An addition to the endemic Indian radiation of Eutropis: Phylogenetic position of Eutropis dissimilis Hallowell (Squamata: Scincidae)

Skinks of the genus Eutropis represent one of the most widespread and speciose lizard groups in tropical Asia. Numerous recent studies have utilized a variety of genes and methods to reconstruct the phylogeny of these lizards, however these studies have not resolved the placement of one of the widely distributed Eutropis Fitzinger, E. dissimilis. We have sequenced a specimen of E. dissimilis from the type locality and our result suggests that it is part of the Indian radiation of Eutropis and not related to African Trachylepis Fitzinger or Southeast Asian Dasia Gray as previously suggested. Furthermore, we report that the sequence of E. dissimilis used in an earlier study of the once cosmopolitan genus `Mabuya' may have been erroneously identified and appears to be a sequence of E. novemcarinata. We also demonstrate that the evolution of a clear lower eyelid, which was considered a synapomorphy for the sister genus Trachylepis, has arisen multiple times in Eutropis.

Paraphyly of Chinese Amolops (Anura, Ranidae) and phylogenetic position of the rare Chinese frog, Amolops tormotus

In order to evaluate the five species groups of Chinese Amolops based on morphological characteristics, and to clarify the phylogenetic position of the concave-eared torrent frog Amolops tormotus, we investigated the phylogeny of Amolops by maximum parsim

The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata)

The mitochondrial genome complete sequence of Achalinus meiguensis was reported for the first time in the present study. The complete mitochondrial genome of A. meiguensis is 17239 bp in length and contains 13 protein-coding genes, 22 tRNA, 2 rRNA, and 2 non-coding regions (Control regions). On the basis of comparison with the other complete mitochondrial sequences reported, we explored the characteristic of structure and evolution. For example, duplication control regions independently occurred in the evolutionary history of reptiles; the pseudo-tRNA of snakes occurred in the Caenophidia; snake is shorter than other vertebrates in the length of tRNA because of the truncations of T psi C arm (less than 5 bp) and "DHU" arm. The phylogenic analysis by MP and BI analysis showed that the phylogenetic position of A. meiguensis was placed in Caenophidia as a sister group to other advanced snakes with the exclusion of Acrochordus granulatus which was rooted in the Caenophidia. Therefore we suggested that the subfamily Xenodermatinae, which contains A. meiguensis, should be raised to a family rank or higher rank. At the same time, based on the phylogenic statistic test, the tree of Bayesian was used for estimating the divergence time. The results showed that the divergence time between Henophidia and Caenophidia was 109.50 Mya; 106.18 Mya for divergence between Acrochordus granulatus and the other snakes of the Caenophidia; the divergence time of A. meiguensis was 103 Mya, and Viperidae diverged from the unilateral of Elapidae and Colubridae was 96.06 Mya.

The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae

To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L crocea individuals and two L polyactis individuals. Interestingly, all seven CR sequences from L crocea were identical while the three sequences from L polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys. (c) 2008 Elsevier B.V. All rights reserved.

Phylogenetic position and morphology of thecae and cysts of Scrippsiella (Dinophyceae) species in the East China Sea

Resting cysts of the marine phytoplanktonic dinoflagellate Scrippsiella spp. are encountered in coastal habitats and shallow seas all over the world. Identification of Scrippsiella species requires information on cyst morphology because the plate pattern of the flagellated cell is conserved. Cysts from sediments of the East China Sea were identified based on traits from both the cysts and the thecal patterns of germinated cells. Calcareous cysts belonged predominantly to S. trochoidea (F. Stein) A. R. Loebl., S. rotunda J. Lewis, and S. precaria Montresor et Zingone. The former two species also produced smooth and noncalcified cysts in the field. A new species, S. donghaienis H. Gu sp. nov, was obtained from six noncalcified cysts with organic spines. These cysts are spherical, full of pale white and greenish granules with a mesoepicystal archeopyle. The vegetative cells consist of a conical epitheca and a round hypotheca with a plate formula of po, x, 4', 3a, 7 '', 6c (5c + t), 6 s, 5''', 2'''' and are morphologically indistinguishable from S. trochoidea. Results of internal transcribed spacer (ITS) sequence comparisons revealed that S. donghaienis was distinct from the S. trochoidea complex and appeared nested within the Calciodinellum/Calcigonellum clade. Culture experiments showed that the presence of a red body in the cyst and the shape of the archeopyle were constant within cell lines from one generation to the next, while the morphological features of the cyst wall, such as calcification and spine shape, appeared to be phenotypically plastic.

