Phylogenetic Reassessment Research Articles

Redescription of three basal anomodonts: a phylogenetic reassessment of the holotype of Eodicynodon oelofseni (NMQR 2913)

The Dicynodontia (Therapsida: Anomodontia) is one of the most successful Permo-Triassic terrestrial tetrapod clades and the oldest specimens are recorded from the middle Permian Eodicynodon Assemblage Zone of South Africa. Their fossil record is abundant and species-rich across Pangea. By contrast, the fossil record of the basal-most anomodonts, which includes non-dicynodont anomodonts and early forms of dicynodonts, is patchy and their morphology and phylogeny are deduced from relatively few specimens. Discovered in 1982 and described in 1990, the holotype of Eodicynodon oelofseni (NMQR 2913) is one of the better-preserved early anomodont specimens. However, it has been suggested that E. oelofseni does not belong to the genus Eodicynodon. Here, using CT-scanning and 3D modeling, the skull of Eodicynodon oelofseni, Patranomodon nyaphulii and Eodicynodon oosthuizeni are redescribed. In the framework of this study, the application of 3D scanning technology to describe anatomical structures which were previously inaccessible in these fossils has enabled detailed redescription of the cranial morphology of the basal anomodonts Patranomodon, Eodicynodon oelofseni and E. oosthuizeni and led to a greater understanding of their cranial morphology and phylogenetic relationships. Based on an anatomical comparison and phylogenetic analyses (Bayesian and cladistics) the phylogenetic relationships of basal anomodonts are reassessed and it is suggested that NMQR 2913 does not belong to the genus Eodicynodon but likely represents a separate genus basal to other dicynodonts. A new genus is erected for NMQR 2913. This presents one of the first applications of Bayesian Inference of phylogeny on Therapsida.

More cryptic diversity among spiny lizards of the Sceloporus torquatus complex discovered through a multilocus approach

Abstract A phylogenetic reassessment of the Sceloporus torquatus species complex is presented using a multilocus approach. Topological conflicts related to a clade belonging to disjunct southern populations of S. madrensis are resolved, confirming the identity of such populations as distinct from the nominal populations of S. madrensis located 175 kilometres to the north. We describe this southern clade as a new species distributed in the Sierra Madre Oriental based on its phylogenetic distinctiveness and a combination of morphological characters and measurements, increasing the number of recognised species in the S. torquatus complex to seven.

Correction to: A stomach plate to divide them all: a phylogenetic reassessment of the family Tritoniidae (Nudibranchia: Cladobranchia)

Correction to: A stomach plate to divide them all: a phylogenetic reassessment of the family Tritoniidae (Nudibranchia: Cladobranchia)

Cranial osteology of the Brazilian dinocephalian Pampaphoneus biccai (Anteosauridae: Syodontinae)

Abstract The Anteosauridae (Dinocephalia) were the largest predators of Guadalupian (Middle Permian) land communities. The, thus far, only known South American anteosaurid is the medium-sized syodontine Pampaphoneus biccai. This taxon was, until now, known only by its holotype, recovered from an outcrop of the Rio do Rasto Formation, Southern Brazil. Here we describe in detail an almost complete Pampaphoneus biccai skull associated with a few postcranial remains (UNIPAMPA 759) recently recovered from the type locality. The novel morphological information provided by this novel, better-preserved, specimen revealed that most characters previously proposed to distinguish Pampaphoneus biccai from Syodon biarmicum are probably ontogenetically constrained. We identify, however, new features that clearly distinguish these two taxa, and provide an updated diagnosis for Pampaphoneus biccai. Our phylogenetic reassessment of the taxon echoes previous propositions in which Pampaphoneus biccai was recovered as an early-divergent Syodontinae. Additionally, we tentatively indicate that a larger fragmentary specimen (UFRGS-PV-0249-P) may represent the mature size of the species, with the similar-sized holotype and UNIPAMPA 759 probably representing subadult individuals.

A stomach plate to divide them all: a phylogenetic reassessment of the family Tritoniidae (Nudibranchia: Cladobranchia)

Abstract The phylogeny of the family Tritoniidae has recently been studied with significant advances, but the relationships between genera are still controversial. In our study, we investigated the phylogeny of Tritoniidae using the most diverse taxon sampling possible. We applied an integrative approach based on new sequences of two mitochondrial genes (COI and 16S), a nuclear gene (H3) and morpho-anatomical characters. The monophyly of the family Tritoniidae was not recovered in our phylogenetic analyses. In view of our results, we propose a new rearrangement at the subfamily and genus levels. The plate-bearing genera are raised to the subfamily level as the monophyletic Marioniinae subfam. nov., formed by Marionia and the reinstated Marioniopsis. The remaining plate-less genera are raised to the subfamily level as the monophyletic Tritoniinae Lamarck, 1809. The genus Myrella is reinstated to assign the Antarctic and sub-Antarctic tritoniids. The taxonomic status of the monotypic Tritonidoxa is confirmed. Species delimitation analyses reveal a new large Marionia species from the Gulf of Cádiz (south-west Spain, Atlantic Ocean) and evidence for the pseudocryptic speciation of numerous Atlantic–Mediterranean and Indo-Pacific tritoniids. Finally, taxonomic notes are provided for several species according to the proposed rearrangement.

