Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus)

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.

The functional divergence of two glgP homologues in Synechocystis sp PCC 6803

Glycogen phosphorylase (GlgP, EC 2.4.1.1) catalyzes the cleavage of glycogen into glucose-1-phosphate (Glc-1-P), the first step in glycogen catabolism. Two glgP homologues are found in the genome of Synechocystis sp. PCC 6803, a unicellular cyanobacterium: sll1356 and slr1367. We report on the different functions of these glgP homologues. sll1356, rather than slr1367, is essential for growth at high temperatures. On the other hand, when CO2-fixation and the supply of glucose are both limited, slr1367 is the key factor in glycogen metabolism. In cells growing autotrophically, sll1356 plays a more important role in glycogen digestion than slr1367. This functional divergence is also supported by a phylogenetic analysis of glgP homologues in cyanobacteria.

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.

Reduced divergence angle of photonic crystal vertical-cavity surface-emitting laser

The reduced divergence angle of the photonic crystal vertical-cavity surface-emitting laser (PC-VCSEL) was investigated in both theory and experiment. The photonic crystal waveguide possessed the weakly guiding waveguide characteristic, which accounted for the reduction of the divergence angle. The three-dimensional finite-difference time-domain method was used to simulate the designed PC-VCSEL, and a calculated divergence angle of 5.2 degrees was obtained. The measured divergence angles of our fabricated PC-VCSEL were between 5.1 degrees and 5.5 degrees over the entire drive current range, consistent with the numerical results. This is the lowest divergence angle of the fabricated PC-VCSEL ever reported.

Theoretical investigation on quantum well lasers with extremely low vertical beam divergence and low threshold current

A specially designed quantum well laser for achieving extremely low vertical beam divergence was reported and theoretically investigated. The laser structure was characterized by two low index layers inserted between the waveguide layers and the cladding layers. The additional layers were intended to achieve wide optical spread in the cladding layers and strong confinement in the active region. This enabled significant reduction of beam divergence with no sacrifice in threshold current density. The numerical results showed that lasers with extremely low vertical beam divergence from 20 degrees down to 11 degrees and threshold current density of less than 131 A/cm(2) can be easily achieved by optimization of the structure parameters. Influences of individual key structure parameters on beam divergence and threshold current density are analyzed. Attention is also paid to the minimum cladding layer thicknesses needed to maintain low threshold current densities and low internal loss. The near and far field patterns are given and discussed. (C) 1998 American Institute of Physics.

Single-mode holey vertical-cavity surface-emitting laser with ultra-narrow beam divergence

We demonstrated oxide-confined 850-nm vertical-cavity surface-emitting lasers (VCSELs) with a two-dimensional petal-shaped holey structure composed of several annular-sector-shaped holes. Four types of devices with different hole numbers were designed and fabricated. The measured results showed that the larger hole number was beneficial to purifying the lasing mode, and realizing the single-mode operation. The side mode suppression ratio (SMSR) exceeded 30 dB throughout the entire drive current. Mode selective loss mechanism was used to explain the single-mode characteristic. The single-mode devices possessed good beam profiles, and the lowest divergence angle was as narrow as 3.2 degrees (full width at half maximum), attributed to the graded index profile and the shallow etching in the top distributed Bragg reflector (DBR).

Small-divergence singlemode emitting tapered distributed-feedback quantum cascade lasers

A tapered distributed feedback quantum cascade laser emitting at lambda similar to 8.1 mu m is reported. Utilising a tapered waveguide structure with a surface metal grating, the device exhibited singlemode operation over the temperature range of 100 to 214 K, with sidemode suppression ratio > 20 dB and a nearly diffraction limited far-field beam divergence angle of 5.4 degrees.

Narrow-beam divergence 1.55μm laser diodes with integrated self-aligned spotsize conVerter

This paper describes the high performance of narrow-beam divergence spot size converter (SSC) integrated separately confined heterostructure (SCH) LD. The upper optical confinement layer (OCL) and the butt-coupled tapered thickness waveguide were regrown simultaneously, which not only offered the separated optimization of the active region and the integrated spotsize converter, but also reduced the difficulty of the butt-joint selective regrowth. The threshold current was as low as 5.4 mA, the output power at 55 mA was 10.1 mW, the vertical and horizontal far field divergence angles were as low as 9°and 15°, and the 1-dB misalignment tolerances were 3.6 and 3.4μm, respectively.

