HEXT, a software supporting tree-based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test.

PubMed

Schneider, Kevin; Koblmüller, Stephan; Sefc, Kristina M

2015-11-11

The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support).We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written in r language and accepts binary data (0/1; e.g. AFLP) as well as co-dominant SNP and genotype data.We demonstrate the usefulness of hext in large SNP data sets containing putative hybrids and their parents. For instance, using published data of the genus Vitis (~6,000 SNP loci), hext output supports V. × champinii as a hybrid between V. rupestris and V. mustangensis .With simulated SNP and AFLP data sets, excess increases in bootstrap support were not always connected with the hybrid taxon (false positives), whereas the expected bootstrap signal failed to appear on several occasions (false negatives). Potential causes for both types of spurious results are discussed.With both empirical and simulated data sets, the taxon-jackknife output generated by hext provided additional signatures of hybrid taxa, including changes in tree topology across trees, consistent effects of exclusions of the hybrid and the parent taxa, and moderate (rather than excessive) increases in bootstrap support. hext significantly facilitates the taxon-jackknife approach to hybrid taxon detection, even though the simple test for excess bootstrap increase may not reliably identify hybrid taxa in all applications.

Estimation of food consumption from pellets cast by captive Ural Owls (Strix uralensis)

Treesearch

Aki Higuchi; Manabu T. Abe

1997-01-01

There is considerable data in the literature on the diet of the Ural Owl (Strix uralensis) based on pellet analysis. Though it is possible to identify prey items by this method, the volume of food consumption is still unknown. The population of Ural Owls in Japan is declining due to the reduction of old-growth forest and the concurrent loss of...

Mountain Building in the Uralides: Pangea to the Present

NASA Astrophysics Data System (ADS)

Brown, Dennis; Juhlin, Christopher; Puchkov, Victor

Extending for more than 2000 kilometers from the islands of Novaya Zemlya in the north to the Aral Sea in the south, the Uralide orogen forms the geographical and geological divide between Europe and Asia. For more than a century the Uralides have been one of the key areas of geological research in Russia, and have provided much of its mineral and petroleum wealth for the last 50 years. Nevertheless, the geology and tectonic evolution of the Uralide orogen were relatively unknown in the international literature until recently, when EUROPROBE and GEODE (European Science Foundation scientific programmes) brought together Russian, European, and American earth scientists to work in the Uralides project and the Urals Mineral Province project, respectively. Much of the recent research has focused around two deep seismic surveys, Europrobe's Seismic Reflection Profiling in the Urals (ESRU) survey in the Middle Urals and the multicomponent Urals Seismic Experiment and Integrated Studies (URSEIS) survey in the South Urals. These experiments were accompanied by a large number of geological, geochemical, geochronological, and geophysical studies.

Preface

NASA Astrophysics Data System (ADS)

Brown, Dennis; Juhlin, Christopher; Puchkov, Victor

Extending for more than 2000 kilometers from the islands of Novaya Zemlya in the north to the Aral Sea in the south, the Uralide orogen forms the geographical and geological divide between Europe and Asia. For more than a century the Uralides have been one of the key areas of geological research in Russia, and have provided much of its mineral and petroleum wealth for the last 50 years. Nevertheless, the geology and tectonic evolution of the Uralide orogen were relatively unknown in the international literature until recently, when EUROPROBE and GEODE (European Science Foundation scientific programmes) brought together Russian, European, and American earth scientists to work in the Uralides project and the Urals Mineral Province project, respectively. Much of the recent research has focused around two deep seismic surveys, Europrobe's Seismic Reflection Profiling in the Urals (ESRU) survey in the Middle Urals and the multicomponent Urals Seismic Experiment and Integrated Studies (URSEIS) survey in the South Urals. These experiments were accompanied by a large number of geological, geochemical, geochronological, and geophysical studies.

Long-range correlations and burstiness in written texts: Universal and language-specific aspects

NASA Astrophysics Data System (ADS)

Constantoudis, Vassilios; Kalimeri, Maria; Diakonos, Fotis; Karamanos, Konstantinos; Papadimitriou, Constantinos; Chatzigeorgiou, Manolis; Papageorgiou, Harris

2016-08-01

Recently, methods from the statistical physics of complex systems have been applied successfully to identify universal features in the long-range correlations (LRCs) of written texts. However, in real texts, these universal features are being intermingled with language-specific influences. This paper aims at the characterization and further understanding of the interplay between universal and language-specific effects on the LRCs in texts. To this end, we apply the language-sensitive mapping of written texts to word-length series (wls) and analyse large parallel (of same content) corpora from 10 languages classified to four families (Romanic, Germanic, Greek and Uralic). The autocorrelation functions of the wls reveal tiny but persistent LRCs decaying at large scales following a power-law with a language-independent exponent ˜0.60-0.65. The impact of language is displayed in the amplitude of correlations where a relative standard deviation >40% among the analyzed languages is observed. The classification to language families seems to play a significant role since, the Finnish and Germanic languages exhibit more correlations than the Greek and Roman families. To reveal the origins of the LRCs, we focus on the long words and perform burst and correlation analysis in their positions along the corpora. We find that the universal features are linked more to the correlations of the inter-long word distances while the language-specific aspects are related more to their distributions.

iss009e18679

NASA Image and Video Library

2004-08-17

ISS009-E-18679 (17 August 2004) --- Ural River Delta, Kazakhstan is featured in this image photographed by an Expedition 9 crewmember on the International Space Station (ISS). The Ural River is one of two major rivers (the other river is the Volga) that empty into the northern coast of the Caspian Sea, creating extensive wetlands. This image shows details of the Ural's tree-like (or “digitate”) delta. According to NASA scientists studying the Space Station imagery, this type of delta forms when wave action is low and sediment content in the river is high. New distributary channels form in the delta when the river breaches natural levees formed by sediment deposition. The dark regions running along the coast are the wetlands that support high biodiversity due to the unique environment and relative isolation of the Caspian Sea. The coastal wetlands are especially important to migrating birds as an important stop-over along the Asian flyway. The Ural River's trek to the Caspian is long — roughly 2400 kilometers (1500 miles) from the Ural Mountains in Russia south to empty into the northern Caspian Sea in Kazakhstan. Although the current sea level of the Caspian is more than 26 meters below global mean sea level the water levels have risen roughly 2 meters since 1980. This has lead to flooding of much of the coastal region, including the Ural delta, and endangers these coastal wetland environments. The coastal flooding has also impacted the oil exploration infrastructure bordering the Caspian coastline, scientists report.

Treeline advances along the Urals mountain range - driven by improved winter conditions?

PubMed

Hagedorn, Frank; Shiyatov, Stepan G; Mazepa, Valeriy S; Devi, Nadezhda M; Grigor'ev, Andrey A; Bartysh, Alexandr A; Fomin, Valeriy V; Kapralov, Denis S; Terent'ev, Maxim; Bugman, Harald; Rigling, Andreas; Moiseev, Pavel A

2014-11-01

High-altitude treelines are temperature-limited vegetation boundaries, but little quantitative evidence exists about the impact of climate change on treelines in untouched areas of Russia. Here, we estimated how forest-tundra ecotones have changed during the last century along the Ural mountains. In the South, North, Sub-Polar, and Polar Urals, we compared 450 historical and recent photographs and determined the ages of 11,100 trees along 16 altitudinal gradients. In these four regions, boundaries of open and closed forests (crown covers above 20% and 40%) expanded upwards by 4 to 8 m in altitude per decade. Results strongly suggest that snow was an important driver for these forest advances: (i) Winter precipitation has increased substantially throughout the Urals (~7 mm decade(-1) ), which corresponds to almost a doubling in the Polar Urals, while summer temperatures have only changed slightly (~0.05°C decade(-1) ). (ii) There was a positive correlation between canopy cover, snow height and soil temperatures, suggesting that an increasing canopy cover promotes snow accumulation and, hence, a more favorable microclimate. (iii) Tree age analysis showed that forest expansion mainly began around the year 1900 on concave wind-sheltered slopes with thick snow covers, while it started in the 1950s and 1970s on slopes with shallower snow covers. (iv) During the 20th century, dominant growth forms of trees have changed from multistemmed trees, resulting from harsh winter conditions, to single-stemmed trees. While 87%, 31%, and 93% of stems appearing before 1950 were from multistemmed trees in the South, North and Polar Urals, more than 95% of the younger trees had a single stem. Currently, there is a high density of seedlings and saplings in the forest-tundra ecotone, indicating that forest expansion is ongoing and that alpine tundra vegetation will disappear from most mountains of the South and North Urals where treeline is already close to the highest peaks. © 2014 John Wiley & Sons Ltd.

Structural evolution of the Ural-Tian Shan junction: A view from Karatau ridge, South Kazakhstan

NASA Astrophysics Data System (ADS)

Alexeiev, Dmitriy V.; Cook, Harry E.; Buvtyshkin, Vasiliy M.; Golub, Lyudmila Y.

2009-02-01

The deformation history of the Late Palaeozoic Ural-Tian Shan junction is discussed for the example of the Karatau ridge in southern Kazakhstan. Three deformation events are recognized. The Late Carboniferous D1 event is characterized by Laramide-style thrust-and-fold structures on the southern margin of Kazakhstan with shortening in a NE-SW direction. The Latest Permian and Triassic D2 event is controlled by compression in an east-west direction, which reflects collisional deformation in the Urals. The main structures are submeridional folds and north-west-striking sinistral strike-slip faults. The Triassic D3 event with shortening in a north-south direction reflects collision of the Turan microcontinent against the southern margin of Kazakhstan. The main structures are north-west-striking dextral strike-slip faults. Our new data provides important clues for the reconstruction of pre-Cretaceous structures between the Urals and the Tian Shan.

[Hygienic evaluation of transboundary pollution of the Ural River basin].

PubMed

Iskakov, A Zh; Lestsova, N A; Zasorin, B V; Boev, M V

2009-01-01

The anthropogenic pollution of the Ural River and its tributaries is the most important problem of the Ural-Caspian basin. Transboundary inflow from Kazakhstan to Russian is 30.9 km3/year. The border Ilek river pollution was hygienically evaluated and the contribution of pollution sources was ascertained, with the seasonal variations and hydrochemical background being kept in mind, from 2002 to 2007. The monitoring data on the content of priority pollutants of the surface waters of the basin of the Ilek River, a tributary of the Ural River, which come from the Republic of Kazakhstan, are given. Semiquantitative spectral estimation and the atomic absorption method were used to study the chemical composition of bottom sediments in the Ilek River and its tributaries. The magnitude and sources of influence of man-caused pollution on the quality of the river water were established.

Geology of the Volga-Ural petroleum province and detailed description of the Ramashkino and Arlan oil fields

USGS Publications Warehouse

Peterson, James A.; Clarke, James W.

1983-01-01

The Volga-Ural petroleum province is in general coincident with the Volga-Ural regional high, a broad upwarp of the east-central part of the Russian (East European) platform. The central part of the province is occupied by the Tatar arch, which contains the major share of the oil fields of the province. The Perm-Bashkir arch forms the northeastern part of the regional high, and the Zhigulevsko-Orenburg arch makes up the southern part. These arches are separated from one another by elongate downwarps. The platform cover overlies an Archean crystalline basement and consists of seven main sedimentation cycles as follows: 1) Riphean (lower Bavly) continental sandstone, shale, and conglomerate beds from 500 to 5,000 m thick deposited in aulacogens. 2) Vendian (upper Bavly) continental and marine shale and sandstone up to 3,000 m thick. 3) Middle Devonian-Tournaisian transgressive deposits, which are sandstone, siltstone, and shale in the lower part and carbonates with abundant reefs in the upper; thickness is 300-1,000 m. In the upper carbonate part is the Kamsko-Kinel trough system, which consists of narrow interconnected deep-water troughs. 4) The Visean-Namurian-Bashkirian cycle, which began with deposition of Visean clastics that draped over reefs of the previous cycle and filled in an erosional relief that had formed in some places on the sediments of the previous cycle. The Visean clastics are overlain by marine carbonates. Thickness of the cycle is 50-800 m. 5) Early Moscovian-Early Permian terrigenous clastic deposits and marine carbonate beds 1,000-3,000 m thick. 6) The late Early Permian-Late Permian cycle, which reflects maximum growth of the Ural Mountains and associated Ural foredeep. Evaporites were first deposited, then marine limestones and dolomites, which intertongue eastward with clastic sediments from the Ural Mountains. 7) Continental redbeds of Triassic age and mixed continental and marine elastic beds of Jurassic and Cretaceous age, which were deposited on the southern, southwestern, and northern margins of the Russian platform; they are generally absent in the Volga-Ural province, however. The Volga-Ural oil and gas basin is a single artesian system that contains seven aquifers separated by seals. The areas of greatest hydraulic head are in the eastern parts of the basin near areas where the aquifers crop out on the western slopes of the Ural Mountains. The Peri-Caspian basin is the principal drainage area of the artesian system. Approximately 600 oil and gas fields and 2,000 pools have been found in the Volga-Ural province. Nine productive sequences are recognized as follows: 1) Upper Proterozoic (Bavly beds), which are promising but not yet commercial. 2) Clastic Devonian, which contains the major reserves and includes the main pays of the super-giant Romashkino field. 3) Carbonate Upper Devonian and lowermost Carboniferous, which is one of the main reef-bearing intervals. 4) Visean (Lower Carboniferous) elastics, which are the main pays in the super-giant Arian field. 5) Carbonate Lower and Middle Carboniferous. 6) Clastic Middle Carboniferous Moscovian. 7) Carbonate Middle and Upper Carboniferous. 8) Carbonate-evaporite Lower Permian, which contains the major gas reserves and the lower part of the Melekess tar deposits. 9) Clastic-carbonate Upper Permian, which contains the major part of the Melekess tar deposits. The Volga-Ural province is divided into several productive regions on a basis of differences in structure, distribution of reservoir and source-rock facies, and general composition of the petroleum accumulations. These regions are the Tatar arch, Birsk saddle, Upper Kama depression, Perm-Bashkir arch, Ufa-Orenburg monocline, Melekess-Sernovodsko-Abdulino basin, Zhligulevsko-Orenburg arch, Ural foredeep, and north borders of the Peri-Casplan depression. Exploration activity has declined in recent years; however, interest remains high in several parts of the province, particula

Ordovician volcanic and plutonic complexes of the Sakmara allochthon in the southern Urals

NASA Astrophysics Data System (ADS)

Ryazantsev, A. V.; Tolmacheva, T. Yu.

2016-11-01

The Ordovician terrigenous, volcanic-sedimentary and volcanic sequences that formed in rifts of the active continental margin and igneous complexes of intraoceanic suprasubduction settings structurally related to ophiolites are closely spaced in allochthons of the Sakmara Zone in the southern Urals. The stratigraphic relationships of the Ordovician sequences have been established. Their age and facies features have been specified on the basis of biostratigraphic and geochronological data. The gabbro-tonalite-trondhjemite complex and the basalt-andesite-rhyolite sequence with massive sulfide mineralization make up a volcanic-plutonic association. These rock complexes vary in age from Late Ordovician to Early Silurian in certain structural units of the Sakmara Allochthon and to the east in the southern Urals. The proposed geodynamic model for the Ordovician in Paleozoides of the southern Urals reconstructs the active continental margin, whose complexes formed under extension settings, and the intraoceanic suprasubduction structures. The intraoceanic complexes display the evolution of a volcanic arc, back-, or interarc trough.

Structural evolution of the Ural-Tian Shan junction: A view from Karatau ridge, South Kazakhstan

USGS Publications Warehouse

Alexeiev, D.V.; Cook, H.E.; Buvtyshkin, V.M.; Golub, L.Y.

2009-01-01

The deformation history of the Late Palaeozoic Ural-Tian Shan junction is discussed for the example of the Karatau ridge in southern Kazakhstan. Three deformation events are recognized. The Late Carboniferous D1 event is characterized by Laramide-style thrust-and-fold structures on the southern margin of Kazakhstan with shortening in a NE-SW direction. The Latest Permian and Triassic D2 event is controlled by compression in an east-west direction, which reflects collisional deformation in the Urals. The main structures are submeridional folds and north-west-striking sinistral strike-slip faults. The Triassic D3 event with shortening in a north-south direction reflects collision of the Turan microcontinent against the southern margin of Kazakhstan. The main structures are north-west-striking dextral strike-slip faults. Our new data provides important clues for the reconstruction of pre-Cretaceous structures between the Urals and the Tian Shan. ?? 2008 Acad??mie des sciences.

Ural Mountains, Russia

NASA Image and Video Library

2015-10-06

This image from NASA Terra spacecraft shows the Ural Mountains, which run 2500 km north-south through western Russia, and form the boundary between Europe and Asia. Since the 17th century, the mountains were exploited for their deposits of iron, copper, gold, coal, oil, mica and gemstones. The Urals are among the world's oldest existing mountain ranges, having been formed about 275 million years ago due to the collision of the Laurussia supercontinent with the continent of Kazakhstania. The image was acquired July 13, 2011, covers an area of 39 by 62 km, and is located near 65.5 degrees north, 59.9 degrees east. http://photojournal.jpl.nasa.gov/catalog/PIA19795

The Hirnantian δ13C Positive Excursion in the Nabiullino Section (South Urals)

NASA Astrophysics Data System (ADS)

Yakupov, R. R.; Mavrinskaya, T. M.; Smoleva, I. V.

2018-02-01

The upper Sandbian, Katian, and Hirnantian complexes of conodonts in the upper Ordovician section of the western slope of the Southern Urals near the village of Nabiullino were studied. The δ13C positive excursion with a maximum of 3.3‰ associated with the global Hirnantian isotopic event, HICE, was fixed for the first time. This excursion shows the beginning of the Hirnantian stage in the terrigenous-carbonate section of the upper Ordovician in the Southern Urals. It coincides with the first occurrence of the Hirnantian conodont species of Gamachignathus ensifer and the conodonts of shallow-water biophacies, Aphelognathus-Ozarkodina, reflecting the global glacio-eustatic event.

Developing the mechatronics and robotics at Nizhny Tagil Technological Institute of Ural Federal University

NASA Astrophysics Data System (ADS)

Goman, V. V.; Fedoreev, S. A.

2018-02-01

This report concerns the development trends of education in the field of the Mechatronics and Robotics at Nizhny Tagil Technological Institute (branch of Ural Federal University). The paper considers new teaching technologies, experience in upgrade of the laboratory facilities and some results of development Mechatronics and Robotics educational courses.

Experience gained at the Ural Turbine Works with retrofitting steam turbine units for thermal power stations

NASA Astrophysics Data System (ADS)

Valamin, A. E.; Kultyshev, A. Yu.; Gol'dberg, A. A.; Shibaev, T. L.; Paneque Aguilera, H. C.

2013-08-01

Examples of projects on retrofitting, modernizing, and renovating steam turbine units at thermal power stations implemented with participation of the Ural Turbine Works are given. Advanced construction and layout solutions were used in implementing these projects both on the territory of Russia and abroad.

Improving Energy Efficiency of Buildings in the Urals

NASA Astrophysics Data System (ADS)

Kiyanets, A. V.

2017-11-01

The article is devoted to the results of studies of energy efficiency improvements of the buildings which are constructed under the climatic conditions of the Ural Federal District of the Russian Federation. The relevance of the stated problem is corroborated. The requirements of the existing regulatory legal acts of the Russian Federation on energy conservation and energy efficiency in construction are given. The article specifies that energy efficiency in construction refers to a set of measures aimed at the reduction of energy resources which are consumed by buildings and are necessary to maintain the required microclimate parameters indoors. The main modern measures for improving the energy efficiency of buildings are presented, and their application under the climatic conditions of the Urals are analyzed and calculated. Each of the proposed methods is evaluated. Basing on the research results, it is concluded that most of the currently known measures for improving the energy efficiency of buildings are significantly limited in the Ural Federal District due to the small economic effect connected with the complexity and high cost of their implementation and operation, the peculiarities of climatic conditions and the conditions of the population density of the territories or significant ineffectiveness of the measures themselves; the most promising measures for improving the energy efficiency of buildings under the climatic and economic conditions of the Urals are the measures for reducing heat loss through the building envelopes (for improving the heat-insulation characteristics of the applied materials and structures).

The reconstruction of Lymantria dispar outbreaks by dendrochronological methods in the South Urals

Treesearch

Sergei Kucherov

1991-01-01

Interest in investigating the influence of extreme ecological factors on the radial growth of oak (Quercus robur L.) is bound up with oak dieback in the South Urals during the last decade. Factors contributing to this problem in the study area are hard winter frosts, late spring frosts, and Lymantria dispar L. outbreaks. To...

Assessment of undiscovered continuous oil and gas resources in the Domanik-type formations of the Volga-Ural Region Province, Russia, 2017

USGS Publications Warehouse

Klett, Timothy R.; Brownfield, Michael E.; Finn, Thomas M.; Gaswirth, Stephanie B.; Le, Phuong A.; Leathers-Miller, Heidi M.; Marra, Kristen R.; Mercier, Tracey J.; Pitman, Janet K.; Schenk, Christopher J.; Tennyson, Marilyn E.; Woodall, Cheryl A.

2018-02-27

Using a geology-based assessment methodology, the U.S. Geological Survey estimated mean undiscovered, technically recoverable continuous resources of 2.8 billion barrels of oil and 34 trillion cubic feet of gas in the Domanik-type formations of the Volga-Ural Region Province, Russia.

Results of in vivo measurements of strontium-90 body-burden in Urals residents: analyses of data obtained 2006-2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tolstykh, E. I.; Bougrov, N. G.; Krivoshchapov, Victor A.

2012-06-01

A part of the Urals territory was contaminated with 90Sr and 137Cs in the 1950s as a result of accidents at the "Mayak" Production Association. The paper describes the analysis of in vivo 90Sr measurements in Urals residents. The measurements were performed with the use of whole-body-counter SICH-9.1M in 2006-2012. Totally 5840 measurements for 4876 persons were performed from 2006 to 2012; maximal measured value was 24 kBq. Earlier, similar measurements were performed with SICH-9.1 (1974-1997). Comparison of the results obtained with SICH-9.1 and SICH-9.1M has shown a good agreement of the two data sets.

Assessment of undiscovered oil and gas resources of the Volga-Ural Region Province, Russia and Kazakhstan, 2010

USGS Publications Warehouse

Klett, T.R.; Schenk, Christopher J.; Charpentier, Ronald R.; Brownfield, Michael E.; Pitman, Janet K.; Cook, Troy A.; Tennyson, Marilyn E.

2010-01-01

The U.S. Geological Survey estimated mean volumes of technically recoverable, conventional, undiscovered petroleum resources at 1.4 billion barrels of crude oil, 2.4 trillion cubic feet of natural gas, and 85 million barrels of natural gas liquids for the Volga-Ural Region Province, using a geology-based assessment methodology.

Morphological and molecular observations on the cereal cyst nematode Heterodera filipjevi from the Volga and South Ural regions of Russia

USDA-ARS?s Scientific Manuscript database

During 2010-2012, a survey was conducted to determine the distribution and species diversity of the cereal cyst nematode Heterodera filipjevi within the Volga and South Ural regions of the Russian Federation. A total of 270 soil samples were collected. Seven populations of CCN were found in the rhiz...

Petroleum geology and resources of the Volga-Ural province, U.S.S.R.

USGS Publications Warehouse

Peterson, James A.; Clarke, James W.

1983-01-01

The Volga-Ural petroleum province is, in general, coincident with the Volga-Ural regional high, a broad upwarp of the east-central part of the Russian (East European) Platform. The central part of the province is occupied by the Tatar arch, which contains the major share of the oilfields of the province. The Komi-Perm arch forms the northeastern part of the regional high, and the Zhigulevsko-Pugachev and Orenburg arches make up the southern part. These arches are separated from one another by elongate downwarps. The platform cover overlies an Archean crystalline basement and consists of seven main sedimentation cycles. (1) Riphean (lower Bavly) continental sandstone, shale, and conglomerate beds, from 500 to 5,000 m thick, were deposited in aulacogens. (2) Vendian (upper Bavly) continental and marine shale and sandstone are up to 3,000 m thick. (3) Middle Devonian-Tournaisian transgressive deposits, which are sandstone, siltstone, and shale in the lower part and carbonates and abundant reefs in the upper part, range from 300 to 1,000 m in thickness. The upper carbonate part includes the Kamsko-Kinel trough system, which consists of narrow, interconnected, deepwater troughs. (4) The Visean-Namurian-Bashkirian cycle began with deposition of Visean clastic deposits, which draped over reefs of the previous cycle and filled in an erosional relief that had formed in some places on the sediments of the previous cycle. The Visean clastic deposits are overlain by marine carbonate beds. The cycle is from 50 to 800 m thick. (5) The lower Moscovian-Lower Permian cycle consists of 1,000 to 3,000 m of terrigenous clastic deposits and marine carbonate beds. (6) The upper Lower Permian-Upper Permian cycle reflects the maximum growth of the Ural Mountains and the associated Ural foredeep. Evaporite deposits were first laid down, followed by marine limestones and dolomites, which intertongue eastward with clastic sediments from the Ural Mountains. (7) Continental red beds of Triassic age and mixed continental and marine clastic beds of Jurassic and Cretaceous age were deposited on the western, southwestern, and northern margins of the Russian Platform; they are generally absent in the Volga-Ural province, however. Approximately 600 oilfields and gasfields and 2,000 pools have been found in the Volga-Ural province. Nine productive sequences are recognized; these are, in general, the same as the sedimentation cycles, although some subdivisions have been added. The clastic section of Middle and early Late Devonian age contains the major recoverable oil accumulations, including the supergiant Romashkino field. Cumulative production to 1980 is estimated at 30 to 35 billion barrels of oil equivalent, identified reserves at about 10 billion barrels of oil equivalent, and undiscovered resources at about 7 billion barrels of oil equivalent. Identified reserves of natural gas are estimated at 100 trillion cubic feet and undiscovered resources at 63 trillion cubic feet.

The Role of Nutrition in the Biological Adaptation of the Medieval Population of the Cis-Ural Perm Region (Archeological and Anthropological Evidence)

ERIC Educational Resources Information Center

Krylasova, Natalya B.; Brykhova, Natalya G.; Burova, Natalya D.

2016-01-01

The aim of this article is to reconstruct the nutrition system of the medieval inhabitants of the Perm Territory located in the western foothills of the Ural mountain range. The investigation is built on a comprehensive analysis of archaeological sources available and on the basis if anthropological materials with involvement of radioactive tracer…

Occurrence modes of As, Sb, Te, Bi, Ag in sulfide assemblages of gold deposits of the Urals

NASA Astrophysics Data System (ADS)

Vikent'eva, O.; Vikentev, I.

2016-04-01

Review of occurrence modes of trace toxic elements ("potential pollutants") in ores from large gold deposits (the Urals) of different genetic types is presented. Mineral forms of these elements as well as their presence in main minerals from gold-bearing sulfide assemblages according to SEM, EPMA, INAA, ICP-MS and LA-ICP-MS are demonstrated.

Bulgar Factories (Trading Posts) in the Kama River Area as a Factor of Adjustment to Feudalism

ERIC Educational Resources Information Center

Krylasova, Natalia B.; Belavin, Andrei M.; Podosenova, Yulia A.

2016-01-01

At the start of the 2nd ML AD a number of trading posts, or factories, emerged in the Cis-Ural region with participation of Bulgar handicraftsmen and merchants. They were townships populated by various ethnic groups. Several centuries later similar factories were set up by natives of the Cis-Ural region in Western Siberia. These factories have…

North Atlantic Origin of Interdecadal variability of Siberian High

NASA Astrophysics Data System (ADS)

Kim, Seon-Hwa; Sung, Mi-Kyung; Kim, Baek-Min

2017-04-01

We suggest that the changes in the mean atmospheric circulation structure in the North Atlantic Ocean upstream region of Eurasian continent play an important role in the interdecadal variability of Siberian High (SH) through the modulation of Ural blocking frequency. Previous studies suggested that the interdecadal variability of SH is partly explained by the Arctic Oscillation. However, in this study, we emphasize the role of 'Warm Arctic and Cold Eurasia (WACE)', which is the second mode of winter surface air temperature variability over Eurasia. We show that the correlation between SH and WACE is high in general compared to that between SH and AO. However, the correlation between SH and WACE does not always exhibit high constant value. It shows a distinctive interdecadal fluctuation in the correlation. We found that this fluctuation in the correlation is due to the interdecadal fluctuation of the continental trough over the North Atlantic and the resultant strengthening of in-situ atmospheric baroclinicity. This accompanies changes in the transient vorticity flux divergence which leads to the downstream wave development and anomalous anticyclonic flow near Ural region. Obviously, the existence of anticyclonic flow over Ural region helps more frequent occurrence of Ural blocking and it is shown that this condition favors positive WACE event, which links to an intensified SH.

Towards an Artificial Space Object Taxonomy

NASA Astrophysics Data System (ADS)

Wilkins, M.; Schumacher, P.; Jah, M.; Pfeffer, A.

2013-09-01

Object recognition is the first step in positively identifying a resident space object (RSO), i.e. assigning an RSO to a category such as GPS satellite or space debris. Object identification is the process of deciding that two RSOs are in fact one and the same. Provided we have appropriately defined a satellite taxonomy that allows us to place a given RSO into a particular class of object without any ambiguity, one can assess the probability of assignment to a particular class by determining how well the object satisfies the unique criteria of belonging to that class. Ultimately, tree-based taxonomies delineate unique signatures by defining the minimum amount of information required to positively identify a RSO. Therefore, taxonomic trees can be used to depict hypotheses in a Bayesian object recognition and identification process. This work describes a new RSO taxonomy along with specific reasoning behind the choice of groupings. An alternative taxonomy was recently presented at the Sixth Conference on Space Debris in Darmstadt, Germany. [1] The best example of a taxonomy that enjoys almost universal scientific acceptance is the classical Linnaean biological taxonomy. A strength of Linnaean taxonomy is that it can be used to organize the different kinds of living organisms, simply and practically. Every species can be given a unique name. This uniqueness and stability are a result of the acceptance by biologists specializing in taxonomy, not merely of the binomial names themselves. Fundamentally, the taxonomy is governed by rules for the use of these names, and these are laid down in formal Nomenclature Codes. We seek to provide a similar formal nomenclature system for RSOs through a defined tree-based taxonomy structure. Each categorization, beginning with the most general or inclusive, at any level is called a taxon. Taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a diagnosis, a statement intended to supply characters that differentiate the taxon from others with which it is likely to be confused. Each taxon will have a set of uniquely distinguishing features that will allow one to place a given object into a specific group without any ambiguity. When a new object does not fall into a specific taxon that is already defined, the entire tree structure will need to be evaluated to determine if a new taxon should be created. Ultimately, an online learning process to facilitate tree growth would be desirable. One can assess the probability of assignment to a particular taxon by determining how well the object satisfies the unique criteria of belonging to that taxon. Therefore, we can use taxonomic trees in a Bayesian process to assign prior probabilities to each of our object recognition and identification hypotheses. We will show that this taxonomy is robust by demonstrating specific stressing classification examples. We will also demonstrate how to implement this taxonomy in Figaro, an open source probabilistic programming language.

