Comparative molecular cytogenetic studies in the order Carnivora: mapping chromosomal rearrangements onto the phylogenetic tree

We have made a set of chromosome-specific painting probes for the American mink by degenerate oligonucleotide primed-PCR (DOP-PCR) amplification of flow-sorted chromosomes. The painting probes were used to delimit homologous chromosomal segments among human, red fox, dog, cat and eight species of the family Mustelidae, including the European mink, steppe and forest polecats, least weasel, mountain weasel, Japanese sable, striped polecat, and badger. Based on the results of chromosome painting and G-banding, comparative maps between these species have been established. The integrated map demonstrates a high level of karyotype conservation among mustelid species. Comparative analysis of the conserved chromosomal segments among mustelids and outgroup species revealed 18 putative ancestral autosomal segments that probably represent the ancestral chromosomes, or chromosome arms, in the karyotype of the most recent ancestor of the family Mustelidae. The proposed 2n = 38 ancestral Mustelidae karyotype appears to have been retained in some modern mustelids, e.g., Martes, Lutra, ktonyx, and Vormela. The derivation of the mustelid karyotypes from the putative ancestral state resulted from centric fusions, fissions, the addition of heterochromatic arms, and occasional pericentric inversions. Our results confirm many of the evolutionary conclusions suggested by other data and strengthen the topology of the carnivore phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. Copyright (C) 2002 S. KargerAG, Basel.

Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

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.

Utility of ITS1-5.8S-ITS2 sequences for species discrimination and phylogenetic inference of two closely related bucephalid digeneans (Digenea : Bucephalidae): Dollfustrema vaneyi and Dollfustrema hefeiensis

The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from 60 specimens belonging to two closely related bucephalid digeneans (Dollfustrema vaneyi and Dollfustrema hefeiensis) from different localities, hosts, and microhabitat sites were cloned to examine the level of sequence variation and the taxonomic levels to show utility in species identification and phylogeny estimation. Our data show that these molecular markers can help to discriminate the two species, which are morphologically very close and difficult to separate by classical methods. We found 21 haplotypes defined by 44 polymorphic positions in 38 individuals of D. vaneyi, and 16 haplotypes defined by 43 polymorphic positions in 22 individuals of D. hefeiensis. There is no shared haplotypes between the two species. Haplotype rather than nucleotide diversity is similar between the two species. Phylogenetic analyses reveal two robustly supported clades, one corresponding to D. vaneyi and the other corresponding to D. hefeiensis. However, the population structures between the two species seem to be incongruent and show no geographic and host-specific structure among them, further indicating that the two species may have had a more complex evolutionary history than expected.

Comparative cytogenetics of bats (Chiroptera): The prevalence of Robertsonian translocations limits the power of chromosomal characters in resolving interfamily phylogenetic relationships

Although the monophyly of Chiroptera is well supported by many independent studies, higher-level systematics, e.g. the monophyly of microbats, remains disputed by morphological and molecular studies. Chromosomal rearrangements, as one type of rare genomic changes, have become increasingly popular in phylogenetic studies as alternatives to molecular and other morphological characters. Here, the representatives of families Megadermatidae and Emballonuridae are studied by comparative chromosome painting for the first time. The results have been integrated into published comparative maps, providing an opportunity to assess genome-wide chromosomal homologies between the representatives of eight bat families. Our results further substantiate the wide occurrence of Robertsonian translocations in bats, with the possible involvement of whole-arm reciprocal translocations (WARTs). In order to search for valid cytogenetic signature(s) for each family and superfamily, evolutionary chromosomal rearrangements identified by chromosomal painting and/or banding comparison are subjected to two independent analyses: (1) a cladistic analysis using parsimony and (2) the mapping of these chromosomal changes onto the molecularly defined phylogenetic tree available fromthe literature. Both analyses clearly indicate the prevalence of homoplasic events that reduce the reliability of chromosomal characters for resolving interfamily relationships in bats.