Morphological and phylogenetic reassessment of Sclerococcum simplex from China

Sclerococcum is a species rich lichenicolous genus in Ascomycota. However, many species of Sclerococcum have been described based only on morphology. This study provides sequences for the large-subunit ribosomal RNA (LSU), internal transcribed spacer (ITS) and mitochondrial small-subunit ribosomal RNA (mtSSU) for the first time for Sclerococcum simplex, and the first geographical record of the genus from China. Phylogenetic analyses confirmed that S. simplex clustered within Sclerococcum sensu stricto while the genus was recovered as paraphyletic in Dactylosporaceae. Our asexual specimen of Sclerococcum simplex was collected on a corticolous Pertusaria thallus. The taxonomic affinity of Sclerococcum simplex is investigated based on phylogenetic and morphological evidence.

Phylogenetic re-assessment of the delimitation of Plocama and its species relationships and limits (Rubiaceae, Putorieae): resurrection of the monospecific genus Aitchisonia and a description of trib. nov. Aitchisonieae

Phylogenetic re-assessment of the delimitation of Plocama and its species relationships and limits (Rubiaceae, Putorieae): resurrection of the monospecific genus Aitchisonia and a description of trib. nov. Aitchisonieae

Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi

The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.

Taxonomic and phylogenetic reassessment of a large-bodied dinosaur from the earliest dinosaur-bearing beds (Carnian, Upper Triassic) from southern Brazil

Upper Triassic (Carnian) strata from the Candelária Sequence of southern Brazil bear the oldest records of dinosaurs worldwide. In consequence, investigation of the specimens yielded by these fossiliferous units is crucial for a more comprehensive knowledge regarding the origin, early diversification and radiation of dinosaurs. Herein we reassess a dinosaur specimen from Brazil, informally known as the ‘Big Saturnalia’, a supposed large-sized sauropodomorph unearthed at the ‘Cerro da Alemoa’ locality in Santa Maria municipality, Rio Grande do Sul State. However, our phylogenetic analyses and comparisons of the known elements of this specimen resulted in herrerasaurid affinities instead. In fact, it is the largest specimen so far of a herrerasaurid from the Candelária Sequence. It preserves cranial and postcranial elements, with the former being unprecedented for dinosaurs from the Alemoa local fauna. The morphology of the specimen allows new insights into the anatomy, evolution and distribution of some character states among Herrerasauridae, including but not limited to the typical craniocaudally short caudal dorsal vertebrae. Moreover, the specimen adds to the dinosauromorph diversity in the Carnian units of southern Brazil and its large size provides further support for herrerasaurids as top-tier predators during the dawn of dinosaurs in south-western Pangaea.

Morphological variation among the species of Armigatus (Teleostei, Clupeomorpha, Ellimmichthyiformes) and new material of Armigatus alticorpus from the Upper Cretaceous (Cenomanian) of Hakel, Lebanon

The clupeomorph genus Armigatus is an extinct group of fish which comprises five species of small marine fishes described from the Late Cretaceous Tethys Sea. Of the five species, A. alticorpus is the least well known and least studied species. The most recent cladistic analyses of the group exclude A. alticorpus due to a lack of sufficient information for the taxon. Here we report new material of Armigatus from the Cenomanian of Hakel, Lebanon. The mass mortality slab preserves multiple clupeomorph fishes including specimens of two species of Armigatus, A. namourensis and A. alticorpus, which have previously been known only from Namoura, Lebanon. The good preservation of skull elements and caudal skeletons of the A. alticorpus specimens provides necessary information for inclusion of this species in a phylogenetic analysis. Results of the phylogenetic reassessment of A. alticorpus indicate that the species had close affinities to the two younger species of the genus, A. oligodentatus and A. dalmaticus. The three species together (A. alticorpus (A. oligodentatus + A. dalmaticus)) belong to a separate lineage from their sister-clade, (A. brevissimus + A. namourensis). Comparative examination of the multiple specimens of each species enabled us to establish a set of morphological traits which allow a more reliable delimitation of the species of Armigatus; this includes number of abdominal scutes, vertebrae, predorsal bones, as well as position of the dorsal fin.