Phylogenetic position of Dendropsophus gaucheri (Lescure and Marty 2000) highlights the need for an in-depth investigation of the phylogenetic relationships of Dendropsophus (Anura: Hylidae)

Dendropsophus gaucheri is a recently described species which inhabits open areas of the eastern part of the Guiana Shield and is currently assigned to the D. parviceps species group based on the presence of a subocular cream spot. Herein we investigate its phylogenetic position including material from the type locality and newly documented populations from Suriname and Brazil based on mtDNA sequences. The species, as well as D. riveroi which is assigned to the D. minimus species group, were recovered nested within the D. microcephalus species group which implies the paraphyly of the three Dendropsophus species groups. Such result, along with other evidences, highlights the need for a thorough revision of the genus. The genetic distances among D. gaucheri samples studied are low confirming their conspecificity and suggesting recent connections among populations from open areas currently isolated by rainforest in the lowlands of the Guiana Shield.

Phylogenetic position of Dendropsophus gaucheri (Lescure and Marty 2000) highlights the need for an in-depth investigation of the phylogenetic relationships of Dendropsophus (Anura: Hylidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Reassessment of the phylogenetic position of conulariids (?Ediacaran-Triassic) within the subphylum medusozoa (Phylum Cnidaria)

Fossil taxa of uncertain phytogenetic affinities can play a crucial role in the analysis of character evolution within major extant groups. Marques & Collins (2004) concluded that conulariids (?Ediacaran-Triassic) are an extinct group of medusozoan cnidarians most closely related to Stauromedusae. However, only six of the 87 characters used by these authors can be observed in conulariid fossils. Rescoring the character states of conulariids in a conservative manner yields a new hypothesis for the phylogenetic position of conulariids, namely that they are the sister group of the scyphozoan order Coronatae rather than Stauromedusae, which is revealed as the earliest diverging lineage of Medusozoa. This new hypothesis also implies several different sequences of character evolution within Cnidaria. Specifically, the presence of a periderm completely covering the polyp in conutariids and coronates appears to be derived within Scyphozoa. Strobilation appears to be a synapomorphy uniting conulariids, Coronatae, Rhizostomeae and Semaeostomeae. This result supports the controversial interpretation of one exceptionally preserved conulariid that potentially shows that these animals produced ephyrae by strobilation. Finally, the pelagic adult medusa stage and the giant fibre nerve net appear to be features that are derived within Medusozoa.

A New Miniature Characid (Ostariophysi: Characiformes: Characidae), with Phylogenetic Position Inferred from Morphological and Molecular Data

Erythrocharax altipinnis is described from the Serra do Cachimbo, Pará, Brazil. The new taxon is distinguished from all of the Characidae genera by having the pelvic bones firmly attached through the isquiatic processes; a nearly triangular hiatus in the musculature covering the anterior chamber of the swim bladder between the first and second pleural ribs (pseudotympanum); the pedunculate, notably expanded and distally compressed teeth in both jaws; circumorbital series represented by antorbital and four infraorbital bones with laterosensory canals not enclosed; a single tooth row in the premaxillary with the teeth perfectly aligned and similar in shape and cusp number; the first three branched dorsal-fin rays distinctly elongate in males; a bright red adipose and caudal fins in life; a conspicuous dark midlateral stripe extending from the opercle to the tip of the median caudal-fin rays; and by the absence of a humeral spot. The phylogenetic position of the new taxon is discussed using morphological and molecular datasets, with conflicting results of both approaches discussed. Additionally, a summarized discussion on the current problems in the Characidae taxonomy is presented and the principal biases in the morphological dataset are also discussed. © 2013 Netto-Ferreira et al.

