The Stegana (sensu stricto) species from China,with morphological and molecular evidence (Diptera: Drosophilidae)

Four new species of the subgenus Stegana (sensu stricto) were found and described from China: S. (S.) antha sp. nov., S. (S.) latiorificia sp. nov., S. (S.) huangjiai sp. nov. and S. (S.) nigrifoliacea sp. nov. Three known Stegana (s. str.) species from China: S. (S.) antlia Okada, 1991, S. (S.) cheni Sidorenko, 1997 Sidorenko, V. S. (1997). New Asian species and new records of the genus Stegana Meigen (Diptera, Drosophilidae). I. Subgenera Oxyphortica Duda and Stegana s. str. Annales d la Société Entomologique de France (N. S.), 33, 65–79.[Web of Science ®] , [Google Scholar] and S. (S.) emeiensis Sidorenko, 1997 Sidorenko, V. S. (1997). New Asian species and new records of the genus Stegana Meigen (Diptera, Drosophilidae). I. Subgenera Oxyphortica Duda and Stegana s. str. Annales d la Société Entomologique de France (N. S.), 33, 65–79.[Web of Science ®] , [Google Scholar] are redescribed as supplementary information. A key to the species, based on morphological characters, is provided. The phylogenetic relationships among 14 species of the subgenus Stegana are reconstructed with the combined sequences of the mitochondrial genes, ND2 (NADH dehydrogenase subunit 2) and COI (cytochrome c oxidase, subunit I). Moreover, the intra- and interspecific pairwise K-2P (Kimura's two-parameter) distances among these species are summarized, and the availability of mitochondrial markers in the species identification of the subgenus Stegana are further discussed.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:368C55C3-B101-457C-BD61-BDD8F1B780E5     

A review of the genus Paraphyllanthoxylon

Thirteen species of petrified wood have been assigned previously to the genus Paraphyllanthoxylon which was established by Bailey (1924) as representative of the section Phyllanthoideae of the family Euphorbiaceae. Mädel (1962) considered the genus Paraphyllanthoxylon representative of only the Glochidion wood group of the section Phyllanthoideae. This necessitates the establishment of a new genus, Phyllanthoideoxylon, for fossil woods which have characteristics in common with several of the other wood groups in the section Phyllanthoideae. The thirteen previously identified species of Paraphyllanthoxylon are reviewed and compared with the characteristics of the genus. Eleven of these species are retained in Paraphyllanthoxylon Bailey (emend. Mädel), one (P. bangalamodense) is assigned to Phyllanthoideoxylon nov. gen. and one (P. keriense) is transferred to Bridelioxylon Ramanujam.     

Sociogenetic organisation of two desert ants

Desert ants of the genus Cataglyphis evolved a remarkable diversity in their reproductive strategies. In Cataglyphis species where social organisation was described so far, colonies are headed by one or multiple queens, queens being singly or multiply mated, and workers and/or queens possess the ability to reproduce asexually via thelytokous parthenogenesis. Here, we investigate the social organisation of C. bombycina (group bombycinus) and C. theryi (group albicans) using highly polymorphic microsatellite markers. Our results show that both species are characterized by monogynous colonies and multiply mated queens, supporting the idea that polyandry is an ancestral trait of the genus. No evidence for parthenogenetic reproduction by queens was found. One distinctive feature of the species C. bombycina among the genus is the presence of a morphologically distinct soldier caste, with highly developed scythe blades jaws. In the only colony where a significant number of soldiers have been sampled, the distribution of patrilines is fundamentally different between the soldier and the worker caste. This result suggests a genetic contribution to worker caste determination in this species, and certainly awaits further investigation.     

Phylogenetic relationships of the algae scraping cyprinid genus Capoeta (Teleostei: Cyprinidae)

We reconstructed the matrilineal phylogeny of Asian algae-eating fishes of the genus Capoeta based on complete mitochondrial gene for cytochrome b sequences obtained from 20 species sampled from the majority of the range and 44 species of closely related barbs of the genera Barbus s. str. and Luciobarbus. The results of this study show that Capoeta forms a strongly supported monophyletic subclade nested within the Luciobarbus clade, suggesting that specialized scraping morphology appeared once in the evolutionary history of the genus. We detected three main groups of Capoeta: the Mesopotamian group, which includes three species from the Tigris-Euphrates system and adjacent water bodies, the Anatolian-Iranian group, which has the most diversified structure and encompasses many species distributed throughout Anatolian and Iranian inland waters, and the Aralo-Caspian group, which consists of species distributed in basins of the Caspian and Aral Seas, including many dead-end rivers in Central Asia and Northern Iran. The most probable origination pathway of the genus Capoeta is hypothesized to occur as a result of allopolyploidization. The origin of Capoeta was found around the Langhian-Serravallian boundary according to our molecular clock. The diversification within the genus occurred along Middle Miocene-Late Pliocene periods.     

