Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei : Cyprinidae) in China inferred from cytochrome b sequences

Aim: To test a vicariant speciation hypothesis derived from geological evidence of large-scale changes in drainage patterns in the late Miocene that affected the drainages in the south-eastern Tibetan Plateau. Location: The Tibetan Plateau and adjacent areas. Methods: The cytochrome b DNA sequences of 30 species of the genus Schizothorax from nine different river systems were analysed. These DNA sequences were analysed using parsimony, maximum likelihood and Bayesian methods. The approximately unbiased and Shimodaira-Hasegawa tests were applied to evaluate the statistical significance of the shortest trees relative to alternative hypotheses. Dates of divergences between lineages were estimated using the nonparametric rate smoothing method, and confidence intervals of dates were obtained by parametric bootstrapping. Results: The phylogenetic relationships recovered from molecular data were inconsistent with traditional taxonomy, but apparently reflected geographical associations with rivers. Within the genus Schizothorax, we observed a divergence between the lineages from the Irrawaddy-Lhuit and Tsangpo-Parlung rivers, and tentatively dated this vicariant event back to the late Miocene (7.3-6.8 Ma). We also observed approximately simultaneous geographical splits within drainages of the south-eastern Tibetan Plateau, the Irrawaddy, the Yangtze and the Mekong-Salween rivers in the late Miocene (7.1-6.2 Ma). Main conclusions: Our molecular evidence tentatively highlights the importance of palaeoriver connections and the uplift of the Tibetan Plateau in understanding the evolution of the genus Schizothorax. Molecular estimates of divergence times allowed us to date these vicariant scenarios back to the late Miocene, which agrees with geological suggestions for the separation of these drainages caused by tectonic uplift in south-eastern Tibet. Our results indicated the substantial role of vicariant-based speciation in shaping the current distribution pattern of the genus Schizothorax.

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp - Cyprinus carpio haematopterus, Yuanjiang River wild common carp Cyprinus carpio rubrofuscus and Volga River wild common carp - Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus.

Molecular systematics of Xenocyprinae (Teleostei : Cyprinidae): Taxonomy, biogeography, and coevolution of a special group restricted in east Asia

We surveyed mitochondrial DNA (mtDNA) sequence variation in the subfamily Xenocyprinae from China and used these data to estimate intraspecific, interspecific, and intergeneric phylogeny and assess biogeographic scenarios underlying the geographic structure of lineages. We sequenced 1140 bp of cytochrome b from 30 individuals of Xenocyprinae and one putative outgroup (Myxocypris asiaticus) and also sequenced 297 bp of ND4L, 1380 bp of ND4, 68 bp of tRNA(His), and 69 bp of tRNA(Ser) from 17 individuals of Xenocyprinae and the outgroup (M. asiaticus). We detected high levels of nucleotide variation among populations, species, and genera. The phylogenetic analysis suggested that Distoechodon hupeinensis might be transferred to the genus Xenocypris, the taxonomic status of the genus Plagiognathops might be preserved, and species of Xenocypris and Plagiognathops form a monophyletic group that is sister to the genus Distoechodon and Pseudobrama. The introgressive hybridization might occur among the populations of X. argentea and X. davidi, causing the two species to not be separated by mtDNA patterns according to their species identification, and the process and direction of hybridization are discussed. The spatial distributions of mtDNA lineages among populations of Xenocypris were compatible with the major geographic region, which indicated that the relationship between Hubei + Hunan and Fujian is closer than that between Hubei + Hunan and Sichuan, From a perspective of parasite investigation, our data suggested that the fauna of Hexamita in Xenocyprinae could be used to infer the phylogeny of their hosts. (C) 2001 Academic Press.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

Formation of GaAs/AlGaAs and InGaAs/GaAs nanorings by droplet molecular-beam epitaxy

GaAs/AlGaAs lattice-matched nanorings are formed on GaAs (100) substrates by droplet epitaxy. The crucial step in the formation of nanorings is annealing Ga droplets under As flux for proper time. The observed morphologic evolution of Ga droplets during annealing does not support the hypothesis that As atoms preferentially react with Ga around the periphery of the droplets, but somehow relates to a dewetting process similar to that of unstable films. Photoluminescene (PL) test results confirm the quantum-confinement effect of these GaAs nanorings. Using similar methods, we have fabricated InGaAs/GaAs lattice-mismatched rings. (c) 2005 American Institute of Physics.