Phylogenetic reassessment of gorals with new evidence from northern Myanmar reveals five distinct species

AbstractResearchers have recognised one to seven species of goral (Naemorhedus spp., Caprinae, Bovidae). We compared all available whole mitogenomic sequences, including eight new ones from northern Myanmar, and now recognise five distinct species. Naemorhedus caudatus remains a valid species. Naemorhedus griseus is a synonym of Naemorhedus goral. Naemorhedus evansi is a valid species, with a geographic range that extends northwards into southwestern China. Naemorhedus cranbrooki and Naemorhedus baileyi are distinct species, not synonyms. Molecular divergence analyses suggest that goral speciation was closely related to the rapid uplift of the Qinghai‐Tibetan Plateau and Hengduan Mountains from the early Pliocene to the Pleistocene.

Step changes in evolution

Summary Lineages changing their mode of locomotion are among the most conspicuous manifestations of evolutionary change. The appearance and disappearance of legs in events like the transition from fish to tetrapods, lizards to snakes, and tetrapods to whales has long fascinated biologists and lay people alike. Now genetics, developmental biology and paleontology are converging on a better understanding of these crucial transitions. Michael Gross reports.

Redescription and phylogenetic reassessment of the enigmatic anuran Eorubeta nevadensis (Amphibia) based on new specimens from ?latest Cretaceous–Paleocene beds of the Sheep Pass Formation, Nevada

ABSTRACTEorubeta nevadensis was originally based on a poorly preserved specimen from a well core in Member B of the Late Cretaceous–Eocene Sheep Pass Formation, White Pine County, Nevada. Originally thought to be a member of Leptodactylidae, E. nevadensis was later determined to have uncertain affinities with other anurans. Additional specimens of E. nevadensis recently collected from the outcrop from Members B and C of the Sheep Pass Formation in the Sheep Pass Canyon area, White Pine County, fill many gaps in knowledge about this poorly understood anuran. The new information allows for the first time a phylogenetic analysis of Eorubeta using parsimony. This analysis places E. nevadensis as the sister taxon of Acosmanura. Eorubeta nevadensis was originally reported as early Eocene but is now considered to be ?latest Cretaceous–Paleocene, based on invertebrates and pollen. Thus, although it is uncertain if E. nevadensis spans the Cretaceous–Paleogene boundary, it was at least part of the recovery fauna. The anuran fossil record from this time interval in North America is based on very fragmentary material of mostly uncertain relationships, making E. nevadensis the only nearly complete, well-preserved anuran fossil known. Eorubeta nevadensis, one of the larger fossil anurans recorded, is remarkable for being the only fossil anuran documented from a high-elevation environment, which has been compared to the modern Puna-Altiplano or the Tibetan Plateau.

Controversies over the scientific name of the principal mosquito vector of yellow fever virus - expediency versus validity.

The history of the scientific name of the yellow fever mosquito, the vector of yellow fever virus, ranges from 1757 to the early twenty-first century. In his 1757 work Iter Palaestinum, Frederic Hasselquist gave the name Culex aegypti to a mosquito species responsible for fierce attacks on humans in Egypt. That name was never later ascribed to Hasselquist as author, but to Linnaeus, although the name never appeared in any of Linnaeus' publications. In Cuba, at the end of the nineteenth century, the vector of the unknown infectious agent of yellow fever was first identified as Culex mosquito and later more validly named Stegomyia fasciata. Mosquito taxonomists differed strongly about the name of the mosquito through much of the twentieth century. Interventions by the International Commission on Zoological Nomenclature imposed a biologically invalid specific name, and in the early twenty-first century a phylogenetic analysis of the culicid tribe Aedini restored the genus Stegomyia from a century earlier. That action was short-lived. A phylogenetic reassessment resulted in the return of Stegomyia to subgeneric rank in Aedes; thus, the name of the yellow fever mosquito survives in the traditional classification of convenience as the trinomial Aedes (Stegomyia) aegypti (Linnaeus).