Conodont assemblages: A new functional model

A functional model for the conodont apparatus is proposed based on Carboniferous bedding plane assemblages. It is proposed that the conodont assemblage functioned as a filter feeding and respiratory organ in organisms of unknown affinities, and that the organisation of elements in the assemblage genus Scottognathus can be used as a basic plan for interpreting the arrangement of conodont elements in other assemblages. In our model the Platform Blades opened and closed the anterior end of the system, the sieve consisted of Arched Blades, Pick-shaped Blades (assemblage genera Lewistownella and Lochriea) and the main cusps of the Elongate Blades; the denticulated bars of Elongate Blades and Pick-shaped Blades (form genera Scottognathus and Westphalicus) acted as a support for ciliated tissue. A radial and bilateral arrangement for the Elongate Blades is presented and discussed. Using this model as a guide we have reconstructed the assemblage genus Duboisella.The success of conodont organisms is attributed to the genetic plasticity of elements of the filter respiratory system, which enabled the system to adapt to evolutionary changes in the marine plankton. Ideas for further research are presented. In this account we have chosen to refer to the morphological form of conodont elements (Rhodes, 1954) rather than to the form generic and specific names assigned to them in the literature, e.g., we use the term Elongate Blades, instead of Hindeodella.     

Phylogenetic incongruence in Cymbidium orchids

Cymbidium, which includes approximately 80 species, is one of the most ornamental and cultivated orchid genera. However, a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus. In the present study, we reconstructed the phylogenetic relationships by utilizing one nuclear DNA (nrITS) and seven plastid genes (rbcL, trnS, trnG, matK, trnL, psbA, and atpI) from 70 species (varieties) in Cymbidium. We also examined the occurrence of phylogenetic conflict between nuclear (nrITS) and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus. We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics. Our results do not support previous classification of the subgenera and sections within Cymbidium. Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium. Overall, our study indicates that Cymbidium has undergone a complex evolution.     

Phylogenetic and molecular dating analysis of Taiwan Blue Pheasant (Lophura swinhoii)

The Swinhoe's Pheasant (Lophura swinhoii) is an endemic and most endangered species to Taiwan, China. It belongs to the genus Lophura, family Phasianidae. To further investigate the evolutionary history of L. swinhoii, we determined its complete mitochondrial genome and reconstructed a single, robust phylogenetic tree. Our results showed that L. swinhoii is clustered with Lophura nycthemera and forms a sister group of Lophura ignita. The genus Lophura is strongly supported as the sister taxon of the genus Crossoptilon. The molecular clock analysis showed that the genetic divergence of L. swinhoii occurred in 2.71 (1.31–4.22) Mya. The most common ancestor of L. swinhoii might have migrated from mainland of South East Asia to Taiwan Island by the land bridge at 2.71 Mya ago. Taiwan Island is separated from the mainland by the sea (Taiwan Strait) and formed a separate island at around 2.5 Mya because of the transgression and regression. Therefore, geographical isolation and climate change may accelerate the evolution of L. swinhoii. In this study, we propose a biogeographic hypothesis for speciation of the L. swinhoii based on known events of the geographic and geological history of South East Asia and southeast China, which would benefit the understanding of evolutionary history of L. swinhoii as well as other galliform birds.     

A new species of the genus Borealites Klimova, 1969 (Ammonitida,Craspeditidae) from the Boreal Berriasian of Siberia

The diagnosis of the genus Borealites Klimova, 1969 is revised and amended. Polymorphism, typical of this group, is described. The new species Borealites (Borealites) schulginae sp. nov. and B. (Pseudocraspedites) compressus sp. nov. are described.     

Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae)

Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).     

Molecular Phylogeny of Weakfish Species of the Stellifer Group (Sciaenidae,Perciformes) of the Western South Atlantic Based on Mitochondrial and Nuclear Data

