Molecular phylogenetics of the family Cyprinidae (Actinopterygii : Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichotvensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages. (c) 2008 Published by Elsevier Inc.

Transport-determined early growth and development of jack mackerel Trachurus japonicus juveniles immigrating into Sagami Bay, Japan

Oceanographic conditions and transport processes are often critical factors that affect the early growth, survival and recruitment of marine fishes. Sagittal otoliths were analysed to determine age and early growth for 381 jack mackerel (Trachurus japonicus) juveniles from Sagami Bay on the Pacific coast of Japan. Two separate hatching periods ( December and February-March) were identified. They originated from the spawning grounds in the East China Sea. Early growth and developmental rates of December-hatching fish were lower than those for February-March-hatching fish. It is likely that these differences were determined in the Kuroshio Current during transport from the spawning grounds to Sagami Bay, and the lower December water temperatures in the bay. Origin and hatch dates of juveniles in Sagami Bay were in contrast to previous research on Fukawa Bay, where April-or-later-hatching fish from spawning grounds in the coastal waters of southern Japan constituted about half of the juvenile population. Management of these two jack mackerel stocks needs to consider these differences in hatch date composition and spawning origins, as these differences could affect early growth and subsequent mortality.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei : Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence (1140bp). Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G. eckloni of the Yellow River specific haplotype A1 was a founder and it radiated all haplotypes of G. przewalskii which suggested G. przewalskii might only originate from one of two maternals of G. eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades A1 and A21 with the most recent common ancestor (TMRCA) about 0.2308 +/- 0.01 Ma and 0.1319 +/- 0.015 Ma, respectively, which were within the geological age range of "Gonghe Movement" event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qinghai-Tibetan Plateau in the Late Pleistocene.

Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei : Cypriniformes) derived from the nuclear recombination activating gene 2 sequences

The family Cyprinidae is one of the largest families of fishes in the world and a well-known component of the East Asian freshwater fish fauna. However, the phylogenetic relationships among cyprinids are still poorly understood despite much effort paid on the cyprinid molecular phylogenetics. Original nucleotide sequence data of the nuclear recombination activating gene 2 were collected from 109 cyprinid species and four non-cyprinid cypriniform outgroup taxa and used to infer the cyprinid phylogenetic relationships and to estimate node divergence times. Phylogenetic reconstructions using maximum parsimony, maximum likelihood, and Bayesian analysis retrieved the same clades, only branching order within these clades varied slightly between trees. Although the morphological diversity is remarkable, the endemic cyprinid taxa in East Asia emerged as a monophyletic clade referred to as Xenocypridini. The monophyly for the subfamilies including Cyprininae and Leuciscinae, as well as the tribes including Labeonini, Gobionini, Acheilognathini, and Leuciscini, was also well resolved with high nodal support. Analysis of the RAG2 gene supported the following cyprinid molecular phylogeny: the Danioninae is the most basal subfamily within the family Cyprinidae and the Cyprininae is the sister group of the Leuciscinae. The divergence times were estimated for the nodes corresponding to the principal clades within the Cyprinidae. The family Cyprinidae appears to have originated in the mid-Eocene in Asia, with the cladogenic event of the key basal group Danioninae occurring in the early Oligocene (about 31-30 MYA), and the origins of the two subfamilies, Cyprininae and Leuciscinae, occurring in the mid-Oligocene (around 26 MYA). (c) 2006 Elsevier Inc. All rights reserved.

Vertical variation in dissolved alkaline phosphatase activity in a shallow eutrophic lake determined in reverse micelles

We evaluated the feasibility of microencapsulating dissolved alkaline phosphatase of a water body into reverse micelle systems prepared by hexadecyltrimethylammonium bromide as a surfactant in cyclohexane and 1-butanol as co-surfactant. The dissolved alkaline phosphatase activity within the micelle was described, including its kinetic parameters and the effects of pH and temperature on catalytic activity in surface, overlying and interstitial water of Lake Donghu. We found the similarities on the behavior of dissolved alkaline phosphatase of surface and interstitial water in reverse micelles, which was distinctly different from its behavior in the overlying water. This difference likely reflected the different origins of the dissolved alkaline phosphatase in the vertical profile of the lake. This system provides a novel tool with which to study the diversity and ecological significance of extracellular enzymes in aquatic environments.

