bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity
Authors: JANZEN DANIEL H. , HALLWACHS WINNIE , BLANDIN PATRICK , BURNS JOHN M. , CADIOU JEAN‐MARIE , CHACON ISIDRO , DAPKEY TANYA , DEANS ANDREW R. , EPSTEIN MARC E. , ESPINOZA BERNARDO , FRANCLEMONT JOHN G. , HABER WILLIAM A. , HAJIBABAEI MEHRDAD , HALL JASON P. W. , HEBERT PAUL D. N. , GAULD IAN D. , HARVEY DONALD J. , HAUSMANN AXEL , KITCHING IAN J. , LAFONTAINE DON , LANDRY JEAN‐FRANÇOIS , LEMAIRE CLAUDE , MILLER JACQUELINE Y. , MILLER JAMES S. , MILLER LEE , MILLER SCOTT E , MONTERO JOSE , MUNROE EUGENE , GREEN SUZANNE RAB , RATNASINGHAM SUJEEVAN , RAWLINS JOHN E. , ROBBINS ROBERT K. , RODRIGUEZ JOSEPHINE J. , ROUGERIE RODOLPHE , SHARKEY MICHAEL J. , SMITH M. ALEX , SOLIS M. ALMA , SULLIVAN J. BOLLING , THIAUCOURT PAUL , WAHL DAVID B. , WELLER SUSAN J. , WHITFIELD JAMES B. , WILLMOTT KEITH R. , WOOD D. MONTY , WOODLEY NORMAN E. , WILSON JOHN J.
Published: April 2009

Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0–2000 m elevation contains at least 10 000 species of non‐leaf‐mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG‐reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co‐authors. DNA barcoding — the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species — was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to ‘variation’ or thought to be insignificant for species‐level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.
The front‐end logistics of DNA barcoding: challenges and prospects
Authors: BORISENKO ALEX V. , SONES JAYME E. , HEBERT PAUL D. N.
Published: April 2009

Building a global library of DNA barcodes will require efficient logistics of pre‐laboratory specimen processing and seamless interfacing with molecular protocols. If not addressed properly, the task of aggregating specimens may become the biggest bottleneck in the analytical chain. Three years of experience in developing a collection management system to facilitate high‐throughput DNA barcoding have allowed the Canadian Centre for DNA Barcoding to recognize and resolve the most common logistical obstacles. Dealing with these challenges on a larger scale will be an important step towards building a solid collection‐based foundation for the international DNA barcoding effort.
DNA barcoding and the mediocrity of morphology
Authors: PACKER LAURENCE , GIBBS JASON , SHEFFIELD CORY , HANNER ROBERT
Published: April 2009

A small but vocal community of critics has questioned the epistemological value of DNA barcoding by suggesting that either it ‘cannot work’ for the identification or discovery of species or that it ignores the ‘richness’ inherent in traditional approaches. We re‐examine these arguments through a comparison of DNA barcoding and morphological taxonomy in terms of their accuracy and diversity of characters employed. We conclude that morphology often does not work and that it is often nowhere near as ‘rich’ as has been argued. Morphology is particularly poor in numerous important situations, such as the association of larvae with adults and discrimination among cryptic species. The vehemence of some of the criticisms is surprising given that morphology alone is known to be inadequate to the task of species‐level identification in many instances.
Biological agent detection technologies
Authors: JAKUPCIAK JOHN P. , COLWELL RITA R.
Published: April 2009

The challenge for first responders, physicians in the emergency room, public health personnel, as well as for food manufacturers, distributors and retailers is accurate and reliable identification of pathogenic agents and their corresponding diseases. This is the weakest point in biological agent detection capability today.

There is intense research for new molecular detection technologies that could be used for very accurate detection of pathogens that would be a concern to first responders. These include the need for sensors for multiple applications as varied as understanding the ecology of pathogenic micro‐organisms, forensics, environmental sampling for detect‐to‐treat applications, biological sensors for ‘detect to warn’ in infrastructure protection, responses to reports of ‘suspicious powders’, and customs and borders enforcement, to cite a few examples.

The benefits of accurate detection include saving millions of dollars annually by reducing disruption of the workforce and the national economy and improving delivery of correct countermeasures to those who are most in need of the information to provide protective and/or response measures.
Barcoding diatoms: Is there a good marker?
Authors: MONIZ MÓNICA B. J. , KACZMARSKA IRENA
Published: April 2009

The promise of DNA barcoding is based on a small DNA fragment divergence coinciding with biological species separation. Here we evaluated the performance of three markers as diatom barcodes, the small ribosomal subunit (1600 bp), a 5′ end fragment of cytochromecoxidase subunit 1 (430 bp), and the second internal transcribed spacer region combined with the 5.8S gene (5.8S + ITS‐2, 300–400 bp). Forty‐four sequences per marker representing 28 species from all diatom classes were analysed. Sequence alignment of the three genetic markers and uncorrected genetic distances (P) were calculated at the intra‐ and heterospecific level. All three markers correctly separated the species examined and had advantages which contribute to their feasibility as a DNA barcode. Small ribosomal subunit had the largest GenBank data set, its success rate in amplification and sequencing was assumed to be the highest of all three and was readily aligned. However, it required a long fragment to recover divergence sufficient for species separation and small genetic distances increased the potential for misidentifications. Cytochromecoxidase subunit 1 demonstrated a substantial heterospecific divergence level and was also readily alignable, but it showed very low amplification and sequencing success rates with currently existing primers. 5.8S + ITS‐2 was amplified and sequenced with high success rate and was the most variable of the three markers, but its secondary structure was needed to aid in alignment. However, since it has been recently suggested that ITS‐2 may provide insight into sexual compatibility, this marker offers an additional advantage. We therefore propose that the 5.8S + ITS‐2 fragment is the best candidate as a diatom DNA barcode.
Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths
Authors: MOSZCZYNSKA ANNA , LOCKE SEAN A. , McLAUGHLIN J. DANIEL , MARCOGLIESE DAVID J. , CREASE TERESA J.
Published: April 2009