New species and emendations of Orphella: taxonomic and phylogenetic reassessment of the genus to establish the Orphellales, for stonefly gut fungi with a twist

ABSTRACTWe consolidate and present data for the sexual stages of five North American species of Orphella, fungal members of trichomycetes previously classified within Harpellales. Three species emendations accommodate the newly recognized characters, including not only the coiled zygospores and accompanying cells but also other morphological traits not provided in the original descriptions for O. avalonensis, O. haysii, and O. hiemalis. We describe three new species, Orphella cataloochensis from both the Smoky Mountains in USA and two provinces in Canada as well as O. pseudoavalonensis and O. pseudohiemalis, both from the Cascade Range, in Oregon, USA. Key morphological features for all known species are summarized and reviewed, with illustrations of some of the North American taxa to update and supplement the literature. The entire suite of morphological characters is discussed, with emphasis on species relationships and hypotheses on possible vicariant origins. We also present a molecular phylogeny based on nuc rDNA 18S and 28S, which supports Orphella as a lineage distinct from Harpellales, and we establish a new order, Orphellales, for it. With the combination of sexual features, now known for 12 of the 14 species of Orphella, and new molecular data, the group is now better characterized, facilitating and hopefully also promoting future studies toward a better understanding of their relationships, origins, and evolutionary history as stonefly gut–dwelling fungi.

Systematic revision and phylogenetic reassessment of the centipede genera Rhysida Wood, 1862 and Alluropus Silvestri, 1912 (Chilopoda: Scolopendromorpha) in Southeast Asia, with further discussion of the subfamily Otostigminae

Phylogenetic relationships of two morphologically similar scolopendrid genera, Rhysida Wood, 1862, and Alluropus Silvestri, 1912, were investigated based on broad-scale taxonomic sampling from SE Asia, India and Australia. Morphological revision and molecular phylogenetics using three loci validate seven Rhysida species in SE Asia and Australia: R. lithobioides (Newport, 1845), R. longipes (Newport, 1845), R. immarginata (Porat, 1876), R. nuda (Newport, 1845), R. carinulata (Haase, 1887), R. singaporiensis Verhoeff, 1937 and R. polyacantha Koch, 1985. The nominal SE Asian species R. leviventer Attems, 1953 and R. marginata Attems, 1953 are placed in junior subjective synonymy with R. lithobioides and Alluropus calcaratus (Pocock, 1891), respectively. The monotypic genus Alluropus is redescribed, molecular phylogeny recovering it nesting together with Indo-Australian Rhysida. Taxonomic revision reassigned R. calcarata Pocock, 1891 to Alluropus based on its morphological and molecular similarity to the type, A. demangei Silvestri, 1912, the differences between putative species being sexual variation. Two morphologically distinct allopatric populations of A. calcaratus, comb. nov. (= A. demangei, syn. nov.) were found in the Indochina subregion. Phylogenetic relationships in Otostigminae remain unsettled because clades within several genera lack significant support, although Rhysida consistently falls into two clades that are not each other’s closest relative.

The oldest Asian hesperornithiform from the Upper Cretaceous of Japan, and the phylogenetic reassessment of Hesperornithiformes

Asian hesperornithiforms are extremely rare in contrast to the much more abundant record from North America. In Asia, these fossil birds are only known from fragmentary materials from Mongolia. Here we describe the skeletal remains of a new hesperornithiform Chupkaornis keraorum gen. et sp. nov. from the Upper Cretaceous Kashima Formation (Coniacian to Santonian) of the Yezo Group in Mikasa City, Hokkaido, Japan. This is the best-preserved hesperornithiform material from Asia and it is the first report of hesperornithiforms from the eastern margin of the Eurasian continent. Chupkaornis has a unique combination of characters: finger-like projected tibiofibular crest of femur, deep, emarginated lateral excavation with a sharply defined edge of the ventral margin of the thoracic vertebrae, and the heterocoelous articular surface of the thoracic vertebrae. Our new phylogenetic analysis revises the phylogenetic relationships of Hesperornithiformes. In contrast to previous studies, Enaliornis is assigned as the most basal taxon and Baptornis is positioned as more derived than Brodavis. Chupkaornis is a sister taxon to the clade of Brodavis and higher taxa. Parahesperornis and Hesperornis are positioned within Hesperornithidae, the derived Hesperornithiformes. Many of the skeletal character changes are concentrated at the base of Hesperornithidae (Parahesperornis and more derived taxa), and involve the modification of the pelvic girdle and hind limb morphology (e.g. dorsal directed antitrochanter of pelvis, short and sprawled femur, including probable lobe-toed feet suggested by the specialized distal articular surface of first digit of fourth toe, and predominantly robust digit IV phalanges). These skeletal modifications are likely adaptations for foot-propelled diving behaviour.http://zoobank.org/urn:lsid:zoobank.org:pub:FB783237-E565-4B74-9386-EADF8E12DFD4

Phylogenetic reassessment of Nigrospora: Ubiquitous endophytes, plant and human pathogens.

