Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces : Teleostei): A new insight

The Otocephala, a clade including ostariophysan and clupeomorph telcosts, represents about a quarter of total fish species diversity, with about 1000 gencra and more than 7000 species. A series of recent papers have defended that the origin of this clade and of its major groups may be significantly older than the oldest fossils of each of these groups suggest. Some of these recent papers explicitly defend a Pangean origin for some otocephalan groups Such as the Siluriformes or Cypriniformes. To know whether or not the otocephalans as a whole, and particularly the mainly freshwater, cosmopolitan otophysans could have originated before the splitting of the Pangean Supercontinent is of extreme importance, since otophysan fishes are among the most useful animal groups for the determination of historical continental relationships. In the present work we examined divergence times for each major otocephalan group by an analysis of complete mtDNA sequences, in order to investigate if these divergence times support the hypotheses advanced in recent studies. The complete mtDNA sequences of nine representative non-otocephalan fish species and of twenty-one representative otocephalan species was compared. The present study is thus, among the studies dealing with molecular divergence times of telcosts, the one in which a greater number of otocephalan species are included. The divergence times obtained support that the major otocephalan groups had a much older origin than the oldest fossil records available for these groups suggest. The origin of the Otocephala is estimated as having occurred about 282 Mya, with the origin of the Otophysi being estimated at about 251 Mya. (c) 2005 Elsevier B.V. All rights reserved.

Origin of the double- and multi-pulse structure of echolocation signals in Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientialis)

The signals of dolphins and porpoises often exhibit a multi-pulse structure. Here, echolocation signal recordings were made from four geometrically distinct positions of seven Yangtze finless porpoises temporarily housed in a relatively small, enclosed area. Some clicks demonstrated double-pulse, and others multi-pulse, structure. The interpulse intervals between the first and second pulse of the double- and multi-pulse clicks were significantly different among data from the four different positions (p < 0.01, one-way ANOVA). These results indicate that the interpulse interval and structure of the double- and multi-pulse echolocation signals depend on the hydrophone geometry of the animal, and that the double- and multi-pulse structure of echolocation signals in Yangtze finless porpoise is not caused by the phonating porpoise itself, but by the multipath propagation of the signal. Time delays in the 180 degrees phase-shifted surface reflection pulse and the nonphase-shifted bottom reflection pulse of the multi-pulse structures, relative to the direct signal, can be used to calculate the distance to a phonating animal. (c) 2005 Acoustical Society of America.

Genetic divergence between Cyprinus carpio carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis, with emphasis on origin of European domestic carp

Although common carp is the major fish species in Asian and European aquaculture and many domestic varieties have occurred, there is a controversy about the origination of European domestic common carp. Some scientists affirmed that the ancestor of European domestic common carp was Danube River wild common carp, but others considered it might be Asian common carp. For elucidating origination of European domestic common carp, we chose two representative European domestic common carp strains (German mirror carp and Russian scattered scaled mirror carp) and one wild common carp strain of Cyprinus carpio carpio subspecies (Volga River wild common carp) and two Asian common carp strains, the Yangtze River wild common carp (Cyprinus carpio haematopterus) and traditionally domestic Xingguo red common carp, as experimental materials. ND5-ND6 and D-loop segments of mitochondrial DNA were amplified by polymerase chain reaction and analyzed through restriction fragment length polymorphism (RFLP) and sequencing respectively. The results revealed that HaeIII and DdeI digestion patterns of ND5-ND6 segment and sequences of control region were different between European subspecies C. carpio carpio and Asian subspecies C. carpio haematopterus. Phylogenetic analysis showed that German mirror carp and Russian scattered scaled mirror carp belonged to two subspecies, C. carpio carpio and C. carpio haematopterus, respectively. Therefore, there were different ancestors for domestic carp in Europe: German mirror carp was domesticated from European subspecies C. carpio carpio and Russian scattered scaled mirror carp originated from Asian subspecies C. carpio haematopterus.

