Intergeneric phylogenetic relationships in catfishes of the Loricariinae (Siluriformes: Loricariidae), with the description of Fonchiiloricaria nanodon: a new genus and species from Peru

Recent investigations in the upper Río Huallaga in Peru revealed the presence of an intriguing species of the Loricariinae. To characterize and place this species within the evolutionary tree of the subfamily, a molecular phylogeny of this group was inferred based on the 12S and 16S mitochondrial genes and the nuclear gene F-reticulon4. The phylogeny indicated that this distinctive species was a member of the subtribe Loricariina. Given its phylogenetic placement, and its unusual morphology, this species is described as a new genus and new species of Loricariinae: Fonchiiloricaria nanodon. This new taxon is diagnosed by usually possessing one to three premaxillary teeth that are greatly reduced; lips with globular papillae on the surface; the distal margin of lower lip bearing short, triangular filaments; the premaxilla greatly reduced; the abdomen completely covered by plates, with the plates between lateral abdominal plates small and rhombic; a caudal fin with 14 rays; the orbital notch absent; five lateral series of plates; dorsal-fin spinelet absent; preanal plate present, large and solid, and of irregular, polygonal shape, the caudal peduncle becoming more compressed posteriorly for the last seven to 10 plates.     

Turbellaria Lecithoepitheliata: morphology,systematics, phylogeny

A review of the literature on the world fauna of lecithoepitheliata and Prolecithophora and extensive observations by the author on species of the Prorhynchidae, including cosmopolitan species as well as some endemic to Lake Baikal, and on endemic species of Baicalarctiinae (Prolecithophora) show that the Prorhynchidae and Gnosonesimidae are properly classified in the Neoophora. The morphological similarity of the Prorhynchidae and Prolecithophora proves these taxa are closely related. A hypothesis relating the Lecithoepitheliata Prorhynchidae to primitive prolecithophorans appears to be the only tenable hypothesis on the phylogeny of Lecithoepitheliata. The question of whether the Lecithoepitheliata is monophyletic still needs investigation; more evidence on the phylogeny of the Gnosonesimidae is needed.     

Implications of Molecular and Morphological Data for Understanding Ateline Phylogeny

The ateline monkeys constitute as certain a monophyletic group as there is among primates. The group is intriguing because while their adaptations are well-documented and their monophyly as a group is unquestioned, their phylogenetic interrelationships are controversial. Molecular data indicate a phylogeny at odds with their morphology. Traditional morphological comparisons isolate Alouatta from the atelins, and link Ateles and Brachyteles as a sister group to the exclusion of Lagothrix. In contrast, several recent molecular studies point to a closer relationship between Brachyteles and Lagothrix than between Brachyteles and Ateles. At the heart of the problem lie the assumptions we make about the validity of data and the homology of observed traits. The fossil record further confounds the issue. We must account for the fossil record because it is positive evidence. But we cannot control how much of it there is or how much of it ever will be known. At this point in time, the ateline molecular and fossil record provoke us to examine critically our morphological approach to phylogenetic modeling.     

Taxonomic redescriptions of two ciliates, Protogastrostyla pulchra n. g., n. comb. and Hemigastrostyla enigmatica (ciliophora: spirotrichea, stichotrichia), with phylogenetic analyses based on 18S and 28S rRNA gene sequences

The morphology and infraciliature of two stichotrichid ciliates, Gastrostyla pulchra(Perejaslawzewa 1886) Kahl, 1932 and Hemigastrostyla enigmatica(Dragesco and Dragesco-Kernéis 1986) Song & Wilbert, 1997, collected from marine and brackish sediments, were investigated by using living observations and protargol impregnations. Both 18S and 28S rRNA genes of these two species were sequenced. The 18S rDNA show high similarities (98.4%-99.7%) among populations of each species. There is about 94% similarity in 18S rDNA genes between G. pulchra and Gastrostyla steinii, the type species of the genus, which has been confirmed to be an oxytrichid by previous studies. In the phylogenetic trees of 18S, 28S, and combined 18S and 28S rDNA, both G. pulchra and H. enigmatica are consistently placed outside the well-established oxytrichid clade. Based on our analyses and previous ontogenetic data, we conclude that these two species may represent some lower groups in the subclass Stichotrichia, and that G. pulchra should represent a new genus, Protogastrostyla n. g. This new genus, which is morphologically similar to Gastrostyla, differs in its morphogenesis: the apical part of the old AZM is retained combining with the newly built membranelles that develop from the proter's oral primordium; the primary primordia of the dorsal kinety; and marginal primordia commence de novo without a definite contribution from the old structure.     