The phylogenetic relationships within the Stellifer group of weakfishes (Stellifer, Odontoscion, Ophioscion, and Bairdiella) were evaluated using 2723 base pairs comprising sequences of nuclear (rhodopsin, TMO-4C4, RAG-1) and mitochondrial (16S rRNA and COI) markers obtained from specimens of nine species. Our results indicate a close relationship between Bairdiella and Odontoscion, and also that the genus Stellifer is not monophyletic, but rather that it consists of two distinct lineages, one clade containing S. microps/S. naso/S. brasiliensis and the other, S. rastrifer/S. stellifer/Stellifer sp. B, which is closer to Ophioscion than the former clade. The O. punctatissimus populations from the northern and southern Brazilian coast were also highly divergent in both nuclear (0.8% for rhodopsin and 0.9% for RAG-1) and mitochondrial sequences (2.2% for 16S rRNA and 7.3% for COI), which we conclude is consistent with the presence of two distinct species. The morphological similarities of the members of the Stellifer group is reinforced by the molecular data from both the present study and previous analyses, which have questioned the taxonomic status of the Stellifer group. If, on the one hand, the group is in fact composed of four genera (Stellifer, Ophioscion, Odontoscion, and Bairdiella), one of the two Stellifer clades should be reclassified as a new genus. However, if the close relationship and the reduced genetic divergence found within the group is confirmed in a more extensive study, including representatives of additional taxa, this, together with the morphological evidence, would support downgrading the whole group to a single genus. Obviously, these contradictory findings reinforce the need for a more systematic taxonomic revision of the Stellifer group as a whole.     

A review of the cleptoparasitic bee genus Townsendiella (Apidae,Nomadinae, Townsendiellini), with the description of a new species from Pinnacles National Park

The cleptoparasitic bee genus Townsendiella Crawford (Nomadinae, Townsendiellini) is a rare group restricted to the southwestern United States and adjacent Mexico, whose taxonomy and biology remain poorly known. This paper describes Townsendiella ensifera sp. n., the first known record of this genus from Pinnacles National Park. A key to the species of the genus is provided. Several potential areas of future research are also discussed.     

Genetic diversity and population structure in the Brazilian Cattleya labiata (Orchidaceae) using RAPD and ISSR markers

Brazilian orchids are currently threatened with extinction due to habitat loss and, because of their high ornamental value, intense collecting pressure. Genetic diversity can play a key role in the survival of endangered orchid species. Here we provide the first data on genetic diversity and structure of wild populations in the genus Cattleya, in particular C.?labiata, using random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) markers. We studied 130 individuals, 117 belonging to Cattleya?labiata and 13 from 10 other species in the same genus. Data generated from 12 ISSR and 12 RAPD primers were used to determine genetic variability via a model-based Bayesian procedure (Structure) and molecular variance analysis. In addition, Shannon index, genetic diversity and Jaccard coefficients were also estimated. The marker data indicated that C. labiata has a high level of polymorphism, and five reconstructed populations were identified by Structure. The unweighted pair group method with arithmetic mean dendrogram did not group the samples by origin, which was also confirmed by Bayesian analysis, demonstrating the complex genetic structure of C.?labiata. Other Cattleya species showed no relationship with any C.?labiata sample. This genetic characterization of Cattleya from northeast Brazil contributes to knowledge of the genetic structure of the species and can be used to define strategies for conservation and breeding programmes.     

The characterization of complete mitochondrial genome and phylogenetic relationship within Rattus genus (Rodentia: Muridae)

The genus Rattus is one of the main pest genus of rodent. Most species of the genus carry all kinds of pathogenic bacteria to human being. They are traditionally considered to be a least understood group. The complete mitochondrial genome of the White-Footed Indochinese Rat, Rattus nitidus was determined in this study. The characterization of mitochondrial genomes of Rattus genus was also analyzed based on comprehensive comparison. The result of evolutionary patterns of protein-coding genes (PCGs) suggested purifying selection was the predominant evolutionary forces in the mitochondrial genomes of Rattus genus. The NADH dehydrogenase 4 gene (ND4) showed a highly elevated Ka/Ks ratio compared to the other protein-coding genes, which indicated ND4 was most likely under relaxed selection pressure. Phylogenetic analysis provided a well-supported outline of Rattus genus, and revealed two groups in the genus. R. nitidus had a sister relationship with R. norvegicus.     

Phylogenic analysis of the genus Leishmania by cytochrome b gene sequencing

In a previous report (Luyo-Acero et al., 2004), we demonstrated that cytochrome b (Cyt b) gene analysis is an effective method for classifying several isolates of the genus Leishmania; hence, we have further applied this method to other Leishmania species in an effort to enhance the accuracy of the procedure and to construct a new phylogenic tree. In this study, a total of 30 Leishmania and Endotrypanum WHO reference strains, clinical isolates from our patients assigned to 28 strains (human and non-human pathogenic species) and two species of the genus Endotrypanum were analyzed. The Cyt b gene in each sample was amplified by PCR, and was then sequenced by several primers, as reported previously. The phylogenic tree was constructed based on the results obtained by the computer software MEGA v3.1 and PAUP* v4.0 Beta. The present phylogenic tree was almost identical to the traditional method of classification proposed by Lainson and Shaw (1987). However, it produces the following suggestions: (1) exclusion of L. (Leishmania) major from the L. (L.) tropica complex; (2) placement of L.tarentolae in the genus Sauroleishmania; (3) L. (L.) hertigi complex and L. (V.) equatorensis close to the genus Endotrypanum; (4) L. (L.) enrietti, defined as L. (L.) mexicana complex, placed in another position; and (5) L. (L.) turanica and L. (L.) arabica are located in an area far from human pathogenic Leishmania strains. Cyt b gene analysis is thus applicable to the analyzing phylogeny of the genus Leishmania and may be useful for separating non-human pathogenic species from human pathogenic species.     