Comparative study of Ga2O3 : Dy3+ phosphors prepared by three methods

Trivalent dysprosium (Dy3+)-activated beta-gallium oxide (beta-Ga2O3) phosphors were synthesized by solid-state (SS), coprecipitation (CP), and citrate gel (CG) methods, respectively. The resulting beta-Ga2O3:Dy3+ phosphors were well characterized by X-ray diffraction, field-emission scanning electron microscopy (FESEM), and by photoluminescence and cathodoluminescence spectra. The phosphors prepared by different methods show different luminescence properties under the excitation of UV and low-voltage cathode rays. There exists an energy transfer from the beta-Ga2O3 host lattices to Dy3+, and the energy transfer efficiency was higher in the CG-derived phosphors than those of the SS- and CP-derived phosphors. Factors influencing the intensity of luminescence and the energy transfer efficiency from beta-Ga2O3 host to Dy3+ in beta-Ga2O3:Dy3+ phosphors were investigated in detail. It is shown that the CG method is the most respected process for the preparation of beta-Ga2O3:Dy3+ phosphors.

Comparative study on the luminescent properties of Y3Al5O12 : RE3+ (RE : Eu, Dy) phosphors synthesized by three methods

By using metal nitrates and oxides as the starting materials, Y3Al5O12 (YAG) and YAG: RE3+ (RE: Eu, Dy) powder phosphors were prepared by solid state (SS), coprecipitation (CP) and citrate-gel (CG) methods, respectively. The resulting YAG based phosphors were characterized by XRD and photoluminescent excitation and emission spectra as well as lifetimes. The purified crystalline phases of YAG were obtained at 800degreesC (CG) and 900degreesC (CP and SS), respectively. Great differences were observed for the excitation and emission spectra of Eu3+ and Dy3+ between crystalline and amorphous states of YAG, and their emission intensities increased with increasing the annealing temperature. At an identical annealing temperature and doping concentration, the Eu3+ and Dy3+ showed the strongest and weakest emission intensity in CP- and CG-derived YAG phosphors, respectively. The poor emission intensity for CG-derived phosphors is mainly caused by the contamination organic impurities from citric acid in the starting materials. Furthermore, the lifetimes for the samples derived from CG and CP routes are shorter than those derived from the SS route.

Comparative studies on electrochemical behavior and electrocatalytic properties of heteropolyanion-containing multilayer films prepared by two methods

Two modification methods for multilayer formation, i.e. immersion growth and electrochemical growth, were studied comparatively for their influence on the electrochemical behavior and the electrocatalytic properties of the thus-fabricated SiMo11V-containing multilayer films. Electrochemical growth was proven to be a more suitable method than immersion growth in preparing uniform ultrathin multilayer self-assemblies with good functions. We investigated the effects of scan rate and pH on the electrochemical behavior of the monolayer and multilayer films. We also compared the electrocatalytic effects on the reduction of BrO3- and HNO2 by the multilayer films prepared by the two methods. Moreover, the influence of multilayer thickness and the identity of the outermost layer on the electrocatalytic properties were studied. Much higher catalytic currents appeared on the thicker multilayer films than those on the thinner ones. On the other hand, the catalytic currents became smaller when the multilayer films with SiMo11V as the outermost layer were covered with an additional quarternized poly(4-vinylpyridine) layer partially complexed with osmium bis(2,2'-bypyridine) chloride (QPVP-Os layer). These influences were believed to be due to the different quantities of electrocatalyst loaded in the multilayer films and the blocking effect of the QPVP-Os outermost layer. (C) 2000 Elsevier Science S.A. All rights reserved.