Common evolutionary origin of aquareoviruses and orthoreoviruses revealed by genome characterization of Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus (genus Aquareovirus, family Reoviridae)

Full-length and partial genome sequences of four members of the genus Aquareovirus, family Reoviridae (Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus) were characterized. Based on sequence comparison, the unclassified Grass carp reovirus was shown to be a member of the species Aquareovirus C The status of golden ide reovirus, another unclassified aquareovirus, was also examined. Sequence analysis showed that it did not belong to the species Aquareovirus A or C, but assessment of its relationship to the species Aquareovirus B, D, E and F was hampered by the absence of genetic data from these species. In agreement with previous reports of ultrastructural resemblance between aquareoviruses and orthoreoviruses, genetic analysis revealed homology in the genes of the two groups. This homology concerned eight of the 11 segments of the aquareovirus genome (amino acid identity 17-42%), and similar genetic organization was observed in two other segments. The conserved terminal sequences in the genomes of members of the two groups were also similar. These data are undoubtedly an indication of the common evolutionary origin of these viruses. This clear genetic relatedness between members of distinct genera is unique within the family Reoviridae. Such a genetic relationship is usually observed between members of a single genus. However, the current taxonomic classification of aquareoviruses and orthoreoviruses in two different genera is supported by a number of characteristics, including their distinct G+C contents, unequal numbers of genome segments, absence of an antigenic relationship, different cytopathic effects and specific econiches.

Origin of antiferromagnetism in CoO: A density functional theory study

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Origin of insulating behavior of the p-type LaAlO3/SrTiO3 interface: Polarization-induced asymmetric distribution of oxygen vacancies

It is revealed from first-principles calculations that polarization-induced asymmetric distribution of oxygen vacancies plays an important role in the insulating behavior at p-type LaAlO3/SrTiO3 interface. The formation energy of the oxygen vacancy (V-O) is much smaller than that at the surface of the LaAlO3 overlayer, causing all the carriers to be compensated by the spontaneously formed V-O's at the interface. In contrast, at an n-type interface, the formation energy of V-O is much higher than that at the surface, and the V-O's formed at the surface enhance the carrier density at the interface. This explains the puzzling behavior of why the p-type interface is always insulating but the n-type interface can be conducting.

Interface as the origin of ferromagnetism in cobalt doped ZnO film grown on silicon substrate

We have investigated the magnetic properties of Co-doped zinc oxide (ZnO) film deposited on silicon substrate by magnetron sputtering. Co ions have a valence of 2+ and substitute for Zn sites in the lattice. By using a chemical etching method, an extrinsic ferromagnetism was demonstrated. The observed ferromagnetism is neither associated with magnetic precipitates nor with contamination, but originates from the silicon/silicon oxide interface. This interface ferromagnetism is characterized by being temperature independent and by having a parallel magnetic anisotropy. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.2989128]

Investigation on the structural origin of n-type conductivity in InN films

This work presents a study of the correlation between the electrical properties and the structural defects in nominally undoped InN films. It is found that the density of edge-type threading dislocations (TDs) considerably affects the electron concentration and mobility in InN films. The Hall-effect measured electron concentration increases, while the Hall mobility decreases with the increase in the edge-type TD density. With the combination of secondary ion mass spectrometry and positron annihilation analysis, we suggest that donor-type point defects at the edge-type TD lines may serve as dominant donors in InN films and affect the carrier mobility.

Origin of the doping bottleneck in semiconductor quantum dots: A first-principles study

Doping difficulty in semiconductor nanocrystals has been observed and its origin is currently under debate. It is not clear whether this phenomenon is energetic or depends on the growth kinetics. Using first-principles method, we show that the transition energies and defect formation energies of the donor and acceptor defects always increase as the quantum dot sizes decrease. However, for isovalent impurities, the changes of the defect formation energies are rather small. The origin of the calculated trends is explained using simple band-energy-level models.

Possible origin of ferromagnetism in undoped anatase TiO2

Using first-principles electronic structure calculations we find that the titanium vacancy and divacancy may be responsible for the unexpected ferromagnetism in undoped anatase TiO2. An isolated titanium vacancy produces a magnetic moment of 3.5 mu(B), and an isolated titanium divacancy produces a magnetic moment of 2.0 mu(B). The origin of the collective magnetic moments is the holes introduced by the titanium vacancy or divacancy in the narrow nonbonding oxygen 2p(pi) band. At the center of the divacancy, an O-2 dimer forms during the relaxation, which lowers the total energy of the system and leads to the decrease in the total magnetic moment due to a hole compensation mechanism. For both the two native defects, the ferromagnetic state is more stable than the antiferromagnetic state.

