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.

Identification of novel SINEs from Cyprinidae and their evolutionary significance

Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.

A possible evolutionary lag in the relationship between freshwater mussels and European bitterling

The coevolutionary dynamics between European bitterling Rhodeus amarus and freshwater unionid mussels, which the former parasitize by laying eggs on their gills, were tested. In a series of experiments fish preferences and mussel responses were compared in parasites and hosts of recent (Europe) and ancient (Asia) sympatry. Rhodeus amarus readily oviposited on the gills of all mussel species tested. Fish that laid their eggs on the gills of Asian Anodonta woodiana, however, suffered a dramatic reduction in reproductive success compared to fish that oviposited on the gills of European mussels: Unio pictorum, Unio tumidus, Anodonta anatina and Anodonta cygnea. This difference was the result of egg ejection behaviour by mussels rather than the unsuitability of the internal gill environment for European bitterling embryo development. The ejection response of mussels with a long sympatry with European bitterling was considerably more pronounced than that of mussels with a substantially shorter sympatry. The data support a coevolutionary arms race between bitterling and mussels and point to an evolutionary lag in the relationship between R. amarus and its European mussel hosts. (c) 2007 The Authors. Journal compilation (c) 2007 The Fisheries Society of the British Isles.

The co-evolutionary relationship between bitterling fishes and freshwater mussels: insights from interspecific comparisons

Hypothesis: In parasites that use hosts for offspring development, adults may base oviposition decisions on a range of host traits related either to host quality or the co-evolutionary relationship between parasite and host. We examined whether host quality or co-evolutionary dynamics drive the use of hosts in the bitterling-mussel relationship. Organisms: Six species of bitterling fish (Acheilognathinae) and eight species of freshwater mussels (Unionidae, Corbiculidae) that are used by bitterling for oviposition. Site of experiments: Experimental tanks in Wuhan, China, at the site of the natural distribution of the studied species. Methods: Three experiments that controlled for host accessibility and interspecific interactions were conducted to identify host preferences among bitterling fishes and their mussel hosts. We started with a broad interspecific comparison. We then tested bitterling behavioural choices, their temporal stability, and mussel host ejection behaviour of the eggs of generalist and specialist bitterling species. Finally, we measured host mussel quality based on respiration rate and used published studies on mussel gill structure to infer mussel suitability as hosts for bitterling eggs. Results: We found significant interspecific differences among bitterling species in their use of mussel hosts. Bitterling species varied in their level of host specificity and identity of preferred hosts. Host preferences were flexible even among apparently specialized species and fishes switched their preferences adaptively when the quality of individuals of preferred host species declined. Mussels varied considerably in their response to oviposition through egg ejections. Host preference by a generalist bitterling species correlated positively with host quality measured as the efficiency of the mussel gills to extract oxygen from inhaled water. Host ability to eject bitterling eggs correlated positively with their relative respiration rate, probably due to a higher velocity of water circulating in the mussel gill chamber.

Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei : Cypriniformes)

It is widely accepted that mitochondrial DNA (mtDNA) control region evolves faster than protein encoding genes with few exceptions. In the present study, we sequenced the mitochondrial cytochrome b gene (cyt b) and control region (CR) and compared their rates in 93 specimens representing 67 species of loaches and some related taxa in the Cobitoidea (Order Cypriniformes). The results showed that sequence divergences of the CR were broadly higher than those of the cyt b (about 1.83 times). However, in considering only closely related species, CR sequence evolution was slower than that of cyt b gene (ratio of CR/cyt b is 0.78), a pattern that is found to be very common in Cypriniformes. Combined data of the cyt b and CR were used to estimate the phylogenetic relationship of the Cobitoidea by maximum parsimony, neighbor-joining, and Bayesian methods. With Cyprinus carpio and Danio rerio as outgroups, three analyses identified the same four lineages representing four subfamilies of loaches, with Botiinae on the basal-most clade. The phylogenctic relationship of the Cobitoidea was ((Catostomidae + Gyrinocheilidae) + (Botiinae + (Balitorinae + (Cobitinae + Nemacheilinae)))), which indicated that Sawada's Cobitidae (including Cobitinae and Botiinae) was not monophyletic. Our molecular phylogenetic analyses are in very close agreement with the phylogenetic results based on the morphological data proposed by Nalbant and Bianco, wherein these four subfamilies were elevated to the family level as Botiidae, Balitoridae, Cobitidae, and Nemacheilidae. (c) 2005 Elsevier Inc. All rights reserved.

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.

Evaluation of holonomic quantum computation: Adiabatic versus nonadiabatic

Based on the analytical solution to the time-dependent Schrodinger equations, we evaluate the holonomic quantum computation beyond the adiabatic limit. Besides providing rigorous confirmation of the geometrical prediction of holonomies, the present dynamical resolution offers also a practical means to study the nonadiabaticity induced effects for the universal qubit operations.