Seismic and Geophysical Characterization of Northern Asia

DTIC Science & Technology

2010-09-01

seismic networks in Russia and Japan. The geographic scope of this project covers Russia from the Urals to the Bering Strait and from the Arctic Ocean to...Russia and Japan. The geographic scope of this project covers Russia from the Urals to the Bering Strait and from the Arctic Ocean to the North Korean...between these somewhat correspond to the boundaries of the microplates , it is our intention to use significantly more data from the region to define

Parkerite and bismutohauchecornite in chromitites of the Urals: Example of the Uralian Emerald Mines

NASA Astrophysics Data System (ADS)

Koroteev, V. A.; Popov, M. P.; Erokhin, Yu. V.; Khiller, V. V.

2017-04-01

An unusual ore mineralization represented by parkerite, millerite, bismutohauchecornite, bismuthinite, and nickeline was registered in altered chromitite from the Mariinsk emerald-beryllium deposit. Such mineralization is typical of Cu-Ni sulfide ores and hydrothermal veins from the five-element formation. This mineral assemblage was not registered in ophiolitic ultrabasic rocks and related chromitites. The find of bismutohauchecornite is the first in the Urals; the find of parkerite is the third.

[Genetic structure of people from the Volga-Ural region and Central Asia from data of Alu-polymorphism].

PubMed

Khusainova, R I; Akhmetova, V L; Kutuev, I A; Salimova, A Z; Korshunova, T Iu; Lebedev, Iu B; Khusnutdinova, E K

2004-04-01

Nine Alu loci (Ya5NBC5, Ya5NBC27, Ya5NBC148, Ya5NBC182, YA5NBC361, ACE, ApoA1, PV92, TPA25) were analyzed in six ethnic populations (Trans-Ural Bashkirs, Tatars-Mishars, Mordovians-Moksha, Mountain Maris, Udmurts, and Komi-Permyaks) of the Volga-Ural region and in three Central Asian populations (Uzbeks, Kazakhs, and Uigurs). All Alu insertions analyzed appeared to be polymorphic in all populations examined. The frequency of insertion varied from 0.110 in Mountain Maris at the Ya5NBC5 locus to 0.914 in Tatars at the ApoA1 locus. The data on the allele frequency distribution at nine loci point to the existence of substantial genetic diversity in the populations examined. The value of the observed heterozygosity averaged over nine Alu insertions varied from 0.326 in Mountain Maris to 0.445 in Kazakhs and Uigurs. The level of the interpopulation genetic differences for the Volga-Ural population (Fst = 0.061) was higher than for the populations of Central Asia (Fst = 0.024), Europe (Fst = 0.02), and Southeastern Asia (Fst = 0.018). The populations examined were highly differentiated both in respect of linguistic characteristics and the geographical position. The data obtained confirmed the effectiveness of the marker system used for the assessment of genetic differentiation and the relationships between the ethnic groups.

Assessment of Inhalation Risk to Public Health in the Southern Ural

NASA Astrophysics Data System (ADS)

Ulrikh, D. V.; Ivanova, S. V.; Riabchikova, I. A.

2017-11-01

A large number of iron and steel companies in the Southern Ural cause severe air pollution in the towns of Karabash (Chelyabinsk region), Sibay (Republic of Bashkortostan), Gai (Orenburg region). The article aims to assess the inhalation effects of hazardous substances on the Southern Ural population. The analysis focused on cancer and non-cancer risks to public health that arise from the surface air pollution caused by the metallurgical industry emissions. The assessment was carried out on the basis of methodological guidelines R 2.1.10.1920-04 using modern sanitary and hygienic standards. We analysed the level of ambient air pollution in the impact area of the metallurgical industry of Karabash, Sibay and Gai over the past eleven years. We established that the ambient air of all the studied towns contain carcinogenic substances that cause unacceptable cancer risks. Formaldehyde has the main share in this risk. We calculated the hazard quotients HQ for the identified priority pollutants and the total hazard indices HI. It is shown that the non-cancer inhalation risk to the Southern Ural population exceeds the safe level manyfold. Sulfur dioxide has the main share in this risk. The conducted assessment showed that in 2006-2016, there was a continuous inhalation exposure of the population to hazardous substances. Sanitary and technological solutions that will allow a reduction of risk to acceptable values are required.

Origin of the Words Denoting Some of the Most Ancient Old World Pulse Crops and Their Diversity in Modern European Languages

PubMed Central

Mikić, Aleksandar

2012-01-01

This preliminary research was aimed at finding the roots in various Eurasian proto-languages directly related to pulses and giving the words denoting the same in modern European languages. Six Proto-Indo-European roots were indentified, namely arnk(')- (‘a leguminous plant’), *bhabh- (‘field bean’), * (‘a kernel of leguminous plant’, ‘pea’), ghArs- (‘a leguminous plant’), *kek- (‘pea’) and *lent- (‘lentil’). No Proto-Uralic root was attested save hypothetically *kača (‘pea’), while there were two Proto-Altaic roots, *bŭkrV (‘pea’) and * (‘lentil’). The Proto-Caucasianx root * denoted pea, while another one, *hōwł(ā) (‘bean’, ‘lentil’) and the Proto-Basque root *iłha-r (‘pea’, ‘bean’, ‘vetch’) could have a common Proto-Sino-Caucasian ancestor, *hVwłV (‘bean’) within the hypothetic Dené-Caucasian language superfamily. The Modern Maltese preserved the memory of two Proto-Semitic roots, *'adaš- (‘lentil’) and *pūl- (‘field bean’). The presented results prove that the most ancient Eurasian pulse crops were well-known and extensively cultivated by the ancestors of all modern European nations. The attested lexicological continuum witnesses the existence of a millennia-long links between the peoples of Eurasia to their mutual benefit. This research is meant to encourage interdisciplinary concerted actions between plant scientists dealing with crop evolution and biodiversity, archaeobotanists and language historians. PMID:22973458

New data concerning the age and specific features of magmatism of timanides in the southern part of the Lyapin structure (Northern Urals)

NASA Astrophysics Data System (ADS)

Petrov, G. A.; Ronkin, Yu. L.; Gerdes, A.; Maslov, A. V.

2017-10-01

New data on composition and age of Precambrian granites and volcanic rocks in the southern part of the Lyapin structure (Northern Urals) are considered. The geochemical features of the igneous rocks are similar to those of the rocks formed in both divergent and convergent environments. In the Late Precambrian (583-553 Ma), the investigated area is assumed to have been a part of the active margin above the mantle plume.

Renewable Energy Sources in Formation of South Urals Modern Urban Systems

NASA Astrophysics Data System (ADS)

Khudyakov, A. Ju; Shabiev, S. G.

2017-11-01

The article considers the vital problems of renewable energy sources using by the example of the South Urals as a part of a general energy system of the Russian Federation, makes a forecast and gives recommendations on the application of specific technologies: solar energy, wind energy, deep heat energy and geothermal energy. It also considers the influence of the climatology on selection of the development pattern for the alternative energy industry. The article contains an example of wind energy used as a driver of the Karabash company town development in the Chelyabinsk region. The development of the economic energy sector is extremely important for the Russian Federation, both from the point of view of strategic security and from the point of view of integration into a modern development on the principles of Sustainable Development. To provide a full understanding of the role of alternative energy in the energy sector of the country, the article presents the materials illustrating the regional potential in terms of alternative energy sources use. This article is a part of the global research on the settlement system evolution in the South Urals. The authors studied the historical, geographical, demographic, economic characteristics of the region. Finally, a forecast for development at the regional level was made. Some of the aforementioned results were obtained due to the testing research in the learning process of the students from the South Ural State University (national research university).

Using the CAE technologies of engineering analysis for designing steam turbines at ZAO Ural Turbine Works

NASA Astrophysics Data System (ADS)

Goloshumova, V. N.; Kortenko, V. V.; Pokhoriler, V. L.; Kultyshev, A. Yu.; Ivanovskii, A. A.

2008-08-01

We describe the experience ZAO Ural Turbine Works specialists gained from mastering the series of CAD/CAE/CAM/PDM technologies, which are modern software tools of computer-aided engineering. We also present the results obtained from mathematical simulation of the process through which high-and intermediate-pressure rotors are heated for revealing the most thermally stressed zones, as well as the results from mathematical simulation of a new design of turbine cylinder shells for improving the maneuverability of these turbines.

Braconid wasps of subfamily Alysiinae (Hymenoptera: Braconidae) as endoparasitoids of Selachops flavocinctus Wahlberg, 1844 (Diptera: Agromyzidae) in the Central Urals, Russia.

PubMed

Kostromina, Tatiana S; Timokhov, Alexander V; Belokobylskij, Sergey A

2016-11-29

The Agromyzidae fly Selachops flavocinctus Wahlberg, 1844 as host of the Alysiinae genera Asyntactus Marshall, 1898 (Alysiini) and Protochorebus Perepechaenko, 1997 (Dacnusini) is recorded for the first time. A new species from Central Urals, Protochorebus pervushini sp. nov., is described and illustrated. The new material for Asyntactus rhogaleus Marshall, 1898 is studied. A key to Protochorebus species is provided. Description of puparium of Selachops flavocinctus and new data on its life history are published for the first time.

[Contamination of protozoa by enteroviruses in fresh water and sewages].

PubMed

Skachkov, M V; Al'misheva, A Sh; Plotnikov, A O; Nemtseva, N V; Skvortsov, V O

2009-01-01

To determine rate of infection of protozoa by enteroviruses to assess the potential role of protozoa as a natural reservoir of enteroviruses. The samples were collected from flowing and stagnant water reservoirs in Orenburg region in summer and autumn. The samples of sewages were taken in all stages of their treatment. Cultures of protozoa were isolated with micromanipulator equipped with micropipette, incubated on Pratt's medium at 25 degrees C and fed with Pseudomonas fluorescens culture. RNA of enteroviruses was detected by reverse transcription polymerase chain reaction (RT-PCR). Seventy-two protozoan species were found in Ural river, whereas 15 and 38 species were found in lakes and sewages respectively. Enteroviruses were detected by RT-PCR in 61.8% cultures of protozoa belonging to 23 species of flagellates, amoebae and ciliates isolated from natural water bodies undergoing anthropogenic impact as well as from sewages in all stages of their treatment. Predominant localization of enteroviruses in dominant taxons of protozoa (Paraphysomonas sp., Spumella sp., Petalomonas poosilla, Amoeba sp.) was noted. Obtained data confirm presence of enteroviruses in protozoa living both in flowing and stagnant recreation natural water bodies as well as in sewages and confirm the hypothesis of persistence of enteroviruses in protozoa and the reservoir role of the latter. Contingency of life cycles of viruses and protozoa allows to explain the seasonality of aseptic meningitis incidence caused by enteroviruses, which peaks in summer and autumn when protozoa massively multiply in water bodies.

"My naturesound" - nature observations with sound recordings

PubMed Central

Runnel, Veljo; Peterson, Marko; Zirk, Allan

2017-01-01

Abstract Background Online systems for observation reporting by citizen scientists have been operating for many years. iNaturalist (California Academy of Sciences 2016), eBird (Cornell Lab of Ornithology 2016) and Observado (Observation International 2016) are well-known international systems, Artportalen (Swedish Species Information Centre 2016) and Artsobservasjoner (Norwegian Biodiversity Information Centre 2016) are Scandinavian. In addition, databases and online solutions exist that are more directly research-oriented but still offer participation by citizen scientists, such as the PlutoF (University of Tartu Natural History Museum 2016) platform. The University of Tartu Natural History Museum maintains the PlutoF platform (Abarenkov et al. 2010) for storing and managing biodiversity data, including taxon observations. In 2014, development was started to integrate an observation app "Minu loodusheli"/"My naturesound" (University of Tartu Natural History Museum 2017b) (My naturesound, Fig. 1) within PlutoF system. In 2017, an English language version of the app (University of Tartu Natural History Museum 2017c) was launched that includes nearly all major sound-producing taxon groups in its taxonomy. The application also acts as a practical tool for collecting and publishing occurrence data for the Global Biodiversity Information Facility (Global Biodiversity Information Facility 2017) in standardized Darwin Core format together with download links to the multimedia files. Although the sound recording ability of mobile phones opens new opportunities to validate taxon occurrences, current technological solutions limit the use of recordings in biodiversity research. The "My naturesound" allows the user to record taxon occurrences and to provide audio recordings as evidence. After installing the application, the user is promted to login with PlutoF system credentials or to register with PlutoF. The application is targeted primarely to citizen scientists, but researchers themselves can also use it as a tool for easy annotation of taxon occurrences. New information The dataset consists observation data of birds, amphibians and insects by citizen scientists with on site audio recordings. The dataset gives the possibility to analyze the suitablility of mobile devices for recording animal vocalizations and their use in reporting. PMID:29104438

Climate change-driven treeline advances in the Urals alter soil microbial communities

NASA Astrophysics Data System (ADS)

Djukic, Ika; Moiseev, Pavel; Hagedorn, Frank

2016-04-01

Climatic warming may affect microbial communities and their functions either directly through increased temperatures or indirectly by changes in vegetation. Treelines are temperature-limited vegetation boundaries from tundra to forests. In unmanaged regions of the Ural mountains, there is evidence that the forest-tundra ecotone has shifted upward in response to climate warming during the 20th century. Little is known about the effects of the treeline advances on the microbial structure and function and hence they feedbacks on the belowground carbon and nitrogen cycling In our study, we aimed to estimate how ongoing upward shifts of the treeline ecotone might affect soil biodiversity and its function and hence soil carbon (C) and nitrogen (N) dynamics in the Southern and Polar Ural mountains. Along altitudinal gradients reaching from the tundra to forests, we determined the soil microbial community composition (using Phospholipid Fatty Acids method) and quantified the activity of several extracellular enzymes involved in the C and nutrient cycling. In addition, we measured C pools in biomass and soils and quantified C and N mineralization. The results for the top soils, both in South Urals and in the Polar Ural, indicate a close link between climate change driven vegetation changes and soil microbial communities. The observed changes in microbial structure are induced through the resulting more favorable conditions than due to a shift in litter quality. The activities of chitinase were significantly higher under trees than under herbaceous plants, while activities of cellulase and protease declined with altitude from the tundra to the closed forest. In contrast to enzymatic activities, soil carbon stocks did not change significantly with altitude very likely as a result of a balancing out of increased C inputs from vegetation by an enhanced C output through mineralization with forest expansion. The accelerated organic matter turnover in the forest than in the tundra leads to higher contents of mineral N and net nitrification rates. In turn, the increasing N availability may stimulate plant growth and hence, induce a positive feedback between treeline advances and soil nitrogen cycling through soil microbial communities.

The Ufa indenter: stratigraphic and geophysic evidences for an actual indentation of the Southern Urals by the East European craton

NASA Astrophysics Data System (ADS)

Lefort, Jean-Pierre; Danukalova, Guzel

2014-07-01

Study of the altitudes of the lowest part of the Upper Cretaceous-Eocene and Aktschagylian-Quaternary stratigraphic ensembles known on the western slope of the Southern Urals evidences the existence of an East-West elongated dome which follows the N53° latitude. This ridge is superimposed at depth with the remnants of the Sernovodsk-Abdulino Aulacogen and with the Belaya tear fault, which support the existence of a recent rejuvenation of these old structures. North of these disruptions the Southern Urals display a clear bent towards the East. Detailed microstructural studies show that this curvature is associated with a typical stress pattern which suggests the existence of an indentation of the fold belt by the East European craton. The hypothesis of an Ufa indenter is not supported by an equivalent East-West deep fault north of the bend. However, a long N100° magnetic anomaly, interpreted as a shear zone, suggests that the indenter is a reality. Quaternary uplift and crustal thickening at its front as well as seismological data support our interpretation. It is not stressed that the curvature of the Urals observed at 56° latitude results solely from this recent indentation. It is only assumed that the actual indentation is rejuvenating a former unevenness which existed before in the East European craton. Study of the inner part of the indenter shows that this type of structure is not necessarily rigid and undeformed. Some of the structures described on the URSEIS deep seismic line could be much younger than previously expected.

The Age of Dinosaurs in Russia and Mongolia

NASA Astrophysics Data System (ADS)

Benton, Michael J.; Shishkin, Mikhail A.; Unwin, David M.; Kurochkin, Evgenii N.

2003-12-01

The former Soviet Union covers a vast area of land, and over the last 200 years, many dozens of extraordinary dinosaurs and other fossil amphibians, reptiles, birds and mammals have been found in Mesozoic rocks in its territories. The Permo-Triassic of the Ural Mountains of Russia have produced hundreds of superb specimens, and many of the dinosaurs from Mongolia are unique. This is the first compilation in any Western language of this large body of Russian research and the first time so much of this research, previously unexplored by the West, has been introduced in English. The Age of Dinosaurs in Russia and Mongolia is written by a unique mix of Russian and Western palaeontologists, and provides an entrée to a range of fossil faunas, in particular reptiles, that have been little known outside Russia. It will undoubtedly become a major reference work for all vertebrate palaeontologists.

Quintinite-1 M from the Mariinsky Deposit, Ural Emerald Mines, Central Urals, Russia

NASA Astrophysics Data System (ADS)

Zhitova, E. S.; Popov, M. P.; Krivovichev, S. V.; Zaitsev, A. N.; Vlasenko, N. S.

2017-12-01

The paper describes the first finding of quintinite [Mg4Al2(OH)12][(CO3)(H2O)3] at the Mariinsky deposit in the Central Urals, Russia. The mineral occurs as white tabular crystals in cavities within altered gabbro in association with prehnite, calcite, and a chlorite-group mineral. Quintinite is the probable result of late hydrothermal alteration of primary mafic and ultramafic rocks hosting emerald-bearing glimmerite. According to electron microprobe data, the Mg: Al ratio is 2: 1. IR spectroscopy has revealed hydroxyl and carbonate groups and H2O molecules in the mineral. According to single crystal XRD data, quintinite is monoclinic, space group C2/ m, a =5.233(1), b = 9.051(2), c = 7.711(2) Å, β = 103.09(3)°, V = 355.7(2) Å3. Based on structure refinement, the polytype of quintinite should be denoted as 1M. This is the third approved occurrence of quintinite-1M in the world after the Kovdor complex and Bazhenovsky chrysotile-asbestos deposit.

[Natural selection associated with color vision defects in some population groups of Eurasia].

PubMed

Evsiukov, A N

2014-01-01

Fitness coefficients and other quantitative parameters of selection associated with the generalized color blindness gene CB+ were obtained for three ethnogeographic population groups, including Belarusians from Belarus, ethnic populations of the Volga-Ural region, and ethnic populations of Siberia and the Far East of Russia. All abnormalities encoded by the OPN1LW and OPN1MW loci were treated as deviations from normal color perception. Coefficients were estimated from an approximation of the observed CB+ frequency distributions to the theoretical stationary distribution for the Wright island model. This model takes into account the pressure of migrations, selection, and random genetic drift, while the selection parameters are represented in the form of the distribution parameters. In the populations of Siberia and Far East, directional selection in favor of normal color vision and the corresponding allele CB- was observed. In the Belarusian and ethnic populations of the Volga-Ural region, stabilizing selection was observed. The selection intensity constituted 0.03 in the Belarusian; 0.22 in the ethnic populations of the Volga-Ural region; and 0.24 in ethnic populations of Siberia and Far East.

Modern Church Construction in Urals. Problems and Prospects

NASA Astrophysics Data System (ADS)

Surin, D. N.; Tereshina, O. B.

2017-11-01

The article analyzes the problems of the modern Orthodox church architecture in Russia, special attention is paid to the problems of the Ural region. It justifies the importance of addressing to this issue connected with the Orthodox traditions revival in Russia over the last decades and the need to compensate for tens of thousands of the churches destroyed in the Soviet period. The works on the theory and history of the Russian architecture and art, studies of the architectural heritage and the art of building of the Ural craftsmen are used as a scientific and methodological base for the church architecture development. The article discloses the historically formed architectural features of the Russian Orthodox churches the artistic image of which is designed to create a certain religious and aesthetic experience. It is stated that the restoration of the Russian church construction tradition is possible on the background of architectural heritage. It sets the tendencies and vital tasks in church construction and outlines a complex of measures to solve these tasks at the public and regional levels.

Undiscovered porphyry copper resources in the Urals—A probabilistic mineral resource assessment

USGS Publications Warehouse

Hammarstrom, Jane M.; Mihalasky, Mark J.; Ludington, Stephen; Phillips, Jeffrey; Berger, Byron R.; Denning, Paul; Dicken, Connie; Mars, John; Zientek, Michael L.; Herrington, Richard J.; Seltmann, Reimar

2017-01-01

A probabilistic mineral resource assessment of metal resources in undiscovered porphyry copper deposits of the Ural Mountains in Russia and Kazakhstan was done using a quantitative form of mineral resource assessment. Permissive tracts were delineated on the basis of mapped and inferred subsurface distributions of igneous rocks assigned to tectonic zones that include magmatic arcs where the occurrence of porphyry copper deposits within 1 km of the Earth's surface are possible. These permissive tracts outline four north-south trending volcano-plutonic belts in major structural zones of the Urals. From west to east, these include permissive lithologies for porphyry copper deposits associated with Paleozoic subduction-related island-arc complexes preserved in the Tagil and Magnitogorsk arcs, Paleozoic island-arc fragments and associated tonalite-granodiorite intrusions in the East Uralian zone, and Carboniferous continental-margin arcs developed on the Kazakh craton in the Transuralian zone. The tracts range from about 50,000 to 130,000 km2 in area. The Urals host 8 known porphyry copper deposits with total identified resources of about 6.4 million metric tons of copper, at least 20 additional porphyry copper prospect areas, and numerous copper-bearing skarns and copper occurrences.Probabilistic estimates predict a mean of 22 undiscovered porphyry copper deposits within the four permissive tracts delineated in the Urals. Combining estimates with established grade and tonnage models predicts a mean of 82 million metric tons of undiscovered copper. Application of an economic filter suggests that about half of that amount could be economically recoverable based on assumed depth distributions, availability of infrastructure, recovery rates, current metals prices, and investment environment.

Reconstruction of radionuclide intakes for the residents of East Urals Radioactive Trace (1957–2011)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tolstykh, Evgenia I.; Peremyslova, Lyudmila M.; Degteva, Marina O.

The East Urals Radioactive Trace (EURT) was formed after a chemical explosion in the radioactive waste-storage facility of the Mayak Production Association in 1957 (Southern Urals, Russia) and resulted in an activity dispersion of 7.4 × 10 16 Bq into the atmosphere. Internal exposure due to ingestion of radionuclides with local foodstuffs was the main factor of public exposure at the EURT. The EURT cohort, combining residents of most contaminated settlements, was formed for epidemiological study at the Urals Research Center for Radiation Medicine, Russia (URCRM). For the purpose of improvement of radionuclide intake estimates for cohort members, the followingmore » data sets collected in URCRM were used: (1) Total β-activity and radiochemical measurements of 90Sr in local foodstuffs over all of the period of interest (1958–2011; n = 2200), which were used for relative 90Sr intake estimations. (2) 90Sr measurements in human bones and whole body ( n = 338); these data were used for average 90Sr intake derivations using an age- and gender-dependent Sr-biokinetic model. Non-strontium radionuclide intakes were evaluated on the basis of 90Sr intake data and the radionuclide composition of contaminated foodstuffs. Validation of radionuclide intakes during the first years after the accident was first carried out using measurements of the feces β-activity of EURT residents ( n = 148). The comparison of experimental and reconstructed values of feces β-activity shows good agreement. 90Sr intakes for residents of settlements evacuated 7–14 days after the accident were also obtained from 90Sr measurements in human bone and whole body. Furthermore, the results of radionuclide intake reconstruction will be used to estimate the internal doses for the members of the EURT cohort.« less

Reconstruction of radionuclide intakes for the residents of East Urals Radioactive Trace (1957–2011)

DOE PAGES

Tolstykh, Evgenia I.; Peremyslova, Lyudmila M.; Degteva, Marina O.; ...

2017-01-19

The East Urals Radioactive Trace (EURT) was formed after a chemical explosion in the radioactive waste-storage facility of the Mayak Production Association in 1957 (Southern Urals, Russia) and resulted in an activity dispersion of 7.4 × 10 16 Bq into the atmosphere. Internal exposure due to ingestion of radionuclides with local foodstuffs was the main factor of public exposure at the EURT. The EURT cohort, combining residents of most contaminated settlements, was formed for epidemiological study at the Urals Research Center for Radiation Medicine, Russia (URCRM). For the purpose of improvement of radionuclide intake estimates for cohort members, the followingmore » data sets collected in URCRM were used: (1) Total β-activity and radiochemical measurements of 90Sr in local foodstuffs over all of the period of interest (1958–2011; n = 2200), which were used for relative 90Sr intake estimations. (2) 90Sr measurements in human bones and whole body ( n = 338); these data were used for average 90Sr intake derivations using an age- and gender-dependent Sr-biokinetic model. Non-strontium radionuclide intakes were evaluated on the basis of 90Sr intake data and the radionuclide composition of contaminated foodstuffs. Validation of radionuclide intakes during the first years after the accident was first carried out using measurements of the feces β-activity of EURT residents ( n = 148). The comparison of experimental and reconstructed values of feces β-activity shows good agreement. 90Sr intakes for residents of settlements evacuated 7–14 days after the accident were also obtained from 90Sr measurements in human bone and whole body. Furthermore, the results of radionuclide intake reconstruction will be used to estimate the internal doses for the members of the EURT cohort.« less

Influence of anglers' specializations on catch, harvest, and bycatch of targeted taxa

USGS Publications Warehouse

Pope, Kevin L.; Chizinski, Christopher J.; Wiley, Christopher L.; Martin, Dustin R.

2016-01-01

Fishery managers often use catch per unit effort (CPUE) of a given taxon derived from a group of anglers, those that sought said taxon, to evaluate fishery objectives because managers assume CPUE for this group of anglers is most sensitive to changes in fish taxon density. Further, likelihood of harvest may differ for sought and non-sought taxa if taxon sought is a defining characteristic of anglers’ attitude toward harvest. We predicted that taxon-specific catch across parties and reservoirs would be influenced by targeted taxon after controlling for number of anglers in a party and time spent fishing (combine to quantify fishing effort of party); we also predicted similar trends for taxon-specific harvest. We used creel-survey data collected from anglers that varied in taxon targeted, from generalists (targeting “anything” [no primary target taxa, but rather targeting all fishes]) to target specialists (e.g., anglers targeting largemouth bass Micropterus salmoides) in 19 Nebraska reservoirs during 2009–2011 to test our predictions. Taxon-specific catch and harvest were, in general, positively related to fishing effort. More importantly, we observed differences of catch and harvest among anglers grouped by taxon targeted for each of the eight taxa assessed. Anglers targeting a specific taxon had the greatest catch for that taxon and anglers targeting anything typically had the second highest catch for that taxon. In addition, anglers tended to catch more of closely related taxa and of taxa commonly targeted with similar fishing techniques. We encourage managers to consider taxon-specific objectives of target and non-target catch and harvest.

Methods for Ensuring High Quality of Coding of Cause of Death. The Mortality Register to Follow Southern Urals Populations Exposed to Radiation.

PubMed

Startsev, N; Dimov, P; Grosche, B; Tretyakov, F; Schüz, J; Akleyev, A

2015-01-01

To follow up populations exposed to several radiation accidents in the Southern Urals, a cause-of-death registry was established at the Urals Center capturing deaths in the Chelyabinsk, Kurgan and Sverdlovsk region since 1950. When registering deaths over such a long time period, quality measures need to be in place to maintain quality and reduce the impact of individual coders as well as quality changes in death certificates. To ensure the uniformity of coding, a method for semi-automatic coding was developed, which is described here. Briefly, the method is based on a dynamic thesaurus, database-supported coding and parallel coding by two different individuals. A comparison of the proposed method for organizing the coding process with the common procedure of coding showed good agreement, with, at the end of the coding process, 70  - 90% agreement for the three-digit ICD -9 rubrics. The semi-automatic method ensures a sufficiently high quality of coding by at the same time providing an opportunity to reduce the labor intensity inherent in the creation of large-volume cause-of-death registries.

EXPLORATORY PLASMA BIOCHEMISTRY REFERENCE INTERVALS FOR URAL OWLS (STRIX URALENSIS, PALLAS 1771) FROM THE AUSTRIAN REINTRODUCTION PROJECT.

PubMed

Scope, Alexandra; Schwendenwein, Ilse; Stanclova, Gabriela; Vobornik, Angela; Zink, Richard

2016-06-01

The Ural owl (Strix uralensis) is the biggest forest-living owl in Austria; however, it became extinct in Austria through poaching and habitat loss more than half a century ago. The birds examined in the present study were breeding pairs from the reintroduction project with the aim of determining exploratory plasma biochemistry reference intervals in Ural owls and evaluating the amount of biological variation between seasons, sexes, and ages. A total of 45 birds were sampled, including 13 adult males, 14 adult females, and 18 juvenile birds. Remarkably, almost all of the analytes showed significant differences between the subgroups, primarily between seasons, followed by age and sex. Only creatinkinase, glucose, lactatdehydrogenase, and triglycerides did not show any significant variations. Despite partitioning of reference values into subgroups according to biological variation diminishing the number of reference individuals in the respective groups, the resulting smaller reference intervals will improve medical assessment. The results of the present study once again demonstrate that significant seasonal fluctuations must be expected and considered in the interpretation. It can be assumed that these differences are probably even greater in free-range birds with considerable changes in food quantity and quality during and between years.

Lower Carboniferous Siderites: A Product of Bottom Seeps and Bacterial Metanogenesis (Subpolar Urals)

NASA Astrophysics Data System (ADS)

Antoshkina, A. I.; Ryabinkina, N. N.

2018-02-01

Complex modern micro- and spectroscopic methods for study of siderite concretions in the Lower Carboniferous terrigenous strata on the Kozhym River (Subpolar Urals) have shown that its formation was caused by destruction of clay minerals due to the activity of bacterial communities. The abundance of these bacteria was caused by gas-fluid seeps and bacterial methanogenesis processes in bottom deposits. In basins with normal marine fauna, this led to local desalination, hydrogen sulfide contamination, mass collapse of primary organisms, and the development of element-specific bacteria. The occurrence of these bacteria caused the formation of specific authigenic mineralization in the concretion of sideritic bacteriolites: the framboidal pyrite, sphalerite, galenite, barite, sulfoselenides, and tellurides.