The phylum Platyhelminthes is a diverse group of flatworms that includes parasites with serious impacts on human health, animal husbandry, aquaculture and wildlife management. Here we present degenerate primers for the barcode region of the mitochondrial cytochrome c oxidase I (COI) gene in flatworms. Although amplicons were obtained from a wide taxonomic range in the Cestoda and Trematoda, COI fragments from many taxa in these classes did not amplify. Primers specific to trematodes in the family Diplostomidae were also developed. Amplification success was much higher with diplostomid‐specific primers and sequences were obtained from 504 of 585 specimens of Diplostomum and Tylodelphys. Sequences from the barcode region resolved all specimens to the species level, with mean divergence between congeners of 19% (3.9–25%). Because many of our specimens were small, we initially amplified part of the nuclear small subunit ribosomal (r) RNA gene to evaluate the quality and quantity of DNA in our specimens. Short sequences (~380 nt) of this gene were recovered from most specimens and can be used to distinguish specimens at the family level and often the generic level. We suggest that rRNA genes could be used to screen samples of completely unknown taxonomy, after which specific COI primers could be used to obtain species‐level identifications.
Progress towards DNA barcoding of fungi
Authors: SEIFERT KEITH A.
Published: April 2009

The use of DNA sequences for identifying fungi and fungus‐like organisms predates the DNA barcoding movement by at least 10 years. A brief overview of the mycological shift from phenotypic to molecular taxonomy is provided. Exploration of the animal barcode marker, cytochrome oxidase 1, by Canadian mycologists has been fruitful for some fungi, but intron issues and lack of resolution in other taxa prevent its universal application. The momentum established by 15 years of research on the fungal nuclear ribosomal internal transcribed spacer (ITS) sequences will lead to a proposal to the Consortium for the Barcode of Life on the adoption of this marker as the fungal barcode. Existing mycological research networks should facilitate the rapid development of DNA barcoding of fungi once the marker issue is settled. Some available online fungal identification databases are briefly described.
Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium
Authors: GILMORE SCOTT R. , GRÄFENHAN TOM , LOUIS‐SEIZE GERRY , SEIFERT KEITH A.
Published: April 2009

Using data from published mitochondrial or complete genomes, we developed and tested primers for amplification and sequencing of the barcode region of cytochrome oxidase 1 (COX1) of the fungal genus Fusarium, related genera of the order Hypocreales, and degenerate primers for fungi in the subdivision Pezizomycotina. The primers were successful for amplifying and sequencing COX1 barcodes from 13 genera of Hypocreales (Acremonium, Beauveria, Clonostachys, Emericellopsis, Fusarium, Gliocladium, Hypocrea, Lanatonectria, Lecanicillium, Metarhizium, Monocillium, Neonectria and Stilbella), 22 taxa of Fusarium, and two genera in other orders (Arthrosporium, Monilochaetes). Parologous copies of COX1 occurred in several strains of Fusarium. In some, copies of the same length were detected either by heterozygous bases in otherwise clean sequences or in different replicates of amplification and sequencing events; this may indicate multiple transcribed copies. Other strains included one or two introns. Two intron insertion sites had at least two nonhomologous intron sequences among Fusarium species. Irrespective of whether the multiple copy issue could be resolved by sequencing RNA transcripts, developing a precise COX1‐based barcoding system for Fusarium may not be feasible. The overall divergence among homologous COX1 sequences obtained so far is rather low, with many species sharing identical sequences.
Evaluation of mitochondrial genes as DNA barcode for Basidiomycota
Authors: VIALLE AGATHE , FEAU NICOLAS , ALLAIRE MATHIEU , DIDUKH MARYNA , MARTIN FRANCIS , MONCALVO JEAN‐MARC , HAMELIN RICHARD C.
Published: April 2009

Our study evaluated in silico the potential of 14 mitochondrial genes encoding the subunits of the respiratory chain complexes, including cytochrome c oxidase I (CO1), as Basidiomycota DNA barcode. Fifteen complete and partial mitochondrial genomes were recovered and characterized in this study. Mitochondrial genes showed high values of molecular divergence, indicating a potential for the resolution of lower‐level relationships. However, numerous introns occurred in CO1 as well as in six other genes, potentially interfering with polymerase chain reaction amplification. Considering these results and given the minimal length of 600‐bp that is optimal for a fungal barcode, the genes encoding for the ATPase subunit 6, the cytochrome oxidase subunit 3 and the NADH dehydrogenase subunit 6 have the most promising characteristics for DNA barcoding among the mitochondrial genes studied. However, biological validation on two fungal data sets indicated that no single mitochondrial gene gave a better taxonomic resolution than the ITS, the region already widely used in fungal taxonomy.
Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae)
Authors: STARR JULIAN R. , NACZI ROBERT F. C. , CHOUINARD BRIANNA N.
Published: April 2009