Nonadiabatic geometric quantum computation with trapped ions

We propose a nonadiabatic scheme for geometric quantum computation with trapped ions. By making use of the Aharonov-Anandan phase, the proposed scheme not only preserves the globally geometric nature in quantum computation, but also provides the advantage of nonadiabaticity that overcomes the problem of slow evolution in the existing adiabatic schemes. Moreover, the present scheme requires only two atomic levels in each ion, making it an appealing candidate for quantum computation.

Quantum computation with coupled quantum dots embedded in optical microcavities

Based on an idea that spatial separation of charge states can enhance quantum coherence, we propose a scheme for a quantum computation with the quantum bit (qubit) constructed from two coupled quantum dots. Quantum information is stored in the electron-hole pair state with the electron and hole located in different dots, which enables the qubit state to be very long-lived. Universal quantum gates involving any pair of qubits are realized by coupling the quantum dots through the cavity photon which is a hopeful candidate for the transfer of long-range information. The operation analysis is carried out by estimating the gate time versus the decoherence time.

Analog computation using quantum-dot cell network

A novel analog-computation system using a quantum-dot cell network is proposed to solve complex problems. Analog computation is a promising method for solving a mathematical problem by using a physical system analogous to the problem. We designed a novel quantum-dot cell consisting of three-stacked. quantum dots and constructed a cell network utilizing the nearest-neighbor interactions between the cells. We then mapped a graph 3-colorability problem onto the network so that the single-electron configuration of the network in the ground state corresponded to one of the solutions. We calculated the ground state of the cell network and found solutions to the problems. The results demonstrate that analog computation is a promising approach for solving complex problems.

Computation of resonant frequencies and quality factors of cavities by FDTD technique and Pade approximation

The finite-difference time domain (FDTD) technique and the Pade approximation with Baker's algorithm are used to calculate the mode frequencies and quality factors of cavities. Comparing with the fast Fourier transformation/Pade method, we find that the Fade approximation and the Baker's algorithm can obtain exact resonant frequencies and quality factors based on a much shorter time record of the FDTD output.

Pipeline Architecture and Parallel Computation-Based Real-Time Stereovision Tracking System for Surgical Navigation

This paper studies the development of a real-time stereovision system to track multiple infrared markers attached to a surgical instrument. Multiple stages of pipeline in field-programmable gate array (FPGA) are developed to recognize the targets in both left and right image planes and to give each target a unique label. The pipeline architecture includes a smoothing filter, an adaptive threshold module, a connected component labeling operation, and a centroid extraction process. A parallel distortion correction method is proposed and implemented in a dual-core DSP. A suitable kinematic model is established for the moving targets, and a novel set of parallel and interactive computation mechanisms is proposed to position and track the targets, which are carried out by a cross-computation method in a dual-core DSP. The proposed tracking system can track the 3-D coordinate, velocity, and acceleration of four infrared markers with a delay of 9.18 ms. Furthermore, it is capable of tracking a maximum of 110 infrared markers without frame dropping at a frame rate of 60 f/s. The accuracy of the proposed system can reach the scale of 0.37 mm RMS along the x- and y-directions and 0.45 mm RMS along the depth direction (the depth is from 0.8 to 0.45 m). The performance of the proposed system can meet the requirements of applications such as surgical navigation, which needs high real time and accuracy capability.

Pipeline Architecture and Parallel Computation-Based Real-Time Stereovision Tracking System for Surgical Navigation

This paper studies the development of a real-time stereovision system to track multiple infrared markers attached to a surgical instrument. Multiple stages of pipeline in field-programmable gate array (FPGA) are developed to recognize the targets in both left and right image planes and to give each target a unique label. The pipeline architecture includes a smoothing filter, an adaptive threshold module, a connected component labeling operation, and a centroid extraction process. A parallel distortion correction method is proposed and implemented in a dual-core DSP. A suitable kinematic model is established for the moving targets, and a novel set of parallel and interactive computation mechanisms is proposed to position and track the targets, which are carried out by a cross-computation method in a dual-core DSP. The proposed tracking system can track the 3-D coordinate, velocity, and acceleration of four infrared markers with a delay of 9.18 ms. Furthermore, it is capable of tracking a maximum of 110 infrared markers without frame dropping at a frame rate of 60 f/s. The accuracy of the proposed system can reach the scale of 0.37 mm RMS along the x- and y-directions and 0.45 mm RMS along the depth direction (the depth is from 0.8 to 0.45 m). The performance of the proposed system can meet the requirements of applications such as surgical navigation, which needs high real time and accuracy capability.