The first Lu-Hf zircon isotope data for gabbro-diorite-tonalite associations of the Urals

NASA Astrophysics Data System (ADS)

Ronkin, Yu. L.; Smirnov, V. N.; Ivanov, K. S.; Gerdes, A.

2017-01-01

The Lu-Hf isotope systematics of zircon from the gabbro-plagiogranite association (gabbro, diorite, tonalite, and plagiogranite), which is one of the most typical associations of igneous rocks in the Urals, was studied for the first time. The isotope study yielded a unified age limit of 433 Ma, which corresponds to the time of formation of this rock association. The younger "rejuvenated" ages characterize superimposed thermal impact events, induced by the volcanic arc activity, as well as collisional and postcollisional processes. Here, the initial 176Hf/177Hf( t) ratio in the studied zircon from gabbro and plagiogranite corresponds in fact to a highly LILE-depleted (DM) mantle.

Development of the work on fuel cells in the Ministry for Atomic Energy of Russian Federation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lubovin, B.Y.; Novitski, E.Z.

1996-04-01

This paper describes research on fuel cells in the Russian Federation. The beginning of the practical work on fuel cells in Russia dates back to the 50`s and 60`s when the Ural Electrochemical Plant and the Ural Electromechanical Plant of the Ministry of Medium Machine-Building of the USSR, all Russian Research Institute of the power sources and many other institutes of the Ministry of Electrotechnical Industry of the USSR got to the development of the alkaline fuel cells for the spaceships according to the tasks of the SPC `Energy` and for the submarines on the tasks of the Ministry ofmore » Defense.« less

Phytomining Perspectives in Rehabilitation of Mining and Industrial Areas of South Ural

NASA Astrophysics Data System (ADS)

Timofeeva, S. S.; Ulrikh, D. V.; Timofeev, S. S.

2017-05-01

The ability of midland hawthorn (Crataegus laevigata (Poir)), common barberry (Berberis vulgaris), red elder (Sambucus racemosa), cinnamon rose (Rosa cinnamomea L.), couch grass (Elytrigia repens), crested wheat grass (Agropyron cristatum), meadow fescue (Festuca pratensis) and meadow grass (Poa pratensis) for phytoextraction of heavy metals from technogenic soil is proved in the article. The possibility of effective phytoextraction with the use of hawthorn and elder is shown. Maximum accumulation of zinc takes place in the surface mass of couch grass and meadow fescue. In regard to the conditions of South Ural, planting of elder and hawthorn with seeding of couch grass and meadow fescue is recommended for phytomining purposes.

Uranium-Bearing Srilankite from High-Pressure Garnetites of the Southern Urals: First Data

NASA Astrophysics Data System (ADS)

Gottman, I. A.; Pushkarev, E. V.; Khiller, V. V.

2018-04-01

This work presents the results of studying srilankite, a rare zirconium titanate (ZrTi2O6), associated with ilmenite, rutile, zircon, uraninite, and other minerals discovered in high-pressure garnetites of the lherzolite Mindyak massif (Southern Urals). Srilankite occurs as inclusions in ilmenite and rutile of up to several tens of microns in size. It was established for the first time that srilankite contains a significant UO2 admixture (up to 20%). The negative correlation between Zr and U is evidence of isomorphism in the srilankite-brannerite system. The association of srilankite with high-Zr rutile indicates that formation of these minerals occurred at T > 850°C.

Investigation of ancient DNA from Western Siberia and the Sargat culture.

PubMed

Bennett, Casey C; Kaestle, Frederika A

2010-04-01

Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th-12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis.

Geochemistry of Thorium and Uranium in Soils of the Southern Urals

NASA Astrophysics Data System (ADS)

Asylbaev, I. G.; Khabirov, I. K.; Gabbasova, I. M.; Rafikov, B. V.; Lukmanov, N. A.

2017-12-01

Specific features of the horizontal and vertical distribution of uranium and thorium in soils and parent materials of the Southern Urals within the Bashkortostan Republic have been studied with the use of mass spectrometry with inductively coupled plasma. The dependence of distribution patterns of these elements on the local environmental conditions is shown. A scale for soil evaluation according to the concentrations of uranium and thorium (mg/kg) is suggested: the low level, up to 3; medium, up to 9; high, up to 15; and very high, above 15 mg/kg. On the basis of to this scale, the ecological state of the soils is evaluated, and the schematic geochemical map of the region is compiled. The territory of Bashkortostan is subdivided into two parts according to the contents of radioactive elements in soils: the western part with distinct accumulation of uranium and the eastern part with predominant thorium accumulation. This finding supports the charriage (thrust fault) nature of the fault zone of the Southern Urals. The vertical distribution patterns of uranium and thorium in soils of the region are of the same character. The dependence between the contents of these two elements and rare-earth elements has been established. The results of this study are applied for assessing the ecological state of soils in the region.

Granitoids of the Ufalei block (South Urals): Sr-Nd isotope systematics, geodynamic position and genetic reconstructions

NASA Astrophysics Data System (ADS)

Ronkin, Yu. L.; Shardakova, G. Yu.; Maslov, A. V.; Shagalov, E. S.; Lepikhina, O. P.

2009-04-01

Petrogeochemical and isotopic-geochronological signatures in granitoids developed in structures with complex geological history represent an important feature for reconstructing paleogeodynamic settings. Granitoids are widespread in the western slope of the Urals, where the Uralian Orogen contacts via a collage of different-age blocks of the east European Platform. The Ufalei block located in the Central Urals megazone at the junction between the South and Middle Urals’ segments represents one such boundary structure with multistage geological evolution. The isotopic ages obtained by different methods for acid igneous rocks range from 1290 to 245 Ma. We determined close Rb-Sr and Sm-Nd ages (317 Ma) for granites of the Nizhnii Ufalei Massif. By their petrochemical parameters, granitoids and host granite-gneisses differ principally from each other: the former are close to subduction-related, while the latter, to continental-riftogenic varieties. The primary ratio (87Sr/86Sr)0 = 0.70428 and ɛNd ≈ +4 values indicate significant contribution of oceanic (island-arc?) material to the substrate, which served as a source for granites of the Nizhnii Ufalei Massif. Model Nd ages of granites vary from 641 to 550 Ma. Distinct oceanic rocks and varieties with such ages are missing from the surrounding structures. New isotopic dates obtained for ultramafic and mafic rocks from different zones of the Urals related to the Cadomian cycle imply development of unexposed Upper Riphean-Vendian “oceanic” rocks in the central part of the Ufalei block, which played a substantial role in the formation of the Nizhnii Ufalei granitoids. Such rocks could be represented, for example, by fragments of the Precambrian Timanide-type ophiolite association. The analysis of original materials combined with published data point to the heterogeneous composition and structure of the Ufalei block and a significant part of the western segment of the Central Uralian Uplift and extremely complex geological history of the region coupling the Uralian Orogen with the East European Platform in the present-day structure.

Paleomagnetic and Geochronologic Data from Central Asia: Inferences for Early Paleozoic Tectonic Evolution and Timing of Worldwide Glacial Events

NASA Astrophysics Data System (ADS)

Gregory, L. C.; Meert, J. G.; Levashova, N.; Grice, W. C.; Gibsher, A.; Rybanin, A.

2007-12-01

The Neoproterozoic to early Paleozoic Ural-Mongol belt that runs through Central Asia is crucial for determining the enigmatic amalgamation of microcontinents that make up the Eurasian subcontinent. Two unique models have been proposed for the evolution of Ural-Mongol belt. One involves a complex assemblage of cratonic blocks that have collided and rifted apart during diachronous opening and closing of Neoproterozoic to Devonian aged ocean basins. The opposing model of Sengor and Natal"in proposes a long-standing volcanic arc system that connected Central Asian blocks with the Baltica continent. The Aktau-Mointy and Dzabkhan microcontinents in Kazakhstan and Central Mongolia make up the central section of the Ural-Mongol belt, and both contain glacial sequences characteristic of the hypothesized snowball earth event. These worldwide glaciations are currently under considerable debate, and paleomagnetic data from these microcontients are a useful contribution to the snowball controversy. We have sampled volcanic and sedimentary sequences in Central Mongolia, Kazakhstan and Kyrgyzstan for paleomagnetic and geochronologic study. U-Pb data, 13C curves and abundant fossil records place age constraints on sequences that contain glacial deposits of the hypothesized snowball earth events. Carbonates in the Zavkhan Basin in Mongolia are likely remagnetized, but fossil evidence within the sequence suggests a readjusted age control on two glacial events that were previously labeled as Sturtian and Marinoan. U-Pb ages from both Kazakhstan and Mongolian volcanic sequences imply a similar evolution history of the areas as part of the Ural-Mongol fold belt, and these ages paired with paleomagnetic and 13C records have important tectonic implications. We will present these data in order to place better constraints on the Precambrian to early Paleozoic tectonic evolution of Central Asia and the timing of glacial events recorded in the area.

Magnetic Characterization of Proposed Tektite-like Objects (Urengoites, South-Ural Glass) from Siberia, Russia

NASA Astrophysics Data System (ADS)

Bezaeva, N. S.; Rochette, P.; Masaitis, V. L.; Badyukov, D. D.; Kosterov, A.

2017-12-01

Urengoites and South-Ural glass are proposed `tektite-like' objects from Western Siberia (Russia), previously described in [1-3]. Urengoites (U-1, U-2, U-3; 24 Ma [1]) were discovered near the West-Siberian town of Novy Urengoi [1-2]. Total recovered mass: 21.65 g. The only recovered South-Ural glass A-1 was found near Magnitogorsk ( 90 g) [3]. In spite of previous works [1-3], the magnetic properties of urengoites and South-Ural glass remain unknown. Here we present a comprehensive magnetic characterization for all three currently known urengoite specimens and the only discovered South-Ural glass. Rock magnetic investigations revealed the presence of ferrimagnetic minerals in all samples. Low-temperature magnetometry (ZFC-FC dataset) points out to magnetite, which was detected in the most magnetic urengoite sample (U-3) via its characteristic Verwey transition at 120K (<1 ppm). Contrary to previous investigations [2], we could measure NRM for all samples and acquire alternating field demagnetization spectra for the biggest samples (U-1 and A-1). The following SIRM values were recorded: 4.33 μAm2/kg (U-1). 13.20 μAm2/kg (U-2), 62.40 μAm2/kg (U-3) and 9.36 μAm2/kg (A-1). The obtained χ0 values for all four samples (U-1 to U-3: from 9.98 to 19.90·10-9 m3/kg; A-1: 4.66·10-9 m3/kg) are close to those for Libyan glassed (see Table 1 in [4]). Anisotropy of magnetic susceptibility (AMS) measurements for A-1 sample revealed 28% of anisotropy. SIRM values and non-isotropic susceptibility demonstrate a composite ferrimagnetic and paramagnetic origin of susceptibility. U-1 and A-1 do not demonstrate any field nor frequency dependence of χ0, which likely indicates the absence of superparamagnetic grains of nanometric size. Acknowledgements: The work is supported by Act 211 Government of the Russian Federation, agreement № 02.A03.21.0006 and is performed according to the Russian Government Program of Competitive Growth of Kazan Federal University. This research has been conducted using the facilities of St. Petersburg University Scientific Park, RCs Geomodel, DFM, and ITCN. Refs: [1] Deutsch A. et al. (1997) MAPS 32:679-686. [2] Masaitis V.L. et al. (1988) LPS XIX:728-729. [3] Koroteev V.A. et al. (1994) Zapisky Vseross. Mineral. Obsh. 123:44-48 (in Russian). [4] Rochette et al. (2015) EPSL 432:381-390.

The Ural train-gas pipeline catastrophe: the report of the IDF medical corps assistance.

PubMed

Benmeir, P; Levine, I; Shostak, A; Oz, V; Shemer, J; Sokolova, T

1991-08-01

Following the destruction of two trains in the Urals 2000 km east of Moscow, as a consequence of the conflagration caused by an explosion from a leaking natural gas pipeline, 3000 people were injured;* most of them (2200) died* immediately and the others (about 800) were badly burned. At the request of the Soviet Union Government a medical military delegation was sent to give assistance to the injured people. This report describes the treatment given by the delegation to 40 patients with burns of between 40 and 90 per cent TBSA during a period of 10 days. An insight into a Soviet Union Trauma Center is given and the good treatment given by the Soviet colleagues is emphasized.

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

Polyhedral geometry of phylogenetic rogue taxa.

PubMed

Cueto, María Angélica; Matsen, Frederick A

2011-06-01

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.

Early Permian conodont fauna and stratigraphy of the Garden Valley Formation, Eureka County, Nevada

USGS Publications Warehouse

Wardlaw, Bruce R.; Gallegos, Dora M.; Chernykh, Valery V.; Snyder, Walter S.

2015-01-01

The lower Part of the Garden Valley Formation yields two distinct conodont faunas. One of late Asselian age dominated by Mesogondolella and Streptognathodus and one of Artinskian age dominated by Sweetognathus with Mesogondolella. The Asselian fauna contains the same species as those found in the type area of the Asselian in the southern Urals including Mesogondolella dentiseparata, described for the first time outside of the Urals. Apparatuses for Sweetognathus whitei, Diplognathodus stevensi, and Idioprioniodus sp. are described. The Garden Valley Formation represents a marine pro-delta basin and platform, and marine and shore fan delta complex deposition. The fan-delta complex was most likely deposited from late Artinskian to lateWordian. The Garden Valley Formation records tremendous swings in depositional setting from shallow-water to basin to shore.

Early Permian conodont fauna and stratigraphy of the Garden Valley Formation, Eureka County, Nevada

USGS Publications Warehouse

Wardlaw, Bruce R.; Gallegos, Dora M.; Chernykh, Valery V.; Snyder, Walter S.

2015-01-01

The lower part of the Garden Valley Formation yields two distinct conodont faunas. One of late Asselian age dominated by Mesogondolella and Streptognathodus and one of Artinskian age dominated by Sweetognathus with Mesogondolella. The Asselian fauna contains the same species as those found in the type area of the Asselian in the southern Urals including Mesogondolella dentiseparata, described for the first time outside of the Urals. Apparatuses for Sweetognathus whitei, Diplognathodus stevensi, and Idioprioniodus sp. are described. The Garden Valley Formation represents a marine pro-delta basin and platform, and marine and shore fan delta complex deposition. The fan-delta complex was most likely deposited from late Artinskian to late Wordian. The Garden Valley Formation records tremendous swings in depositional setting from shallow-water to basin to shore.

Coral bleaching response index: a new tool to standardize and compare susceptibility to thermal bleaching.

PubMed

Swain, Timothy D; Vega-Perkins, Jesse B; Oestreich, William K; Triebold, Conrad; DuBois, Emily; Henss, Jillian; Baird, Andrew; Siple, Margaret; Backman, Vadim; Marcelino, Luisa

2016-07-01

As coral bleaching events become more frequent and intense, our ability to predict and mitigate future events depends upon our capacity to interpret patterns within previous episodes. Responses to thermal stress vary among coral species; however the diversity of coral assemblages, environmental conditions, assessment protocols, and severity criteria applied in the global effort to document bleaching patterns creates challenges for the development of a systemic metric of taxon-specific response. Here, we describe and validate a novel framework to standardize bleaching response records and estimate their measurement uncertainties. Taxon-specific bleaching and mortality records (2036) of 374 coral taxa (during 1982-2006) at 316 sites were standardized to average percent tissue area affected and a taxon-specific bleaching response index (taxon-BRI) was calculated by averaging taxon-specific response over all sites where a taxon was present. Differential bleaching among corals was widely variable (mean taxon-BRI = 25.06 ± 18.44%, ±SE). Coral response may differ because holobionts are biologically different (intrinsic factors), they were exposed to different environmental conditions (extrinsic factors), or inconsistencies in reporting (measurement uncertainty). We found that both extrinsic and intrinsic factors have comparable influence within a given site and event (60% and 40% of bleaching response variance of all records explained, respectively). However, when responses of individual taxa are averaged across sites to obtain taxon-BRI, differential response was primarily driven by intrinsic differences among taxa (65% of taxon-BRI variance explained), not conditions across sites (6% explained), nor measurement uncertainty (29% explained). Thus, taxon-BRI is a robust metric of intrinsic susceptibility of coral taxa. Taxon-BRI provides a broadly applicable framework for standardization and error estimation for disparate historical records and collection of novel data, allowing for unprecedented accuracy in parameterization of mechanistic and predictive models and conservation plans. © 2016 John Wiley & Sons Ltd.

Coral bleaching response index: a new tool to standardize and compare susceptibility to thermal bleaching

PubMed Central

SWAIN, TIMOTHY D.; VEGA-PERKINS, JESSE B.; OESTREICH, WILLIAM K.; TRIEBOLD, CONRAD; DUBOIS, EMILY; HENSS, JILLIAN; BAIRD, ANDREW; SIPLE, MARGARET; BACKMAN, VADIM; MARCELINO, LUISA

2017-01-01

As coral bleaching events become more frequent and intense, our ability to predict and mitigate future events depends upon our capacity to interpret patterns within previous episodes. Responses to thermal stress vary among coral species; however the diversity of coral assemblages, environmental conditions, assessment protocols, and severity criteria applied in the global effort to document bleaching patterns creates challenges for the development of a systemic metric of taxon-specific response. Here, we describe and validate a novel framework to standardize bleaching response records and estimate their measurement uncertainties. Taxon-specific bleaching and mortality records (2036) of 374 coral taxa (during 1982–2006) at 316 sites were standardized to average percent tissue area affected and a taxon-specific bleaching response index (taxon-BRI) was calculated by averaging taxon-specific response over all sites where a taxon was present. Differential bleaching among corals was widely variable (mean taxon-BRI = 25.06 ± 18.44%, ± SE). Coral response may differ because holobionts are biologically different (intrinsic factors), they were exposed to different environmental conditions (extrinsic factors), or inconsistencies in reporting (measurement uncertainty). We found that both extrinsic and intrinsic factors have comparable influence within a given site and event (60% and 40% of bleaching response variance of all records explained, respectively). However, when responses of individual taxa are averaged across sites to obtain taxon-BRI, differential response was primarily driven by intrinsic differences among taxa (65% of taxon-BRI variance explained), not conditions across sites (6% explained), nor measurement uncertainty (29% explained). Thus, taxon-BRI is a robust metric of intrinsic susceptibility of coral taxa. Taxon-BRI provides a broadly applicable framework for standardization and error estimation for disparate historical records and collection of novel data, allowing for unprecedented accuracy in parameterization of mechanistic and predictive models and conservation plans. PMID:27074334

International Field School on Permafrost, Polar Urals, 2012

NASA Astrophysics Data System (ADS)

Streletskiy, D. A.; Grebenets, V.; Ivanov, M.; Sheinkman, V.; Shiklomanov, N. I.; Shmelev, D.

2012-12-01

The international field school on permafrost was held in the Polar Urals region from June, 30 to July 9, 2012 right after the Tenth International Conference on Permafrost which was held in Salekhard, Russia. The travel and accommodation support generously provided by government of Yamal-Nenets Autonomous Region allowed participation of 150 permafrost young research scientists, out of which 35 students from seven countries participated in the field school. The field school was organized under umbrella of International Permafrost Association and Permafrost Young Research Network. The students represented diverse educational backgrounds including hydrologists, engineers, geologists, soil scientists, geocryologists, glaciologists and geomorphologists. The base school camp was located near the Harp settlement in the vicinity of Polar Urals foothills. This unique location presented an opportunity to study a diversity of cryogenic processes and permafrost conditions characteristic for mountain and plain regions as well as transition between glacial and periglacial environments. A series of excursions was organized according to the following topics: structural geology of the Polar Urals and West Siberian Plain (Chromite mine "Centralnaya" and Core Storage in Labitnangy city); quaternary geomorphology (investigation of moraine complexes and glacial conditions of Ronamantikov and Topographov glaciers); principles of construction and maintains of structures built on permafrost (Labitnangy city and Obskaya-Bovanenkovo Railroad); methods of temperature and active-layer monitoring in tundra and forest-tundra; cryosols and soil formation in diverse landscape condition; periglacial geomorphology; types of ground ice, etc. Every evening students and professors gave a series of presentations on climate, vegetation, hydrology, soil conditions, permafrost and cryogenic processes of the region as well as on history, economic development, endogenous population of the Siberia and the Russian Arctic in general. Series of discussions were focused on methodological aspects of permafrost research, data mining techniques, international projects, job opportunities etc. The experience gained by students during the field school, new networking opportunities and good spirit of polar research cannot be adequately replaced by any classroom demonstrations. That is why it is critically important to conduct such filed schools in the future. We are grateful to administration of Yamal-Nenets Autonomous region for providing financial support and to Yamal Tour for the organization and logistics in the field.

Regional changes in vertebra morphology during ontogeny reflect the life history of Atlantic cod (Gadus morhua L.)

PubMed Central

Fjelldal, Per G; Totland, Geir K; Hansen, Tom; Kryvi, Harald; Wang, Xiyuan; Søndergaard, Jens L; Grotmol, Sindre

2013-01-01

This study examined vertebra formation, morphology, regional characters, and bending properties of the vertebral column of Atlantic cod throughout its life cycle (0–6 years). The first structure to form was the foremost neural arch, 21 days post hatching (dph), and the first vertebra centrum to form – as a chordacentrum – was the 3rd centrum at 28 dph. Thereafter, the notochord centra developed in a regular sequence towards the head and caudal fin. All vertebrae were formed within 50 dph. The vertebral column consisted of 52 (± 2) vertebrae (V) and could be divided into four distinct regions: (i) the cervical region (neck) (V1 and V2), characterized by short vertebra centra, prominent neural spines and absence of articulations with ribs; (ii) the abdominal region (trunk) (V3–V19), characterized by vertebrae with wing-shaped transverse processes (parapophyses) that all articulate with a rib; (iii) the caudal region (tail) (V20–V40), where the vertebra centra have haemal arches with prominent haemal spines; (iv) the ural region (V41 to the last vertebra), characterized by broad neural and haemal spines, providing sites of origin for muscles inserting on the fin rays – lepidotrichs – of the tail fin. The number of vertebrae in the cervical, abdominal and caudal regions was found to be constant, whereas in the ural region, numbers varied from 12 to 15. Geometric modelling based on combination of vertebra lengths, diameters and intervertebral distances showed an even flexibility throughout the column, except in the ural region, where flexibility increased. Throughout ontogeny, the vertebra centra of the different regions followed distinct patterns of growth; the relative length of the vertebrae increased in the cervical and abdominal regions, and decreased in the caudal and ural regions with increasing age. This may reflect changes in swimming mode with age, and/or that the production of large volumes of gametes during sexual maturation requires a significant increase in abdominal cavity volume. PMID:23587057

Rana computatrix to human language: towards a computational neuroethology of language evolution.

PubMed

Arbib, Michael A

2003-10-15

Walter's Machina speculatrix inspired the name Rana computatrix for a family of models of visuomotor coordination in the frog, which contributed to the development of computational neuroethology. We offer here an 'evolutionary' perspective on models in the same tradition for rat, monkey and human. For rat, we show how the frog-like taxon affordance model provides a basis for the spatial navigation mechanisms that involve the hippocampus and other brain regions. For monkey, we recall two models of neural mechanisms for visuomotor coordination. The first, for saccades, shows how interactions between the parietal and frontal cortex augment superior colliculus seen as the homologue of frog tectum. The second, for grasping, continues the theme of parieto-frontal interactions, linking parietal affordances to motor schemas in premotor cortex. It further emphasizes the mirror system for grasping, in which neurons are active both when the monkey executes a specific grasp and when it observes a similar grasp executed by others. The model of human-brain mechanisms is based on the mirror-system hypothesis of the evolution of the language-ready brain, which sees the human Broca's area as an evolved extension of the mirror system for grasping.

ScienceCast 93: What Happened Over Russia?

NASA Image and Video Library

2013-02-25

Two weeks after an asteroid exploded over Russia's Ural mountains, scientists are making progress understanding the origin and make-up of the unexpected space rock. This week's ScienceCast presents their latest results.

A Study of the Invertebrates and Fishes of Salt Marshes in Two Oregon Estuaries.

DTIC Science & Technology

1981-06-01

TAXON Level Level Debris TAXON Level Level Debris Marsh Marsh Line Marsh Marsh Line Cnidaria Coleopr era Halaoampa s? p. A Carabidae A A A Turbellaria A...HAB ITAT H fAB ITAT TAXON Tidal Tidal Flat Tidal Tidal Flat Lan Creek Sandy Mudd TAXON PA Creek SandyMdd Cnidaria A A Tanaidacea Nemertea A A Pancolus...INVERTEBRATES Phylum Protozoa Subphylum Sarcomastigophora Class Rhizopodea Order Foraminifera Phylum Cnidaria Class Anthozoa Subclass Zoantharia Order

Clusterons as a tool for monitoring populations of tick-borne encephalitis virus.

PubMed

Kovalev, Sergey Y; Mukhacheva, Tatyana A

2014-02-01

Tick-borne encephalitis (TBE) is a natural focal viral neuroinfection that is widespread in the temperate zone of Eurasia. Knowledge of the genetic structure of tick-borne encephalitis virus (TBEV) populations is important for understanding, not only the origin and evolution of the virus, but also the formation and maintenance of natural foci. A new approach to the differentiation of TBEV strains within subtype, with clusterons as the basis of analysis, has recently been proposed. In the present study, the genetic structure of TBEV-Sib populations has been investigated based on 387 strains isolated in the Middle Urals (Sverdlovsk region). Fourteen of the 18 currently known TBEV-Sib clusterons were identified. They belong to the Asian and Eastern European (Baltic) groups. It was shown that each TBE foci could be characterized by a unique clusteron profile. Three clusterons that emerged within the last 50 years have been identified which implies an active evolutionary process in the TBEV-Sib populations. The greatest diversity of clusterons was observed in the south of the Middle Urals along the Trans-Siberian Way. Such a pattern could reflect the history of colonization of the area and is closely related to the roads passing from Siberia to the European part of Russia through the Urals. In this article, the principles of continuous monitoring in the regional and local TBE foci are proposed, based on the quantitative and qualitative analysis of TBEV-Sib clusteron profiles. © 2013 Wiley Periodicals, Inc.

Lead Isotope Characteristics of the Mindyak Gold Deposit, Southern Urals: Evidence for the Source of Metals

NASA Astrophysics Data System (ADS)

Chugaev, A. V.; Znamensky, S. E.

2018-01-01

The isotopic composition of Pb in pyrite of the Mindyak orogenic gold deposit located in the Main Ural Fault Zone, the Southern Urals, has been studied by the high-precision MC-ICP-MS method. Orebodies at the deposit are composed of early pyrite and late polysulfide-carbonate-quartz mineral assemblages. The orebodies are localized in olistostrome with carbonaceous clayey-cherty cement. Pyrites from early and late mineral assemblages are close in Pb isotope ratios. For early pyrite 206Pb/204Pb = 18.250-18.336, 207Pb/204Pb = 15.645-15.653, 208Pb/204Pb = 38.179-38.461; while for late pyrite 206Pb/204Pb = 18.102-18.378, 207Pb/204Pb = 15.635-15.646, 208Pb/204Pb = 38.149-38.320. The model parameters μ2 (238U/204Pb = 9.91 ± 2), ω2 (232Th/204Pb = 38.5 ± 4), and 232Th/238U = 3.88 ± 3 indicate that an upper crustal Pb source played a leading role in ore formation. Carbonaceous shale as an olistostrome cement and syngenetic sulfide mineralization are considered to be the main Pb sources of both early and late mineral assemblages. An additional recept in apparently magmatic lead is suggested for the late veinlet mineralization. The involvement of lead from several sources in ore formation is consistent with the genetic model, which assumes a two-stage formation of orebodies at the Mindyak deposit.

Oil and gas reserve growth-a model for the Volga-Ural Province, Russia

USGS Publications Warehouse

Verma, M.K.; Ulmishek, G.F.; Gilbershtein, A.P.

2000-01-01

An understanding of reserve growth in known oil and gas fields has become a critical component of energy resource analysis. Significant statistical studies of reserve growth have been published in the U.S., whereas little information is available on other regions of the world. It may be expected that in many countries the magnitude of reserve growth is different from that in the U.S. because of differences in reporting systems and in exploration and production practices. This paper describes the results of a reserve growth study in a group of largest oil and gas fields of the Volga-Ural petroleum province, Russia. The dynamics of reserve growth in these fields shows rapid reserve additions during the first 5 years of field exploration and development, which results from intensive step-out and delineation drilling. Later reserve growth is slow and is related to improvements in recovery technologies and discoveries of new pools and extensions. These two stages of reserve growth are described by two different groups of empirical models. A comparison of these models with the models developed for the lower 48 states and Gulf Coast offshore of the U.S. demonstrates that the reserve growth in the Volga-Ural province is significantly lower than in the U.S. The proposed models may be used for assessment of future reserve additions in known fields of countries that presently have or recently had a centrally-planned economic system.

Conversational sensing

NASA Astrophysics Data System (ADS)

Preece, Alun; Gwilliams, Chris; Parizas, Christos; Pizzocaro, Diego; Bakdash, Jonathan Z.; Braines, Dave

2014-05-01

Recent developments in sensing technologies, mobile devices and context-aware user interfaces have made it pos- sible to represent information fusion and situational awareness for Intelligence, Surveillance and Reconnaissance (ISR) activities as a conversational process among actors at or near the tactical edges of a network. Motivated by use cases in the domain of Company Intelligence Support Team (CoIST) tasks, this paper presents an approach to information collection, fusion and sense-making based on the use of natural language (NL) and controlled nat- ural language (CNL) to support richer forms of human-machine interaction. The approach uses a conversational protocol to facilitate a ow of collaborative messages from NL to CNL and back again in support of interactions such as: turning eyewitness reports from human observers into actionable information (from both soldier and civilian sources); fusing information from humans and physical sensors (with associated quality metadata); and assisting human analysts to make the best use of available sensing assets in an area of interest (governed by man- agement and security policies). CNL is used as a common formal knowledge representation for both machine and human agents to support reasoning, semantic information fusion and generation of rationale for inferences, in ways that remain transparent to human users. Examples are provided of various alternative styles for user feedback, including NL, CNL and graphical feedback. A pilot experiment with human subjects shows that a prototype conversational agent is able to gather usable CNL information from untrained human subjects.

INDICES OF TAXON-BY-TAXON DISAGREEMENT BETWEEN OBSERVED AND EXPECTED ASSEMBLAGES

EPA Science Inventory

RIVPACS-type models infer impairment from the level of disagreement between observed and expected assemblages. The popular O/E index measures the disagreement between the observed and expected number of taxa. Thus, O/E ignores the additional information offered by a taxon-by-taxo...

A revised geological range (Late Pliocene) for foraminifer taxon Bolliella adamsi Banner et Blow, 1959

NASA Astrophysics Data System (ADS)

Reddy, A. Nallapa; Nagendra, R.

