracea from the shuffling of preexisting SINE portions. Finally, the comparative evolution history of SINE families present in Arabidopsis thaliana and Brassica oleracea revealed that SINEs were in general more active in the Brassica lineage. The importance of these new data for the use of Brassicaceae SINEs as molecular markers in future applications is discussed.     

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: infraorder Furnariides)

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods.     

Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides)

Phylogenetic relationships among the Tyrannides were assessed using over 4000 base pairs of nuclear recombination activating 1 (RAG-1) and 2 (RAG-2) DNA sequence data from about 93% of all described genera, which represents the most complete assessment of relationships for this diverse New World radiation to date. With this sampling we propose a significantly expanded interpretation of higher-level relationships within the group. The Tyrannides are shown to be comprised of six major lineages, all of which represent traditional family-level taxa ( sensu Fitzpatrick, 2004a and Snow, 2004a,b ; del Hoyo et al., 2004 ): (i) manakins (Pipridae); (ii) cotingas (Cotingidae); (iii) the sharpbill ( Oxyruncus ) + onychorhynchine flycatchers (Onychorhynchini); (iv) tityrines (Tityridae); (v) rhynchocycline flycatchers (Rhynchocyclidae); and (vi) the tyrant flycatchers (Tyrannidae). In addition, the RAG data recovered isolated lineages with uncertain relationships, including Neopipo , Platyrinchus , Piprites , and Tachuris . The Pipridae are the sister-group to all the other Tyrannides. Within the latter, the clade ((Oxyruncidae + Tityridae) + Cotingidae) is the sister-group of the Tyrannoidea. Within the Tyrannoidea, the Rhynchocyclidae and their allies are sisters to Neopipo  + Tyrannidae. Using our phylogenetic hypothesis, we propose the first comprehensive phylogenetic classification that attempts to achieve isometry between the tree and a classification scheme using subordination and phyletic sequencing. This study thus provides a phylogenetic framework for understanding the evolution of this diverse New World assemblage, and identifies many avenues for further systematic study.
 © The Willi Hennig Society 2009.     

A new Late Jurassic turtle from Spain: phylogenetic implications,taphonomy and palaeoecology

Abstract: The Jurassic was an important period in the evolution of Testudinata and encompasses the origin of many clades, and this is especially true of Jurassic turtles from Western Europe. A new genus and species of Late Jurassic turtle, Hispaniachelys prebetica gen. et sp. nov. from the upper Oxfordian of the Prebetic (Southern Spain), is described on the basis of postcranial material. The specimen is the only known tetrapod from the Mesozoic of the Prebetic and the oldest turtle from southern Europe. A mosaic of characters indicates this is a new genus: it displays basal features including dorsal epiplastral processes/reduced cleithra, no medial contact of the extragulars and a long first thoracic rib, alongside derived characters including an absence of mesoplastra and the vertebral 3/4 sulcus crossing neural 5. The phylogenetic position of the new taxon is hard to resolve, and it might be either a paracryptodire or a basal testudine, but it is distinct from Plesiochelys. A complex taphonomic history is shown by a range of overlying grazing traces and bioerosion on the carapace. The carapace was subsequently overturned and buried ventrally up, terminating grazing activity, and was then bored by sponges before final burial. Scanning electron microscopy reveals phosphatic microspheroids associated with bacterial decay in the vascular cavities of the cancellous bone, suggesting the carapace may have acted as a closed microenvironment in which decay‐derived authigenic minerals formed.     

Outbreak of Cutaneous Leishmaniasis among military personnel in French Guiana, 2020: Clinical,phylogenetic, individual and environmental aspects

BackgroundCutaneous Leishmaniasis (CL) is endemic in French Guiana but cases are usually sporadic. An outbreak signal was issued on May 15^th 2020 with 15 suspected cases after a military training course in the rainforest. An outbreak investigation was carried out.Methodology/Principal findingsThirty cases were confirmed. Leishmania guyanensis was the most frequent species (90%). The most frequent presentation was ulcerative (90%). Lesions on the face and hands were frequent (40% each). Eight cases (26%) presented a poor outcome after treatment with pentamidine and required a second line with amphotericin B. Three of them required further treatments with meglumine antimoniate or miltefosine. Two spots within the training area were deemed as likely sites of contamination, due to illegal logging. The isolated Leishmania strains did not form a separate cluster. Participation in Week 13 of year 2020 was associated with infection (OR = 4.59 [1.10–19.83]; p = 0.016) while undergoing only the “Fighting” exercise was protective (OR = 0.1 [0–0.74]; p = 0.021). There was no association between infection and other risk factors at the individual level. The attack rate of Regiment B (14/105 = 13.3%) was significantly higher (OR = 4.22 [1.84–9.53], p = 0.0001) compared to Regiment A (16/507 = 3.2%). The attack rate during this training course (30/858 = 3.5%) was significantly higher (OR 2.29 [1.28–4.13]; p = 0.002) than for other missions in French Guiana during the same period (22/1427 = 1.5%).ConclusionsThis outbreak could be explained by a combination of factors: climatic conditions around week 13, at-risk activities including night trainings, absence of impregnation, a lesser experience of rainforest duties in Regiment B and illegal logging attracting sandflies on military training grounds.