We investigate the species discriminatory power of a subset of the proposed plant barcoding loci (matK, rbcL, rpoC1, rpoB, trnH‐psbA) in Carex, a cosmopolitan genus that represents one of the three largest plant genera on earth (c. 2000 species). To assess the ability of barcoding loci to resolve Carex species, we focused our sampling on three of the taxonomically best‐known groups in the genus, sections Deweyanae (6/8 species sampled), Griseae (18/21 species sampled), and Phyllostachyae (10/10 species sampled). Each group represents one of three major phylogenetic lineages previously identified in Carex and its tribe Cariceae, thus permitting us to evaluate the potential of DNA barcodes to broadly identify species across the tribe and to differentiate closely related sister species. Unlike some previous studies that have suggested that plant barcoding could achieve species identification rates around 90%, our results suggest that no single locus or multilocus barcode examined will resolve much greater than 60% of Carex species. In fact, no multilocus combination can significantly increase the resolution and statistical support (i.e., ≥ 70% bootstrap) for species than matK alone, even combinations involving the second most variable region, trnH‐psbA. Results suggest that a matK barcode could help with species discovery as 47% of Carex taxa recently named or resolved within cryptic complexes in the past 25 years also formed unique species clusters in upgma trees. Comparisons between the nrDNA internal transcribed spacer region (ITS) and matK in sect. Phyllostachyae suggest that matK not only discriminates more species (50–60% vs. 25%), but it provides more resolved phylogenies than ITS. Given the low levels of species resolution in rpoC1 and rpoB (0–13%), and difficulties with polymerase chain reaction amplification and DNA sequencing in rbcL and trnH‐psbA (alignment included), we strongly advocate that matK should be part of a universal plant barcoding system. Although identification rates in this study are low, they can be significantly improved by a regional approach to barcoding.
Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae)
Authors: STEVEN G. NEWMASTER , SUBRAMANYAM RAGUPATHY
Published: April 2009

Acacia species are quite difficult to differentiate using morphological characters. Routine identification of Acacia samples is important in order to distinguish invasive species from rare species or those of economic importance, particularly in the forest industry. The genus Acacia is quite abundant and diverse comprising approximately 1355 species, which is currently divided into three subgenera: subg. Acacia (c. 161 species), subg. Aculiferum (c. 235 species), and subg. Phyllodineae (c. 960 species). It would be prudent to utilize DNA barcoding in the accurate and efficient identification of acacias. The objective of this research is to test barcoding in discriminating multiple populations among a sister‐species complex in pantropical Acacia subg. Acacia, across three continents. Based on previous research, we chose three cpDNA regions (rbcL, trnH‐psbA and matK). Our results show that all three regions (rbcL, matK and trnH‐psbA) can distinguish and support the newly proposed genera of Vachellia Wight & Arn. from Acacia Mill., discriminate sister species within either genera and differentiate biogeographical patterns among populations from India, Africa and Australia. A morphometric analysis confirmed the cryptic nature of these sister species and the limitations of a classification based on phenetic data. These results support the claim that DNA barcoding is a powerful tool for taxonomy and biogeography with utility for identifying cryptic species, biogeograhic patterns and resolving classifications at the rank of genera and species.
DNA barcode accumulation curves for understudied taxa and areas
Authors: SMITH M. ALEX , FERNANDEZ‐TRIANA JOSE , ROUGHLEY ROB , HEBERT PAUL D. N.
Published: April 2009

Frequently, the diversity of umbrella taxa is invoked to predict patterns of other, less well‐known, life. However, the utility of this strategy has been questioned. We tested whether a phylogenetic diversity (PD) analysis of CO1 DNA barcodes could act as a proxy for standard methods of determining sampling efficiency within and between sites, namely that an accumulation curve of barcode diversity would be similar to curves generated using morphology or nuclear genetic markers. Using taxa at the forefront of the taxonomic impediment — parasitoid wasps (Ichneumonidae, Braconidae, Cynipidae and Diapriidae), contrasted with a taxon expected to be of low diversity (Formicidae) from an area where total diversity is expected to be low (Churchill, Manitoba), we found that barcode accumulation curves based on PD were significantly different in both slope and scale from curves generated using names based on morphological data, while curves generated using nuclear genetic data were only different in scale. We conclude that these differences clearly identify the taxonomic impediment within the strictly morphological alpha‐taxonomy of these hyperdiverse insects. The absence of an asymptote within the barcode PD trend of parasitoid wasps reflects the as yet incomplete sampling of the site (and more accurately its total diversity), while the morphological analysis asymptote represents a collision with the taxonomic impediment rather than complete sampling. We conclude that a PD analysis of standardized DNA barcodes can be a transparent and reproducible triage tool for the management and conservation of species and spaces.
Characterization of 12 polymorphic microsatellite markers for a facultatively eusocial sweat bee (Megalopta genalis)
Authors: KAPHEIM KAREN M. , POLLINGER JOHN P. , WCISLO WILLIAM T. , WAYNE ROBERT K.
Published: April 2009