2017-12-01

The foraminifer taxon Bolliella adamsi Banner et Blow, 1959 is found to co-occur with index planktic foraminifer taxa of the Late Pliocene (Zone N21) in a core of 2.60 m at 1300 m water depth off Tuticorin, Bay of Bengal. This taxon has been previously known as a Holocene taxon of the Indo-Pacific province. This study significantly revises the known stratigraphic range of B. adamsi from the Late Pliocene (uppermost part of Zone N21) to the Holocene in the Bay of Bengal area.

Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles.

PubMed

Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C

2016-04-01

High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments.

Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.

PubMed

Chau, John H; Rahfeldt, Wolfgang A; Olmstead, Richard G

2018-03-01

Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants. We identify and compare a taxon-specific locus set and three general locus sets (conserved ortholog set [COSII], shared single-copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific data set produced the best-supported tree, but all data sets showed improved resolution over previous non-sequence capture data sets. General locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.

Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles

PubMed Central

Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C.

2016-01-01

High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments. PMID:27032533

Treeline advances and associated shifts in the ground vegetation alter fine root dynamics and mycelia production in the South and Polar Urals.

PubMed

Solly, Emily F; Djukic, Ika; Moiseev, Pavel A; Andreyashkina, Nelly I; Devi, Nadezhda M; Göransson, Hans; Mazepa, Valeriy S; Shiyatov, Stepan G; Trubina, Marina R; Schweingruber, Fritz H; Wilmking, Martin; Hagedorn, Frank

2017-02-01

Climate warming is shifting the elevational boundary between forests and tundra upwards, but the related belowground responses are poorly understood. In the pristine South and Polar Urals with shifts of the treeline ecotone documented by historical photographs, we investigated fine root dynamics and production of extramatrical mycorrhizal mycelia (EMM) along four elevational transects reaching from the closed forest to the treeless tundra. In addition, we analysed elevational differences in climate and vegetation structure, and excavated trees to estimate related changes in the partitioning between below- and aboveground biomass. Fine root biomass of trees (<2 mm) increased by 13-79% with elevation, paralleled by a 35-72% increase in ground vegetation fine roots from the closed forest to the tundra. During the first year of decomposition, mass loss of fine root litter from different vegetation types was greater at lower elevations in the forest-tundra ecotone. The ratio between fine roots of trees and stem biomass largely increased with elevation in both regions, but these increases were not accompanied by a distinct production of EMM. Production of EMM, however, increased with the presence of ectomycorrhizal trees at the transition from the tundra to the forest. Our results imply that the recorded upward expansion of forest into former tundra in the Ural Mountains by 4-8 m per decade is decreasing the partitioning of plant biomass to fine roots. They further suggest that climate-driven forest advances will alter EMM production rates with potential feedbacks on soil carbon and nutrient cycling in these ecosystems.

Mapping of Vegetation with the Geoinformation System and Determining of Carrying Capacity of the Pre-Urals Steppe area for a Newly Establishing Population of the Przewalski Horse Equus ferus przewalskii at the Orenburg State Nature Reserve

NASA Astrophysics Data System (ADS)

Fedorov, N. I.; Mikhailenko, O. I.; Zharkikh, T. L.; Bakirova, R. T.

2018-01-01

Mapping of the vegetation (1:25000) of the Pre-Urals Steppe area at the Orenburg State Nature Reserve was completed in 2016. A map created with the geoinformation system contains 1931 simple and complex polygons for 25 types of vegetation. In a drought year, the average stock of palatable vegetation of the whole area is estimated at 8380 tons dry weight. The estimation is based on the size of areas covered by different types of vegetation, their grass production, the correction coefficients for decreasing of pasture forage stocks in winter and decreasing of production of grass communities in dry years. Based on pasture forage stocks the area could tolerate the maximum population size of 1769 individuals of the Przewalski horse, their average density could be 0.11 horse per ha. Yet, as watering places for animals are limited in Pre-Urals Steppe, grazing pressures on the vegetation next to the water sources may increase in dry years. That is why the above-mentioned calculated maximum population size and density must be reduced at least by half until some additional watering places are established and monitoring of the grazing effect on the vegetation next to the places is carried out regularly. Thus, the maximum size of the population is estimated at 800 to 900 individuals, which is almost 1.5 times more than necessary to establish a self-sustained population of the Przewalski horse.

Phylogenomic analysis of ants, bees and stinging wasps: Improved taxon sampling enhances understanding of hymenopteran evolution

USDA-ARS?s Scientific Manuscript database

The importance of taxon sampling in phylogenetic accuracy is a topic of active debate. We investigated the role of taxon sampling in causing incongruent results between two recent phylogenomic studies of stinging wasps (Hymenoptera: Aculeata), a diverse lineage that includes ants, bees and the major...

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.

PubMed

Cui, Hong; Xu, Dongfang; Chong, Steven S; Ramirez, Martin; Rodenhausen, Thomas; Macklin, James A; Ludäscher, Bertram; Morris, Robert A; Soto, Eduardo M; Koch, Nicolás Mongiardino

2016-11-17

Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study.

Upper Permian vertebrates and their sedimentological context in the South Urals, Russia

NASA Astrophysics Data System (ADS)

Tverdokhlebov, Valentin P.; Tverdokhlebova, Galina I.; Minikh, Alla V.; Surkov, Mikhail V.; Benton, Michael J.

2005-02-01

Fossil fishes and tetrapods (amphibians and reptiles) have been discovered at 81 localities in the Upper Permian of the Southern Urals area of European Russia. The first sites were found in the 1940s, and subsequent surveys have revealed many more. Broad-scale stratigraphic schemes have been published, but full documentation of the rich tetrapod faunas has not been presented before. The area of richest deposits covers some 900,000 km 2 of territory between Samara on the River Volga in the NW, and Orenburg and Sakmara in the SW. A continental succession, some 3 km thick, of mudstones, siltstones, and sandstones, deposited on mudflats and in small rivers flowing off the Ural Mountain chain, span the last two stages of the Permian (Kazanian, Tatarian). The succession is divided into seven successive units of Kazanian (Kalinovskaya, Osinovskaya, and Belebey svitas, in succession) and Tatarian age, which is further subdivided into the early Tatatian Urzhumian Gorizont (Bolshekinelskaya and Amanakskaya svitas, in succession), and the late Tatarian Severodvinian (Vyazovskaya and Malokinelskaya svitas, of equivalent age) and Vyatkian gorizonts (Kulchumovskaya and Kutulukskaya svitas, of equivalent age). This succession documents major climatic changes, with increasing aridity through the Late Permian. The climate changes are manifested in changing sedimentation and the spread of dryland plants, and peak aridity was achieved right at the Permo-Triassic (PTr) boundary, coincident with global warming. Uplift of the Urals and extinction of land plants led to stripping of soils and massive run-off from the mountains; these phenomena have been identified at the PTr boundary elsewhere (South Africa, Australia) and this may be a key part of the end-Permian mass extinction. The succession of Late Permian fish and tetrapod faunas in Russia documents their richness and diversity before the mass extinction. The terminal Permian Kulchomovskaya and Kutulukskaya svitas have yielded respectively some 6 and 13 species of fishes (sharks, bony fishes, lungfishes) and 11 and 14 species of tetrapods (aquatic amphibians, herbivorous and carnivorous reptiles of all sizes up to the hippo-sized pareiasaurs and sabre-toothed gorgonopsians). Immediately following the end-Permian environmental catastrophe, earliest Triassic faunas consisted only of a few fish taxa and small, aquatic tetrapods, in low-diversity, low-abundance assemblages.

Main consistent patterns of Stromatoporoid Development in the Late Ordovician and Silurian in the North Urals Palaeobasin

NASA Astrophysics Data System (ADS)

Antropova, E.

2009-04-01

In the history of the Earth there have been no basins with similar characteristics. The North Urals palaeobasin had its own unique features. The dominant benthic organisms of basin ecosystem during the Ordovician and Silurian were stromatoporoids, corals, and brachiopods. This fauna is vitally important for the aims of stratigraphy so long as conodonts are extremely rare in sections of the Northern Urals area. The most complete ordering of stromatoporoid complexes has been established and made it possible to estimate rates and measures of extinction at a level of the province. It was also found out that stromatoporoids were organisms responsive to subtle changes of environment and that they accommodated differently to those changing conditions. The evolution of stromatoporoids was accompanied by phylogenetic reorganization and formation of endemic communities in the Late Ordovician and Early Silurian. In the Late Silurian taxonomical diversity of stromatoporoids was mainly controlled by migration processes and cosmopolites with wide palaeogeographic links prevailed in the palaeobasin. Therefore palaeobasin at that time was open to stromatoporoid fauna migration which is confirmed by the occurrence of genera and species that disperse in coeval deposits of many areas, for example, Baltic States, Sweden, Ukraine (Podolia), Western Siberia, Arctic islands of Russia, Mongolia, Canada (islands). The evolution of stromatoporoid communities in the Ordovician-Silurian was intermitted by biotic crises. The analysis of stromatoporoid development helps to define crucial points of ecosystem's reorganizations coinciding with critical geological and biotic events in the history of the North Urals palaeobasin existence, as well as global events during the Ordovician and Silurian (Hirnantian Event, Ireviken Event, Lau Event). The analysis of crises indicates local dependence of stromatoporoid biodiversity on depositional environments. Large local biocenos reorganizations and biotic crises were connected with regressive phases of basin development. Maximum diversity was associated with transgressions. Forming buildups in Middle Llandovery, Wenlock and Early Ludlow favoured development of stromatoporoid migration. Distinct changes of communities are confined to large taxa boundaries. A lot of factors influenced dispersal and development of stromatoporoids: the depth of palaeobasin, temperature and water salinity, shape of bottom, food chains and etc. In different times some factors dominated thus causing reorganization of communities, alteration of their taxonomical composition, expansion or extinction of communities. In its turn the above-listed factors were defined by geologic events.

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification

PubMed Central

2014-01-01

Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner. PMID:25077800

Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.

PubMed

Pongor, Lőrinc S; Vera, Roberto; Ligeti, Balázs

2014-01-01

Next generation sequencing (NGS) of metagenomic samples is becoming a standard approach to detect individual species or pathogenic strains of microorganisms. Computer programs used in the NGS community have to balance between speed and sensitivity and as a result, species or strain level identification is often inaccurate and low abundance pathogens can sometimes be missed. We have developed Taxoner, an open source, taxon assignment pipeline that includes a fast aligner (e.g. Bowtie2) and a comprehensive DNA sequence database. We tested the program on simulated datasets as well as experimental data from Illumina, IonTorrent, and Roche 454 sequencing platforms. We found that Taxoner performs as well as, and often better than BLAST, but requires two orders of magnitude less running time meaning that it can be run on desktop or laptop computers. Taxoner is slower than the approaches that use small marker databases but is more sensitive due the comprehensive reference database. In addition, it can be easily tuned to specific applications using small tailored databases. When applied to metagenomic datasets, Taxoner can provide a functional summary of the genes mapped and can provide strain level identification. Taxoner is written in C for Linux operating systems. The code and documentation are available for research applications at http://code.google.com/p/taxoner.

7 CFR 360.501 - Petitions to remove a taxon from the noxious weed lists.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 5 2013-01-01 2013-01-01 false Petitions to remove a taxon from the noxious weed...) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.501 Petitions to remove a taxon from the noxious weed lists. A person may petition the Administrator to remove a...

Variance Component Selection With Applications to Microbiome Taxonomic Data.

PubMed

Zhai, Jing; Kim, Juhyun; Knox, Kenneth S; Twigg, Homer L; Zhou, Hua; Zhou, Jin J

2018-01-01

High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Microbiome data are summarized as counts or composition of the bacterial taxa at different taxonomic levels. An important problem is to identify the bacterial taxa that are associated with a response. One method is to test the association of specific taxon with phenotypes in a linear mixed effect model, which incorporates phylogenetic information among bacterial communities. Another type of approaches consider all taxa in a joint model and achieves selection via penalization method, which ignores phylogenetic information. In this paper, we consider regression analysis by treating bacterial taxa at different level as multiple random effects. For each taxon, a kernel matrix is calculated based on distance measures in the phylogenetic tree and acts as one variance component in the joint model. Then taxonomic selection is achieved by the lasso (least absolute shrinkage and selection operator) penalty on variance components. Our method integrates biological information into the variable selection problem and greatly improves selection accuracies. Simulation studies demonstrate the superiority of our methods versus existing methods, for example, group-lasso. Finally, we apply our method to a longitudinal microbiome study of Human Immunodeficiency Virus (HIV) infected patients. We implement our method using the high performance computing language Julia. Software and detailed documentation are freely available at https://github.com/JingZhai63/VCselection.

Knowledge Management in Taxonomy and Biostratigraphy using TaxonConcept Software

NASA Astrophysics Data System (ADS)

Klump, J.; Huber, R.; Goetz, S.

2005-12-01

The use of fossils to constrain age models for geological samples is not as straightforward as it might seem. Even though index fossils have been defined as biostratigraphic time markers ambiguity arises from the synonymous use of taxonomic names. Progress in our understanding of the origin of certain species have sometimes lead to substantial changes in the taxonomic classification of these organisms. TaxonConcept was created as part of the Stratigraphy.net initiative as a tool to manage taxonomic information and complex knowledge networks to help resolve taxonomic ambiguities in biostratigraphy. Its workflow is based on the principles of open nomenclature. Open nomenclature allows researchers to comment on the identification of a specimen which cannot exactly be determined and is frequently used in synonymy lists. The use of such synonymy lists in TaxonConcept allows to work with taxonomic classifications that are uncertain, or where several versions exist. Every single taxonomic entity in TaxonConcept is recorded with its relevant citations in the literature. This allows to manage information on taxonomy. The members of working groups using TaxonConcept can record their opinion on the taxonomic classification of each taxon in the framework of open nomenclature and annotate it in free text. This managed and structured collection of taxonomic opinions is an example of knowledge management. Taxonomic opinions are otherwise dispersed throughout the literature, if recorded at all, and are only available to the specialist. Assembled as a collection, they represent our knowledge on the taxonomy of a certain group of organisms. In the terminology of computer science, the semantic relationships between taxonomic terms are an ontology. Open nomenclature offers a formal framework that lends itself very well to describe the nature of the relations between taxonomic terms. The use of such synonymy lists in a taxonomic information system allows interesting search options, ranging from tracking name changes to the investigation of complex taxonomic topologies. In addition to its synonymy and literature management, TaxonConcept allows to store many other information categories such as textual descriptions (e.g. diagnoses and comments), images, bioevents and specimen and collection data. Ecological information is scheduled for a later stage of the project. Already now TaxonConcept is linked to taxon names in paleoenvironmental data of the World Data Center for Marine Environmental Sciences (WDC-MARE), interfaces to other databases are planned. WDC-MARE stores environmental, marine and geological research data and frequently uses taxon names in its parameters. By linking TaxonConcept and WDC-MARE, synonymous names can be included in queries, e.g. when researching for stable isotope data measured on microfossils. TaxonConcept is not a project on authoritative taxonomic information, but is a tool for taxonomic projects to use to find a taxonomic consensus, e.g. to define a taxonomic framework for biostratigraphic studies. Both, the project specific hierarchical classification of selected taxa, as well as a project specific selection of any other information categories is supported by TaxonConcept. The results of such a taxonomic consensus can be used to create Fossilium Catalogus style summaries in various output formats which can later be used to create online or print publications.

"Social Anxiety Disorder Carved at its Joints": evidence for the taxonicity of social anxiety disorder.

PubMed

Weeks, Justin W; Carleton, R Nicholas; Asmundson, Gordon J G; McCabe, Randi E; Antony, Martin M

2010-10-01

Previous findings suggest that social anxiety disorder may be best characterized as having a dimensional latent structure (Kollman et al., 2006; Weeks et al., 2009). We attempted to extend previous taxometric investigations of social anxiety by examining the latent structure of social anxiety disorder symptoms in a large sample comprised of social anxiety disorder patients (i.e., putative taxon members) and community residents/undergraduate respondents (i.e., putative complement class members). MAXEIG and MAMBAC were performed with indicator sets drawn from a self-report measure of social anxiety symptoms, the Social Interaction Phobia Scale (Carleton et al., 2009). MAXEIG and MAMBAC analyses, as well as comparison analyses utilizing simulated taxonic and dimensional datasets, yielded converging evidence that social anxiety disorder has a taxonic latent structure. Moreover, 100% of the confirmed social anxiety disorder patients in our overall sample were correctly assigned to the identified taxon class, providing strong support for the external validity of the identified taxon; and k-means cluster analysis results corroborated our taxometric base-rate estimates. Implications regarding the conceptualization, diagnosis, and assessment of social anxiety disorder are discussed. Copyright 2010 Elsevier Ltd. All rights reserved.

Sub-fossil beetle assemblages associated with the "mammoth fauna" in the Late Pleistocene localities of the Ural Mountains and West Siberia.

PubMed

Zinovyev, Evgeniy

2011-01-01

The distribution of beetles at the end of the Middle Pleninglacial (=terminal Quaternary) was examined based on sub-fossil material from the Ural Mountains and Western Siberia, Russia. All relevant localities of fossil insects have similar radiocarbon dates, ranging between 33,000 and 22,000 C14 years ago. Being situated across the vast territory from the southern Ural Mountains in the South to the middle Yamal Peninsula in the North, they allow latitudinal changes in beetle assemblages of that time to be traced. These beetles lived simultaneously with mammals of the so-called "mammoth fauna" with mammoth, bison, and wooly rhinoceros, the often co-occurring mega-mammalian bones at some of the sites being evidence of this. The beetle assemblages found between 59° and 57°N appear to be the most interesting. Their bulk is referred to as a "mixed" type, one which includes a characteristic combination of arcto-boreal, boreal, steppe and polyzonal species showing no analogues among recent insect complexes. These peculiar faunas seem to have represented a particular zonal type, which disappeared since the end of the Last Glaciation to arrive here with the extinction of the mammoth biota. In contrast, on the sites lying north of 60°N, the beetle communities were similar to modern sub-arctic and arctic faunas, yet with the participation of some sub-boreal steppe components, such as Poecilus ravus Lutshnik and Carabus sibiricus Fischer-Waldheim. This information, when compared with our knowledge of synchronous insect faunas from other regions of northern Eurasia, suggests that the former distribution of beetles in this region could be accounted for both by palaeo-environmental conditions and the impact of grazing by large ruminant mammals across the so-called "mammoth savannas".

Russian Ural and Siberian Media Education Centers

ERIC Educational Resources Information Center

Fedorov, Alexander

2014-01-01

The comparative analysis of the models and functions of the media education centres showed that despite having some definite differences and peculiarities, they have the following common features: differentiated financing resources (public financing, grants, business organizations, etc.) and regional media information support; presence of famous…

[Origin of Lepidoptera fauna of the Southern Transural region].

PubMed

Utkin, N A

2000-01-01

The butterfly fauna of the Southern Transural region began mainly through the migration of insects from the Urals and Kazakhstan, since the end of the Cretaceous Period to the end of Paleogen, the Transural region was covered by an epiplatform sea. As this sea was retreating, the first regions of dry land appeared, which had boundaries with Kazakhstan and the Urals. They were the first to be populated by Lepidoptera. During the Pleocene and then after the Pleistocene cooling events, insects settled generally along the valley of the Tobol River and the Turgai depression, because these territories belong to intrazonal elements. At the present time, the greatest species diversity among insects in the southern Transural area is observed specifically in the Turgai depression and in areas directly adjacent to it. This territory is mainly occupied by populations unique to the Transural regions and belonging to the following species: Mantis religiosa (praying mantis), Saga pedo, Parnassius apollo (apollo), Neolycaena rhymnus, Hyponephele lupina (oriental meadow brown), Chazara persephone (dark rockbrown), Epicallia villica (cream-spot tiger), etc.

Radiological medical data preservation in the Southern Urals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melamed, E.

2000-07-01

Information is being microfilmed and scanned in the Southern Urals to ensure the archival preservation of the unique, important and irreplaceable records documenting chromic low-level radiation exposure to workers and neighboring populations of the Mayak Production Association (MAYAK), as well as health effects. The records include dosimetric and epidemiologic information maintained on workers and neighboring populations located at facilities in Ozyorsk and Chelyabinsk. Microfilming is being done in Ozyorsk, and on a more limited basis in Chelyabinsk, where a scanning project has also recently been initiated. Over 1,800 rolls of film have been produced as of the fall of 1999.more » This article describes the background and results of this data preservation effort and includes brief summary tables describing the types of records being preserved. Researchers interested in access to these records should contact Paul Seligman, Deputy Assistant Secretary for the Office of Health Studies at the Department of Energy (DOE) for more information.« less

[MOLECULAR CHARACTERISTICS OF THE MULTIDRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS STRAINS IN THE NORTHWEST RUSSIA].

PubMed

Vyazovaya, A A; Mokrousov, I V; Zhuravlev, V Yu; Solovieva, N S; Otten, T F; Manicheva, O A; Vishnevsky, B I; Narvskaya, O V

2016-01-01

The goal of this work was to study the genotypic characteristics of the multidrug-resistant (MDR, i.e., resistant to at least rifampicine and isoniazid) Mycobacterium tuberculosis strains isolated in 2011-2012 from tuberculosis (TB) patients in the Northwest Russia. Spoligotyping of 195 M. tuberculosis isolates identified 14 different spoligotypes and assigned isolates to the genetic families Beijing (n = 162, 83%), LAM (n = 15), H3/URAL (n = 14), as well as T, Haarlem and X. Spoligotypes SIT1 (Beijing), SIT42 (LAM) and SIT262 (H3/URAL) were the most prevalent. Irrespective to the genotype, all the isolates were resistant to streptomycin. The multidrug resistance was accompanied by the resistance to ethionamide (56%), amikacin (31%), kanamycin (40%), and capreomycin (33%). The ethambutol resistance was found in 71% (n = 115) and 42% (n = 14) of the Beijing and non-Beijing strains, respectively (p < 0.05). In conclusion, the multidrug resistant M. tuberculosis population circulating in the Northwest Russia continues to be dominated by the Beijing family strains.

An unclassified Eubacterium taxon in acute dento-alveolar abscess.

PubMed

Wade, W G; Lewis, M A; Cheeseman, S L; Absi, E G; Bishop, P A

1994-02-01

The microflora of pus samples aspirated from 50 acute dento-alveolar abscesses was examined. A total of 143 bacterial strains was isolated, consisting predominantly of Prevotella spp., alpha-haemolytic Streptococcus spp., Peptostreptococcus spp. and Eubacterium spp. An unclassified asaccharolytic Eubacterium taxon was encountered in 17 (34%) of the abscesses. This taxon was found to have a positive association with Fusobacterium spp. and a negative association with alpha-haemolytic Streptococcus spp.

Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy

NASA Astrophysics Data System (ADS)

Sackett, O.; Armand, L.; Beardall, J.; Hill, R.; Doblin, M.; Connelly, C.; Howes, J.; Stuart, B.; Ralph, P.; Heraud, P.

2014-05-01

Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value, furthermore data on taxon-specific responses is almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate and carbohydrates. In contrast to some previous studies, silicate levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community measurements, highlighting the need for further research into taxon-specific phenotypic responses of phytoplankton to environmental change.

Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy

NASA Astrophysics Data System (ADS)

Sackett, O.; Armand, L.; Beardall, J.; Hill, R.; Doblin, M.; Connelly, C.; Howes, J.; Stuart, B.; Ralph, P.; Heraud, P.

2014-10-01

Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value - furthermore, data on taxon-specific responses are almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate/silicic acid and carbohydrates. In contrast to some previous studies, silicate/silicic acid levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community measurements, highlighting the need for further research into taxon-specific phenotypic responses of phytoplankton to environmental change.

Neural systems language: a formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity.

PubMed

Brown, Ramsay A; Swanson, Larry W

2013-09-01

Systematic description and the unambiguous communication of findings and models remain among the unresolved fundamental challenges in systems neuroscience. No common descriptive frameworks exist to describe systematically the connective architecture of the nervous system, even at the grossest level of observation. Furthermore, the accelerating volume of novel data generated on neural connectivity outpaces the rate at which this data is curated into neuroinformatics databases to synthesize digitally systems-level insights from disjointed reports and observations. To help address these challenges, we propose the Neural Systems Language (NSyL). NSyL is a modeling language to be used by investigators to encode and communicate systematically reports of neural connectivity from neuroanatomy and brain imaging. NSyL engenders systematic description and communication of connectivity irrespective of the animal taxon described, experimental or observational technique implemented, or nomenclature referenced. As a language, NSyL is internally consistent, concise, and comprehensible to both humans and computers. NSyL is a promising development for systematizing the representation of neural architecture, effectively managing the increasing volume of data on neural connectivity and streamlining systems neuroscience research. Here we present similar precedent systems, how NSyL extends existing frameworks, and the reasoning behind NSyL's development. We explore NSyL's potential for balancing robustness and consistency in representation by encoding previously reported assertions of connectivity from the literature as examples. Finally, we propose and discuss the implications of a framework for how NSyL will be digitally implemented in the future to streamline curation of experimental results and bridge the gaps among anatomists, imagers, and neuroinformatics databases. Copyright © 2013 Wiley Periodicals, Inc.

Fatty acid amides from freshwater green alga Rhizoclonium hieroglyphicum.

PubMed

Dembitsky, V M; Shkrob, I; Rozentsvet, O A

2000-08-01

Freshwater green algae Rhizoclonium hieroglyphicum growing in the Ural Mountains were examined for their fatty acid amides using capillary gas chromatography-mass spectrometry (GC-MS). Eight fatty acid amides were identified by GC-MS. (Z)-9-octadecenamide was found to be the major component (2.26%).

Legislative Environmental Impact Statement. M-X Closely Spaced Basing

DTIC Science & Technology

1982-10-18

Improvement Area, Plainview, Texas, Hale County, Austin: Espey, Houston, and Associates. Thordarson , W., R. A. Young, and I. 1. Winograd, 1967...34 Cu:ural Resources Report No. 21. USDA Forest Service, Southwestern3 IRegion, Albuquerque. Winograd, I. 1., and W. Thordarson , 1975. "Hydrologic ana Hydroci

The influence of taxon sampling on Bayesian divergence time inference under scenarios of rate heterogeneity among lineages.

PubMed

Soares, André E R; Schrago, Carlos G

2015-01-07

Although taxon sampling is commonly considered an important issue in phylogenetic inference, it is rarely considered in the Bayesian estimation of divergence times. In fact, the studies conducted to date have presented ambiguous results, and the relevance of taxon sampling for molecular dating remains unclear. In this study, we developed a series of simulations that, after six hundred Bayesian molecular dating analyses, allowed us to evaluate the impact of taxon sampling on chronological estimates under three scenarios of among-lineage rate heterogeneity. The first scenario allowed us to examine the influence of the number of terminals on the age estimates based on a strict molecular clock. The second scenario imposed an extreme example of lineage specific rate variation, and the third scenario permitted extensive rate variation distributed along the branches. We also analyzed empirical data on selected mitochondrial genomes of mammals. Our results showed that in the strict molecular-clock scenario (Case I), taxon sampling had a minor impact on the accuracy of the time estimates, although the precision of the estimates was greater with an increased number of terminals. The effect was similar in the scenario (Case III) based on rate variation distributed among the branches. Only under intensive rate variation among lineages (Case II) taxon sampling did result in biased estimates. The results of an empirical analysis corroborated the simulation findings. We demonstrate that taxonomic sampling affected divergence time inference but that its impact was significant if the rates deviated from those derived for the strict molecular clock. Increased taxon sampling improved the precision and accuracy of the divergence time estimates, but the impact on precision is more relevant. On average, biased estimates were obtained only if lineage rate variation was pronounced. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships.

PubMed

Pick, K S; Philippe, H; Schreiber, F; Erpenbeck, D; Jackson, D J; Wrede, P; Wiens, M; Alié, A; Morgenstern, B; Manuel, M; Wörheide, G

2010-09-01

Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.

TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies.

PubMed

Collin, Rachel; Fredericq, Suzanne; Freshwater, D Wilson; Gilbert, Edward; Madrid, Maycol; Maslakova, Svetlana; Miglietta, Maria Pia; Rocha, Rosana M; Rodríguez, Estefanía; Thacker, Robert W

2016-01-01

Correctly identifying organisms is key to most biological research, and is especially critical in areas of biodiversity and conservation. Yet it remains one of the greatest challenges when studying all but the few well-established model systems. The challenge is in part due to the fact that most species have yet to be described, vanishing taxonomic expertise and the relative inaccessibility of taxonomic information. Furthermore, identification keys and other taxonomic resources are based on complex, taxon-specific vocabularies used to describe important morphological characters. Using these resources is made difficult by the fact that taxonomic documentation of the world's biodiversity is an international endeavour, and keys and field guides are not always available in the practitioner's native language. To address this challenge, we have developed a publicly available on-line illustrated multilingual glossary and translation tool for technical taxonomic terms using the Symbiota Software Project biodiversity platform. Illustrations, photographs and translations have been sourced from the global community of taxonomists working with marine invertebrates and seaweeds. These can be used as single-language illustrated glossaries or to make customized translation tables. The glossary has been launched with terms and illustrations of seaweeds, tunicates, sponges, hydrozoans, sea anemones, and nemerteans, and already includes translations into seven languages for some groups. Additional translations and development of terms for more taxa are underway, but the ultimate utility of this tool depends on active participation of the international taxonomic community.

Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

PubMed Central

2008-01-01

Background Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs). Results Given the Marquesan data, we find strong evidence of simultaneous colonization across all seven cowrie gastropod endemics co-distributed in the Marquesas. In contrast, the lower sample sizes in the Hawaiian data lead to greater uncertainty associated with the Hawaiian estimates. Although, the hyper-parameter estimates point to soft vicariance in a subset of the 11 Hawaiian taxon-pairs, the hyper-prior and hyper-posterior are too similar to make a definitive conclusion. Both results are not inconsistent with what is known about the geologic history of the archipelagos. Simulations verify that our method can successfully distinguish these two histories across a wide range of conditions given sufficient sampling. Conclusion Although soft vicariance and colonization are likely to produce similar genetic patterns when a single taxon-pair is used, our hierarchical Bayesian model can potentially detect if either history is a dominant process across co-distributed taxon-pairs. As comparative phylogeographic datasets grow to include > 100 co-distributed taxon-pairs, the HABC approach will be well suited to dissect temporal patterns in community assembly and evolution, thereby providing a bridge linking comparative phylogeography with community ecology. PMID:19038027

Cross-taxon congruence and environmental conditions.