Late Miocene brackish Loxoconchidae (Crustacea, Ostracoda) from Italy

The Late Miocene Italian brackish Loxoconchidae are herein discussed and illustrated. Three genera and two subgenera have been recognized in the brackish Italian basins: Loxoconcha, Loxocorniculina, Loxoconchissa (Loxoconchissa) and Loxoconchissa (Loxocaspia). Taking into account the diagnostic characters of several Loxoconchidae genera, in this paper Loxocorniculina is raised at a generic rank, Loxocaspia is confirmed as a subgenus within genus Loxoconchissa and several new species are established: Loxoconchissa (Loxoconchissa) kinoi nov. sp., Loxoconchissa (Loxocaspia) cosentinoi nov. sp., Loxoconchissa (Loxocaspia) nuda nov. sp., Loxoconchissa (Loxocaspia) punctata nov. sp., Loxoconchissa (Loxocaspia) reticulata nov. sp., Loxoconchissa (Loxocaspia) tuberosa nov. sp. and Loxoconchissa (Loxocaspia) velonae nov. sp. Loxocorniculina is a typical Paratethyan genus which widespread into the Palaeo-Mediterranean during the late Messinian Lago-Mare event. Loxoconchissa was known to be widespread only in the Paratethyan realm and in this paper it is signalled for the first time in the Late Tortonian-early Messinian of Italy. The palaeobiogeography of these genera is discussed and the observed continuous distribution of Loxocorniculina against the disjunct distribution of Loxoconchissa leads to suggest that this latter genus underwent a passive dispersal via aquatic birds.     

Alectorioid Morphologies in Paleogene Lichens: New Evidence and Re-Evaluation of the Fossil Alectoria succini M?gdefrau

One of the most important issues in molecular dating studies concerns the incorporation of reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria. Several lichen fossils have been used as minimum age constraints in recent studies concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes, an almost exclusively lichen-forming class in the Ascomycota, have utilized the Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation of the type material revealed that this inclusion in fact represents poorly preserved plant remains, most probably of a root. Consequently, this fossil cannot be used as evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene. The new fossils represent either a lineage within the alectorioid group or belong to the genus Oropogon.     

Cristatopecten nov. gen. benoisti (Pectinidae, Bivalvia) du Chattien d'Aquitaine (France). Révision systématique et réflexions sur l'origine et l'évolution des Cristatopecten

The detailed study of a sample of “Pecten (Amussiopecten) benoisti” Cossmann and Peyrot (1914) from the Chattian outcrops of the Adour Basin, allowed to improve our knowledge of this species poorly known till now and to show its important ornamental variability. It follows that some nomenclatural points have been clarified at the generic level: we refute the attribution of this species to the genus Amussiopecten Sacco (1897) as used by authors—genus which was besides emended several times subsequently— and we propose its allocation to Cristatopecten nov. gen. Furthermore, this study allowed to remove the ambiguity existing originally as for the attribution of the species benoisti and burdigalensis to a same genus: our comparison of the latter two taxa shows that if benoisti has to be henceforth included in the new genus Cristatopecten (as its type species), burdigalensis (which is the type species of Amussiopecten) must be incorporated in the genus Flabellipecten Sacco (1897). The two genera Amussiopecten and Flabellipecten are therefore synonymous, as Depéret and Roman had already stated in 1910. The Cristatopecten from the Old World seem to be derived from a group of “Aequipecten” notably known in the Italian Rupelian, the group of “Aequipecten deletus” (Michelotti, 1861), of which we study here a sample from the Aquitaine Chattian. In the Aquitaine Basin, the Cristatopecten are represented, in the Chattian, by Cristatopecten benoisti (Cossmann and Peyrot, 1914); in the Lower Aquitanian, by C. praehaueri (Bongrain, Cahuzac and Freneix, 1994); in the Burdigalian-Langhian of the Saubrigues paleocanyon, by C. haueri (Michelotti, 1847) and C. miogallicus (Cossmann and Peyrot, 1914). During the whole Neogene, they spread and evolved in the Tethys and the Paratethys areas, and seem to have become extinct in the Pliocene with the disappearance of C. cristatus (Bronn, 1827), a species that we consider not as an Amusium s.s., but as the last representative of the Cristatopecten phylum.