Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation

To determine the origin and genetic diversity of Chinese cattle, we analyzed the complete mtDNA D-loop sequences of 84 cattle from 14 breeds/populations from southwest and west China, together with the available cattle sequences in GenBank. Our results sh

Mitochondrial DNA sequence diversity and origin of Chinese domestic yak

In order to clarify the origin and genetic diversity of yak in China, we analysed mitochondrial DNA (mtDNA) control region sequences (similar to 891 bp) in 52 individuals from four domestic yak (Poephagus grunniens) breeds, as well as from a hybrid betwee

Shifting atomic patterns: on the origin of the different atomic-scale patterns of graphite as observed using scanning tunnelling microscopy.

We present an in-depth study of the myriad atomically resolved patterns observed on graphite using the scanning tunnelling microscope (STM) over the past three decades. Through the use of highly resolved atomic resolution images, we demonstrate how the interactions between the different graphene layers comprising graphite affect the local surface atomic charge density and its resulting symmetry orientation, with particular emphasis on interactions that are thermodynamically unstable. Moreover, the interlayer graphene coupling is controlled experimentally by varying the tip-surface interaction, leading to associated changes in the atomic patterns. The images are corroborated by first-principles calculations, further validating our claim that surface graphene displacement, coming both from lateral and vertical displacement of the top graphene layer, forms the basis of the rich variety of atomic patterns observed in STM experiments on graphite.

The nature and origin of deep ocean clay crust from the Gulf of Guinea

Deep ocean sediments off the west coast of Africa exhibit a peculiar undrained strength profile in the form of a crust, albeit of exceptionally high water content, overlying normally consolidated clay. Hot-oil pipelines are installed into these crustal sediments, so their origins and characteristics are of great interest to pipeline designers. This paper provides evidence for the presence of burrowing invertebrates in crust material, and for the way sediment properties are modified through their creation of burrows, and through the deposition of faecal pellets. A variety of imaging techniques are used to make these connections, including photography, scanning electron microscopy and X-ray computer tomography. However, the essential investigative technology is simply the wet-sieving of natural cores, which reveals that up to 60% by dry mass of the crustal material can consist of smooth, highly regular, sand-sized capsules that have been identified as the faecal pellets of invertebrates such as polychaetes. Mechanical tests reveal that these pellets are quite robust under effective stresses of the order of 10 kPa, acting like sand grains within a matrix of fines. Their abundance correlates closely with the measured strength of the crust. While this can easily be accepted in the context of a pellet fraction as high as 60%, the question arises how a smaller proportion of pellets, such as 20%, is apparently able to enhance significantly the strength of a sediment that otherwise appears to be normally consolidated. A hypothesis is suggested based on the composition of the matrix of fines around the pellets. These appear to consist of agglomerates of clay platelets, which may be the result of the breakdown of pellets by other organisms. Their continued degradation at depths in excess of 1 m is taken to explain the progressive loss of crustal strength thereafter.

Origin of transient crosstalk and its reduction in phase-only LCOS wavelength selective switches

The transient crosstalk in a phase-only liquid crystal on silicon (LCOS) based wavelength selective switch using a Fourier transform setup was investigated. Its origin was identified using an in situ test procedure and found to be related to the transient phase patterns displayed by the LCOS device during the switching. Two different methods were proposed to reduce the transient crosstalk without the need to modify the optics or electronics in use. Experimental results show both methods are able to reduce the worst-case transient crosstalk by at least 5 dB. © 1983-2013 IEEE.

First human-caused extinction of a cetacean species?

The Yangtze River dolphin or baiji ( Lipotes vexillifer), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multivessel visual and acoustic survey carried out in November-December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise ( Neophocaena phocaenoides asiaeorientalis).

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei : Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence (1140bp). Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G. eckloni of the Yellow River specific haplotype A1 was a founder and it radiated all haplotypes of G. przewalskii which suggested G. przewalskii might only originate from one of two maternals of G. eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades A1 and A21 with the most recent common ancestor (TMRCA) about 0.2308 +/- 0.01 Ma and 0.1319 +/- 0.015 Ma, respectively, which were within the geological age range of "Gonghe Movement" event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qinghai-Tibetan Plateau in the Late Pleistocene.

Triploid origin of the gibel carp as revealed by 5S rDNA localization and chromosome painting

5S ribosomal DNA (rDNA) was isolated and sequenced from the gibel carp Carassius auratus gibelio with 162 chromosomes and crucian carp Carassius auratus with 100 chromosomes, and fluorescent probes for chromosome localization were prepared to ascertain the ploidy origin and evolutionary relationship between the two species. Using fluorescence in-situ hybridization (FISH), major 5S rDNA signals were localized to the short arms of three subtelocentric chromosomes in the gibel carp and to the short arms of two subtelocentrics in the crucian carp. In addition, some minor signals were detected on other chromosomes of both species. Simultaneously, six chromosomes were microdissected from the gibel carp metaphase spreads using glass needles, and the isolated chromosomes were amplified in vitro by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR). Significantly, when the DOP-PCR-generated probes prepared from each single chromosome were hybridized, three same-sized chromosomes were painted in each gibel carp metaphase, whereas only two painted chromosomes were observed in each crucian carp metaphase spread. The data indicate that gibel carp is of triploid origin in comparison with diploid crucian carp.

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]