Species of Nigrospora commonly occur as plant pathogens, endophytes or saprobes, and have been shown to be extremely interesting for the discovery of novel metabolites. The familial placement, as well as phylogenetic relationships among Nigrospora species remain ambiguous. In this study, Nigrospora (= Khusia) is confirmed as a monophyletic genus belonging to Apiosporaceae (Xylariales), based on a phylogeny inferred from LSU sequence data. A multi-locus phylogeny based on ITS, TEF1-α and TUB2, in conjunction with morphological characters, host associations, and ecological data was employed for species delimitation in Nigrospora, as well as identification of 165 recently collected isolates from China, and three from Europe. In total 13 novelties are proposed including 12 new species and 1 new combination. Five species are re-described based on an examination of type specimens and/or fresh collections. New species described in this paper include: N. aurantiaca, N. bambusae, N. camelliae-sinensis, N. chinensis, N. guilinensis, N. hainanensis, N. lacticolonia, N. osmanthi, N. pyriformis, N. rubi, N. vesicularis and N. zimmermanii. Furthermore, N. vietnamensis is transferred to Arthrinium. Our results indicate a high level of species diversity within Nigrospora, with a general lack in host specificity. Taxa that cluster basal in Nigrospora have wide host ranges, whereas those that diverged later tend to have narrow host ranges. The currently available data suggest, therefore, that the general evolutionary direction in the genus Nigrospora is from a wide to a narrow host range.

Powdery mildew of Chrysanthemum × morifolium: phylogeny and taxonomy in the context of Golovinomyces species on Asteraceae hosts

ABSTRACTThe taxonomic history of the common powdery mildew of Chrysanthemum × morifolium (chrysanthemum, florist’s daisy), originally described in Germany as Oidium chrysanthemi, is discussed. The position of O. chrysanthemi was investigated on the basis of morphological traits and molecular phylogenetic analyses. Based on the results of this study, this species, which is closely related to Golovinomyces artemisae, was reassessed and reallocated to Golovinomyces. The phylogenetic analysis and taxonomic reassessment of the chrysanthemum powdery mildew is supplemented by a morphological description, a summary of its worldwide distribution data, and a brief discussion of the introduction of this fungus to North America. G. chrysanthemi differs from true G. artemisiae in that it has much longer conidiophores, is not constricted at the base, and has much larger and most importantly longer conidia. The close affinity of Golovinomyces to Artemisia and Chrysanthemum species signifies a coevolutionary event between the powdery mildews concerned and their host species in the subtribe Artemisiinae (Asteraceae tribe Anthemideae). This conclusion is fully supported by the current phylogeny and taxonomy of the host plant genera and the coevolution that occurred with the host and pathogen. The following powdery mildew species, which are associated with hosts belonging to the tribe Anthemideae of the Asteraceae, are epitypified: Alphitomorpha depressa β artemisiae (≡ Alphitomorpha artemisiae), Erysiphe artemisiae, and Oidium chrysanthemi. Erysiphe macrocarpa is neotypified. Their sequences were retrieved from the epitype collections and have been added to the phylogenetic tree. Golovinomyces orontii, an additional powdery mildew species on Chrysanthemum ×morifolium, is reported. This species is rarely found as a spontaneous infection and was obtained from inoculation experiments.

Bone histology sheds light on the nature of the "dermal armor" of the enigmatic sauropod dinosaur Agustinia ligabuei Bonaparte, 1999.

Agustinia ligabuei is an Early Cretaceous sauropod dinosaur from the northwest of Patagonia that is currently the topic of debate with respect to its phylogenetic position and atypical dermal armor. The presence of four morphotypes of laminar and transversely elongated putative osteoderms was used to consider Agustinia as an armored sauropod. Regarding the different hypotheses about the identity of the bony structures of Agustinia (e.g., osteoderms, cervical or dorsal ribs, hypertrophied elements), a comparative histological analysis has been carried out. Histological evidence is presented herein and reveals that none of the morphotypes of Agustinia shows a primary bone tissue formed by structural fiber bundles as in other sauropod dinosaur osteoderms. Furthermore, on the basis of their gross morphology and microstructure, the bony structures originally classified as types 1+4 and 3 are more comparable respectively with dorsal and cervical ribs than any other kind of dermal or bony element. Due to poor preservation, the nature of the type 2 cannot be assessed but is here tentatively assigned to a pelvic girdle element. Although a phylogenetic reassessment of Agustinia is not the purpose of this paper, our paleohistological analyses have broader implications: by not supporting the dermal armor hypothesis for Agustinia, its inclusion in Lithostrotia is not justified in the absence of other diagnostic features.