The skull of the Upper Cretaceous snake Dinilysia patagonica Smith-Woodward, 1901, and its phylogenetic position revisited

The cranial anatomy of Dinilysia patagonica, a terrestrial snake from the Upper Cretaceous of Argentina, is redescribed and illustrated, based on high-resolution X-ray computed tomography and better preparations made on previously known specimens, including the holotype. Previously unreported characters reinforce the intriguing mosaic nature of the skull of Dinilysia, with a suite of plesiomorphic and apomorphic characters with respect to extant snakes. Newly recognized plesiomorphies are the absence of the medial vertical flange of the nasal, lateral position of the prefrontal, lizard-like contact between vomer and palatine, floor of the recessus scalae tympani formed by the basioccipital, posterolateral corners of the basisphenoid strongly ventrolaterally projected, and absence of a medial parietal pillar separating the telencephalon and mesencephalon, amongst others. We also reinterpreted the structures forming the otic region of Dinilysia, confirming the presence of a crista circumfenestralis, which represents an important derived ophidian synapomorphy. Both plesiomorphic and apomorphic traits of Dinilysia are treated in detail and illustrated accordingly. Results of a phylogenetic analysis support a basal position of Dinilysia, as the sister-taxon to all extant snakes. The fossil taxa Yurlunggur, Haasiophis, Eupodophis, Pachyrhachis, and Wonambi appear as derived snakes nested within the extant clade Alethinophidia, as stem-taxa to the crown-clade Macrostomata. The hypothesis of a sister-group relationship between Dinilysia and Najash rionegrina, as suggested by some authors, is rejected by the results of our analysis.

A new species of the catfish genus Trichomycterus from the La Plata River basin, southern Brazil, with comments on its putative phylogenetic position (Siluriformes: Trichomycteridae)

The genus Trichomycterus is a highly diverse group of Neotropical catfishes that encompass almost 60% of all the currently recognized species of the Trichomycteridae. A new species of this genus, T. perkos, is herein described from tributaries of the Paranapanema and Uruguai River basins, southern Brazil. The new species exhibits a remarkable ontogenetic change in its pigmentation, having a unique color pattern when adult. The adult pigmentation consists of three wide dark brown stripes, located in an inner skin layer of trunk and caudal peduncle, combined with a superficial light brown freckled pattern on the dorsum and caudal peduncle. Small, presumably juvenile specimens lack the superficial freckles but already have the dark stripes, thus resembling the color pattern of a few other congeners. Nevertheless, several unequivocal morphological features distinguish both juveniles and adults of T. perkos from these congeners. In spite of the difficulties in estimating phylogenetic relationships within Trichomycterus, the new species is tentatively proposed as being the sister-taxon of a small group of species composed by T. crassicaudatus, T. igobi, and T. stawiarski.

A revision of Askeptosaurus italicus and other thalattosaurs from the European Triassic, the interrelationships of thalattosaurs, and their phylogenetic position within diapsid reptiles (Amniota, Eureptilia)