PubMed

Toranza, Carolina; Arim, Matías

2010-07-16

Diversity patterns of different taxa typically covary in space, a phenomenon called cross-taxon congruence. This pattern has been explained by the effect of one taxon diversity on taxon diversity, shared biogeographic histories of different taxa, and/or common responses to environmental conditions. A meta-analysis of the association between environment and diversity patterns found that in 83 out of 85 studies, more than 60% of the spatial variability in species richness was related to variables representing energy, water or their interaction. The role of the environment determining taxa diversity patterns leads us to hypothesize that this would explain the observed cross-taxon congruence. However, recent analyses reported the persistence of cross-taxon congruence when environmental effect was statistically removed. Here we evaluate this hypothesis, analyzing the cross-taxon congruence between birds and mammals in the Brazilian Cerrado, and assess the environmental role on the spatial covariation in diversity patterns. We found a positive association between avian and mammal richness and a positive latitudinal trend for both groups in the Brazilian Cerrado. Regression analyses indicated an effect of latitude, PET, and mean temperature over both biological groups. In addition, we show that NDVI was only associated with avian diversity; while the annual relative humidity, was only correlated with mammal diversity. We determined the environmental effects on diversity in a path analysis that accounted for 73% and 76% of the spatial variation in avian and mammal richness. However, an association between avian and mammal diversity remains significant. Indeed, the importance of this link between bird and mammal diversity was also supported by a significant association between birds and mammal spatial autoregressive model residuals. Our study corroborates the main role of environmental conditions on diversity patterns, but suggests that other important mechanisms, which have not been properly evaluated, are involved in the observed cross-taxon congruence. The approaches introduced here indicate that the prevalence of a significant association among taxa, after considering the environmental determinant, could indicate both the need to incorporate additional processes (e.g. biogeographic and evolutionary history or trophic interactions) and/or the existence of a shared trend in detection biases among taxa and regions.

The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries.

PubMed

Ribeiro, Apoena Aguiar; Azcarate-Peril, Maria Andrea; Cadenas, Maria Belen; Butz, Natasha; Paster, Bruce J; Chen, Tsute; Bair, Eric; Arnold, Roland R

2017-01-01

Dental caries is the most prevalent disease in humans globally. Efforts to control it have been invigorated by an increasing knowledge of the oral microbiome composition. This study aimed to evaluate the bacterial diversity in occlusal biofilms and its relationship with clinical surface diagnosis and dietary habits. Anamneses were recorded from thirteen 12-year-old children. Biofilm samples collected from occlusal surfaces of 46 permanent second molars were analyzed by 16S rRNA amplicon sequencing combined with the BLASTN-based search algorithm for species identification. The overall mean decayed, missing and filled surfaces modified index [DMFSm Index, including active white spot lesions (AWSL)] value was 8.77±7.47. Biofilm communities were highly polymicrobial collectively, representing 10 bacterial phyla, 25 classes, 29 orders, 58 families, 107 genera, 723 species. Streptococcus sp_Oral_Taxon_065, Corynebacterium matruchotii, Actinomyces viscosus, Actinomyces sp_Oral_Taxon_175, Actinomyces sp_Oral_Taxon_178, Actinomyces sp_Oral_Taxon_877, Prevotella nigrescens, Dialister micraerophilus, Eubacterium_XI G 1 infirmum were more abundant among surfaces with AWSL, and Streptococcus gordonii, Streptococcus sp._Oral_Taxon_058, Enterobacter sp._str._638 Streptococcus australis, Yersinia mollaretii, Enterobacter cloacae, Streptococcus sp._Oral_Taxon_71, Streptococcus sp._Oral_Taxon_F11, Centipeda sp._Oral_Taxon_D18 were more abundant among sound surfaces. Streptococcus mutans was detected on all surfaces in all patients, while Streptococcus sobrinus was detected only in three patients (mean relative abundances 7.1% and 0.6%, respectively). Neither species differentiated healthy from diseased sites. Diets of nine of the subjects were scored as high in fermentable carbohydrates (≧2X/day between meals). A direct association between relative abundances of bacteria and carbohydrate consumption was observed among 18 species. High consumption of fermentable carbohydrates and sound surfaces were associated with a reduction in bacterial diversity. PCoA plots displayed differences in bacterial community profiles between sound and diseased surfaces. Our study showed that, in addition to mutans streptococci, other species may be associated with the initiation of dental caries on occlusal surfaces, and that biofilm diversity of tooth surfaces is influenced by carbohydrate consumption and a surface's health status.

The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries

PubMed Central

Azcarate-Peril, Maria Andrea; Cadenas, Maria Belen; Butz, Natasha; Paster, Bruce J.; Chen, Tsute; Bair, Eric

2017-01-01

Dental caries is the most prevalent disease in humans globally. Efforts to control it have been invigorated by an increasing knowledge of the oral microbiome composition. This study aimed to evaluate the bacterial diversity in occlusal biofilms and its relationship with clinical surface diagnosis and dietary habits. Anamneses were recorded from thirteen 12-year-old children. Biofilm samples collected from occlusal surfaces of 46 permanent second molars were analyzed by 16S rRNA amplicon sequencing combined with the BLASTN-based search algorithm for species identification. The overall mean decayed, missing and filled surfaces modified index [DMFSm Index, including active white spot lesions (AWSL)] value was 8.77±7.47. Biofilm communities were highly polymicrobial collectively, representing 10 bacterial phyla, 25 classes, 29 orders, 58 families, 107 genera, 723 species. Streptococcus sp_Oral_Taxon_065, Corynebacterium matruchotii, Actinomyces viscosus, Actinomyces sp_Oral_Taxon_175, Actinomyces sp_Oral_Taxon_178, Actinomyces sp_Oral_Taxon_877, Prevotella nigrescens, Dialister micraerophilus, Eubacterium_XI G 1 infirmum were more abundant among surfaces with AWSL, and Streptococcus gordonii, Streptococcus sp._Oral_Taxon_058, Enterobacter sp._str._638 Streptococcus australis, Yersinia mollaretii, Enterobacter cloacae, Streptococcus sp._Oral_Taxon_71, Streptococcus sp._Oral_Taxon_F11, Centipeda sp._Oral_Taxon_D18 were more abundant among sound surfaces. Streptococcus mutans was detected on all surfaces in all patients, while Streptococcus sobrinus was detected only in three patients (mean relative abundances 7.1% and 0.6%, respectively). Neither species differentiated healthy from diseased sites. Diets of nine of the subjects were scored as high in fermentable carbohydrates (≧2X/day between meals). A direct association between relative abundances of bacteria and carbohydrate consumption was observed among 18 species. High consumption of fermentable carbohydrates and sound surfaces were associated with a reduction in bacterial diversity. PCoA plots displayed differences in bacterial community profiles between sound and diseased surfaces. Our study showed that, in addition to mutans streptococci, other species may be associated with the initiation of dental caries on occlusal surfaces, and that biofilm diversity of tooth surfaces is influenced by carbohydrate consumption and a surface’s health status. PMID:28678838

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling.

PubMed

Reddy, Sushma; Kimball, Rebecca T; Pandey, Akanksha; Hosner, Peter A; Braun, Michael J; Hackett, Shannon J; Han, Kin-Lan; Harshman, John; Huddleston, Christopher J; Kingston, Sarah; Marks, Ben D; Miglia, Kathleen J; Moore, William S; Sheldon, Frederick H; Witt, Christopher C; Yuri, Tamaki; Braun, Edward L

2017-09-01

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The Aggregate Behavior of Branch Points - A Proposal for an Atmospheric Turbulence Layer Sensor: Postprint

DTIC Science & Technology

2010-07-01

urbulcncc altitude. A ,~ l,;on ll;ural on ’I urbu enee Condilion:. Num""r Trombone t’W t’o"llIon I’W ~ Iep l’ropagM Ion ’nUb. "’-elncUy , Ensemble of Len

Requirements Engineering and Analysis Workshop Proceedings Held in Pittsburgh, Pennsylvania on 12-14 March 1991

DTIC Science & Technology

1991-12-01

urally. 6.5 Summary of Current or Potential Approaches Many approaches to context analysis were discussed by the group, including: * Causal Trees * SWOT ... Apple Computer, 1988 1 Aseltine, J., Beam, W.R., Palmer, J.D., Sage, A.P., 1989, Introduction To Computer Systems: Analysis, Design and Application

The first data on breithauptite in chromitite from the northern part of the Voykar-Synya ultramafic massif (Polar Urals)

NASA Astrophysics Data System (ADS)

Shaibekov, R. I.; Gaikovich, M. M.; Isaenko, S. I.; Shevchuk, S. S.

2017-11-01

This work presents the results of studying the mineral composition of chromite ores of the Khoila area. For the first time, nickel antimonide (breithauptite), including an Au-bearing type (with intergrowths and microinclusions of auricuprides) was found in the paragenesis with chromespinelides.

The unique peptidome: Taxon-specific tryptic peptides as biomarkers for targeted metaproteomics.

PubMed

Mesuere, Bart; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-09-01

The Unique Peptide Finder (http://unipept.ugent.be/peptidefinder) is an interactive web application to quickly hunt for tryptic peptides that are unique to a particular species, genus, or any other taxon. Biodiversity within the target taxon is represented by a set of proteomes selected from a monthly updated list of complete and nonredundant UniProt proteomes, supplemented with proprietary proteomes loaded into persistent local browser storage. The software computes and visualizes pan and core peptidomes as unions and intersections of tryptic peptides occurring in the selected proteomes. In addition, it also computes and displays unique peptidomes as the set of all tryptic peptides that occur in all selected proteomes but not in any UniProt record not assigned to the target taxon. As a result, the unique peptides can serve as robust biomarkers for the target taxon, for example, in targeted metaproteomics studies. Computations are extremely fast since they are underpinned by the Unipept database, the lowest common ancestor algorithm implemented in Unipept and modern web technologies that facilitate in-browser data storage and parallel processing. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony.

PubMed

Debry, Ronald W

2005-06-01

The effect of taxonomic sampling on phylogenetic accuracy under parsimony is examined by simulating nucleotide sequence evolution. Random error is minimized by using very large numbers of simulated characters. This allows estimation of the consistency behavior of parsimony, even for trees with up to 100 taxa. Data were simulated on 8 distinct 100-taxon model trees and analyzed as stratified subsets containing either 25 or 50 taxa, in addition to the full 100-taxon data set. Overall accuracy decreased in a majority of cases when taxa were added. However, the magnitude of change in the cases in which accuracy increased was larger than the magnitude of change in the cases in which accuracy decreased, so, on average, overall accuracy increased as more taxa were included. A stratified sampling scheme was used to assess accuracy for an initial subsample of 25 taxa. The 25-taxon analyses were compared to 50- and 100-taxon analyses that were pruned to include only the original 25 taxa. On average, accuracy for the 25 taxa was improved by taxon addition, but there was considerable variation in the degree of improvement among the model trees and across different rates of substitution.

Rhenium in ores of the Mikheevskoe porphyry Cu-Mo deposit, South Urals

NASA Astrophysics Data System (ADS)

Plotinskaya, O. Yu.; Grabezhev, A. I.; Seltmann, R.

2015-03-01

The distribution of Re in ores of the Mikheevskoe Mo-Cu deposit in the South Urals is studied. It is established that the grade of Re in the ores usually does not exceed 0.5 g/t. A positive correlation between concentrations of Re and Mo (correlation coefficient 0.94), and Re and Cu (correlation coefficient 0.52) is found. EMPA of individual flakes of molybdenite showed that a Re content higher than the detection limit has been measured in most flakes studied, as a rule as high as 0.4-0.5 wt %, but occasionally reaching 1.34 wt %. Re within flakes of molybdenite is irregularly distributed. Patchy, linear, and concentric-zoned patterns of zones with elevated Re content (usually 0.5-1 wt % Re, sometimes higher) are found against the lower content (up to 0.2 wt % Re) that is regularly distributed within the flake. Later hydrothermal processes and mechanical deformation of flakes result in epigenetic Re redistribution in molybdenite that leads to homogenization of molybdenite composition and smoothing of primary pattern, or removal of Re from molybdenite.

[The Russian gene pool: gene geography of Alu-insertions (ACE, APOA1, B65, PV92 TPA25)].

PubMed

Solov'eva, D S; Balanovskaia, E V; Kuznetsova, M A; Vasinskaia, O A; Frolova, S A; Pocheshkhova, E A; Evseeva, I V; Boldyreva, M N; Balanovskiĭ, O P

2010-01-01

The analysis of five Alu insertion loci (ACE, AP4OA1, B65, PV92, TPA25) has been carried out for the first time in 10 Russian populations (1088 individuals), covered all parts of historical area of the Russian ethnos. Depending on locus, Russian populations exhibit similarity with their western (European populations) or with the eastern (populations of the Ural region) neighbors. Considering frequencies of the studied Alu-insertions, Russian gene pool exhibits low variation: average difference between populations is d = 0.007, whereas on classical markers, mtDNA and Y chromosome heterogeneity of Russian gene pool is essentially higher (0.013, 0.033 and 0.142 respectively). Therefore, this set of five Alu insertions has lower variability on the intra-ethnic level. However in inter-ethnic comparisons the clear pattern was obtained: 13 Eastern European ethnic groups formed three clusters, according with their historical and geographical position--East Slavic, Caucasian and South Ural clusters. The obtained data confirms efficiency of using Alu insertions for studying genetic differentiation and history of a gene pool of the Eastern European populations.

Gold in Accessory Zircon (the Kozhim Massif, Subpolar Urals)

NASA Astrophysics Data System (ADS)

Denisova, Yuliya; Pystin, Aleksandr

2017-12-01

The crystals of zircon due to their resistance to external impact of various processes can reveal information about the environment of their formation and the inclusions observed of them. Zircon contains different mineral inclusions: biotite, plagioclase, quartz, apatite, etc. However, there is no information about gold inclusions in the zircons from granites of the Sudpolar Urals. The study results of the inclusions of gold in accessory zircon of the Kozhim granitic massif are presented in this paper. The studied mineral is a dark-brown translucent short-prismatic crystal containing the inclusion of gold and the allocations of quartz. According to studies, the inclusion of gold formed during the growth of zircon and it is the gold covered with a thin film of oxide gold. It was confirmed that the crystallization of the studied zircon occurred at a temperature of 800°C and above on the stage of formation of granites of Kozhim massif. The assumption is made about the additional temperature in the course of which was caused by decreasing of temperature up to 700° C and below during postmagmatic stage.

Chemical composition and osmium-isotope systematics of primary and secondary PGM assemblages from high-Mg chromitite of the Nurali lherzolite massif, the South Urals, Russia

NASA Astrophysics Data System (ADS)

Malitch, K. N.; Anikina, E. V.; Badanina, I. Yu.; Belousova, E. A.; Pushkarev, E. V.; Khiller, V. V.

2016-01-01

The isotopic and geochemical characteristics of PGE mineralization in high-Mg chromitite from the banded dunite-wehrlite-clinopyroxenite complex of the Nurali lherzolite massif, the South Urals, Russia is characterized for the first time. Electron microprobe analysis and LA MC-ICP-MS mass spectrometry are used for studying Cr-spinel and platinum-group minerals (PGM). Two processes synchronously develop in high-Mg chromitite subject to metamorphism: (1) the replacement of Mg-Al-rich Cr-spinel, orthopyroxene, and diopside by chromite, Cr-amphibole, chlorite, and garnet; (2) the formation of a secondary mineral assemblage consisting of finely dispersed ruthenium or Ru-hexaferrum aggregate and silicate-oxide or silicate matter on the location of primary Ru-Os-sulfides of the laurite-erlichmanite solid solution series. Similar variations of Os-isotopic composition in both primary and secondary PGM assemblages are evidence for the high stability of the Os isotope system in PGM and for the possibility of using model 187Os/188Os ages in geodynamic reconstructions.

Comparative analysis of the roles of Ixodes persulcatus and I. trianguliceps ticks in natural foci of ixodid tick-borne borrelioses in the Middle Urals, Russia.

PubMed

Korenberg, Edward I; Kovalevskii, Yurii V; Gorelova, Natalya B; Nefedova, Valentina V

2015-04-01

Long-term studies on natural foci of ixodid tick-borne borrelioses (ITBB) have been performed in Chusovskoi district of Perm region, the Middle Urals, where the vectors of these infections are represented by two ixodid tick species: the taiga tick Ixodes persulcatus and many times less abundant vole tick I. trianguliceps. Over 10 years, more than 6000 half-engorged ticks were collected from small forest mammals using the standard procedure, and 1027 I. persulcatus and 1142 I. trianguliceps ticks, individually or in pools, were used to inoculate BSK-2 medium. As a result, 199 Borrelia isolates were obtained. Among them, 177 isolates were identified, and the rrf(5S)-rrl(23S) intergenic spacer sequence was determined in 57 isolates. The prevalence of Borrelia infection in I. persulcatus larvae and nymphs averaged 31.0 and 53.3%, while that in I. trianguliceps larvae, nymphs, and adult ticks was five to ten times lower: 2.6, 10.2, and 8.1%, respectively. Each of the two tick species was found to carry both ITBB agents circulating in the Middle Ural foci (Borrelia garinii and B. afzelii), but the set of genogroups and genovariants of these spirochetes in I. trianguliceps proved to be far less diverse. According to the available data, this tick, compared to I. persulcatus, is generally less susceptible to Borrelia infection (especially by B. afzelii). Taking into account of its relatively low abundance, it appears that I. trianguliceps cannot seriously influence the course of epizootic process in ITBB foci of the study region, whereas highly abundant I. persulcatus with the high level of Borrelia infection is obviously a key component of these parasitic systems. A similar situation may well be typical for the entire geographic range shared by the two tick species. Copyright © 2015. Published by Elsevier GmbH.

Seismic wide-angle constraints on the crust of the southern Urals

NASA Astrophysics Data System (ADS)

Carbonell, R.; Gallart, J.; PéRez-Estaún, A.; Diaz, J.; Kashubin, S.; Mechie, J.; Wenzel, F.; Knapp, J.

2000-06-01

A wide-angle seismic reflection/refraction data set was acquired during spring 1995 across the southern Urals to characterize the lithosphere beneath this Paleozoic orogen. The wide-angle reflectivity features a strong frequency dependence. While the lower crustal reflectivity is in the range of 6-15 Hz, the PmP is characterized by frequencies below 6 Hz. After detailed frequency filtering, the seismic phases constrain a new average P wave velocity crustal model that consists of an upper layer of 5.0-6.0 km/s, which correlates with the surface geology; 5-7 km depths at which the velocities increase to 6.2-6.3 km/s; 10-30 km depths at which, on average, the crust is characterized by velocities of 6.6 km/s; and finally, the lower crust, from 30-35 km down to the Moho, which has velocities ranging from 6.8 to 7.4 km/s. Two different S wave velocity models, one for the N-S and one for the E-W, were derived from the analysis of the horizontal component recordings. Crustal sections of Poisson's ratio and anisotropy were calculated from the velocity models. The Poisson's ratio increases in the lower crust at both sides of the root zone. A localized 2-3% anisotropy zone is imaged within the lower crust beneath the terranes east of the root. This feature is supported by time differences in the SmS phase and by the particle motion diagrams, which reveal two polarized directions of motion. Velocities are higher in the central part of the orogen than for the Siberian and eastern plates. These seismic recordings support a 50-56 km crustal thickness beneath the central part of the orogen in contrast to Moho depths of ≈ 45 km documented at the edges of the transect. The lateral variation of the PmP phase in frequency content and in waveform can be taken as evidence of different genetic origins of the Moho in the southern Urals.

Phytophthora species in forest streams in Oregon and Alaska.

PubMed

Reeser, Paul W; Sutton, Wendy; Hansen, Everett M; Remigi, Philippe; Adams, Gerry C

2011-01-01

Eighteen Phytophthora species and one species of Halophytophthora were identified in 113 forest streams in Alaska, western Oregon and southwestern Oregon that were sampled by baiting or filtration of stream water with isolation on selective media. Species were identified by morphology and DNA characterization with single strand conformational polymorphism, COX spacer sequence and ITS sequence. ITS Clade 6 species were most abundant overall, but only four species, P. gonapodyides (37% of all isolates), P. taxon Salixsoil, P. taxon Oaksoil and P. pseudosyringae, were found in all three regions. The species assemblages were similar in the two Oregon regions, but P. taxon Pgchlamydo was absent in Alaska and one new species present in Alaska was absent in Oregon streams. The number of Phytophthora propagules in Oregon streams varied by season and in SW Oregon, where sampling continued year round, P. taxon Salixsoil, P. nemorosa and P. siskiyouensis were recovered only in some seasons.

Resource-aware taxon selection for maximizing phylogenetic diversity.

PubMed

Pardi, Fabio; Goldman, Nick

2007-06-01

Phylogenetic diversity (PD) is a useful metric for selecting taxa in a range of biological applications, for example, bioconservation and genomics, where the selection is usually constrained by the limited availability of resources. We formalize taxon selection as a conceptually simple optimization problem, aiming to maximize PD subject to resource constraints. This allows us to take into account the different amounts of resources required by the different taxa. Although this is a computationally difficult problem, we present a dynamic programming algorithm that solves it in pseudo-polynomial time. Our algorithm can also solve many instances of the Noah's Ark Problem, a more realistic formulation of taxon selection for biodiversity conservation that allows for taxon-specific extinction risks. These instances extend the set of problems for which solutions are available beyond previously known greedy-tractable cases. Finally, we discuss the relevance of our results to real-life scenarios.

DSM-IV antisocial personality disorder and conduct disorder: evidence for taxonic structures among individuals with and without substance use disorders in the general population.

PubMed

Kerridge, Bradley T; Saha, Tulshi D; Hasin, Deborah S

2014-05-01

The categorical-dimensional status of DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition) conduct disorder (CD) and antisocial personality disorder (ASPD) is a source of controversy. This study examined whether the underlying structure of DSM-IV CD and ASPD was dimensional or categorical (taxonic) among individuals with and without substance use disorders. Using a national large representative survey of U.S. adults (n = 43,093), taxometric analyses of DSM-IV CD and ASPD diagnostic criteria were conducted on the total sample and among those with and without substance use disorders. Results of three taxometric procedures were consistent in showing that the structures underlying DSM-IV CD and ASPD were clearly taxonic in the total sample and among individuals with and without substance use disorders. Comparison curve fit indices exceeded 0.57 for each model. Taxonic findings of the present study were in contrast to the dimensional results of prior taxometric research among incarcerated samples with substantial comorbidity of antisocial syndromes and substance use disorders. Results supported the categorical representation and diagnostic thresholds of ASPD and CD as defined in DSM-IV and DSM-5. That the structure of ASPD and CD may be taxonic suggests that further research on these disorders use group comparative designs in which samples with and without these disorders are compared in terms of sociodemographic and clinical correlates, comorbidity, and treatment utilization. The taxonic structure of ASPD and CD may contribute to future research on causal processes through which these antisocial syndromes develop.

76 FR 31171 - Importation of Plants for Planting; Establishing a Category of Plants for Planting Not Authorized...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-27

...We are amending the regulations to establish a new category of regulated articles in the regulations governing the importation of nursery stock, also known as plants for planting. This category will list taxa of plants for planting whose importation is not authorized pending pest risk analysis. If scientific evidence indicates that a taxon of plants for planting is a quarantine pest or a host of a quarantine pest, we will publish a notice that will announce our determination that the taxon is a quarantine pest or a host of a quarantine pest, cite the scientific evidence we considered in making this determination, and give the public an opportunity to comment on our determination. If we receive no comments that change our determination, the taxon will subsequently be added to the new category. We will allow any person to petition for a pest risk analysis to be conducted to consider whether to remove a taxon that has been added to the new category. After the pest risk analysis is completed, we will remove the taxon from the category and allow its importation subject to general requirements, allow its importation subject to specific restrictions, or prohibit its importation. We will consider applications for permits to import small quantities of germplasm from taxa whose importation is not authorized pending pest risk analysis, for experimental or scientific purposes under controlled conditions. This new category will allow us to take prompt action on evidence that the importation of a taxon of plants for planting poses a risk while continuing to allow for public participation in the process.

al-Biruni, Abu Raihan (973-1048)

NASA Astrophysics Data System (ADS)

Murdin, P.

2000-11-01

Born in Kheva near Ural, present-day Uzbekhistan, al-Biruni was a polymath and traveler (to India), making contributions in mathematics, geography and geology, natural history, calendars and astronomy. His book Qanun-i Masoodi, which he dedicated to his patron Sultan Masood, discusses astronomy, trigonometry, solar, lunar and planetary motions, including the question whether the Earth rotates or ...

Problems of College Students' Adaptation to Professional Activity While in College

ERIC Educational Resources Information Center

Federova, E. E.

2008-01-01

Today's specialists are required to be actively involved, independent, flexible, original thinkers, and well trained both generally and professionally. Results of a sociological survey of 2,000 students at Urals State University indicate that a majority of students are at an average level of well-formed professional competence, and less than 1…

Comparative food niche analysis of Strix Owls in Belarus

Treesearch

Alexey K. Tishechkin

1997-01-01

Three Strix species breed sympatrically in Belarus. The Tawny Owl (Strix aluco) is one of two commonest owl species in the country, and is distributed throughout the whole territory. Its' range overlaps widely with two other species, the Ural Owl (S. uralensis) which is common in the forests of the northern part and the Great...

Peculiarities of Educational Environment at Mining and Metallurgical Schools of the Urals

ERIC Educational Resources Information Center

Chapaev, Nikolay K.; Erofeev, Alexander G.; Dvoráková, Lenka

2016-01-01

The relevancy of the issue under study stems from the contradiction between the need for a modern interpretation of the activities of mining and metallurgical schools, which had played a prominent role in the institutionalization of the vocational education environment as well as from moral "obsolescence" of research work results in this…

Problems with the claim of ecotype and taxon status of the wolf in the Great Lakes region

USGS Publications Warehouse

Cronin, Matthew A.; Mech, L. David

2009-01-01

Koblmuller et al. (2009) analysed molecular genetic data of the wolf in the Great Lakes (GL) region of the USA and concluded that the animal was a unique ecotype of grey wolf and that genetic data supported the population as a discrete wolf taxon. However, some of the literature that the researchers used to support their position actually did not, and additional confusion arises from indefinite use of terminology. Herein, we discuss the problems with designation of a wolf population as a taxon or ecotype without proper definition and assessment of criteria.

A new chasmosaurine from northern Laramidia expands frill disparity in ceratopsid dinosaurs.

PubMed

Ryan, Michael J; Evans, David C; Currie, Philip J; Loewen, Mark A

2014-06-01

A new taxon of chasmosaurine ceratopsid demonstrates unexpected disparity in parietosquamosal frill shape among ceratopsid dinosaurs early in their evolutionary radiation. The new taxon is described based on two apomorphic squamosals collected from approximately time equivalent (approximately 77 million years old) sections of the upper Judith River Formation, Montana, and the lower Dinosaur Park Formation of Dinosaur Provincial Park, Alberta. It is referred to Chasmosaurinae based on the inferred elongate morphology. The typical chasmosaurine squamosal forms an obtuse triangle in dorsal view that tapers towards the posterolateral corner of the frill. In the dorsal view of the new taxon, the lateral margin of the squamosal is hatchet-shaped with the posterior portion modified into a constricted narrow bar that would have supported the lateral margin of a robust parietal. The new taxon represents the oldest chasmosaurine from Canada, and the first pre-Maastrichtian ceratopsid to have been collected on both sides of the Canada-US border, with a minimum north-south range of 380 km. This squamosal morphology would have given the frill of the new taxon a unique dorsal profile that represents evolutionary experimentation in frill signalling near the origin of chasmosaurine ceratopsids and reinforces biogeographic differences between northern and southern faunal provinces in the Campanian of North America.

Revisiting the ants of Melanesia and the taxon cycle: historical and human-mediated invasions of a tropical archipelago.

PubMed

Economo, Evan P; Sarnat, Eli M

2012-07-01

Understanding the historical evolution of biotas and the dynamics of contemporary human-mediated species introductions are two central tasks of biology. One hypothesis may address both-the taxon cycle. Taxon cycles are phases of range expansion and contraction coupled to ecological and evolutionary niche shifts. These historical invasion processes resemble human-mediated invasions in pattern and possibly mechanism, but both the existence of historical cycles and the roles of recent introductions are in question. We return to the system that originally inspired the taxon cycle-Melanesian ants-and perform novel tests of the hypothesis. We analyze (i) the habitat distributions of Fiji's entire ant fauna (183 species), (ii) ecological shifts associated with the in situ radiation of Fijian Pheidole in a phylogenetic context, and (iii) the ecological structure of a massive exotic ant invasion of the archipelago. Our analyses indicate lineages shift toward primary habitats, higher elevation, rarity, and ecological specialization with increasing level of endemism, consistent with taxon cycle predictions. The marginal habitats that historically formed a dispersal conduit in the Pacific are now mostly replaced by human-modified habitats dominated by a colonization pulse of exotic species. We propose this may represent the first phase of an incipient global cycle of human-mediated colonization, ecological shifts, and diversification.

Coalescent histories for caterpillar-like families.

PubMed

Rosenberg, Noah A

2013-01-01

A coalescent history is an assignment of branches of a gene tree to branches of a species tree on which coalescences in the gene tree occur. The number of coalescent histories for a pair consisting of a labeled gene tree topology and a labeled species tree topology is important in gene tree probability computations, and more generally, in studying evolutionary possibilities for gene trees on species trees. Defining the Tr-caterpillar-like family as a sequence of n-taxon trees constructed by replacing the r-taxon subtree of n-taxon caterpillars by a specific r-taxon labeled topology Tr, we examine the number of coalescent histories for caterpillar-like families with matching gene tree and species tree labeled topologies. For each Tr with size r≤8, we compute the number of coalescent histories for n-taxon trees in the Tr-caterpillar-like family. Next, as n→∞, we find that the limiting ratio of the numbers of coalescent histories for the Tr family and caterpillars themselves is correlated with the number of labeled histories for Tr. The results support a view that large numbers of coalescent histories occur when a tree has both a relatively balanced subtree and a high tree depth, contributing to deeper understanding of the combinatorics of gene trees and species trees.

The effects of fossil placement and calibration on divergence times and rates: an example from the termites (Insecta: Isoptera).