We developed a library of twelve polymorphic di‐ and tri‐nucleotide microsatellite markers for Megalopta genalis, a facultatively eusocial sweat bee. We tested each locus in a panel of 23 unrelated females and found 7–20 alleles per locus. Observed and expected heterozygosities ranged from 0.65 to 0.96 and from 0.69 to 0.95 respectively. None of the loci deviated from Hardy–Weinberg equilibrium proportions or was found to be in gametic disequilibrium.
Isolation of polymorphic microsatellite markers for the tetraploid Dipteryx odorata, an intensely exploited Amazonian tree species
Authors: VINSON C. C. , RIBEIRO D. O. , HARRIS S. A. , SAMPAIO I. , CIAMPI A. Y.
Published: April 2009

Dipteryx odorata is an intensely exploited Amazonian tree legume. Microsatellite markers were developed to study the genetic structure, gene flow and reproductive biology of D. odorata. Eight highly polymorphic microsatellite markers were isolated from enriched repeat libraries screened for microsatellite repeats. An average of 16 alleles and 0.964 phenotype diversity per locus were found in 76 individuals from the Tapajos National Forest, in the state of Pará in the Brazilian Amazon.
Microsatellite primers for the four Galápagos mockingbird species (Mimus parvulus, Mimus macdonaldi, Mimus melanotis and Mimus trifasciatus)
Authors: HOECK P. E. A. , BUCHER T. B. , WANDELER P. , KELLER L. F.
Published: April 2009

Nineteen di‐ and tetranucleotide and one trinucleotide microsatellite DNA markers were isolated from the Galápagos mockingbird (Mimus parvulus) and tested for cross‐species amplification in the other three mockingbird species in the Galápagos. In addition, primers for two microsatellite loci previously developed for Mimus polyglottos were redesigned to obtain shorter amplification fragments. The number of alleles per locus and species ranged from 1 to 8, and expected heterozygosity varied from 0.0 to 0.809. These microsatellite markers will be useful to study levels of inbreeding in different island populations.
Sedimentary Response of Different Fan Types to the Paleogene–Neogene Basin Transformation in the Kuqa Depression, Tarim Basin, Xinjiang Province
Authors: GAO Zhiyong , GUO Hongli , ZHU Rukai , ZHANG Lijuan , SUN Yushan
Published: April 2009

A group of alluvial fans formed in the early Paleogene represent marginal sedimentary facies at the foot of the South Tianshan Mountain, Kuqa Depression, Tarim Basin, Xinjiang province. Two types of fans occurred in the middle–late Paleogene Kumugeliemu and Suweiyi formations: one alluvial, and the other fan delta deposited in a lacustrine setting. Within the early Neogene Jidike Formation, coastal subaqueous fans developed, probably in a deeper water lacustrine setting. The three types of fans are stacked vertically in outcrop with the sequence in ascending order: bottom alluvial, middle fan‐delta, and top subaqueous. The subaqueous is a typical coarse‐fan deposit occurring in the glutinite member of the Jidike Formation in some wells. Laterally, from the foreland to the lacustrine settings, the distribution pattern of sedimentary facies represents the same three fan types sequentially. The spatial distribution of these fans was controlled by the Paleogene–Neogene Basin transformation, and evolution with different types of fans developed in the Kuqa Depression in response. In the Paleogene, the Kuqa Depression was a rift basin where an alluvial fan was deposited in the foreland setting, which, by early Neogene, became a foreland basin when the lake level changed. With any rise in lake level, fan‐deltas migrated from lacustrine to foreland settings, whereas when the lake level fell, fan migration was reversed. In the early Neogene, with increasing slope and rising lake level, fans progressed and covered the previous fan‐delta and lacustrine mudstone. Eventually, subaqueous fans developed, forming the present spatial configuration of these three fan types.
Cenozoic Stratigraphy Deformation History in the Central and Eastern of Qaidam Basin by the Balance Section Restoration and its Implication
Authors: LIU Dongliang , FANG Xiaomin , GAO Junping , WANG Yadong , ZHANG Weilin , MIAO Yunfa , LIU Yongqian , ZHANG Yuezhong
Published: April 2009

The Qaidam Basin, located in the northern margin of the Qinghai–Tibet Plateau, is a large Mesozoic–Cenozoic basin, and bears huge thick Cenozoic strata. The geologic events of the Indian‐Eurasian plate–plate collision since ∼55 Ma have been well recorded. Based on the latest progress in high‐resolution stratigraphy, a technique of balanced section was applied to six pieces of northeast‐southwest geologic seismic profiles in the central and eastern of the Qaidam Basin to reconstruct the crustal shortening deformation history during the Cenozoic collision. The results show that the Qaidam Basin began to shorten deformation nearly synchronous to the early collision, manifesting as a weak compression, the deformation increased significantly during the Middle and Late Eocene, and then weakened slightly and began to accelerate rapidly since the Late Miocene, especially since the Quaternary, reflecting this powerful compressional deformation and rapid uplift of the northern Tibetan Plateau around the Qaidam Basin.
Structural Evolution of the Eastern Qiulitagh Fold and Thrust Belt, Northern Tarim Basin, China
Authors: YANG Minghui , JIN Zhijun , LU Xiuxiang , SUN Dongsheng , TANG Xuan , PENG Gengxin , LEI Ganglin
Published: April 2009