Zusammenfassung: Thalattosaurier sind eine rein auf die Trias beschränkte Grupper mariner Diapsiden, die derzeit aus Nordamerika, Europa und China bekannt ist. Die europäischen Formen sind über längere Zeit vernachlässigt worden, was speziell für Askeptosaurus italicus aus der Mitteltrias des Monte San Giorgio gilt. Die hier durchgeführte anatomische Revision des Taxons ergibt einige Korrekturen im dorsalen Schädeldach, und ermöglicht erstmalig eine detaillierte Darstellung des ventralen Teils von Gaumen und Gehirnkapsel. Im postcranialen Skelett ergeben sich ebenfalls wichtige Korrekturen, so fehlt z. B. im Gegensatz zu bisherigen Annahmen ein Thyroidfenster im Becken. Weiterhin zeigt die Hand von Askeptosaurus eine intraspezifische Variation in der Verknöcherung. Das aquatische Reptil Endennasaurus acutirostris aus dem Nor der Lombardei wird ebenfalls neu untersucht, speziell im Hinblick auf eine potenzielle Zugehörigkeit zu Thalattosauriern. Letzteres wird bestätigt, zudem werden einige Korrekturen im Schädel durchgeführt, so ist z.B. der für Thalattosaurier typische Prämaxillare/Frontale-Kontakt vorhanden. Im Postcranium wird u.a. erstmals die vollständige Phalangenformel für die Hand ermittelt. Zwei weitere aquatische Trias-Reptilien werden ebenfalls untersucht. Zum einen ein bisher unbeschriebenes Postcranium eines relativ kleinen, hochschwänzigen Thalattosauriers aus der Obertrias von Österreich, der sehr viele Ähnlichkeiten mit dem chinesischen Xinpusaurus zeigt, und zum anderen die nur an Hand von Wirbeln bekannte Form Blezingeria ichthyospondyla aus dem Muschelkalk/Lettenkeuper der Germanischen Trias. Trotz einiger anatomischer Gemeinsamkeiten mit Thalattosauriern kann eine definitive Zugehörigkeit zu dieser Gruppe nicht bestätigt werden. Zur Klärung der verwandtschaftlichen Position der Thalattosaurier innerhalb der diapsiden Reptilien wird eine computergestützte phylogenetische Analyse basaler Diapsiden unter der Verwendung von 182 Merkmalen und 31 Taxa durchgeführt. Thalattosaurier gruppieren sich hierbei außerhalb der Sauria, und zeigen zudem ein gewisses Signal zu einer Monophylie mit Ichthyosauriern. Weitere Ergebnisse sind eine Gruppierung von Schildkröten mit Lepidosauriern, ein Schwestergruppenverhältnis von Drepanosauriern und Kuehneosauriern außerhalb der Sauria, sowie der Verlust des unteren Schläfenbogens in der frühen Evolution der Diapsiden und dessen sekundäre Aquirierung innerhalb der Archo- und Lepidosauromorpha. Eine Innengruppen-Analyse der Thalattosaurier ergibt auf der Basis von 35 Merkmalen eine basale Dichotomie, die Endennasaurus und die monophyletischen Askeptosaurus/Anshunsaurus von den übrigen Thalattosauriern abgrenzt. Die Monte San Giorgio-Taxa Hescheleria und Clarazia sind ebenfalls monophyletisch und zudem die Schwestergruppe zu Thalattosaurus. Die verbleibenden Thalattosaurier sind basal zu diesen drei Taxa positioniert, wobei der chinesische Xinpusaurus und der kalifornische Nectosaurus monophyletisch sind, und die Einbeziehung des österreichischen Thalattosauriers diesen innerhalb letzterer Taxa gruppiert. Auf der Basis dieser Ergebnisse wird ein vorläufiges biogeographisch-evolutives Szenario entworfen. Eine Kiefermuskelrekonstruktion von Askeptosaurus ergibt eine eher plesiomorphe, von posterodorsal nach anteroventral verlaufende Schläfen-Muskulatur. Zusammen mit weiteren osteologischen Merkmalen resultiert daraus eine Konfiguration, die die effektivste Beißkaft bei nur gering geöffneten Kiefern erlaubt. Die lange Schnauze, der flache Kopf und der bewegliche Hals legen eine Jagdstrategie nahe, bei der die wahrscheinlich aus kleinen bis mittelgroßen Wirbeltieren bestehende Beute durch schnelle Seitwärtsbewegungen des Kopfes gefangen wurde. Die übrige aquatische Fortbewegung des Taxons bestand aus einer subundulatorischen Lokomotion ohne Beteiligung der Extremitäten. Im Gegensatz zu Askeptosaurus bevorzugte der vollständig zahnlose Endennasaurus vermutlich nur Invertebraten und kleine Wirbeltiere als Beute, und schien seine Extremitäten im Rahmen eines paraxialen 'Pectoropelvical-Ruderns' explizit mitbenutzt zu haben.

Phylogenetic position of Riemerella anatipestifer based on 16S rRNA gene sequences

Riemerella anatipestifer, the causative agent of septicemia anserum exsudativa (also called new duckling disease), belongs to the family Flavobacteriaceae of gram-negative bacteria. We determined the DNA sequences of the rrs genes encoding the 16S rRNAs of four R. anatipestifer strains by directly sequencing PCR-amplified rrs genes. A sequence similarity analysis confirmed the phylogenetic position of R. anatipestifer in the family Flavobacteriaceae in rRNA superfamily V and allowed fine mapping of R. anatipestifer on a separate rRNA branch comprising the most closely related species, Bergeyella zoohelcum, as well as Chryseobacterium balustinum, Chryseobacterium indologenes, and Chryseobacterium gleum. The sequences of the rrs genes of the four R. anatipestifer strains varied between 0.5 and 1.0%, but all of the strains occupied the same position on the phylogenetic tree. In general, differences in rrs genes were observed among R. anatipestifer strains, even within a given serotype, as shown by restriction fragment length polymorphism of PCR-amplified rrs genes.