PubMed

Ware, Jessica L; Grimaldi, David A; Engel, Michael S

2010-01-01

Among insects, eusocial behavior occurs in termites, ants, some bees and wasps. Isoptera and Hymenoptera convergently share social behavior, and for both taxa its evolution remains poorly understood. While dating analyses provide researchers with the opportunity to date the origin of eusociality, fossil calibration methodology may mislead subsequent ecological interpretations. Using a comprehensive termite dataset, we explored the effect of fossil placement and calibration methodology. A combined molecular and morphological dataset for 42 extant termite lineages was used, and a second dataset including these 42 taxa, plus an additional 39 fossil lineages for which we had only morphological data. MrBayes doublet-model analyses recovered similar topologies, with one minor exception (Stolotermitidae is sister to the Hodotermitidae, s.s., in the 42-taxon analysis but is in a polytomy with Hodotermitidae and (Kalotermitidae + Neoisoptera) in the 81-taxon analysis). Analyses using the r8s program on these topologies were run with either minimum/maximum constraints (analysis a = 42-taxon and analysis c = 81-taxon analyses) or with the fossil taxon ages fixed (ages fixed to be the geological age of the deposit from which they came, analysis b = 81-taxon analysis). Confidence intervals were determined for the resulting ultrametric trees, and for most major clades there was significant overlap between dates recovered for analyses A and C (with exceptions, such as the nodes Neoisoptera, and Euisoptera). With the exception of isopteran and eusiopteran node ages, however, none of the major clade ages overlapped when analysis B is compared with either analysis A or C. Future studies on Dictyoptera should note that the age of Kalotermitidae was underestimated in absence of kalotermitid fossils with fixed ages. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

DSM-IV Antisocial Personality Disorder and Conduct Disorder: Evidence for Taxonic Structures Among Individuals With and Without Substance Use Disorders in the General Population

PubMed Central

Kerridge, Bradley T; Saha, Tulshi D; Hasin, Deborah S

2014-01-01

Objective: The categorical-dimensional status of DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition) conduct disorder (CD) and antisocial personality disorder (ASPD) is a source of controversy. This study examined whether the underlying structure of DSM-IV CD and ASPD was dimensional or categorical (taxonic) among individuals with and without substance use disorders. Method: Using a national large representative survey of U.S. adults (n = 43,093), taxometric analyses of DSM-IV CD and ASPD diagnostic criteria were conducted on the total sample and among those with and without substance use disorders. Results: Results of three taxometric procedures were consistent in showing that the structures underlying DSM-IV CD and ASPD were clearly taxonic in the total sample and among individuals with and without substance use disorders. Comparison curve fit indices exceeded 0.57 for each model. Conclusions: Taxonic findings of the present study were in contrast to the dimensional results of prior taxometric research among incarcerated samples with substantial comorbidity of antisocial syndromes and substance use disorders. Results supported the categorical representation and diagnostic thresholds of ASPD and CD as defined in DSM-IV and DSM-5. That the structure of ASPD and CD may be taxonic suggests that further research on these disorders use group comparative designs in which samples with and without these disorders are compared in terms of sociodemographic and clinical correlates, comorbidity, and treatment utilization. The taxonic structure of ASPD and CD may contribute to future research on causal processes through which these antisocial syndromes develop. PMID:24766762

Identifying bioindicators across trait-taxon space for assessing water quality in marine environments.

PubMed

Xu, Guangjian; Zhong, Xiaoxiao; Al, Mamun Abdullah; Warren, Alan; Xu, Henglong

2018-06-01

The response units of protozoan communities, based on a community-weighted mean (CWM) dataset across trait-taxon space, were investigated in order to determine their utility as bioindicators of marine water quality. From a total of 17 functional categories of seven biological traits, three functional response units (FRUs) were identified at correlation levels of >0.75. FRUs 1 and 3 generally dominated the communities in more polluted areas during warm seasons, while FRU2 appeared to prefer less polluted waters and dominated the communities in spring and winter. Correlation analysis demonstrated that the CWM values of FRUs 1 and 3 were significantly positively correlated to the concentrations of chemical oxygen demand (COD), whereas those of FRU2 were negatively correlated to COD. Across taxon-function space, 16 species were identified as potential bioindicators of water quality. These results suggest that redundancy analysis across trait-taxon space is a useful tool for identifying indicators of environmental quality. Copyright © 2018 Elsevier Ltd. All rights reserved.

Psychopathy as a Taxon: Evidence That Psychopaths Are a Discrete Class.

ERIC Educational Resources Information Center

Harris, Grant T.; And Others

1994-01-01

Applied taxometric analyses to construct of psychopathy (as measured by Psychopathy Checklist) and to several variables reflecting antisocial childhood, adult criminality, and criminal recidivism. Findings from 653 serious offenders assessed or treated in maximum-security institution supported existence of taxon underlying psychopathy. Childhood…

Experience of the Development of a Regional Qualification Framework for the System of Vocational Education

ERIC Educational Resources Information Center

Masalimova, Alfiya R.; Ovchinnikova, Iraida G.; Kurzaeva, Lubov V.; Samarokova, Irina V.

2016-01-01

The article dwells upon the methodological and technological aspects of the project to develop a framework of qualifications of the Ural region, which concerned with some of the features of the procedure of doing research, as well as the development of diagnostic tools. The work presents the methods of the processing of data collected during the…

Continuous control systems for non-contact ECG

NASA Astrophysics Data System (ADS)

Kodkin, Vladimir L.; Yakovleva, Galina V.; Smirnov, Alexey S.

2017-03-01

South Ural State University is still conducting the research work dedicated to innovations in biomedicine. Development of system for continuous control and diagnosis of the functional state in large groups of people is based on studies of non-contact ECG recording reported by the authors at the SPIE conference in 2016. The next stage of studies has been performed this year.

The Competitive Environment of a Higher Educational Institution of Culture and Art: An Experimental Study

ERIC Educational Resources Information Center

Shtoler, N. N.

2012-01-01

An analysis of educational programs in the Urals region of Russia shows how institutions may cooperate more by sharing programs and by specializing in those programs in which they are strongest. While competition is a necessary mechanism for improvements in educational quality, overlapping and redundant programs need to be avoided. (Contains 1…

The Influence of Edaphic and Orographic Factors on Algal Diversity in Biological Soil Crusts on Bare Spots in the Polar and Subpolar Urals

NASA Astrophysics Data System (ADS)

Patova, E. N.; Novakovskaya, I. V.; Deneva, S. V.

2018-03-01

The influence of edaphic and orographic factors on the formation of algal diversity in biological soil crusts was studied in mountain tundras of the Polar and Subpolar Urals. Bare spots developed in the soils on different parent materials and overgrown to different extents were investigated. Overall, 221 algal species from six divisions were identified. Among them, eighty-eight taxa were new for the region studied. The Stigonema minutum, S. ocellatum, Nostoc commune, Gloeocapsopsis magma, Scytonema hofmannii, Leptolyngbya foveolarum, Pseudococcomyxa simplex, Sporotetras polydermatica species and species of the Cylindrocystis, Elliptochloris, Fischerella, Leptosira, Leptolyngbya, Myrmecia, Mesotaenium, Phormidium, Schizothrix genera were permanent components of biological soil crusts. The basis of the algal cenoses in soil crusts was composed of cosmopolitan cyanoprokaryotes, multicellular green algae with thickened covers and abundant mucus. The share of nitrogen fixers was high. The physicochemical properties of primary soils forming under the crusts of spots are described. The more important factors affecting the species composition of algae in the crusts are the elevation gradient, temperature, soil moisture, and the contents of Ca, Mg, mobile phosphorus, and total nitrogen.

Dose reconstruction for the Urals population. Joint Coordinating Committee on Radiation Effects Research, Project 1.1 -- Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Degteva, M.O.; Drozhko, E.; Anspaugh, L.R.

1996-02-01

This work is being carried out as a feasibility study to determine if a long-term course of work can be implemented to assess the long-term risks of radiation exposure delivered at low to moderate dose rates to the populations living in the vicinity of the Mayak Industrial Association (MIA). This work was authorized and conducted under the auspices of the US-Russian Joint Coordinating Committee on Radiation Effects Research (JCCRER) and its Executive Committee (EC). The MIA was the first Russian site for the production and separation of plutonium. This plant began operation in 1948, and during its early days theremore » were technological failures that resulted in the release of large amounts of waste into the rather small Techa River. There were also gaseous releases of radioiodines and other radionuclides during the early days of operation. In addition, there was an accidental explosion in a waste storage tank in 1957 that resulted in a significant release. The Techa River Cohort has been studied for several years by scientists from the Urals Research Centre for Radiation Medicine and an increase in both leukemia and solid tumors has been noted.« less

The Sr, Nd, and Hf isotopic geochemistry of rocks of the gabbro-diorite-tonalite association from the Eastern Segment of the Middle Urals as an indicator of the age of the continental crust in this area

NASA Astrophysics Data System (ADS)

Smirnov, V. N.; Ivanov, K. S.; Ronkin, Yu. L.; Koroteev, V. A.; Serov, P. A.; Gerdes, A.

2017-05-01

According to isotopic analysis of rocks of the Reft gabbro-diorite-tonalite complex (Middle Urals), gabbro and related diorite and dikes and vein-shaped bodies of plagiogranitoids, crosscutting gabbro, are similar to the depleted mantle substance in ɛNd( T) = 8.6-9.7 and ɛHf( T) = 15.9-17.9. Their model Hf ages are correlated with the time of crystallization. Here, the tonalites and quartz diorites constituting most of the Reft massif are characterized by lower values: ɛNd( T) = 3.7-6.0, ɛHf( T) = 11.1-12.7, and T DM values significantly exceeding the age datings. This is evidence that Neoproterozoic crustal rocks were a source of parental magma for these rocks. The primary 87Sr/86Sr ratio in rocks of both groups is highly variable (0.70348-0.70495). The data obtained allow us to reach the conclusion that the Reft gabbro-diorite-tonalite complex was formed as a result of nearly synchronous processes occurring in the crust and the mantle within a limited area.

The U.S.-Russian radiation health effects research program in the Southern Urals.

PubMed

Seligman, P J

2000-07-01

The Joint Coordinating Committee for Radiation Effects Research (JCCRER) was established through a bilateral U.S.-Russian agreement to support research and exchange information on radiation health effects. The U.S. member agencies include the Department of Energy (DOE), Nuclear Regulatory Commission (NRC), Department of Health and Human Services (DHHS), Department of Defense (DoD), National Aeronautics and Space Administration (NASA), and Environmental Protection Agency (EPA). The Russians are represented by the Ministries of Emergencies (EMERCOM), Atomic Energy (MINATOM) and Health (MINZDRAV), and the Russian Academy of Sciences (IBRAE). The focus of this research is on the workers from the Mayak Production Association (MAYAK) in the Southern Urals and on the neighboring populations along the Techa River exposed to contamination from the plant. The goal of the program is to better define the relationship between the health effects and the chronic low dose and dose-rate exposure, these data being essential to validate current radiation protection standards and practices. The current primary areas of JCCRER research include dose reconstruction, epidemiologic health studies, molecular epidemiology/biodosimetry, and the creation of tissue banks. The organization of the ongoing research conducted under the aegis of the JCCRER and the rationale for this work are described.

Temporal variability of the quality of Taraxacum officinale seed progeny from the East-Ural radioactive trace: is there an interaction between low level radiation and weather conditions?

PubMed

Pozolotina, Vera N; Antonova, Elena V

2017-03-01

The multiple stressors, in different combinations, may impact differently upon seed quality, and low-level doses of radiation may enhance synergistic or antagonistic effects. During 1991-2014 we investigated the quality of the dandelion (Taraxacum officinale s.l.) seed progeny growing under low-level radiation exposure at the East-Ural Radioactive Trace (EURT) area (result of the Kyshtym accident, Russia), and in plants from areas exposed to background radiation. The viability of the dandelion seed progeny was assessed according to chronic radiation exposure, accounting for the variability of weather conditions among years. Environmental factors (temperature, precipitation, and their ratio in different months) can modify the radiobiological effects. We found a wide range of possible responses to multiple stressors: inhibition, stimulation, and indifferent effects in different seasons. The intraspecific variability of the quality of dandelion seed progeny was greatly increased under conditions of low doses of chronic irradiation. Temperature was the most significant factor for seed progeny formation in the EURT zone, whereas the sums of precipitation and ratios of precipitation to temperature dominantly affected organisms from the background population.

A New Eusuchian Crocodyliform with Novel Cranial Integument and Its Significance for the Origin and Evolution of Crocodylia

PubMed Central

Holliday, Casey M.; Gardner, Nicholas M.

2012-01-01

Crocodyliforms were one of the most successful groups of Mesozoic tetrapods, radiating into terrestrial, semiaquatic and marine environments, while occupying numerous trophic niches, including carnivorous, insectivorous, herbivorous, and piscivorous species. Among these taxa were the enigmatic, poorly represented flat-headed crocodyliforms from the late Cretaceous of northern Africa. Here we report a new, giant crocodyliform from the early Late Cretaceous (Cenomanian) Kem Kem Formation of Morocco. Represented by a partial braincase, the taxon has an extremely long, flat skull with large jaw and craniocervical muscles. The skull roof is ridged and ornamented with a broad, rough boss surrounded by significant vascular impressions, likely forming an integumentary structure unique among crocodyliforms. Size estimates using endocranial volume indicate the specimen was very large. The taxon possesses robust laterosphenoids with laterally oriented capitate processes and isolated epipterygoids, features allying it with derived eusuchians. Phylogenetic analysis finds the taxon to be a derived eusuchian and sister taxon to Aegyptosuchus, a poorly understood, early Late Cretaceous taxon from the Bahariya formation. This clade forms the sister clade of crown-group Crocodylia, making these taxa the earliest eusuchian crocodyliforms known from Africa. These results shift phylogenetic and biogeographical hypotheses on the origin of modern crocodylians towards the circum-Tethyean region and provide important new data on eusuchian morphology and evolution. PMID:22303441

Comparative host range and aggressiveness of Phytophthora ramorum and Phytophthora kernoviae sp. nov. on North American and European trees

Treesearch

Clive Brasier; Joan Rose; Susan Kirk; Sandra Denman; Joan Webber

2006-01-01

Phytophthora ramorum and P. kernoviae are recently introduced, invasive pathogens in woodlands in southern Britain. P. kernoviae, previously known as Phytophthora taxon C, is a newly discovered taxon, (Brasier and others 2005), found during surveys for P. ramorum in Cornwall...

Brevipalpus phoenicis (Geijskes) species complex – resurrection of E. W. Baker’s species (Acari: Tenuipalpidae)

USDA-ARS?s Scientific Manuscript database

Brevipalpus phoenicis sensu lato has been identified from countries all over the world and has been associated with many different host plant species. As a taxon, it shows a degree of morphological variation. A combination such as this often indicates that the taxon actually represents a complex o...

7 CFR 360.501 - Petitions to remove a taxon from the noxious weed lists.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 5 2014-01-01 2014-01-01 false Petitions to remove a taxon from the noxious weed lists. 360.501 Section 360.501 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.501...

7 CFR 360.501 - Petitions to remove a taxon from the noxious weed lists.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 5 2011-01-01 2011-01-01 false Petitions to remove a taxon from the noxious weed lists. 360.501 Section 360.501 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.501...

7 CFR 360.501 - Petitions to remove a taxon from the noxious weed lists.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 5 2012-01-01 2012-01-01 false Petitions to remove a taxon from the noxious weed lists. 360.501 Section 360.501 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.501...

Distribution and etiology of aerial stem infections of Phytophthora ramorum and Phytophthora kernoviae at three woodland sites in the U.K.

Treesearch

Anna Brown; Clive Brasier; Sandra Denman; Joan Rose; Susan Kirk; Joan Webber

2006-01-01

Phytophthora ramorum and P . kernoviae sp. nov are recently introduced, invasive pathogens in woodlands in southern Britain. P. kernoviae is a newly discovered taxon, previously referred to as Phytophthora taxon C. Both species aggressively infect foliage and shoots of understory rhododendrons...

The Latent Structure of Psychopathy in Youth: A Taxometric Investigation

ERIC Educational Resources Information Center

Vasey, Michael W.; Kotov, Roman; Frick, Paul J.; Loney, Bryan R.

2005-01-01

Using taxometric procedures, the latent structure of psychopathy was investigated in two studies of children and adolescents. Prior studies have identified a taxon (i.e., a natural category) associated with antisocial behavior in adults as well as children and adolescents. However, features of this taxon suggest that it is not psychopathy but…

Phytophthora ×stagnum nothosp. nov., a New Hybrid from Irrigation Reservoirs at Ornamental Plant Nurseries in Virginia

PubMed Central

Yang, Xiao; Richardson, Patricia A.; Hong, Chuanxue

2014-01-01

A novel Phytophthora species was frequently recovered from irrigation reservoirs at several ornamental plant production facilities in eastern Virginia. Initial sequencing of the internal transcribed spacer (ITS) region of this species generated unreadable sequences due to continual polymorphic positions. Cloning and sequencing the ITS region as well as sequencing the mitochondrially encoded cytochrome c oxidase 1 and beta-tubulin genes revealed that it is a hybrid between P. taxon PgChlamydo as its paternal parent and an unknown species genetically close to P. mississippiae as its maternal parent. This hybrid has some diagnostic morphological features of P. taxon PgChlamydo and P. mississippiae. It produces catenulate hyphal swellings, characteristic of P. mississippiae, and chlamydospores, typical of P. taxon PgChlamydo. It also produces both ornamented and relatively smooth-walled oogonia. Ornamented oogonia are another important diagnostic character of P. mississippiae. The relatively smooth-walled oogonia may be indicative of oogonial character of P. taxon PgChlamydo. The new hybrid is described here as Phytophthora ×stagnum. PMID:25072374

What is the latent structure of alcohol use disorders? A taxometric analysis of the Personality Assessment Inventory Alcohol Problems Scale in male and female prison inmates.

PubMed

Walters, Glenn D; Diamond, Pamela M; Magaletta, Philip R

2010-03-01

Three indicators derived from the Personality Assessment Inventory (PAI) Alcohol Problems scale (ALC)-tolerance/high consumption, loss of control, and negative social and psychological consequences-were subjected to taxometric analysis-mean above minus below a cut (MAMBAC), maximum covariance (MAXCOV), and latent mode factor analysis (L-Mode)-in 1,374 federal prison inmates (905 males, 469 females). Whereas the total sample yielded ambiguous results, the male subsample produced dimensional results, and the female subsample produced taxonic results. Interpreting these findings in light of previous taxometric research on alcohol abuse and dependence it is speculated that while alcohol use disorders may be taxonic in female offenders, they are probably both taxonic and dimensional in male offenders. Two models of male alcohol use disorder in males are considered, one in which the diagnostic features are categorical and the severity of symptomatology is dimensional, and one in which some diagnostic features (e.g., withdrawal) are taxonic and other features (e.g., social problems) are dimensional.

Men and women are from Earth: examining the latent structure of gender.

PubMed

Carothers, Bobbi J; Reis, Harry T

2013-02-01

Taxometric methods enable determination of whether the latent structure of a construct is dimensional or taxonic (nonarbitrary categories). Although sex as a biological category is taxonic, psychological gender differences have not been examined in this way. The taxometric methods of mean above minus below a cut, maximum eigenvalue, and latent mode were used to investigate whether gender is taxonic or dimensional. Behavioral measures of stereotyped hobbies and physiological characteristics (physical strength, anthropometric measurements) were examined for validation purposes, and were taxonic by sex. Psychological indicators included sexuality and mating (sexual attitudes and behaviors, mate selectivity, sociosexual orientation), interpersonal orientation (empathy, relational-interdependent self-construal), gender-related dispositions (masculinity, femininity, care orientation, unmitigated communion, fear of success, science inclination, Big Five personality), and intimacy (intimacy prototypes and stages, social provisions, intimacy with best friend). Constructs were with few exceptions dimensional, speaking to Spence's (1993) gender identity theory. Average differences between men and women are not under dispute, but the dimensionality of gender indicates that these differences are inappropriate for diagnosing gender-typical psychological variables on the basis of sex. (c) 2013 APA, all rights reserved.

Subchronic Studies of Chlorotrifluorethylene

DTIC Science & Technology

1989-06-01

colonic nematodiasis, focal myocarditis, renal retention cysts , pulmonary subpl.ural histiocytosis, focal dacryoadenitis, rhinitis, and multifocal...compared to controls (pɘ.01). Among female rats, te incidences of grossly detected paraovarian cysts were 40, 10, 10, and 0% in the cr,-trol, 0.25, 0.5...level. The histopathologic examination also confirmed each paraovarian cyst in female rats and also revealed paraovarian cysts that ,v-re not grossly

Changing Symbolic and Geographical Boundaries between Penal Zones and Rural Communities in the Russian Federation

ERIC Educational Resources Information Center

Pallot, Judith

2012-01-01

The article examines the processes involved in the integration of the USSR's secret places into mainstream rural society in the Russian Federation. Taking the example of one rural district in the Volga-Ural region that has been the site of a large prison complex over a period of ninety years, the article examines how economic changes and local…

Wood wastes and residues generated along the Colorado Front Range as a potential fuel source

Treesearch

Julie E. Ward; Kurt H. Mackes; Dennis L. Lynch

2004-01-01

Throughout the United States there is interest in utilizing renewable fuel sources as an alternative to coal and nat-ural gas. This project was initiated to determine the availability of wood wastes and residues for use as fuel in ce-ment kilns and power plants located along the Colorado Front Range. Research was conducted through literature searches, phone surveys,...

Genes Associated with Food Allergy and Eosinophilic Esophagitis

DTIC Science & Technology

2013-11-01

conserved enzymes present not only in lower life forms but also inmammals that can cleave chitin a nat- urally occurring polysaccharide composed of N...acetylglucosamine re- peats [1,2]. Chitin is highly expressed in insects and crustacean exoskeletons, fungal cell walls, and microfilarial nematode...sheaths [3]. Levels of chitin are regulated by enzymes synthesizing chitin (i.e. chitin synthase) or degrading chitin (i.e. chitinases). Although

JPRS Report, Science & Technology, USSR: Chemistry.

DTIC Science & Technology

1987-12-11

UDC 536.75:541.128.7 BIFURCATIONAL ANALYSIS OF AUTO-OSCILLATING MODEL OF SYSTEM POTASSIUM IODATE - HYDROGEN PEROXIDE - CYSTE1NE - SULFURIC ACID Kiev...the explosive drilling team of the first ore administration of the Ural Potassium Association headed by Hero of Socialist Labor N. P. Savchuk, because...Republic Socialist Republic of Rumania USSR CSSR Mineral fertilizers Nitrogen Phosphate Potassium Mineral fertilizers play a significant role in

The Place of the Family in the System of Values of Inhabitants of a Medium-Sized Urals City

ERIC Educational Resources Information Center

Satybaldina, E. V.

2012-01-01

The processes of modernization in this country's economy require a well-qualified work force that is mobile in social, professional, and geographic terms. The necessary basis of a successful solution to this problem is the stability of the family, which is the basic active agent of the reproduction of new generations of workers. Family stability…

JPRS Report, Soviet Union, Economic Affairs

DTIC Science & Technology

1988-06-28

reducing the application of melamine formaldehyde resins which are used for the final finishing processes of fabrics since a harmful sub- stance...superphosphate and urea for private plots. Many letters arrive from Siberia, the Urals, Moldavia and from the Moscow region. Even in Moscow itself...Progressive types of rolled metal, including galvanized steel sheet, as well as efficient plastics, resins , polymers, timber products etc., are being

Chelyabinsk fireball and Dyatlov pass tragedy

NASA Astrophysics Data System (ADS)

Kochemasov, G. G.

2013-09-01

The Chelyabinsk bolide as well as the Kunashak meteorite in 1949 (Fig. 3, black square) hit ground in ectonically peculiar place in the Ural Mountains. The main explosion was followed by a series of weaker bangs. The long Uralian fold belt (Pz) separates two subsectors (1 & 2, Fig. 1) of the Eurasian sector (1+2) of the Eastern hemisphere sectoral structure (Fig. 1). At the Pamirs-Hindukush massif (the "Pamirs' cross") meet four tectonic sectors of this structure: two opposite differently uplifted (Africa-Mediterranean ++ and Asian +) and separating them two opposite differently subsided (Eurasian - and Indooceanic - -). Tectonic bisectors divide the sectors into two differently tectonically elevated subsectors. The Ural Mountains is one of these bisectors dividing the somewhat risen East-European subsector and the relatively fallen West-Siberian one. Even more important is the sharp tectonic boundary between subsided Eurasian sector and uplifted Asian one (between 2 and 3, Fig. 1). Fig. 3 shows distribution of electrophonic bolides over USSR [1]. Observations numbers are in circles. The total of 343 observations is distributed at relevant districts; accompanied meteorites were found only in 23-24 cases; in the chart are excluded background values of 1-2 observations per district. Two areas are obviously anomalous. These of the Urals, and the Eurasia-Asia sectoral contact (Novosibirsk - Yenisei R. - Tunguska). A location in the long Uralian belt is determined by its intersection with the Timan fold belt coming from the northwest (Fig. 3). The catastrophic Dyatlov pass where nine people mysteriously died at once occurs there (triangle in Fig. 3). Mancy aborigines know this place as deadly where killing white shining spheres appear. Moreover this belt intersection is well known among hunters for UFO as the Permian triangle (Fig. 2). They meet there to observe unusual atmospheric shining and other anomalous phenomena. In the Yenisei-Tunguska-Baikal region lightning balls appear regularly causing broken trees [2]. In conclusion, these two tectonically distinctive regions are famous by anomalously often appearance of bolides part of which is accompanied by meteorite falls. Out of 343 observations meteorites accompanied less than 10 %. Unclear remains a strange attraction of bolides by very pronounced tectonic features.

Body Potassium Content and Radiation Dose from 40K for the Urals Population (Russia)

PubMed Central

Tolstykh, Evgenia I.; Degteva, Marina O.; Bougrov, Nikolay G.; Napier, Bruce A.

2016-01-01

Long-term whole-body monitoring of radionuclides in residents of the Urals Region has been performed at the Urals Research Center for Radiation Medicine (URCRM, Chelyabinsk). Quantification of 40K was achieved by measuring the 40K photopeak with four phoswich detectors in whole body counter SICH-9.1M. The current study presents the results of 40K measurements in 3,651 women and 1,961 t-test; U-test men aged 11–90; measurements were performed in 2006–2014. The residents belonged to two ethnic groups, Turkic (Tatar, Bashkir) and Slavs (mainly Russian). The levels of 40K-body contents depend upon gender, age, and body mass. Significant ethnic-differences were not found in 40K-body contents and 40K concentrations in terms of Bq per kg of body weight (in groups homogenous by age and gender). Both 40K-body contents and concentrations were significantly higher in men than in women in all age-groups; the difference was about 25%. The measured 40K-body content in men of 20–50 years was about 4200 Bq (134 g of K) and about 3000 Bq (95 g of K) in women. By the age of 80 these values decreased to 3200 Bq (102 g of K) in men and 2500 Bq (80 g of K) in women. Annual dose rates were maximal in the age group of 20–30 years– 0.16 mGy/y for men and 0.13 mGy/y for women. Further, the dose-rates decreased with age and in the groups of 60–80 years were 0.13 mGy/y for men and 0.10 mGy/y for women. Within groups homogeneous by age and gender, individual dose rates are described by a normal statistical distribution. The coefficient of variation ranges from 9 to 14%, and on the average is 12.5%. Doses from naturally occurring 40K accumulated over 70 years were found to be 9.9 mGy for men and 8.3 mGy for women; over 90 years - 12.5 and 10.4 mGy. PMID:27111330

Individuals at high risk for suicide are categorically distinct from those at low risk.

PubMed

Witte, Tracy K; Holm-Denoma, Jill M; Zuromski, Kelly L; Gauthier, Jami M; Ruscio, John

2017-04-01

Although suicide risk is often thought of as existing on a graded continuum, its latent structure (i.e., whether it is categorical or dimensional) has not been empirically determined. Knowledge about the latent structure of suicide risk holds implications for suicide risk assessments, targeted suicide interventions, and suicide research. Our objectives were to determine whether suicide risk can best be understood as a categorical (i.e., taxonic) or dimensional entity, and to validate the nature of any obtained taxon. We conducted taxometric analyses of cross-sectional, baseline data from 16 independent studies funded by the Military Suicide Research Consortium. Participants (N = 1,773) primarily consisted of military personnel, and most had a history of suicidal behavior. The Comparison Curve Fit Index values for MAMBAC (.85), MAXEIG (.77), and L-Mode (.62) all strongly supported categorical (i.e., taxonic) structure for suicide risk. Follow-up analyses comparing the taxon and complement groups revealed substantially larger effect sizes for the variables most conceptually similar to suicide risk compared with variables indicating general distress. Pending replication and establishment of the predictive validity of the taxon, our results suggest the need for a fundamental shift in suicide risk assessment, treatment, and research. Specifically, suicide risk assessments could be shortened without sacrificing validity, the most potent suicide interventions could be allocated to individuals in the high-risk group, and research should generally be conducted on individuals in the high-risk group. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Intensive removal of signal crayfish (Pacifastacus leniusculus) from rivers increases numbers and taxon richness of macroinvertebrate species.

PubMed

Moorhouse, Tom P; Poole, Alison E; Evans, Laura C; Bradley, David C; Macdonald, David W

2014-02-01

Invasive species are a major cause of species extinction in freshwater ecosystems, and crayfish species are particularly pervasive. The invasive American signal crayfish Pacifastacus leniusculus has impacts over a range of trophic levels, but particularly on benthic aquatic macroinvertebrates. Our study examined the effect on the macroinvertebrate community of removal trapping of signal crayfish from UK rivers. Crayfish were intensively trapped and removed from two tributaries of the River Thames to test the hypothesis that lowering signal crayfish densities would result in increases in macroinvertebrate numbers and taxon richness. We removed 6181 crayfish over four sessions, resulting in crayfish densities that decreased toward the center of the removal sections. Conversely in control sections (where crayfish were trapped and returned), crayfish density increased toward the center of the section. Macroinvertebrate numbers and taxon richness were inversely correlated with crayfish densities. Multivariate analysis of the abundance of each taxon yielded similar results and indicated that crayfish removals had positive impacts on macroinvertebrate numbers and taxon richness but did not alter the composition of the wider macroinvertebrate community. Synthesis and applications: Our results demonstrate that non-eradication-oriented crayfish removal programmes may lead to increases in the total number of macroinvertebrates living in the benthos. This represents the first evidence that removing signal crayfish from riparian systems, at intensities feasible during control attempts or commercial crayfishing, may be beneficial for a range of sympatric aquatic macroinvertebrates.