The giant zooxanthellae-bearing ciliate Maristentor dinoferus (Heterotrichea) is closely related to folliculinidae

The small subunit rDNA sequence of Maristentor dinoferus (Lobban, Schefter, Simpson, Pochon, Pawlowski, and Foissner, 2002) was determined and compared with sequences from other Heterotrichea and Karyorelictea. Maristentor resembles Stentor in basic morphology and had been provisionally assigned to Stentoridae. However, our phylogenetic analyses show that Maristentor is more closely related to Folliculinidae. Our results support the creation of a separate family for Maristentor, Maristentoridae n. fam., and also confirm the phylogenetic grouping of Folliculindae, Stentoridae, Blepharismidae, and Maristentoridae, which we informally call 'stentorids'. Maristentor, rather than Stentor itself, appears to be most significant in understanding the origins of folliculinids from their aloricate ancestors. Our analyses suggest continued uncertainty in the exact placement of the root of heterotrichs with this phylogenetic marker.

Status of sturgeon aquaculture and sturgeon trade in China: a review based on two recent nationwide surveys

The authors reviewed the aquacultural history of Acipenseriformes in China, related the legal status and examined the current status of the cultured species or hybrids, origins of seedlings, quantities of production, geographic distribution in farming, and the sustainability for both restocking programmes and human consumption. The census shows that since 2000, the production of cultured sturgeons in China appears to have become the largest in the world. As of 2000, the rapid growth of sturgeon farming in China mainly for commercial purposes has shifted harvests in the Amur River from caviar production to the artificial culture of sturgeon seedlings. This dramatic development has also caused a series of extant and potential problems, including insufficient market availability and the impact of exotic sturgeons on indigenous sturgeon species. Annual preservation of sufficient higher-age sturgeons should be a national priority in order to establish a sustainable sturgeon-culture industry and to preserve a gene pool of critically endangered sturgeon species to prevent their extinction.

Molecular analysis of silver crucian carp (Carassius auratus gibelio Bloch) clones by SCAR markers

Random amplified polymorphic DNA (RAPD) molecular markers specific for one, two or three clones have been identified from five gynogenetic clones of silver crucian carp (Carassius auratus gibelio Bloch) using RAPD markers developed earlier. In this study, three RAPD markers (RA1-PA, RA2-EF and RA4-D) produced by Opj-1, and two RAPD DNA fragments (RA3-PAD and RA5-D) produced by Opj-7, were selected for molecular cloning and sequencing. Sequence data indicated that there were identical 801-bp nucleotide sequences in the shared marker RA1-PA cloned respectively from clones P and A, and the shared marker RA2-EF (which was cloned from clones E and F), were also of identical 958-by nucleotide sequences. The nucleotide sequences of the shared marker RA3-PAD fragments were also similar for 1181 by among clones P, A and D. The specific fragment RA4-D was composed of 628 bp, and the fragment RA5-D from clone D contained 385 nucleotides. According to the nucleotide sequences, we designed and synthesized five pairs of sequence characterized amplified regions (SCAR) primers to identify the specific fragments in these gynogenetic clones of silver crucian carp. Only individuals from clones P and A amplified a specific band using a pair of SCI-PA primers synthesized according to the marker RA1-PA sequences, whereas no products were detected in individuals from clones D, E and F. The PCR products amplified using SC2-EF and SC3-PAD primers were as expected. Furthermore, the pair of SC4-D primers amplified specific bands only in individuals from clone D, although weak bands could be produced in all individuals of the five clones when lower annealing temperatures were used. However, an additional pair of SC5-D primers designed from the RA5-D marker sequences could amplify a DNA band in individuals from clones P, A and D, and the same weak band was produced in clone E, whereas no products were detected in individuals from clone F. Searches in GenBank revealed that the 385-bp DNA fragment from RA5-D was homologous to the 5' end of gonadotropin I beta subunit 2 gene and growth hormone gene. No homologous sequences were found for other markers in GenBank. The SCAR markers identified in this study will offer a powerful, easy, and rapid method for discrimination of different clones and for genetic analyses that examine their origins and unique reproductive modes in crucian carp. Furthermore, they will likely benefit future selective breeding programs as reliable and reproducible molecular markers. (C) 2001 Elsevier Science B.V. All rights reserved.