The eastern Qiulitagh fold and thrust belt (EQFTB) is part of the active Kuqa fold and thrust belts of the northern Tarim Basin. Seismic reflection profiles have been integrated with surface geologic and drill data to examine the deformation and structure style of the EQFTB, particularly the deformational history of the Dina 2 gas field. Seismic interpretations suggest that Dongqiu 8 is overall a duplex structure developed beneath a passive roof thrust, which generated from a tipline in the Miocene Jidike Formation, and the sole thrust was initiated from the same Jidike Formation evaporite zone that extends westward beneath the Kuqatawu anticline. Dongqiu 5 is a pop‐up structure at the western part of the EQFTB, also developed beneath the Jidike Formation evaporite. Very gentle basement dip and steep dipping topographic slope in the EQFTB suggest that the Jidike Formation salt provides effective decoupling. The strong deformation in the EQFTB appears to have developed further south, in an area where evaporite may be lacking. Since the Pliocene, the EQFTB has moved farther south over the evaporite and reached the Yaken area. Restoring a balanced cross‐section suggests that the minimum shortening across the EQFTB is more than 7800 m. Assuming that this shortening occurred during the 5.3 Ma timespan, the shortening rate is approximately 1.47 mm/year.
Distribution of the Permian Monodiexodina in Karakorum and Kunlun and its Geological Significance
Authors: YAO Jianxin , WANG Naiwen , XIAO Xuchang , JI Zhansheng , WU Guichun , WU Zhenjie , LI Boqin , WANG Jun , WANG Yong , ZHAI Qingguo
Published: April 2009

The Permian fusulinoidean genus Monodiexodina is widely distributed in east Tethys. The genus might be an important indicator for the northern margin of Gondwana in northwestern China, but this is disputed. Monodiexodina‐bearing areas can be restored as in either northern or southern middle latitudes with a symmetrical distribution between a high latitudinal, cool/cold water climatic realm and a paleotropical, warm water realm. Permian strata bearing Monodiexodina in Karakorum, Muztag Pear, and Buka Daban Pear of the east Kunlun Mountains can be correlated with each other. Faunal analyses and the stratigraphical position of Monodiexodina‐bearing strata indicate that both Karakorum, east Kunlun, and the Pamirs were formed in a cool temperate sea area of the northern hemisphere in middle latitudes during the Permian, rather than at the Gondwana margin.
Deep Fractionation of Clinopyroxene in the East Pacific Rise 13°N: Evidence from High MgO MORB and Melt Inclusions
Authors: ZHANG Guoliang , ZENG Zhigang , YIN Xuebo , WANG Xiaoyuan , CHEN Daigeng
Published: April 2009

Mid‐ocean ridge basalts (MORBs) from East Pacific Rise (EPR) 13°N are analysed for major and trace elements, both of which show a continuous evolving trend. Positive MgO–Al2O3 and negative MgO–Sc relationships manifest the cotectic crystallization of plagioclase and olivine, which exist with the presence of plagioclase and olivine phenocrysts and the absence of clinopyroxene phenocrysts. However, the fractionation of clinopyroxene is proven by the positive correlation of MgO and CaO. Thus, MORB samples are believed to show a “clinopyroxene paradox”. The highest magnesium‐bearing MORB sample E13–3B (MgO = 9.52%) is modelled for isobaric crystallization with COMAGMAT at different pressures. Observed CaO/Al2O3 ratios can be derived from E13–3B only by fractional crystallization at pressure >4 ±1 kbar, which necessitates clinopyroxene crystallization and is not consistent with cotectic crystallization of olivine plus plagioclase in the magma chamber (at pressure ∼1 kbar). The initial compositions of the melt inclusions, which could represent potential parental magmas, are reconstructed by correcting for post‐entrapment crystallization (PEC). The simulated crystallization of initial melt inclusions also produce observed CaO/Al2O3 ratios only at >4±1 kbar, in which clinopyroxene takes part in crystallization. It is suggested that MORB magmas have experienced clinopyroxene fractionation in the lower crust, in and below the Moho transition zone. The MORB magmas have experienced transition from clinopyroxene+plagioclase+olivine crystallization at >4±1 kbar to mainly olivine+plagioclase crystallization at <1 kbar, which contributes to the explanation of the “clinopyroxene paradox”.
A New Sauropod Dinosaur from the Late Cretaceous Gaogou Formation of Nanyang, Henan Province
Authors: ZHANG Xingliao , LÜ Junchang , XU Li , LI Jinhua , YANG Li , HU Weiyong , JIA Songhai , JI Qiang , ZHANG Chengjun
Published: April 2009

A new sauropod dinosaurBaotianmansaurus henanensisgen. et sp. nov. from the Cretaceous Gaogou Formation of Neixiang, Henan Province is erected. It is characterized by somphospondylous presacral vertebrae; a highly‐developed lamina system on the dorsal vertebrae; transverse process supported by four laminae; and the dorsal portion of the anterior centroparapophyseal lamina is bifurcated, with a small branch extending to the ventral surface of the prezygapophysis. It represents a new titanosauriform sauropod.
Comment on “First Record of Hindeodus–Isarcicella Population in Lower Triassic of Slovenia” by Tea Kolar‐Jurkovšek and Bogdan Jurkovšek in Palaeogeography, Palaeoclimatology, Palaeoecology, 252: 72–81
Authors: WU Yasheng , JIANG Hongxia
Published: April 2009