Intensive removal of signal crayfish (Pacifastacus leniusculus) from rivers increases numbers and taxon richness of macroinvertebrate species

PubMed Central

Moorhouse, Tom P; Poole, Alison E; Evans, Laura C; Bradley, David C; Macdonald, David W

2014-01-01

Invasive species are a major cause of species extinction in freshwater ecosystems, and crayfish species are particularly pervasive. The invasive American signal crayfish Pacifastacus leniusculus has impacts over a range of trophic levels, but particularly on benthic aquatic macroinvertebrates. Our study examined the effect on the macroinvertebrate community of removal trapping of signal crayfish from UK rivers. Crayfish were intensively trapped and removed from two tributaries of the River Thames to test the hypothesis that lowering signal crayfish densities would result in increases in macroinvertebrate numbers and taxon richness. We removed 6181 crayfish over four sessions, resulting in crayfish densities that decreased toward the center of the removal sections. Conversely in control sections (where crayfish were trapped and returned), crayfish density increased toward the center of the section. Macroinvertebrate numbers and taxon richness were inversely correlated with crayfish densities. Multivariate analysis of the abundance of each taxon yielded similar results and indicated that crayfish removals had positive impacts on macroinvertebrate numbers and taxon richness but did not alter the composition of the wider macroinvertebrate community. Synthesis and applications: Our results demonstrate that non-eradication-oriented crayfish removal programmes may lead to increases in the total number of macroinvertebrates living in the benthos. This represents the first evidence that removing signal crayfish from riparian systems, at intensities feasible during control attempts or commercial crayfishing, may be beneficial for a range of sympatric aquatic macroinvertebrates. PMID:24634733

How to normalize metatranscriptomic count data for differential expression analysis.

PubMed

Klingenberg, Heiner; Meinicke, Peter

2017-01-01

Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and global scaling can differ widely. Our studies indicate that in real data applications performed with global scaling it might be impossible to distinguish between differential expression in terms of transcriptomic changes and differential composition in terms of changing taxonomic proportions. As in transcriptomics, a proper normalization of count data is also essential for differential expression analysis in metatranscriptomics. Our model implies a taxon-specific scaling of counts for normalization of the data. The application of taxon-specific scaling consequently removes taxonomic composition variations from functional profiles and therefore provides a clear interpretation of the observed functional differences.

Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island

Treesearch

Benjamin D. Cook; Catherine M. Pringle; Jane M. Hughes

2008-01-01

Taxon cycling, i.e. sequential phases of expansions and contractions in species’ distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae:...

Description of the Immature Stages of Anopheles (Nyssorhynchus) rondoni (Neiva & Pinto) (Diptera: Culicidae)

DTIC Science & Technology

1997-05-01

Neiva & Pinto) (Diptera: Culicidae) Maria Anice Mureb Sallum/+, Richard C Wilkerson* Núcleo de Pesquisa Taxonômica e Sistemática em Entomologia ...Taxonômica e Sistemática em Entomologia Médica, Universidade de São Paulo, São Paulo. The following specimens were used for setal counts and measurements (the

Laboratory test of a novel structural model of anxiety sensitivity and panic vulnerability.

PubMed

Bernstein, Amit; Zvolensky, Michael J; Zvolensky, Michael J; Schmidt, Norman B

2009-06-01

The current study evaluated a novel latent structural model of anxiety sensitivity (AS) in relation to panic vulnerability among a sample of young adults (N=216). AS was measured using the 16-item Anxiety Sensitivity Index (ASI; Reiss, Peterson, Gursky, & McNally, 1986), and panic vulnerability was indexed by panic attack responding to a single administration of a 4-minute, 10% CO(2) challenge. As predicted, vulnerability for panic attack responding to biological challenge was associated with dichotomous individual differences between taxonic AS classes and continuous within-taxon class individual differences in AS physical concerns. Findings supported the AS taxonic-dimensional hypothesis of AS latent structure and panic vulnerability. These findings are discussed in terms of their theoretical and clinical implications.

Epiphytic lichenosynusia under conditions of chemical pollution: Dose-effect dependencies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mikhailova, I.N.; Vorobeichik, E.L.

1995-11-01

The dose-effect dependencies, which characterize response of the epiphytic lichenosynusia of southern taiga in the Middle Urals to pollution by discharges of a copper-smelting plant, are substantially non-linear and, in most cases, have an S-shaped form. A transition from background to impact state is very sharp and begins when the background level of pollution is exceeded by 1.5 - 2.3 times.

Indexing and Exploiting a Discourse History to Generate Context-Sensitive Explanations

DTIC Science & Technology

1993-01-01

facility as part of two intelligent systems. The first is a patient education system intended to provide patients with information about their disease...with our patient education system, and is based upon phenomena we observed in nat- urally occurring interviews with physicians. The responses shown in...Elavil has other possible side effects including dry mouth, difficulty urinating, and weight gain. Figure 2: Actual Dialogue with Patient Education System

Rickettsia Felis in Xenopsylla Cheopis, Java, Indonesia

DTIC Science & Technology

2006-08-01

Sardjono TW, Yanuwiadi B, Hernowati TE, et al. Seroepidemiological evidence for murine and scrub typhus in Malang, Indonesia. Am J Trop Med Hyg. 1997;57...and Allen L. Richards* Rickettsia typhi and R. felis, etiologic agents of murine typhus and fleaborne spotted fever, respectively, were detected in...Indonesia and nat- urally occurring R. felis in Oriental rat fleas. Murine typhus (endemic typhus , fleaborne typhus ),caused by Rickettsia typhi, is

A technique for predicting steel corrosion resistance

NASA Astrophysics Data System (ADS)

Novikov, V. F.; Sokolov, R. A.; Neradovskiy, D. F.; Muratov, K. R.

2018-01-01

Research works were carried out to develop a technique with the aim to increase the lifetime of steel items used in corrosive media. The possibility to monitor corrosion parameters of steel samples is analyzed on the basis of magnetic properties obtained by means of a magnetic structuroscope DIUS-1.15M designed by the Institute of Metal Physics of the Ural Branch of the Russian Academy of Sciences (IMP UB RAS).

The U.S.-Russian radiation health effects research program in the Southern Urals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seligman, P.J.

2000-07-01

The Joint Coordinating Committee for Radiation Effects Research (JCCRER) was established through a bilateral US-Russian agreement to support research and exchange information on radiation health effects. The U.S. member agencies include the Department of Energy (DOE), Nuclear Regulatory Commission (NRC), Department of Health and Human Services (DHHS), Department of Defense (DoD), National Aeronautics and Space Administration (NASA), and Environmental Protection Agency (EPA). The Russians are represented by the Ministries of Emergencies (EMERCOM), the Atomic Energy (MINATOM) and Health (MINZDRAV), and the Russian Academy of Sciences (IBRAE). The focus of this research is on the workers from the Mayak Production Associationmore » (MAYAK) in the Southern Urals and on the neighboring populations along the Techa River exposed to contamination from the plant. The goal of the program is to better define the relationship between the health effects and the chronic low dose and dose-rate exposure, these data being essential to validate current radiation protection standards and practices. The current primary areas of JCCRER research include dose reconstruction, epidemiologic health studies, molecular epidemiology/biodosimetry, and the creation of tissue banks. The organization of the ongoing research conducted under the aegis of the JCCRER and the rationale for this work are described.« less

Impact of GRM: New evidence from the Soviet Union

NASA Technical Reports Server (NTRS)

Mcnutt, M.

1985-01-01

Gravity information released by the Soviet Union allows the quantitative assessment of how the geopotential research mission (GRM) mission might effect the ability to use global gravity data for continental tectonic interpretation. The information is of an isostatic response spectra for eight individual tectonic units in the USSR. The regions examined include the Caroathians, Caucasus, Urals, Pamirs, Tien-Shan, Altal, Chersky Ridge, and East Siberian Platform. The 1 deg x 1 deg gravity data are used to calculate the admittances are used in two different sorts of tectonic studies of mountain belts in the USSR: (1) interpretation of isostatic responses in terms of plate models of compensation for mountainous terrain. Using geologic information concerning time of the orogeny, lithospheric plates involved, and polarity of subduction in collision zones, they convert the best-fitting flexural rigidity to an elastic plate thickness for the lithospheric plate inferred to underlie the mountains; the isostatic admittance functions is an attempt to directly model gravity and topography data for a few select regions in the Soviet Union. By knowing the value of the expected correlation between topography and gravity from the admittances, the Artemjev's map in mountainous areas can be calibrated, and the maps are converted back to Bouguer gravity. This procedure is applied to the Caucasus and southern Urals.

Uranium accumulation in modern and ancient Fe-oxide sediments: Examples from the Ashadze-2 hydrothermal sulfide field (Mid-Atlantic Ridge) and Yubileynoe massive sulfide deposit (South Urals, Russia)

NASA Astrophysics Data System (ADS)

Ayupova, N. R.; Melekestseva, I. Yu.; Maslennikov, V. V.; Tseluyko, A. S.; Blinov, I. A.; Beltenev, V. E.

2018-05-01

Fe-oxyhydroxide sediments (gossans) from the Ashadze-2 hydrothermal sulfide field (Mid-Atlantic Ridge) and hematite-carbonate-quartz rocks (gossanites) from the Yubileynoe Cu-Zn VHMS deposit (South Urals) are characterized by anomalously high U contents (up to 352 ppm and 73 ppm, respectively). In gossans from the Ashadze-2 hydrothermal sulfide field, rare isometric anhedral uraninite grains (up to 2 μm) with outer P- and Ca-rich rims, and numerous smaller (<1 μm) grains, occur in Fe-oxyhydroxides and sepiolite, associated with pyrite, isocubanite, chalcopyrite, galena, atacamite and halite. In gossanites from the Yubileynoe deposit, numerous uraninite particles (<3 μm) are associated with apatite, V-rich Mg-chlorite, micro-nodules of pyrite, Se-bearing galena, hessite and acanthite in a hematite-carbonate-quartz matrix. Small (1-3 μm) round grains of uraninite, which locally coalesce to large grains up to 10 μm in size, are associated with authigenic chalcopyrite. The similar diagenetic processes of U accumulation in modern and ancient Fe-oxyhydroxide sediments were the result of U fixation from seawater during the oxidation of sulfide minerals. Uraninite in gossanites was mainly deposited from diagenetic pore fluids, which circulated in the sulfide-hyaloclast-carbonate sediments.

Microfossils in cherts from the Middle Riphean (Mesoproterozoic) Avzyan Formation, southern Ural Mountains, Russian Federation

NASA Technical Reports Server (NTRS)

Sergeev, V. N.; Knoll, A. H. (Principal Investigator)

1994-01-01

A diverse assemblage of well-preserved microorganisms has been detected in black cherts from the approximately 1200 Ma-old Avzyan Formation (Suite) of the southern Ural Mountains, Russian Federation. The lower Kataskin Member contains a diverse, abundant microbiota dominated by mat-forming filamentous cyanobacteria, several types of colonial unicells, and morphologically distinctive stalked cyanobacteria. The upper Revet Member contains a less diverse biota dominated by unicellular cyanobacteria. Palaeoecological evidence indicates that the microbial community of the Kataskin Member inhabited a shallow water, presumably marine, carbonate environment. Revet microorganisms possibly lived in restricted peritidal environments. The biostratigraphic significance of the Avzyan microbiota is limited. Many of the taxa are long-ranging; they were already abundant in Palaeoproterozoic successions and continue into the Neoproterozoic. Nevertheless, in many respects, the Kataskin assemblage is comparable to those reported from the Middle-Late Riphean deposits of Northern America, Australia and Eurasia. The following taxa are here described: Chroococcaceae-Eogloeocapsa avzyanica Sergeev, Gloeodiniopsis lamellosa Schopf emend. Knoll et Golubic; Entophysalidaceae-Eoentophysalis belcherensis Hofmann; Dermocarpaceae-Polybessurus bipartitus Fairchild ex Green et al.; Nostocaceae-Eosphaeronostoc kataskinicum Sergeev; Nostocaceae or Oscillatoriaceae-Siphonophycus robustum (Schopf) emend. Knoll et Golubic emend. Knoll et al., Siphonophycus sp.; Incertae sedis-Eosynechococcus amadeus Knoll et Golubic.

Long-term paradoxical aftermath of the Early Permian climatic warming in the Northern Hemisphere: biotic and abiotic aspects

NASA Astrophysics Data System (ADS)

Kossovaya, Olga

2014-05-01

Far distant influence of the climatic changes is rather variable and sometimes paradoxical. One of the examples is the flourish of the Photozoan association in the Northern Hemisphere during time of Southern Hemisphere glaciation (P2) and it following collapse in the interglacial phase. Modelling of the possible extrinsic factors using isotope data from the Urals has demonstrated the complex succession of abiotic changes including circulation changes and penetration of cold water from Northern Panthalassa. The invasion of cold water into the Uralian Basin led to disarray of the coastal circulation and rising of cold water via upwelling. It was resulted by change of biota and wide distribution of the heterozoan biota. The replacement took place both in carbonate ramp and reef facies. The depletion of δ18O during the early Artinskian was demonstrated by analyses of the biogenic carbonates from Belaya Gora (Most) section. This coincides with the previously known trend for d18O shown for low latitudes from the Sakmarian to early Artinskian with a minimum during the middle Artinskian and is in accordance with recent data from the South Urals. The heterochrony of the impact in the far-distant and discrete photozoan assemblages depends on their bathymetric and paleo-latitudinal position.

Divergence is not enough: the use of ecological niche models for the validation of taxon boundaries.

PubMed

Dagnino, D; Minuto, L; Casazza, G

2017-11-01

Delimiting taxon boundaries is crucial for any evolutionary research and conservation regulation. In order to avoid mistaken description of species, the approach of integrative taxonomy recommends considering multidisciplinary lines of evidence, including ecology. Unfortunately, ecological data are often difficult to quantify objectively. Here we test and discuss the potential use of ecological niche models for validating taxon boundaries, using three pairs of closely related plant taxa endemic to the south-western Alps as a case study. We also discuss the application of ecological niche models for species delimitation and the implementation of different approaches. Niche overlap, niche equivalency and niche similarity were assessed both in multidimensional environmental space and in geographic space to look for differences in the niche of three pairs of closely related plant taxa. We detected a high degree of niche differentiation between taxa although this result seems not due to differences in habitat selection. The different statistical tests gave contrasting outcomes between environmental and geographic spaces. According to our results, niche divergence does not seem to support taxon boundaries at species level, but may have had important consequences for local adaptation and in generating phenotypic diversity at intraspecific level. Environmental space analysis should be preferred to geographic space as it provides more clear results. Even if the different analyses widely disagree in their conclusions about taxon boundaries, our study suggests that ecological niche models may help taxonomists to reach a decision. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound

USGS Publications Warehouse

Harvey, J.B.J.; Hoy, M.S.; Rodriguez, R.J.

2009-01-01

Non-native marine species have been and continue to be introduced into Puget Sound via several vectors including ship's ballast water. Some non-native species become invasive and negatively impact native species or near shore habitats. We present a new methodology for the development and testing of taxon specific PCR primers designed to assess environmental samples of ocean water for the presence of native and non-native bivalves, crustaceans and algae. The intergenic spacer regions (IGS; ITS1, ITS2 and 5.8S) of the ribosomal DNA were sequenced for adult samples of each taxon studied. We used these data along with those available in Genbank to design taxon and group specific primers and tested their stringency against artificial populations of plasmid constructs containing the entire IGS region for each of the 25 taxa in our study, respectively. Taxon and group specific primer sets were then used to detect the presence or absence of native and non-native planktonic life-history stages (propagules) from environmental samples of ballast water and plankton tow net samples collected in Puget Sound. This methodology provides an inexpensive and efficient way to test the discriminatory ability of taxon specific oligonucleotides (PCR primers) before creating molecular probes or beacons for use in molecular ecological applications such as probe hybridizations or microarray analyses. This work addresses the current need to develop molecular tools capable of diagnosing the presence of planktonic life-history stages from non-native marine species (potential invaders) in ballast water and other environmental samples. ?? 2008 Elsevier B.V.

Re-Structuring of Marine Communities Exposed to Environmental Change: A Global Study on the Interactive Effects of Species and Functional Richness

PubMed Central

Wahl, Martin; Link, Heike; Alexandridis, Nicolaos; Thomason, Jeremy C.; Cifuentes, Mauricio; Costello, Mark J.; da Gama, Bernardo A. P.; Hillock, Kristina; Hobday, Alistair J.; Kaufmann, Manfred J.; Keller, Stefanie; Kraufvelin, Patrik; Krüger, Ina; Lauterbach, Lars; Antunes, Bruno L.; Molis, Markus; Nakaoka, Masahiro; Nyström, Julia; bin Radzi, Zulkamal; Stockhausen, Björn; Thiel, Martin; Vance, Thomas; Weseloh, Annika; Whittle, Mark; Wiesmann, Lisa; Wunderer, Laura; Yamakita, Takehisa; Lenz, Mark

2011-01-01

Species richness is the most commonly used but controversial biodiversity metric in studies on aspects of community stability such as structural composition or productivity. The apparent ambiguity of theoretical and experimental findings may in part be due to experimental shortcomings and/or heterogeneity of scales and methods in earlier studies. This has led to an urgent call for improved and more realistic experiments. In a series of experiments replicated at a global scale we translocated several hundred marine hard bottom communities to new environments simulating a rapid but moderate environmental change. Subsequently, we measured their rate of compositional change (re-structuring) which in the great majority of cases represented a compositional convergence towards local communities. Re-structuring is driven by mortality of community components (original species) and establishment of new species in the changed environmental context. The rate of this re-structuring was then related to various system properties. We show that availability of free substratum relates negatively while taxon richness relates positively to structural persistence (i.e., no or slow re-structuring). Thus, when faced with environmental change, taxon-rich communities retain their original composition longer than taxon-poor communities. The effect of taxon richness, however, interacts with another aspect of diversity, functional richness. Indeed, taxon richness relates positively to persistence in functionally depauperate communities, but not in functionally diverse communities. The interaction between taxonomic and functional diversity with regard to the behaviour of communities exposed to environmental stress may help understand some of the seemingly contrasting findings of past research. PMID:21611170

The description of Rovnoeucoila tympanomorpha Buffington & Perkovsky, a new genus and species of fossil eucoiline,with observations on the asynchronous evolution of Diglyphosematini (Hymenoptera: Figitidae: Eucoilinae)

USDA-ARS?s Scientific Manuscript database

A new genus and species of Eucoilinae, Rovnoeucoila tympanomorpha Buffington & Perkovsky, from a Rovno Amber inclusion, is described. This new taxon differs from extant eucoilines by having a clearly segmented metasoma and singular flagellomere morphology in the antenna. The new taxon is included ...

Categories versus dimensions in personality and psychopathology: a quantitative review of taxometric research.

PubMed

Haslam, N; Holland, E; Kuppens, P

2012-05-01

Taxometric research methods were developed by Paul Meehl and colleagues to distinguish between categorical and dimensional models of latent variables. We have conducted a comprehensive review of published taxometric research that included 177 articles, 311 distinct findings and a combined sample of 533 377 participants. Multilevel logistic regression analyses have examined the methodological and substantive variables associated with taxonic (categorical) findings. Although 38.9% of findings were taxonic, these findings were much less frequent in more recent and methodologically stronger studies, and in those reporting comparative fit indices based on simulated comparison data. When these and other possible confounds were statistically controlled, the true prevalence of taxonic findings was estimated at 14%. The domains of normal personality, mood disorders, anxiety disorders, eating disorders, externalizing disorders, and personality disorders (PDs) other than schizotypal yielded little persuasive evidence of taxa. Promising but still not definitive evidence of psychological taxa was confined to the domains of schizotypy, substance use disorders and autism. This review indicates that most latent variables of interest to psychiatrists and personality and clinical psychologists are dimensional, and that many influential taxonic findings of early taxometric research are likely to be spurious.

Tree Species Traits but Not Diversity Mitigate Stem Breakage in a Subtropical Forest following a Rare and Extreme Ice Storm

PubMed Central

Nadrowski, Karin; Pietsch, Katherina; Baruffol, Martin; Both, Sabine; Gutknecht, Jessica; Bruelheide, Helge; Heklau, Heike; Kahl, Anja; Kahl, Tiemo; Niklaus, Pascal; Kröber, Wenzel; Liu, Xiaojuan; Mi, Xiangcheng; Michalski, Stefan; von Oheimb, Goddert; Purschke, Oliver; Schmid, Bernhard; Fang, Teng; Welk, Erik; Wirth, Christian

2014-01-01

Future climates are likely to include extreme events, which in turn have great impacts on ecological systems. In this study, we investigated possible effects that could mitigate stem breakage caused by a rare and extreme ice storm in a Chinese subtropical forest across a gradient of forest diversity. We used Bayesian modeling to correct stem breakage for tree size and variance components analysis to quantify the influence of taxon, leaf and wood functional traits, and stand level properties on the probability of stem breakage. We show that the taxon explained four times more variance in individual stem breakage than did stand level properties; trees with higher specific leaf area (SLA) were less susceptible to breakage. However, a large part of the variation at the taxon scale remained unexplained, implying that unmeasured or undefined traits could be used to predict damage caused by ice storms. When aggregated at the plot level, functional diversity and wood density increased after the ice storm. We suggest that for the adaption of forest management to climate change, much can still be learned from looking at functional traits at the taxon level. PMID:24879434

Evidence of taxon cycles in an Indo-Pacific passerine bird radiation (Aves: Pachycephala)

PubMed Central

Jønsson, Knud Andreas; Irestedt, Martin; Christidis, Les; Clegg, Sonya M.; Holt, Ben G.; Fjeldså, Jon

2014-01-01

Many insular taxa possess extraordinary abilities to disperse but may differ in their abilities to diversify and compete. While some taxa are widespread across archipelagos, others have disjunct (relictual) populations. These types of taxa, exemplified in the literature by selections of unrelated taxa, have been interpreted as representing a continuum of expansions and contractions (i.e. taxon cycles). Here, we use molecular data of 35 out of 40 species of the avian genus Pachycephala (including 54 out of 66 taxa in Pachycephala pectoralis (sensu lato), to assess the spatio-temporal evolution of the group. We also include data on species distributions, morphology, habitat and elevational ranges to test a number of predictions associated with the taxon-cycle hypothesis. We demonstrate that relictual species persist on the largest and highest islands across the Indo-Pacific, whereas recent archipelago expansions resulted in colonization of all islands in a region. For co-occurring island taxa, the earliest colonists generally inhabit the interior and highest parts of an island, with little spatial overlap with later colonists. Collectively, our data support the idea that taxa continuously pass through phases of expansions and contractions (i.e. taxon cycles). PMID:24403319

Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds.

PubMed

Hansen, Mie Johanne; Bertelsen, Mads Frost; Christensen, Henrik; Bojesen, Anders Miki; Bisgaard, Magne

2012-11-01

A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae. Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges-Proskauer and indole; no X- or V-factor dependency; and acid production from L-arabinose (slow), L-fucose, maltose and trehalose, but not from dulcitol, D-mannitol, D-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994(T)) are C(14:0), C(16:0), C(16:1)ω7c and the summed feature C(14:0) 3-OH/iso-C(16:1) I. This fatty acid profile is characteristic of members of the Pasteurellaceae. The quinone profile of Bisgaard taxon 57 (DSM 23800(T)) was similar to that of other genera in the Pasteurellaceae. The DNA G+C content of strain Baika1(T) is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae. On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1(T) (=CCUG 59994(T)=DSM 23800(T)), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.

Strategies for improving approximate Bayesian computation tests for synchronous diversification.

PubMed

Overcast, Isaac; Bagley, Justin C; Hickerson, Michael J

2017-08-24

Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Ψ), as well as the optimal strategies for data summarization. Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice of prior on Ψ on the estimation of co-divergence variability. We also introduce a new setting (β) that can potentially improve estimation of Ψ by enforcing a minimal temporal difference between pulses of co-divergence. We apply this new method to three empirical datasets: one dataset each of co-distributed taxon pairs of Panamanian frogs and freshwater fishes, and a large set of Neotropical butterfly sister-taxon pairs. We demonstrate that the choice of prior on Ψ has little impact on inference, but that sorting summary statistics yields substantially more reliable estimates of co-divergence variability despite violations of assumptions about exchangeability. We find the implementation of β improves estimation of Ψ, with improvement being most dramatic given larger numbers of taxon pairs. We find equivocal support for synchronous co-divergence for both of the Panamanian groups, but we find considerable support for asynchronous divergence among the Neotropical butterflies. Our simulation experiments demonstrate that using sorted summary statistics results in improved estimates of the variability in divergence times, whereas the choice of hyperprior on Ψ has negligible effect. Additionally, we demonstrate that estimating the number of pulses of co-divergence across co-distributed taxon-pairs is improved by applying a flexible buffering regime over divergence times. This improves the correlation between Ψ and the true variability in isolation times and allows for more meaningful interpretation of this hyperparameter. This will allow for more accurate identification of the number of temporally distinct pulses of co-divergence that generated the diversification pattern of a given regional assemblage of sister-taxon-pairs.

Pedoinformatics Approach to Soil Text Analytics

NASA Astrophysics Data System (ADS)

Furey, J.; Seiter, J.; Davis, A.

2017-12-01

The several extant schema for the classification of soils rely on differing criteria, but the major soil science taxonomies, including the United States Department of Agriculture (USDA) and the international harmonized World Reference Base for Soil Resources systems, are based principally on inferred pedogenic properties. These taxonomies largely result from compiled individual observations of soil morphologies within soil profiles, and the vast majority of this pedologic information is contained in qualitative text descriptions. We present text mining analyses of hundreds of gigabytes of parsed text and other data in the digitally available USDA soil taxonomy documentation, the Soil Survey Geographic (SSURGO) database, and the National Cooperative Soil Survey (NCSS) soil characterization database. These analyses implemented iPython calls to Gensim modules for topic modelling, with latent semantic indexing completed down to the lowest taxon level (soil series) paragraphs. Via a custom extension of the Natural Language Toolkit (NLTK), approximately one percent of the USDA soil series descriptions were used to train a classifier for the remainder of the documents, essentially by treating soil science words as comprising a novel language. While location-specific descriptors at the soil series level are amenable to geomatics methods, unsupervised clustering of the occurrence of other soil science words did not closely follow the usual hierarchy of soil taxa. We present preliminary phrasal analyses that may account for some of these effects.

Characterization of Elastic Properties of Interfaces in Composite Materials

DTIC Science & Technology

1990-09-01

ceramic Imatrix composites. These types of composite materials offer the advantages of being lighter, stiffer, stronger, and more resistant to creep and...actual composite materials. śi 3 II. Introduction The advantages offered by metal and ceramic matrix composites for strw, ural aerispace applications...minimum when ( VST /Vs) 2 = 0.8453... This corresponds to a situation analogous to a Rayleigh wave. As the ratio of the displacements increases, the ratio of

Simulations of Flame Acceleration and Deflagration-to-Detonation Transitions in Methane-Air Systems

DTIC Science & Technology

2010-03-17

are neglected. 3. Model parameter calibration The one-step Arrhenius kinetics used in this model cannot ex- actly reproduce all properties of laminar...with obstacles are compared to previ- ously reported experimental data. The results obtained using the simple reaction model qualitatively, and in...have taken in developing a multidimensional numerical model to study explosions in large-scale systems containing mixtures of nat- ural gas and air

High-Fidelity Multidisciplinary Design Using an Integrated Design Environment

DTIC Science & Technology

2007-08-14

Leovirivakit and A. .Jamneson, -- Case Studies ini Aero-St ruc(t ural NWing Planiforiii aiid Section Op- tifiization". 22`1~ AIAA Applied Aerodynamaiics...design of complete aircraft configurations. The work was focused on four main areas: (1) Flow solution algorithms for unstructured meshes, (2) Aero...Multi-Fidelity Design Optimization Studies for Supersonic lIets" . 13"’" AIAA Aerospace Sciences Meeting kc E’xhibit, AIAA Paper 2005- (0531, Reno. NV

European Missile Defense and Russia

DTIC Science & Technology

2014-07-01

defense system in Europe by 2018 , which involved four phases at the time. The first phase consisted of an early warning radar estab- lished in Turkey...bal- listic missile interceptor site in Europe, slated to be operational in Redizkowo, Poland, by 2018 , equipped with the SM-3 Block IIA interceptor...fourth phases, that is towards 2018 and 2020, the U.S. missile defence sector almost reaches Russia’s Urals. This is not what we have agreed on.29

Repressive States and Insurgencies: Implications for Future Campaigns

DTIC Science & Technology

2006-03-12

dissatisfied with the legitimacy of their government who sought to overthrow the ruling power by force. In contrast, “liberation insurgencies” pit insurgents...nuclear war. The history of the fighting behind the German lines, pitting various German security divisions, commands, and leaders against Soviet...Russian revolution was to Vasili Bliukher, who received the Order of the Red Banner for leading his 6,000 man ‘Urals Partisan Army’ on a 900-mile raid

Body Size Is a Significant Predictor of Congruency in Species Richness Patterns: A Meta-Analysis of Aquatic Studies

PubMed Central

Velghe, Katherine; Gregory-Eaves, Irene

2013-01-01

Biodiversity losses over the next century are predicted to result in alterations of ecosystem functions that are on par with other major drivers of global change. Given the seriousness of this issue, there is a need to effectively monitor global biodiversity. Because performing biodiversity censuses of all taxonomic groups is prohibitively costly, indicator groups have been studied to estimate the biodiversity of different taxonomic groups. Quantifying cross-taxon congruence is a method of evaluating the assumption that the diversity of one taxonomic group can be used to predict the diversity of another. To improve the predictive ability of cross-taxon congruence in aquatic ecosystems, we evaluated whether body size, measured as the ratio of average body length between organismal groups, is a significant predictor of their cross-taxon biodiversity congruence. To test this hypothesis, we searched the published literature and screened for studies that used species richness correlations as their metric of cross-taxon congruence. We extracted 96 correlation coefficients from 16 studies, which encompassed 784 inland water bodies. With these correlation coefficients, we conducted a categorical meta-analysis, grouping data based on the body size ratio of organisms. Our results showed that cross-taxon congruence is variable among sites and between different groups (r values ranging between −0.53 to 0.88). In addition, our quantitative meta-analysis demonstrated that organisms most similar in body size showed stronger species richness correlations than organisms which differed increasingly in size (radj 2 = 0.94, p = 0.02). We propose that future studies applying biodiversity indicators in aquatic ecosystems consider functional traits such as body size, so as to increase their success at predicting the biodiversity of taxonomic groups where cost-effective conservation tools are needed. PMID:23468903

Phytophthora morindae, a new species causing black flag disease on noni (Morinda citrifolia L) in Hawaii.