Evolution of InAs nanostructures grown by droplet epitaxy

The authors report the growth evolution of InAs dot and ring nanostructures with the indium deposition amount on GaAs (001) by droplet molecular beam epitaxy. There is a critical flux for the indium to form InAs dots even when there is no droplet. When the flux exceeds a critical value, In droplets form, which act as nucleation centers for the formation of InAs rings. (C) 2007 American Institute of Physics.

Growth of low-density InAs/GaAs quantum dots on a substrate with an intentional temperature gradient by molecular beam epitaxy

InAs was deposited by molecular beam epitaxy (MBE) on a GaAs substrate with an intentional temperature gradient from centre to edge. Two-dimensional (2D) to three-dimensional (3D) morphology evolution was found along the direction in which the substrate temperature was decreasing. Quantum dots (QDs) with density as low as similar to 8 x 10(6) cm(-2) were formed in some regions. We attribute the morphological evolution to the temperature-dependent desorption of deposited indium and the intermixing between deposited indium and gallium from the buffer.

Size evolution and optical properties of self-assembled InAs quantum dots on different matrix

InAs quantum dots have been grown by solid source molecular beam epitaxy on different matrix to investigate the effect on the structure and optical properties. High density of 1.02 x 10(11) cm(-2) of InAs islands on In0.15Ga0.85As and In0.15Al0.85As underlying layer has been achieved. Atomic force microscopy and photoluminescence spectra show the size evolution of InAs islands on In0.15Ga0.85As underlying layer. A strong 1.3 mum photoluminescence from InAs islands on In0.15Ga0.85As underlying layer and with InGaAs strain-reduced layer has been obtained. Single-mirror light emitting diode structures with InAs quantum dots capped by InGaAs grown on InGaAs layer as active layer were fabricated and the corresponding radiative efficiency was deduced to be as high as 20.5%. Our results provide important information for optimizing the epitaxial structures of 1.3 mum wavelength quantum dots devices. (C) 2003 Elsevier B.V. All rights reserved.

The evolution of InAs/InAlAs/InGaAlAs quantum dots after rapid thermal annealing

We have studied how the optical properties of InAs self-assembled quantum dots (QDs) grown on GaAs substrate are affected when depositing an InAlAs/InGaAs combination overgrowth layer directly on it by rapid thermal annealing (RTA). The photoluminescence measurement demonstrated that the InAs QDs experiences an abnormal variation during the course of RTA. The model of transformation of InAs-InAlAs-InGaAlAs could be used to well explain the phenomena. (C) 2003 Elsevier Science B.V. All rights reserved.

Size and shape evolution of self-assembled coherent InAs/GaAs quantum dots influenced by seed layer

The size and shape Evolution of self-assembled InAs quantum dots (QDs) influenced by 2.0-ML InAs seed layer has been systematically investigated for 2.0, 2.5, and 2.9-ML deposition on GaAs(1 0 0) substrate. Based on comparisons with the evolution of InAs islands on single layer samples at late growth stage, the bimodal size distribution of InAs islands at 2.5-ML InAs coverage and the formation of larger InAs quantum dots at 2.9-ML deposition have been observed on the second InAs layer. The further cross-sectional transmission electron microscopy measurement indicates the larger InAs QDs: at 2.9-ML deposition on the second layer are free of dislocation. In addition, the interpretations for the size and shape evolution of InAs/GaAs QDs on the second layer will be presented. (C) 2001 Elsevier Science B.V. All lights reserved.