Experimental verification on the origin of plateau-like current-voltage characteristics of resonant tunneling diodes

Current-voltage (I-V) characteristics of GaAs-based resonant tunneling diodes have been investigated in the presence of a perpendicular magnetic field. Electron resonant tunneling is strongly suppressed by the applied magnetic field, leading to peak current decreasing with increasing magnetic field. The observed plateau-like structures appear in negative differential resistance region on the I-V curves and are magnetic-field dependent. The plateau-like structures are due to the coupling between the energy levels in the emitter well and in the main quantum well. (C) 2004 American Institute of Physics.

Origin of the blueshift in the infrared absorbance of intersubband transitions in AlxGa1-x/GaN multiple quantum wells

A self-consistent calculation of the subband energy levels of n-doped quantum wells is studied. A comparison is made between theoretical results and experimental data. In order to account for the deviations between them, the ground-state electron-electron exchange interactions, the ground-state direct Coulomb interactions, the depolarization effect, and the exciton-like effect are considered in the simulations. The agreement between theory and experiment is greatly improved when all these aspects are taken into account. The ground-to-excited-state energy difference increases by 8 meV from its self-consistent value if one considers the depolarization effect and the exciton-like effect only. It appears that the electron-electron exchange interactions account for most of the observed residual blueshift for the infrared intersubband absorbance in AlxGa1-xN/GaN multiple quantum wells. It seems that electrons on the surface of the k-space Fermi gas make the main contribution to the electron-electron exchange interactions, while for electrons further inside the Fermi gas it is difficult to exchange their positions. (C) 2004 Elsevier B.V. All rights reserved.

Origin of deep level defect related photoluminescence in annealed InP

Deep level defects in annealed InP have been studied by using photoluminescence spectroscopy (PL), thermally stimulated current (TSC), deep level transient spectroscopy (DLTS), and positron annihilation lifetime (PAL). A noticeable broad PL peak centered at 1.3 eV has been observed in the InP sample annealed in iron phosphide ambient. Both the 1.3 eV PL emission and a defect at E-C-0.18 eV correlate with a divacancy detected in the annealed InP sample. The results make a divacancy defect and related property identified in the annealed InP. (c) 2006 American Institute of Physics.

Investigation on the origin of crystallographic tilt in lateral epitaxial overgrown GaN using selective etching

The crystallographic tilt of the lateral epitaxial overgrown (LEO) GaN on sapphire Substrate with SiNx mask is investiaated by double crystal X-ray diffraction. Two wing peaks beside the GaN 0002 peak can be observed for the as-grown LEO GaN. During the selective etching of SiNx mask, each wing peak splits into two peaks, one of which disappears as the mask is removed, while the other remains unchanged. This indicates that the crystallographic tilt of the overgrown region is caused not only by the plastic deformation resulted from the bending of threading dislocations, but by the non-uniformity elastic deformation related with the GaN, SiNx interfacial forces. The widths of these two peaks are also studied in this paper. (C) 2002 Elsevier Science B.V. All rights reserved.

Origin of the vertical-anticorrelation arrays of InAs/InAlAs nanowires with a fixed layer-ordering orientation

InAs/In0.52Al0.48As nanowire multilayer arrays were grown on (001) InP substrate by molecular-beam epitaxy. The structural property of the arrays was investigated by transmission electron microscopy. The results clearly showed the formation of InAs nanowires, evolution of InAs/InAlAs interface, and composition and thickness modulations in the InAlAs spacer layer. A fixed spatial ordering of InAs/InAlAs nanowires was revealed for all the samples. Regardless of the change in InAlAs spacer thickness of different samples, (i) the nanowires of one InAs layer are positioned above the nanowire spacing in the previous InAs layer and (ii) the layer-ordering orientation angle of nanowires is fixed. The results were explained from the viewpoint of the growth kinetics. The effect of InAlAs spacers is suggested to play an important role on the spatial ordering of the nanowire arrays. (C) 2002 American Institute of Physics.