Some conodonts described by Tea Kolar‐Jurkovsek and Bogdan Jurkovsek (2007) from the Permian‐Triassic boundary section in the Žiri area of western Slovenia are revised in this paper. One specimen that they assigned to Hindeodus parvus is tentatively regarded as Hindeodus cf. scalaris Wu 2005. Two specimens that they assigned to Isarcicella sp. A is changed to Hindeodus parvus. One specimen that they described as Isarcicella lobata Perri and Farabegoli is changed to Hindeodus crenatus Wu (2006). One specimen that they assigned to Isarcicella turgida (Kozur, Mostler and Rahimi‐Yazd) is changed to Hindeodus cf. parvus. Since these revisions, the three conodont zones that they defined have been correspondingly revised. Their first zone may belong to Hindeodus parvus zone, but it is not certain. Their second zone is changed to the Hindeodus parvus zone, and their third one remains as is.
Three‐dimensional Evolutionary Models of the Qiongxi Structures, Southwestern Sichuan Basin, China: Evidence from Seismic Interpretation and Geomorphology
Authors: JIA Qiupeng , JIA Dong , LUO Liang , CHEN Zhuxin , LI Yiquan , DENG Fei , SUN Shengsi , LI Haibin
Published: April 2009

Fold terminations are key features in the study of compressional fault‐related folds. Such terminations could be due to loss of displacement on the thrust fault or/and forming a lateral or oblique ramp. Thus, high‐quality seismic data would help unambiguously define which mechanism should be responsible for the termination of a given fault‐related fold. The Qiongxi and Qiongxinan structures in the Sichuan Basin, China are examples of natural fault‐propagation folds that possess a northern termination and a structural saddle between them. The folds/fault geometry and along‐strike displacement variations are constrained by the industry 3‐D seismic volume. We interpret that the plunge of the fold near the northern termination and the structural saddle are due to the loss of displacement along strike. The fault geometry associated with the northern termination changes from a flat‐ramp at the crest of the Qiongxinan structure, where displacement is the greatest, to simply a ramp near the northern tip of the Qiongxi structure, without forming a lateral or oblique ramp. In this study, we also use the drainage pattern, embryonic structure preserved in the crest of the Qiongxinan structure and the assumption that displacement along a fault is proportional to the duration of thrusting to propose a model for the lateral propagation of the Qiongxinan and Qiongxi structures. Specifically, we suggest that the structure first initiated as an isolated fault ramp within brittle units. With increased shortening, the fault grows to link with lower detachments in weaker shale units to create a hybridized fault‐propagation fold. Our model suggests a possible explanation for the lateral propagation history of the Qiongxinan and Qiongxi structures, and also provides an alternative approach to confirming the activity of the previous Pingluoba structure in the southwestern Sichuan Basin in the late Cenozoic.
Lisiguangite, CuPtBiS3, a New Platinum‐Group Mineral from the Yanshan Mountains, Hebei, China
Authors: YU Zuxiang , CHENG Fanyun , MA Hongwei
Published: April 2009

Lisiguangite, CuPtBiS3, is a new mineral species discovered in a PEG‐bearing, Co‐Cu sulfide vein in garnet pyroxenite of the Yanshan Mountains, Chengde Prefecture, Hebei Province, China. It is associated with chalcopyrite and bornite, galena, minor pyrite, carrolite, molybdenite and the platinum‐group minerals daomanite (CuPtAsS2), Co‐bearing malanite (Cu(Pt, Co)2S4) sperrylite, moncheite, cooperite and malyshevite (CuPdBiS3), rare damiaoite (Pt2In3) and yixunite (Pt3In). Lisiguangite occurs as idiomorphic crystals, tabular or lamellae (010) and elongated [100] or as aggregates, up to 2 mm long and 0.5 mm wide. The mineral is opaque, has lead‐gray color, black streak and metallic luster. The mineral is non‐fluorescent The observed morphology displays the following forms: pinacoids {100}, {010}, {001}, and prism {110}. No twining is observed. The a:b:c ratio, calculated from unit‐cell parameters, is 0.6010:1:0.3836. Cleavage: {010} perfect, {001} distinct, {100} may be visible. H Mohs: 2½ VHN25= 46.7–49.8 (mean 48.3) kg/mm2. Tenacity: brittle. Lisiguangite is bright white with a yellowish tint In reflected light it shows neither internal reflections nor bireflectance or pleochroism. It has weak to moderate anisotropy (blue‐greenish to brownish) and parallel‐axial extinction. The reflectance values in air (and in oil) for R3, R4 and (imR3, imR4), at the standard Commission on Ore Mineralogy wavelengths are: 37.5, 35.7 (23.4, 22.3) at 470 nm; 38.6, 36.5 (23.6, 22.6) at 546 nm; 39.4, 37.5 (23.6, 22.7) at 589 nm and 40.3, 38.2 (23.7, 22.9) at 650 nm. The average of eight electron‐microprobe analyses: Cu 12.98, Pt 30.04, Pd 2.69, Bi 37.65 and S 17.55, totaling 100.91%, corresponding to Cu1.10(Pt0.83, Pd0.14)Σ0.97Bi0.97S2.96 based on six atoms apfu. The ideal formula is CuPtBiS3. The mineral is orthorhombic. Space group: P212121, a= 7.7152(15)Å, b= 12.838(3) Å, c= 4.9248(10)Å, V= 487.80(17)Å3, Z= 4. The six strongest lines in the X‐ray powder‐diffraction pattern [d in Å (I) (h k l) are 6.40(30)(020), 3.24(80)(031), 3.03(100)(201), 2.27(40)(051), 2.14(50)(250), 1.865(60)(232).
Migration of Depocenters and Accumulation Centers and its Indication of Subsidence Centers in the Mesozoic Ordos Basin
Authors: ZHAO Junfeng , LIU Chiyang , WANG Xiaomei , ZHANG Can
Published: April 2009