A Single Mode 980nm InGaAs/GaAs/AlGaAs Large Optical Cavity Quantum Well Laser with Low Vertical Divergence Angle

To achieve high optical power as well as low vertical divergence angle, a new kind of optimized large optical cavity (LOC) structure is applied to a ridge waveguide 980nm InGaAs/GaAs/AlGaAs multi-quantum well laser. The optical power density in the waveguide is successfully reduced. The maximum output power is more than 400mW with a slope efficiency of 0.89W/A and the far-field vertical divergence angle is lowered to 23°.

High efficiency, low vertical divergence angle 980nnn Al-free active region lasers with novel large optical cavity and asymmetrical cladding layers

980nm InGaAs/InGaAsP/AlGaAs strained quantum well lasers,vitta novel large optical cavity and asymmetrical claddings was fabricated bg MOCVD. Very high differential quantum efficiency elf 90% (1.15W/A) and low vertical divergence angle of 24 degrees at long cavity length were obtained for 100 mu m stripe lasers. The differential quantum efficiency is up to 94% (1.20) at cavity length of 500 mu m.

An estimate of divergence time of parazoa and eumetazoa and that of cephalochordata and vertebrata by aldolase and triose phosphate isomerase clocks

Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary distances, It was shown that the evolutionary rates remain essentially unchanged in comparisons not only between different classes of vertebrates but also between vertebrates and arthropods and even between animals and plants, irrespective of the models used, Thus these enzymes might be useful molecular clocks for inferring divergence times of animal phyla, To know the divergence time of Parazoa and Eumetazoa and that of Cephalochordata and Vertebrata, the aldolase cDNAs from Ephydatia fluviatilis, a freshwater sponge, and the TPI cDNAs from Ephydatia fluviatilis and Branchiostoma belcheri an amphioxus, have been cloned and sequenced, Comparisons of the deduced amino acid sequences of aldolase and TPI from the freshwater sponge with known sequences revealed that the Parazoa-Eumetazoa split occurred about 940 million years ago (Ma) as determined by the average of two proteins and three models, Similarly, the aldolase and TPI clocks suggest that vertebrates and amphioxus last shared a common ancestor around 700 Ma and they possibly diverged shortly after the divergence of deuterostomes and protostomes.

Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

The complete mitochondrial genomes of the whistling duck (Dendrocygna javanica) and black swan (Cygnus atratus): dating evolutionary divergence in Galloanserae

Galloanserae is an ancient and diverse avian group, for which comprehensive molecular evidence relevant to phylogenetic analysis in the context of molecular chronology is lacking. In this study, we present two additional mitochondrial genome sequences of Galloanserae (the whistling duck, Dendrocygna javanica, and the black swan, Cygnus atratus) to broaden the scope of molecular phylogenetic reconstruction. The lengths of the whistling duck's and black swan's mitochondrial genomes are 16,753 and 16,748 bases, respectively. Phylogenetic analyses suggest that Dendrocygna is more likely to be in a basal position of the branch consisting of Anatinae and Anserinae, an affiliation that does not conform to its traditional classification. Bayesian approaches were employed to provide a rough timescale for Galloanserae evolution. In general, a narrow range of 95% confidence intervals gave younger estimates than those based on limited genes and estimated that at least two lineages originated before the Coniacian epoch around 90 MYA, well before the Cretaceous-Tertiary boundary. In addition, these results, which were compatible with estimates from fossil evidence, also imply that the origin of numerous genera in Anseriformes took place in the late Oligocene to early Miocene. Taken together, the results presented here provide a working framework for future research on Galloanserae evolution, and they underline the utility of whole mitochondrial genome sequences for the resolution of deep divergence.

Thermodynamical versus log-Poisson distribution in turbulence

The thermodynamical model of intermittency in fully developed turbulence due to Castaing (B. Castaing, J. Phys. II France 6 (1996) 105) is investigated and compared with the log-Poisson model (Z-S, She, E. Leveque, Phys. Rev. Lett. 72 (1994) 336). It is shown that the thermodynamical model obeys general scaling laws and corresponds to the degenerate class of scale-invariant statistics. We also find that its structure function shapes have physical behaviors similar to the log-Poisson's one. The only difference between them lies in the convergence of the log-Poisson's structure functions and divergence of the thermodynamical one. As far as the comparison with experiments on intermittency is concerned, they are indifferent.