On quality of evidence in phylogeny reconstruction: a reply to Zrzavý's defence of the 'Ecdysozoa' hypothesis

Zrzavý’s arguments against the critical analyses of data supporting the Ecdysozoa hypothesis (Wägele et al., J. Zool. Syst. Evol. Res. 37, 211–223, 1999) are discussed. Zrzavý does not understand that the same basic principle of a priori weighting can be applied to sequence data as well as to morphological characters. Quality of evidence is the same as probability of homology, which is estimated from the number of discernible identical details. In sequences it is the number of identical nucleotides. Spectral analyses, dismissed by Zrzavý, visualize patterns of putative homologies present in alignments and also the number of positions supporting splits by chance alone. In cases in which old phylogenetic signals for a given monophylum are eroded in a gene, plesiomorphies and chance patterns will have strong influence on tree topologies and spectra. If plesiomorphies are a cause of errors, the addition of taxa that shorten internal branches is a remedy, although, in many cases such taxa may be extinct. The place of a priori estimations of data quality in a sequence of steps necessary for a phylogenetic analysis is shown. Morphological complexity is used as a proxy for a complex genetic basis and is used as a major criterion to compare characters of the Ecdysozoa and the Articulata. The details associated with the character ‘complex cuticle’ are discussed. Neither moulting nor the known components of the cuticle are novelties occurring only in Ecdysozoa. A published total evidence analysis is used to show that the number of coded characters does not necessarily reflect the quality of the data set. Zrzavý’s misunderstanding of the role of evolutionary scenarios is clarified and the importance of the use of additional biological data for plausibility arguments is explained. Plausibility arguments in favour of the Articulata hypothesis rely on facts found in functional morphology and in the fossil record. Zrzavý’s critique follows the actual mainstream but does not uncover logical mistakes or erroneous data analyses in the work of 86 . It is concluded that the Articulata hypothesis is a well‐founded alternative to the Ecdysozoa; it is based on much better morphological evidence and supported by plausibility arguments that currently do not exist for the Ecdysozoa.     

Permian terebratulids of Eurasia: Morphology,systematics, and phylogeny

The Permian terebratulids of Eurasia are revised. The taxonomic composition of the Permian terebratulids of the Russian Platform, Northern Caucasus, Transcaucasia, northern and southeastern Pamirs, and northern China (Inner Mongolia) is elucidated. Fifty-one species (13 described here as new), 21 genera (3 described here as new), 7 families, and 6 superfamilies are described. During the progress of the study, the author (Smirnova, 2004a, 2004b, 2006a, 2006b) and Smirnova and Grunt (2002, 2003a, 2003b) described for the first time 19 species, nine genera, two families, and one superfamily. Morphofunctional analysis reveals a great diversity of internal structures, of the time of their appearance in the ontogeny, and of their taxonomic significance. Ontogenetic study reveals phylogenetic relationships between the Permian and Meso-Cenozoic terebratulids, the presence of the superfamilies Terebratuloidea and Loboidothyroidea in the Permian, and a new type of brachidium ontogeny characterizing the superfamily Compositelasmatoidea. This book is intended for paleontologists and biologists interested in problems of taxonomy and phylogeny, and includes 5 plates, 80 figures, and 75 bibliographic references.     

Evidence for a phylogenetic position of button quails (Turnicidae: Aves) among the Gruiformes

The phylogenetic position of the Turnicidae (Aves) was unresolved. Historically, they were classified as members of the Struthioniformes, Galliformes, Charadriiformes, Columbiformes or the Gruiformes. In these classifications they had taxonomic rank of order 'Turniciformes' or family 'Turnicidae'. However, most of these studies followed phenetic methodology and used morphological similarity of taxa and plesiomorphic characters to classify Turnix . Recent phylogenetic studies on the basis of morphological character analyses or phenetic comparisons based on DNA-DNA hybridization experiments failed to clarify the phylogenetic realtionship of Turnix and suggested a position as 'incerte sedis', either among the Gruiformes or as the parvclass 'Turnicac'as a sistergroup to the 'Neoaves'.
We studied skeletal and myological material of Turnix to resolve its phylogenetic position. Further, we considered all characters that were previously discussed in literature to classify Turnix and tested them for their potential use in phylogenetic analysis. We added several yet unemployed morphological characters of phylogenetic significance to the analysis. The Struthioniformes, 'Galloanseres', and Columbiformes are each characterized by a clear set of autapomorpies. Only one autapomorphy in known for the Gruiformes but this character is of satisfying consistency and can be found in all families of the Gruiformes (Gruidae, Psophiidae, Aramidae. Rallidae) and Turnix. Turnix and the Rallidae share four complex morphological characters implying a close phylogenetic relationship. The data presented in this paper support the hypothesis that Turnix is a member of the Gruiformes with close relationships to the Rallidae. No evidence was found that would support a parvclass 'Turnicae'as sistergroup to the 'Neoaves'.