Based on the integrated study of structure attributions and characteristics of the original basin in combination with lithology and lithofacies, sedimentary provenance analysis and thickness distribution of the Mesozoic Ordos Basin, it is demonstrated that the depocenters migrated counterclockwise from southeast to the north and then to the southwest from the Middle‐Late Triassic to the Early Cretaceous. There were no unified and larger‐scale accumulation centers except several small isolated accumulation centers before the Early Cretaceous. The reasons why belts of relatively thick strata were well developed in the western basin in several stages are that this area is near the west boundary of the original Ordos Basin, there was abundant sediment supply and the hydrodynamic effect was strong. Therefore, they stand for local accumulation centers. Until the Early Cretaceous, depocenters, accumulation centers and subsidence centers were superposed as an entity in the southwest part of the Ordos Basin. Up to the end of the Middle Jurassic, there still appeared a paleogeographic and paleostructural higher‐in‐west and lower‐in‐east framework in the residual basin to the west of the Yellow River. The depocenters of the Ordos Basin from the Middle–Late Triassic to the Middle Jurassic were superposed consistently. The relatively high thermal maturation of Mesozoic and Paleozoic strata in the depocenters and their neighborhood suggest active deep effects in these areas. Generally, superposition of depocenters in several periods and their consistency with high thermal evolution areas reveal the control of subsidence processes. Therefore, depocenters may represent the positions of the subsidence centers. The subsidence centers (or depocenters) are located in the south of the large‐scale cratonic Ordos Basin. This is associated with flexural subsidence of the foreland, resulting from the strong convergence and orogenic activity contemporaneous with the Qinling orogeny.
Basic Types and Structural Characteristics of Uplifts: An Overview of Sedimentary Basins in China
Authors: HE Dengfa , LI Desheng , WU Xiaozhi , WEN Zhu
Published: April 2009

The uplift is a positive structural unit of the crust It is an important window for continental dynamics owing to its abundant structural phenomena, such as fault, fold, unconformity and denudation of strata. Meanwhile, it is the very place to store important minerals like oil, natural gas, coal and uranium. Giant and large‐scale oil and gas fields in China, such as the Daqing Oilfield, Lunnan‐Tahe Oilfield, Penglai 19–3 Oilfield, Puguang Gas Field and Jingbian Gas Field, are developed mainly on uplifts. Therefore, it is the main target both for oil and gas exploration and for geological study. The uplift can be either a basement uplift, or one developed only in the sedimentary cover. Extension, compression and wrench or their combined forces may give rise to uplifts. The development process of uplifting, such as formation, development, dwindling and destruction, can be taken as the uplifting cycle. The uplifts on the giant Precambrian cratons are large in scale with less extensive structural deformation. The uplifts on the medium‐ and small‐sized cratons or neo‐cratons are formed in various shapes with strong structural deformation and complicated geological structure. Owing to changes in the geodynamic environment, uplift experiences a multi‐stage or multi‐cycle development process. Its geological structure is characterized in superposition of multi‐structural layers. Based on the basement properties, mechanical stratigraphy and development sequence, uplifts can be divided into three basic types — the succession, superposition and destruction ones. The succession type is subdivided into the maintaining type and the lasting type. The superposition type can be subdivided into the composite anticlinal type, the buried‐hill draped type, the faulted uplift type and the migration type according to the different scales and superimposed styles of uplifts in different cycles. The destruction type is subdivided into the tilting type and the negative inverted type. The development history of uplifts and their controlling effects on sedimentation and fluids are quite different from one another, although the uplifts with different structural types store important minerals. Uplifts and their slopes are the main areas for oil and gas accumulation. They usually become the composite oil and gas accumulation zones (belts) with multiple productive formations and various types of oil and gas reservoirs.
Re‐encountering Cuban Tastes in Australia1
Authors: Cardona Euridice T. Charon
Published: April 2009

This paper explores the challenges presented to the everyday praxis of maintaining Cuban identity in the Australian context through an examination of the preparation and eating of Cuban food by migrants in Sydney. I argue that the very different demographic configuration of Cubans in Australia and the US is played out through the different experiences of eating. Cuban identity in the US contrasts markedly with the situation in NSW where the small population of Cubans focus on maintaining a Cuban world in their domestic space through the practice of eating Cuban food, rather than in the public domain. The struggle to find and prepare Cuban food in Australia reflects a distance and separation from homeland both spatially and temporally. The paper suggests that the eating habits of this group constitute a significant ethnic marker used by members of the group to differentiate themselves as Cubans in Australia. Additionally, I argue that the existence of a substantial multicultural and ethnic food market in Australia allows Cuban migrants to acquire the products needed for the Cuban cuisine, from shops primarily serving numerically larger ethnic groups.
Hard Drink and Cigarettes: Restrictive and Expansive Modes of Consumption in an East Malaysian Community
Authors: Westmacott Karen
Published: April 2009