COMPARATIVE-STUDY OF CA4Y6(SIO4)(6)O-A PHOSPHORS PREPARED BY SOL-GEL AND DRY METHODS (A=PB2+,EU3+, TB3+,DY3+)

Ca4Y6(SiO4)(6)O:A (A = Pb2+, Eu3+, Tb3+, Dy3+) phosphors have been prepared by two methods: the sol-gel method and the conventional dry method. The crystallization processes and the luminescence characteristics of the phosphors were studied, The sol-gel method features low-temperature formation of the phosphor, leading to successful preparation of Pb2+-activated phosphors which could not be prepared by the dry method at high temperature. The (4f)(8-)(4f)(7)(5d)(1) absorption band of Tb3+ and the charge-transfer (CT) band of Eu3+ have higher energies and narrower half-widths in the sol-gel-derived phosphors than in the phosphors prepared by the dry method, respectively. The Tb3+ and Dy3+ ions show stronger emission in the former than in the latter. Both the yellow-to-blue intensity ratio (Y:B) of Dy3+ and the red-to-orange intensity ratio (R:O) of Eu3+ in the sol-gel-derived phosphors are smaller than those for the phosphors derived by the dry method.

Comparative analysis of methods for concentrating venom from jellyfish Rhopilema esculentum Kishinouye

In this study, several methods were compared for the efficiency to concentrate venom from the tentacles of jellyfish Rhopilema esculentum Kishinouye. The results show that the methods using either freezing-dry or gel absorption to remove water to concentrate venom are not applicable due to the low concentration of the compounds dissolved. Although the recovery efficiency and the total venom obtained using the dialysis dehydration method are high, some proteins can be lost during the concentrating process. Comparing to the lyophilization method, ultrafiltration is a simple way to concentrate the compounds at high percentage but the hemolytic activities of the proteins obtained by ultrafiltration appear to be lower. Our results suggest that overall lyophilization is the best and recommended method to concentrate venom from the tentacles of jellyfish. It shows not only the high recovery efficiency for the venoms but high hemolytic activities as well.

A comparative study of Young's modulus of single-walled carbon nanotube by CPMD, MD, and first principle simulations

Carbon nanotubes (CNTs), due to their exceptional magnetic, electrical and mechanical properties, are promising candidates for several technical applications ranging from nanoelectronic devices to composites. Young's modulus holds the special status in material properties and micro/nano-electromechanical systems (MEMS/NEMS) design. The excellently regular structures of CNTs facilitate accurate simulation of CNTs' behavior by applying a variety of theoretical methods. Here, three representative numerical methods, i.e., Car-Parrinello molecular dynamics (CPMD), density functional theory (DFT) and molecular dynamics (MD), were applied to calculate Young's modulus of single-walled carbon nanotube (SWCNT) with chirality (3,3). The comparative studies showed that the most accurate result is offered by time consuming DFT simulation. MID simulation produced a less accurate result due to neglecting electronic motions. Compared to the two preceding methods the best performance, with a balance between efficiency and precision, was deduced by CPMD.

Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting

With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: ( 1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; ( 2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks ( Tamias sibiricus), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (order Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.

Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples

As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cytochrome b genes (1140 bp) of all suggested species of musk deer in order to reconstruct their phylogenetic history through molecular information. Our results showed that the cytochrome b gene tree is rather robust and concurred for all the algorithms employed (parsimony, maximum likelihood, and distance methods). Further, the relative rate test indicated a constant sequence substitution rate among all the species, permitting the dating of divergence events by molecular clock. According to the molecular topology, M. moschiferus branched off the earliest from a common ancestor of musk deer (about 700,000 years ago); then followed the bifurcation forming the M. berezouskii lineage and the lineage clustering M. fuscus, M. chrysogaster, and M. leucogaster (around 370,000 years before present), interestingly the most recent speciation event in musk deer happened rather recently (140,000 years ago), which might have resulted from the diversified habitats and geographic barriers in southwest China caused by gigantic movements of the Qinghai-Tibetan Plateau in history. Combining the data of current distributions, fossil records, and molecular data of this study, we suggest that the historical dispersion of musk deer might be from north to south in China. Additionally, in our further analyses involving other pecora species, musk deer was strongly supported as a monophyletic group and a valid family in Artiodactyla, closely related to Cervidae. (C) 1999 Academic Press.