Evolution from point defects to arsenic clusters in low-temperature grown GaAs/AlGaAs multiple quantum wells

Optical transient current spectroscopy (OTCS), photoluminescence (PL) spectroscopy and excitonic electroabsorption spectroscopy have been used to investigate the evolution of defects in the low-temperature grown GaAs/AlGaAs multiple quantum well structures during the postgrowth rapid thermal annealing. The sample was grown at 350 degrees C by molecular beam epitaxy on miscut (3.4 degrees off (001) towards (111)A) (001) GaAs substrate. After growth, the sample was subjected to 30s rapid thermal annealing in the range of 500-800 degrees C. It is found that the integrated PL intensity first decreases with the annealing temperature, then gets a minimum at 600 degrees C and finally recovers at higher temperatures. OTCS measurement shows that besides As,, antisites and arsenic clusters, there are several relatively shallower deep levels with excitation energies less than 0.3 eV in the as-grown and 500 degrees C-annealed samples. Above 600 degrees C, OTCS signals from As,, antisites and shallower deep levels become weaker, indicating the decrease of these defects. It is argued that the excess arsenic atoms group together to form arsenic clusters during annealing. (C) 2000 Elsevier Science B.V. All rights reserved.

Growth and characterization of strained superlattices delta-GaNxAs1-x/GaAs by molecular beam epitaxy

A series of superlattices delta-GaNxAs1-x/GaAs were grown by a DC plasma-N-2-assisted molecular beam epitaxy. The evolution of the surface reconstruction during the growth has been studied with the use of in situ reflection high-energy electron diffraction. The superlattices have been characterized by high-resolution X-ray diffraction measurements. Distinct satellite peaks indicate that the superlattices are of good quality. The N compositions in strained GaNxAs1-x monolayers are obtained from the dynamical simulations of the measured X-ray diffraction patterns. The periodicity fluctuations of N composition are obtained from a kinematical method dependent on the broadening of the satellite peaks of the X-ray diffraction. (C) 2000 Elsevier Science B.V. All rights reserved.

Growth mode and strain relaxation of InAs on InP (111)A grown by molecular beam epitaxy

Growth mode and strain relaxation of molecular-beam-epitaxy grown InAs/InAlAs/InP (111)A system have been investigated using reflection high-energy electron diffraction, transmission electron microscopy, atomic force microscopy, and photoluminescence measurements. In direct contrast to the well-studied InAs/GaAs system, our experimental results show that the InAs grown on InAlAs/InP (111)A follows the Stranski-Krastanov mode. Both self-organized InAs quantum dots and relaxed InAs islands are formed depending on the InAs coverage. Intense luminescence signals from both the InAs quantum dots and wetting layer are observed. The luminescence efficiency of (111)A samples is comparable to that of (001) samples, suggesting the feasibility of fabricating quantum dot optoelectronic devices on InP (111)A surfaces. (C) 1999 American Institute of Physics. [S0003-6951(99)01010-4].

Surface morphology evolution of strained InAs/GaAs(331)a films

Surface morphology evolution of strained InAs/GaAs(331)A films was systematically investigated in this paper. Under As-rich conditions, InAs elongated islands aligned along [1 (1) over bar0] are formed at a substrate temperature of 510 degrees C. We explained it as a result of the anisotropic diffusion of adatoms. Under In-rich conditions, striking change has occurred with respect to the surface morphology of the InAs layers. Instead of anisotropic InAs elongated islands, unique island-pit pairs randomly distributed on the whole surface were observed. Using cooperative nucleation mechanisms proposed by Jesson et al. [Phys. Rev. Lett. 77, 1330 (1996)], we interpret the resulting surface morphology evolution.

Substrate temperature dependence of ZnTe epilayers grown on GaAs(001) by molecular beam epitaxy

ZnTe thin films have been grown on GaAs(0 0 1) substrates at different temperatures with constant Zn and Te beam equivalent pressures (BEPs) by molecular beam epitaxy (MBE). In situ reflection high-energy electron diffraction (RHEED) observation indicates that two-dimensional (2D) growth mode can be established after around one-minute three-dimensional (3D) nucleation by increasing the substrate temperature to 340 degrees C. We found that Zn desorption from the ZnTe surface is much greater than that of Te at higher temperatures, and estimated the Zn sticking coefficient by the evolution of growth rate. The Zn sticking coefficient decreases from 0.93 to 0.58 as the temperature is elevated from 320 to 400 degrees C. The ZnTe epilayer grown at 360 degrees C displays the narrowest full-width at half-maximum (FWHM) of 660 arcsec from (0 0 4) reflection in double-crystal X-ray rocking curve (DCXRC) measurements. The surface morphology of ZnTe epilayers is strongly dependent on the substrate temperature, and the root-mean-square (RMS) roughness diminishes drastically with the increase in temperature.