Based on field research in a Kayan community in Sarawak, East Malaysia, this paper explores new modes of consumption associated with the growth of wage labour in the timber industry. The paper focuses on tobacco and alcohol, and considers the role of consumption, particularly of the products of the global industrial economy, in local efforts toward the creation and recreation of social and cultural identities. Within this, a significant factor is found to be the teachings of the local Protestant evangelical church which are implicated in the choices people make, and attitudes they express, about expanding opportunities for consuming, and consumption of alcohol and tobacco, in particular. It is also suggested that modes of alcohol and tobacco consumption in this community may be usefully seen in terms of a generalised contrast between the restrictive and the expansive.
Primitivising Anorexia: The Irresistible Spectacle of Not Eating
Authors: Warin Megan
Published: April 2009

This article explores the complexities of disseminating ethnographic research within a field that is already saturated by pervasive cultural systems of representation. People with anorexia are inescapably enmeshed in a whole range of fields that define and represent them, including academic writings, psychiatry and popular imaginings. Although these fields are wide (ranging from discursive constructions and to a much lesser extent ethnography), this analysis argues that there is one dominant trope that underpins popular representations of anorexia. It is through the detailed analysis of the public dissemination of this research, of the meeting between ethnography and the print media, that I demonstrate how people with anorexia come to be known through images and words associated with primitivism. Such a reductionist account reproduces the visual spectacle associated with emaciation, and ignores the profound embodied sensations of power and suffering that are central to experiences of anorexia.
Design of Electrothermally Compliant MEMS With Hexagonal Cells Using Local Temperature and Stress Constraints
Authors: Saxena Rajat , Saxena Anupam
Published: April 2009

In this paper, meso- and microscale electrothermally compliant mechanical systems are synthesized for strength, with polysilicon as the structural material. Local temperature and/or stress constraints are imposed in the topology optimization formulation. This is done to keep the optimal solutions thermally intact and also to keep the local stresses below their allowable limit. Constraint relaxation performed on both temperature and stress constraints allows them to be ignored when the cell material densities approach their nonexisting states. As both local constraints are large in number with the number of cells, an active constraint strategy is employed with gradient based optimization. Honeycomb parametrization, which is a staggered arrangement of hexagonal cells, is used to represent the design region. This ensures at least an edge connection between any two adjacent cells, and thus prevents the appearance of both checkerboard and point flexure singularities without any additional computational load. Both SIMP and SIGMOID material assignment functions are explored to obtain the optimal solutions.
An Efficient Re-Analysis Methodology for Probabilistic Vibration of Large-Scale Structures
Authors: Zhang Geng , Nikolaidis Efstratios , Mourelatos Zissimos P.
Published: April 2009

Probabilistic analysis and design of large-scale structures requires repeated finite-element analyses of large models, and each analysis is expensive. This paper presents a methodology for probabilistic analysis and reliability-based design optimization of large-scale structures that consists of two re-analysis methods, one for estimating the deterministic vibratory response and another for estimating the probability of the response exceeding a certain level. The deterministic re-analysis method can analyze efficiently large-scale finite-element models consisting of tens or hundreds of thousand degrees of freedom and design variables that vary in a wide range. The probabilistic re-analysis method calculates very efficiently the system reliability for different probability distributions of the random variables by performing a single Monte Carlo simulation of one design. The methodology is demonstrated on probabilistic vibration analysis and reliability-based design optimization of a realistic vehicle model. It is shown that the computational cost of the proposed re-analysis method for a single reliability analysis is about 1/20 of the cost of the same analysis using MSC/NASTRAN. Moreover, the probabilistic re-analysis approach enables a designer to perform reliability-based design optimization of the vehicle at a cost almost equal to that of a single reliability analysis. Without using the probabilistic re-analysis approach, it would be impractical to perform reliability-based design optimization of the vehicle.
Dry Methane Reforming Without a Metal Catalyst in a Directly Irradiated Solar Particle Reactor
Authors: Klein Hanna Helena , Karni Jacob , Rubin Rachamim
Published: April 2009

Dry methane reforming with carbon dioxide in a directly irradiated particle receiver seeded with carbon black is presented in this study. Carbon particles were entrained in the reacting gases and acted as heat transfer and reaction surface. The reactions were not catalyzed by a metal catalyst. The molar ratio between the entrained carbon particles and the working gases (Ar, CO2, and CH4) was 4–7 mmol carbon/mol gas. The temperature of the reforming experiments varied from 750°C to 1450°C with CO2/CH4 ratios varying from 1:1 to 1:6. Experimental results show that methane reacts at lower temperatures than expected for its thermal decomposition; this indicates that the decomposing reaction is enhanced by the presence of the carbon black particles. At 1170°C 90% of the methane reacted in the receiver during a residence time of 0.3 s. The reaction between carbon dioxide and carbon black is faster than is documented in the literature, but the reaction rate does not seem to change if only carbon dioxide and carbon black are present in the receiver, compared with experiments where methane is also part of the gas mixture. The experimental results indicate that a high solar flux, i.e., about 2500 kW/m2 or higher, significantly accelerates the reaction rate of methane decomposition. Total or partial blockage of the solar radiation reduced the yield by about 50%, compared with tests when the receiver was exposed to the full solar radiation flux, at the same operating temperature.