First-principles prediction of the magnetism of 3d transition-metal-doped Rocksalt MgO

Using first-principles band structure methods, we have systematically studied the electronic structures, magnetic stabilities, and half-metal properties of 3d transition-metal (TM) doped Rocksalt MgO compounds TMMg3O4 (TM = V, Cr, Mn, Fe, Co, and Ni). The calculations reveal that only CrMg3O4 has a ferromagnetic stability among the six compounds, which is explained by double-exchange mechanism. The magnetic stability is affected by the doping concentration of TM if the top valance band is composed of partially occupied t(2g) states. In addition, CrMg3O4 is a half-metallic ferromagnet. The origins of half-metallic and ferromagnetic properties are explored. The Curie temperature (T-c) of CrMg3O4 is 182 K. And it is hard for CrMg3O4 to deform due to the large bulk modulus and shear modulus, so it is a promising spintronic material. Our calculations provide the first available information on the magnetic properties of 3d TM-doped MgO.

Electronic structures of wurtzite ZnO, BeO, MgO and p-type doping in Zn1-xYxO (Y = Mg, Be)

Using the density function theory within the generalized gradient approximation, the band structures of wurtzite ZnO, BeO and MgO have been calculated. The effective-mass parameters are fitted using the calculated eigenvalues. The Dresselhaus spin-orbit effect appears in the k[1 00] direction, and is zero in the high symmetry direction k[00 1]. The orderings of valence band split by the crystal-field and spin-orbit coupling in wurtzite ZnO, BeO and MgO are identified by analyzing the wave function characters calculated by projecting the wave functions onto p-state in the spherical harmonics. For wurtzite ZnO, the ordering of valence band is Still Gamma(7) > Gamma(9) > Gamma(7) due to the negative spin-orbit coupling splitting energy and the positive crystal-field splitting energy. Thus, the Thomas' conclusion is confirmed. For wurtzite BeO and MgO, although their orderings of valence bands are Gamma(7) > Gamma(9) > Gamma(7) too, the origins of their orderings are different from that of wurtzite ZnO. Zn1-x,YxO (Y = Mg, Be) doped with N and P atoms have been studied using first-principles method. The calculated results show that N atom doped in Zn1-x BexO has more shallow acceptor energy level with increasing the concentration of Be atom. (C) 2008 Elsevier B.V. All rights reserved.

Photoluminescence from heterogeneous SiGe/Si nanostructures prepared via a two-step approach strategy

A two-step approach of preparation for SiGe/Si heterogeneous nanostructures, which combined with ultra-high vacuum chemical deposition and electrochemical anodization techniques, is demonstrated. Uniformly distributed nanostructures with a quite uniform distribution of size and morphology are obtained. A strong room-temperature photoluminescence from the nanostructures was observed with a narrow full-width at half-maximum of around 110 meV. The possible origins of the two main peaks at around 1.6 and 1.8 eV have been discussed in detail. The two-step approach is proved to be a promising method to fabricate new Si-based optoelectronic materials. (C) 2009 Elsevier B.V. All rights reserved.

Photoluminescence characteristics of InP annealed in phosphorus and iron phosphide ambiences

Photo luminescence (PL) spectroscopy has been used to study InP annealed in phosphorus and iron phosphide ambiences. Noticeable PL emissions related with thermally induced defects have been detected in undoped InP annealed in iron phosphide ambience. Origins of the PL emissions have been discussed. (c) 2004 Elsevier Ltd. All rights reserved.

Electrical characterization of Er- and Pr-implanted GaN films

Hall, current-voltage, and deep-level transient spectroscopy measurements were used to characterize the electrical properties of metalorganic chemical vapor deposition grown undoped, Er- and Pr-implanted GaN films. Only one deep level located at 0.270 eV below the conduction band was found in the as-grown GaN films. However, four defect levels located at 0.300, 0.188, 0.600, and 0.410 eV below the conduction band were found in the Er-implanted GaN films after annealing at 900 degrees C for 30 min, and four defect levels located at 0.280, 0.190, 0.610, and 0.390 eV below the conduction band were found in the Pr-implanted GaN films after annealing at 1050 degrees C for 30 min. The origins of the deep defect levels are discussed. (C) 2005 American Institute of Physics.

Cr-doped InAs self-organized diluted magnetic quantum dots with room-temperature ferromagnetism

Cr-doped InAs self-organized diluted magnetic quantum dots (QDs) are grown by low-temperature molecular-beam epitaxy, Magnetic measurements reveal that the Curie temperature of all the InAs:Cr QDs layers with Cr/In flux ratio changing from 0.026 to 0.18 is beyond 400 K. High-resolution cross sectional transmission electron microscopy images indicate that InAs:Cr QDs are of the zincblende structure. Possible origins responsible for the high Curie temperature are discussed.