PubMed

Nelson, Scot C; Abad, Z Gloria

2010-01-01

A homothallic, papillate Phytophthora species causing foliar and fruit blight of noni (Morinda citrifolia var. citrifolia) in Hawaii was identified. The asexual phase of this species is characterized by the production of umbellate sporangiophores and papillate sporangia that are ellipsoid and obpyriform with conspicuously tapered bases and possess caducous, medium to long pedicels. The sexual phase is characterized by the production of oogonia with tapered bases, small amphigynous antheridia and thick-walled, plerotic oospores. The morphology of the taxon does not match any of the valid 95 Phytophthora species described to date. Phylogenetic analysis based on sequences of the internal transcribed spacer rDNA region (ITS) and the translation elongation factor 1 alpha (EF-1 alpha) of this taxon and those from other Phytophthora species from GenBank and the Phytophthora database indicates that the new taxon is most closely related to species in ITS clade 10, including P. kernoviae, P. boehmeriae and the recently described P. gallica. The most closely related species is P. kernoviae, an invasive plant pathogen causing bleeding stem lesions on forest trees (beech, Fagus sylvatica) and foliar necrosis of ornamentals (rhododendron, pieris and magnolia) in the UK, and isolated in New Zealand from necrotic cherimoya shoots and fruits and soil. Although the morphological characters of the sexual phase of P. morindae and P. kernoviae are similar, the umbellate sporangiophores produced by the new taxon marks the main morphological distinction. In this paper we describe the morphological characteristics, the phylogenetic relationships and pathogenicity characteristics that support the description of this taxon as a new species with the proposed name Phytophthora morindae sp. nov.

Phenex: ontological annotation of phenotypic diversity.

PubMed

Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

2010-05-05

Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

Unidirectional hybrid male sterility from crosses between species A and species B of the taxon Anopheles (Cellia) culicifacies Giles.

PubMed

Miles, S J

1981-02-01

Crosses between species A females and species B males of the taxon Anopheles culicifacies give F1 males with undeveloped testes, reduced vasa deferentia, and apparently normal accessory glands. F1 males from the reciprocal cross, and F1 hybrid females from both reciprocal crosses are fertile, though their fertility is less than that of either parental species

Diamond and Unusual Minerals Discovered from the Chromitite in Polar Ural: A First Report

NASA Astrophysics Data System (ADS)

Yang, J.; Bai, W.; Fang, Q.; Meng, F.; Chen, S.; Zhang, Z.

2007-12-01

Ultrahigh pressure (UHP) minerals, such as diamond, coesite, and pseudomorphs of octahedral olivine, and as well as about 80 other mineral species have been recovered from podiform chromitites of the Luobusa ophiolite, southern Tibet, and a new mineral, Luobusaite (Fe0.82Si2), has been approved recently by CNMMN. The UHP minerals from Luobusa are controversial because they have not found in situ and because ophiolites are currently believed to form at shallow levels above oceanic spreading centers. More detailed study and experimental work are needed to understand the origin and significance of these unusual minerals and investigations of other ophiolites are needed to determine if such minerals occur elsewhere. For this purpose, we collected about 1500 kg of chromitite from two orebodies in an ultramafic body in the Polar Urals. Thus far, more than 60 different mineral species have been separated from these ores. The most exciting discovery is the common occurrence of diamond, a typical UHP mineral in the Luobusa chromitites. Diamonds from Ural chromitite are clear, colorless, well-developed crystals with octahedral morphology, generally 0.2-0.3 mm in size. Attached with the diamonds and perhaps also occurring as inclusions within them are many minerals as chromite, MnNiCrFe alloy, native Si and Ta, corundum, zircon, feldspar, garnet, moissanite, confirming their natural origin and suggesting a long residence time in the mantle. Other mineral group include: (1) native elements: Cr, W, Ni, Co, Si, Al and Ta; (2) carbides: SiC and WC; (3) alloys: Cr-Fe, Si-Al-Fe, Ni-Cu, Ag-Au, Ag-Sn, Fe-Si, Fe-P, and Ag-Zn-Sn; (4) oxides: NiCrFe, PbSn, REE, rutile and Si- bearing rutile, ilmenite, corundum, chromite, MgO, and SnO2; (5) silicates: kyanite, pseudomorphs of octahedral olivine, zircon, garnet, feldspar, and quartz,; (6) sulfides of Fe, Ni, Cu, Mo, Pb, Ab, AsFe, FeNi, CuZn, and CoFeNi; and (7) iron groups: native Fe, FeO, and Fe2O3. These minerals are very similar in composition and structure to those reported from the Luobusa chromitites. For examples, some spherules of native iron contain spherical inclusions of FeO, exactly like comparable grains in the Luobusa sample.

Mariinskite, BeCr2O4, a new mineral, chromium analog of chrysoberyl

NASA Astrophysics Data System (ADS)

Pautov, L. A.; Popov, M. P.; Erokhin, Yu. V.; Khiller, V. V.; Karpenko, V. Yu.

2013-12-01

A new mineral, mariinskite, BeCr2O4, the chromium analog of chrysoberyl, has been found at the Mariinsky (Malyshevo) deposit, the Ural Emerald Mines, the Central Urals, Russia. The mineral is named after its type locality. It was discovered in chromitite in association with fluorphlogopite, Cr-bearing muscovite, eskolaite, and tourmaline. Mariinskite occurs as anhedral grains ranging from 0.01 to 0.3 mm in size; in some cases it forms pseudohexagonal chrysoberyl-type twins. The mineral is dark-green, with a pale green streak; the Mohs' hardness is 8.5, microhardness VHN = 1725 kg/mm2. D meas = 4.25(2) g/cm3, D calc = 4.25 g/cm3. Microscopically, it is emerald-green, pleochroic from emerald-green (γ) to yellow-green (β) and greenish yellow (α). The new mineral is biaxial (+), γ = 2.15(1), β = 2.09(3), and α = 2.05(1), 2 V meas = 80 ± (10)°, 2 V calc = 80.5°. In reflected light, it is gray with green reflections; R max (589) = 12.9%; R min (589) = 12.3%, and there are strong, internal green reflections. The strongest absorption bands in the IR spectrum are as follows (cm-1): 935, 700, 614, 534. Space group Pnma, a = 9.727(3), b = 5.619(1), c = 4.499(1) Å, V = 245.9(3) Å3, Z = 4. The strongest reflections in the X-ray powder diffraction pattern are as follows ( d Å, I, hkl): 4.08(40)(101), 3.31(90)(111), 2.629(50)(301), 2.434(50)(220), 2.381(40)(311), 2.139(60)(221), 1.651(100)(222). The average chemical composition of mariinskite (electron microprobe, wt %) is as follows: BeO 16.3, Al2O3 23.89, Cr2O3 58.67, Fe2O3 0.26, V2O3 0.26, TiO2 0.61, total is 99.98. The empirical formula, calculated on the basis of four O atoms is Be1.03(Cr1.22Al0.74Ti0.01Fe0.01V0.01)1.99O4. The compatibility index 1 - (Kp/Kc), 0.019, is excellent. The type specimens are deposited in the Fersman Mineralogical Museum, Russian Academy of Sciences, Moscow, and the Ural Geological Museum, Yekaterinburg, Russia.

CTC Sentinel. Volume 6, Issue 6, June 2013

DTIC Science & Technology

2013-06-01

failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE JUN 2013 2. REPORT...different in a number of other ways. Both communities are in conflict with flee- ing Syrian refugees and rebels in Hatay Province. See Khairi Abaza and...in Damascus on May 28, 2013,24 Ural has been noted among Syria’s fearful coastal Alawite communities as having oratory skills akin to that of a

Visual Enhancement of Laparoscopic Partial Nephrectomy With 3-Charge Coupled Device Camera: Assessing Intraoperative Tissue Perfusion and Vascular Anatomy by Visible Hemoglobin Spectral Response

DTIC Science & Technology

2010-10-01

open nephron spanng surgery a single institution expenence. J Ural 2005; 174: 855 21 Bhayan• SB, Aha KH Pmto PA et al Laparoscopic partial...noninvasively assess laparoscopic intraoperative changes in renal tissue perfusion during and after warm ischemia. Materials and Methods: We analyzed select...TITLE AND SUBTITLE Visual Enhancement of Laparoscopic Partial Nephrectomy With 3-Charge Coupled Device Camera: Assessing Intraoperative Tissue

ASPECTS OF ALTAIC CIVILIZATION, PROCEEDINGS OF THE MEETING OF THE PERMANENT INTERNATIONAL ALTAISTIC CONFERENCE (5TH, INDIANA UNIVERSITY, JUNE 4-9, 1962). URALIC AND ALTAIC SERIES, VOLUME 23.

ERIC Educational Resources Information Center

FRANCIS, DAVID; SINOR, DENIS

THE 25 PAPERS APPEARING IN THIS SELECTION ARE GROUPED BY THE FOLLOWING GENERAL TOPICS AND AUTHORS--(A) "THE DWELLING OF THE ALTAIC PEOPLES"--S. CAMMANN, K. CZEGLEDY, M. ESZTERGAR, A. VON GABAIN, AND A. RONA-TAS, (B) "FORMS OF CULTURAL AND MUSICAL EXPRESSION AMONG THE ALTAIC PEOPLES"--P. AALTO, C. BAWDEN, A. BOMBACI, J. ECKMANN, AND K. SAGASTER,…

City of Troitsk and Sooty Snow, Chelyabinsk, CIS

NASA Technical Reports Server (NTRS)

1992-01-01

This view shows the industrial pollution around the Siberian city of Troitsk (54.0N, 61.0E). Troitsk is the smallest of a group of three heavy industrial cities east of the Urals, the others being Magnitogorsk and Chelyabinsk. All have been cited as being some of the worst industrial polluted cities in the CIS. Despite being the smallest of the three, Troitsk has the largest area of soot blackened snow. Respiratory diseases among the citizens are chronic.

High-throughput SNP-genotyping analysis of the relationships among Ponto-Caspian sturgeon species

PubMed Central

Rastorguev, Sergey M; Nedoluzhko, Artem V; Mazur, Alexander M; Gruzdeva, Natalia M; Volkov, Alexander A; Barmintseva, Anna E; Mugue, Nikolai S; Prokhortchouk, Egor B

2013-01-01

Abstract Legally certified sturgeon fisheries require population protection and conservation methods, including DNA tests to identify the source of valuable sturgeon roe. However, the available genetic data are insufficient to distinguish between different sturgeon populations, and are even unable to distinguish between some species. We performed high-throughput single-nucleotide polymorphism (SNP)-genotyping analysis on different populations of Russian (Acipenser gueldenstaedtii), Persian (A. persicus), and Siberian (A. baerii) sturgeon species from the Caspian Sea region (Volga and Ural Rivers), the Azov Sea, and two Siberian rivers. We found that Russian sturgeons from the Volga and Ural Rivers were essentially indistinguishable, but they differed from Russian sturgeons in the Azov Sea, and from Persian and Siberian sturgeons. We identified eight SNPs that were sufficient to distinguish these sturgeon populations with 80% confidence, and allowed the development of markers to distinguish sturgeon species. Finally, on the basis of our SNP data, we propose that the A. baerii-like mitochondrial DNA found in some Russian sturgeons from the Caspian Sea arose via an introgression event during the Pleistocene glaciation. In the present study, the high-throughput genotyping analysis of several sturgeon populations was performed. SNP markers for species identification were defined. The possible explanation of the baerii-like mitotype presence in some Russian sturgeons in the Caspian Sea was suggested. PMID:24567827

Atlantic Multidecadal Oscillation Modulates the Impacts of Arctic Sea Ice Decline

NASA Astrophysics Data System (ADS)

Li, Fei; Orsolini, Yvan J.; Wang, Huijun; Gao, Yongqi; He, Shengping

2018-03-01

The Arctic sea ice cover has been rapidly declining in the last two decades, concurrent with a shift in the Atlantic Multidecadal Oscillation (AMO) to its warm phase around 1996/1997. Here we use both observations and model simulations to investigate the modulation of the atmospheric impacts of the decreased sea ice cover in the Atlantic sector of the Arctic (AASIC) by the AMO. We find that the AASIC loss during a cold AMO phase induces increased Ural blocking activity, a southeastward-extended snowpack, and a cold continent anomaly over Eurasia in December through northerly cold air advection and moisture transport from the Arctic. The increased Ural blocking activity and more extended Eurasian snowpack strengthen the upward propagation of planetary waves over the Siberian-Pacific sector in the lower stratosphere and hence lead to a weakened stratospheric polar vortex and a negative Arctic Oscillation (AO) phase at the surface in February. However, corresponding to the AASIC loss during a warm AMO phase, one finds more widespread warming over the Arctic and a reduced snowpack over Northern Eurasia in December. The stratosphere-troposphere coupling is suppressed in early winter and no negative AO anomaly is found in February. We suggest that the cold AMO phase is important to regulate the atmospheric response to AASIC decline, and our study provides insight to the ongoing debate on the connection between the Arctic sea ice and the AO.

White-nose syndrome detected in bats over an extensive area of Russia.

PubMed

Kovacova, Veronika; Zukal, Jan; Bandouchova, Hana; Botvinkin, Alexander D; Harazim, Markéta; Martínková, Natália; Orlov, Oleg L; Piacek, Vladimir; Shumkina, Alexandra P; Tiunov, Mikhail P; Pikula, Jiri

2018-06-18

Spatiotemporal distribution patterns are important infectious disease epidemiological characteristics that improve our understanding of wild animal population health. The skin infection caused by the fungus Pseudogymnoascus destructans emerged as a panzootic disease in bats of the northern hemisphere. However, the infection status of bats over an extensive geographic area of the Russian Federation has remained understudied. We examined bats at the geographic limits of bat hibernation in the Palearctic temperate zone and found bats with white-nose syndrome (WNS) on the European slopes of the Ural Mountains through the Western Siberian Plain, Central Siberia and on to the Far East. We identified the diagnostic symptoms of WNS based on histopathology in the Northern Ural region at 11° (about 1200 km) higher latitude than the current northern limit in the Nearctic. While body surface temperature differed between regions, bats at all study sites hibernated in very cold conditions averaging 3.6 °C. Each region also differed in P. destructans fungal load and the number of UV fluorescent skin lesions indicating skin damage intensity. Myotis bombinus, M. gracilis and Murina hilgendorfi were newly confirmed with histopathological symptoms of WNS. Prevalence of UV-documented WNS ranged between 16 and 76% in species of relevant sample size. To conclude, the bat pathogen P. destructans is widely present in Russian hibernacula but infection remains at low intensity, despite the high exposure rate.

Possible mechanisms for four regimes associated with cold events over East Asia

NASA Astrophysics Data System (ADS)

Yang, Zifan; Huang, Wenyu; Wang, Bin; Chen, Ruyan; Wright, Jonathon S.; Ma, Wenqian

2017-09-01

Circulation patterns associated with cold events over East Asia during the winter months of 1948-2014 are classified into four regimes by applying a k-means clustering method based on the area-weighted pattern correlation. The earliest precursor signals for two regimes are anticyclonic anomalies, which evolve into Ural and central Siberian blocking-like circulation patterns. The earliest precursor signals for the other two regimes are cyclonic anomalies, both of which evolve to amplify the East Asian trough (EAT). Both the blocking-like circulation patterns and amplified EAT favor the initialization of cold events. On average, the blocking-related regimes tend to last longer. The lead time of the earliest precursor signal for the central Siberian blocking-related regime is only 4 days, while those for the other regimes range from 16 to 18 days. The North Atlantic Oscillation plays essential roles both in triggering the precursor for the Ural blocking-related regime and in amplifying the precursors for all regimes. All regimes preferentially occur during the positive phase of the Eurasian teleconnection pattern and the negative phase of the El Niño-Southern Oscillation. For three regimes, surface cooling is primarily due to reduced downward infrared radiation and enhanced cold advection. For the remaining regime, which is associated with the southernmost cooling center, sensible and latent heat release and horizontal cold advection dominate the East Asian cooling.

Climate and Vegetation Changes over the Past 7000 Years in the Cis-Ural Steppe

NASA Astrophysics Data System (ADS)

Khokhlova, O. S.; Morgunova, N. L.; Khokhlov, A. A.; Gol'eva, A. A.

2018-05-01

A multilayered archaeological site Turganik Settlement in the valley of the Tok River in the Cis- Ural steppe (Orenburg oblast) was examined with the use of paleopedological and microbiomorph methods. Ancient people inhabited this area in the Latest Neolithic (Eneolithic) (5th millennium BC) and Early Bronze (4th millennium BC) ages. It was found that cultural layers dating back to the Atlantic period of the Holocene had been formed under conditions of a predominance of grassy-forb vegetation with a small portion of tree species and dry climate; the ancient settlement was not affected by floods and was suitable for permanent living. It is probable that soils of the chestnut type with salinization and solonetzic features were developed in that time. The final stages of the accumulation of cultural layers were marked by strong shortterm floods, whose sediments partly masked the features of the previous long arid epoch. The highest degree of aridity was at the end of the Atlantic period. In the Subboreal and Subatlantic periods, soils of the meadowchernozemic type were formed; the spore-pollen spectra of these periods are characterized by a higher portion of tree species and by the presence of phytoliths of meadow grasses. The climatic conditions were generally colder and more humid, though some short-term aridization stages could take place. Some of these stages are recorded in the thickness of the studied sediments.

In utero exposure to radiation and haematological malignancies: pooled analysis of Southern Urals cohorts

PubMed Central

Schüz, Joachim; Deltour, Isabelle; Krestinina, Lyudmila Y; Tsareva, Yulia V; Tolstykh, Evgenia I; Sokolnikov, Mikhail E; Akleyev, Alexander V

2017-01-01

Background: It is scientifically uncertain whether in utero exposure to low-dose ionising radiation increases the lifetime risk of haematological malignancies. Methods: We pooled two cohorts from the Southern Urals comprising offspring of female workers of a large nuclear facility (the Mayak Production Association) and of women living in areas along the Techa River contaminated by nuclear accidents/waste from the same facility, with detailed dosimetry. Results: The combined cohort totalled 19 536 subjects with 700 504 person-years at risk over the period of incidence follow-up, and slightly more over the period of mortality follow-up, yielding 58 incident cases and 36 deaths up to age 61 years. Risk was increased in subjects who received in utero doses of ⩾80 mGy (excess relative risk (ERR): 1.27; 95% confidence interval (CI): −0.20 to 4.71), and the risk increased consistently per 100 mGy of continuous exposure in utero (ERR: 0.77; CI: 0.02 to 2.56). No association was apparent in mortality-based analyses. Results for leukaemia and lymphoma were similar. A very weak positive association was observed between incidence and postnatal exposure. Conclusions: In summary, the results suggest a positive association between in utero exposure to ionising radiation and risk of haematological malignancies, but the small number of outcomes and inconsistent incidence and mortality findings preclude firm conclusions. PMID:27855443

Cyclic variation in seasonal recruitment and the evolution of the seasonal decline in Ural owl clutch size.

PubMed Central

Brommer, Jon E; Pietiäinen, Hannu; Kokko, Hanna

2002-01-01

Plastic life-history traits can be viewed as adaptive responses to environmental conditions, described by a reaction norm. In birds, the decline in clutch size with advancing laying date has been viewed as a reaction norm in response to the parent's own (somatic or local environmental) condition and the seasonal decline in its offspring's reproductive value. Theory predicts that differences in the seasonal recruitment are mirrored in the seasonal decrease in clutch size. We tested this prediction in the Ural owl. The owl's main prey, voles, show a cycle of low, increase and peak phases. Recruitment probability had a humped distribution in both increase and peak phases. Average recruitment probability was two to three times higher in the increase phase and declined faster in the latter part of the season when compared with the peak phase. Clutch size decreased twice as steep in the peak (0.1 eggs day-1) as in the increase phase (0.05 eggs day-1). This result appears to refute theoretical predictions of seasonal clutch size declines. However, a re-examination of current theory shows that the predictions of modelling are less robust to details of seasonal condition accumulation in birds than originally thought. The observed pattern can be predicted, assuming specifically shaped seasonal increases in condition across individuals. PMID:11916482

Application of the soil-ecological multiplicative index to assess suitability of Cis-Ural chernozems for cultivation with due account for economic parameters

NASA Astrophysics Data System (ADS)

Levykin, S. V.; Chibilev, A. A.; Kazachkov, G. V.; Petrishchev, V. P.

2017-02-01

The evolution of Russian concepts concerning the assessment of soil suitability for cultivation in relation to several campaigns on large-scale plowing of virgin steppe soils is examined. The major problems of agricultural land use in steppe areas—preservation of rainfed farming in the regions with increasing climatic risks, underestimation of the potential of arable lands in land cadaster assessments, and much lower factual yields in comparison with potential yields—are considered. It is suggested that the assessments of arable lands should be performed on the basis of the soil-ecological index (SEI) developed by I. Karmanov with further conversion of SEI values into nominal monetary values. Under conditions of land reforms and economic reforms, it is important to determine suitability of steppe chernozems for plowing and economic feasibility of their use for crop growing in dependence on macroeconomic parameters. This should support decisions on optimization of land use in the steppe zone on the basis of the principles suggested by V. Dokuchaev. The developed approach for assessing soil suitability for cultivation was tested in the subzone of herbaceous-fescue-feather grass steppes in the Cis-Ural part of Orenburg oblast and used for the assessment of soil suitability for cultivation in the southern and southeastern regions of Orenburg oblast.

Use of taxon-specific competitive-priming PCR to study host specificity, hybridization, and intergroup gene flow in intersterility groups of Heterobasidion annosum

Treesearch

M. Garbelotto; A. Ratcliff; T.D. Bruns; F.W. Cobb; W.J. Otrosina

1996-01-01

Two intersterility groups (ISGs) of the forest pathogen Heterobasidion annosum are found in California: S and P.We devised a polymerase chain reaction (PCR) method called taxon- specific competitive-priming (TSCP) PCR to differentiate the two ISGs.Using TSCP-PCR, we typed 537 live isolates and dry basidiocarps from 204 trees and 114 stumps from 60 sites in eight...

Homosexuality as a Discrete Class.

PubMed

Norris, Alyssa L; Marcus, David K; Green, Bradley A

2015-12-01

Previous research on the latent structure of sexual orientation has returned conflicting results, with some studies finding a dimensional structure (i.e., ranging quantitatively along a spectrum) and others a taxonic structure (i.e., categories of individuals with distinct orientations). The current study used a sample (N = 33,525) from the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC). A series of taxometric analyses were conducted using three indicators of sexual orientation: identity, behavior, and attraction. These analyses, performed separately for women and men, revealed low-base-rate same-sex-oriented taxa for men (base rate = 3.0%) and women (base rate = 2.7%). Generally, taxon membership conferred an increased risk for psychiatric and substance-use disorders. Although taxa were present for men and women, women demonstrated greater sexual fluidity, such that any level of same-sex sexuality conferred taxon membership for men but not for women. © The Author(s) 2015.

Absolute quantification of microbial taxon abundances.

PubMed

Props, Ruben; Kerckhof, Frederiek-Maarten; Rubbens, Peter; De Vrieze, Jo; Hernandez Sanabria, Emma; Waegeman, Willem; Monsieurs, Pieter; Hammes, Frederik; Boon, Nico

2017-02-01

High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). Our results highlight that both relative and absolute abundances should be considered for a comprehensive biological interpretation of microbiome surveys.

[Recent advance in Geodermatophilaceae--A review].

PubMed

Hongmin, Sun; Liyan, Yu; Yuqin, Zhang

2015-12-04

The family Geodermatophilaceae is a newly established actinobacterial taxon. Normand ever proposed the family Geodermatophilaceae in 1996, which was recognized as an invalid taxon at that time. In 2006, based on the common characteristics of the genera Geodermatophilus, Blastococcus and Modestobacter, Normand summarized the typical characteristics of Geodermatophilaceae, then the family Geodermatophilaceae was finally accommodated as a validly described taxon in the phylum Actinobacteria. Up to date, the family Geodermatophilaceae consisted of 3 genera, i. e., Geodermatophilus, Blastococcus and Modestobacter, including 25 validly described species. The members of the family Geodermatophilaceae were considered as biologic pioneers in extreme environments, exhibiting many potential advantages in the study of mechanism of stress resistance, desertification control and environmental remediation. The objective of this review is to summarize the research advances in the family Geodermatophilaceae, including the establishment and taxonomic characteristics of the family, as well as their application prospect and the roles in the field of ecology.

A new species of broad-nosed bat Platyrrhinus Saussure, 1860 (Chiroptera:   Phyllostomidae) from the Guianan Shield.

PubMed

Velazco, Paúl M; Lim, Burton K

2014-05-16

A new species of broad-nosed bat Platyrrhinus Saussure, 1860 (Chiroptera: Phyllostomidae: Stenodermatinae) from the Guianan Shield is described based on molecular and morphological data. Previously confused with P. helleri and P. recifinus, the new taxon is currently known from only Guyana and Suriname and is most closely related to P. recifinus from eastern Brazil and not to the two sympatric species (P. fusciventris and P. incarum) also recently recognized as distinct from P. helleri. Morphometrically the new taxon overlaps with the smaller species of the genus (P. angustirostris, P. brachycephalus, P. fusciventris, P. helleri, P. incarum, and P. matapalensis), but forms a different cluster from the larger P. recifinus. Morphologically the new taxon is distinguished from its congeners by a combination of external and craniodental characteristics. Platyrrhinus now includes 21 species making it the most speciose genus in the Neotropical family Phyllostomidae.

A reappraisal of the morphology and systematic position of the theropod dinosaur Sigilmassasaurus from the “middle” Cretaceous of Morocco

PubMed Central

Rauhut, Oliver W.M.; Milner, Angela C.; McFeeters, Bradley; Allain, Ronan

2015-01-01

Sigilmassasaurus brevicollis is an enigmatic theropod dinosaur from the early Late Cretaceous (Cenomanian) of Morocco, originally based on a few isolated cervical vertebrae. Ever since its original description, both its taxonomic validity and systematic affinities were contentious. Originally considered to represent its own family, Sigilmassasauridae, the genus has variously been suggested to represent a carcharodontosaurid, an ornithischian, and, more recently, a spinosaurid. Here we describe new remains referrable to this taxon and re-evaluate its taxonomic status and systematic affinities. Based on the new remains, a re-evaluation of the original materials, and comparisons with other spinosaurids, the holotype of Sigilmassasaurus brevicollis is identified as an anterior dorsal, rather than a cervical vertebra, and differences between elements referred to this taxon can be explained by different positions of the elements in question within the vertebral column. Many characters used previously to diagnose the genus and species are found to be more widespread among basal tetanurans, and specifically spinosaurids. However, the taxon shows several autapomorphies that support its validity, including the presence of a strongly rugose, ventrally offset triangular platform that is confluent with a ventral keel anteriorly in the mid-cervical vertebral centra and a strongly reduced lateral neural arch lamination, with no or an incomplete distinction between anterior and posterior centrodiapophyseal laminae in the posterior cervical and anterior dorsal vertebrae. We argue furthermore that Spinosaurus maroccanus, also described on the basis of isolated cervical vertebrae from the same stratigraphic unit and in the same paper as Sigilmassasaurus brevicollis, is a subjective synonym of the latter. Both a detailed comparison of this taxon with other theropods and a formal phylogenetic analysis support spinosaurid affintities for Sigilmassasaurus. However, we reject the recently proposed synonymy of both Spinosaurus maroccanus and Sigilmassasurus brevicollis with Spinosaurus aegyptiacus from the Cenomanian of Egypt, as there are clear differences between the vertebrae of these taxa, and they do not share any derived character that is not found in other spinosaurids. Together with a comparison with other spinosaurid vertebral material from the Kem Kem, this suggests that more than one taxon of spinosaurid was present in the Kem Kem assemblage of Morocco, so the referral of non-overlapping material from this unit to a single taxon should be regarded with caution. PMID:26500829

[Once again about "Gregg paradox" and its solution].

PubMed

Mavrodiev, E V

2002-01-01

"Gregg paradox" means that monotypical groups containing the same species (or groups of species) will be equal each other although systematics considers them as different taxa. Thus if the order of placental mammalia Tubilidentata includes one species aardvark Orycteropus after, the order itself, its single family Orycteropodiaceae, single genus of the family Orycteropus and the single species Orycteropus after can be considered as equal to each other. To solve this disagreement the author asserts that taxa of any level can be regarded as an individual according to the taxa of higher rank. Possibility of such interpretation was already suggested by Georg Cantor (1985). He supposed that a set (class) can be regarded as unity by itself. In this case connections between taxa of different levels can be realized by Peano ratio of intrasitive conformities. In this model a genus will consist of species but not individuals, a type--of classes, etc. Thus, if a taxon x as an individual is an element of taxon y, and taxon y as an individual is an element of taxon z, then z according to x will be not only logical class, but class of classes and, hence we could not consider x as an element of z, because the latter consists of indecomposable individual-class y or some similar classes. In this situation "Gregg paradox" does not arise.

A reappraisal of Polyptychodon (Plesiosauria) from the Cretaceous of England

PubMed Central

2016-01-01

Pliosauridae is a globally distributed clade of aquatic predatory amniotes whose fossil record spans from the Lower Jurassic to the Upper Cretaceous. However, the knowledge of pliosaurid interrelationships remains limited. In part, this is a consequence of a few key taxa awaiting detailed reassessment. Among them, the taxon Polyptychodon is of special importance. It was established on isolated teeth from the mid-Cretaceous strata of East and South East England and subsequently associated with numerous finds of near-cosmopolitan distribution. Here the taxon is reassessed based on the original dental material from England, with special focus on a large collection of late Albian material from the Cambridge Greensand near Cambridge. The dental material is reviewed here from historical and stratigraphic perspective, described in detail, and discussed in terms of its diagnostic nature. The considerable morphological variability observed in the teeth attributed to Polyptychodon, together with a wide stratigraphic range of the ascribed material, possibly exceeding 35 Ma (early Aptian to ?middle Santonian), suggests that the taxon is based on a multispecies assemblage, possibly incorporating members of different plesiosaur clades. Due to the absence of any autapomorphic characters or unique character combinations in the original material, Polyptychodon interruptus, the type species of Polyptychodon, is considered nomen dubium. From a global perspective, Polyptychodon is viewed as a wastebasket taxon whose material originating from different localities should be reconsidered separately. PMID:27190712

BUMPER v1.0: a Bayesian user-friendly model for palaeo-environmental reconstruction

NASA Astrophysics Data System (ADS)

Holden, Philip B.; Birks, H. John B.; Brooks, Stephen J.; Bush, Mark B.; Hwang, Grace M.; Matthews-Bird, Frazer; Valencia, Bryan G.; van Woesik, Robert

2017-02-01

We describe the Bayesian user-friendly model for palaeo-environmental reconstruction (BUMPER), a Bayesian transfer function for inferring past climate and other environmental variables from microfossil assemblages. BUMPER is fully self-calibrating, straightforward to apply, and computationally fast, requiring ˜ 2 s to build a 100-taxon model from a 100-site training set on a standard personal computer. We apply the model's probabilistic framework to generate thousands of artificial training sets under ideal assumptions. We then use these to demonstrate the sensitivity of reconstructions to the characteristics of the training set, considering assemblage richness, taxon tolerances, and the number of training sites. We find that a useful guideline for the size of a training set is to provide, on average, at least 10 samples of each taxon. We demonstrate general applicability to real data, considering three different organism types (chironomids, diatoms, pollen) and different reconstructed variables. An identically configured model is used in each application, the only change being the input files that provide the training-set environment and taxon-count data. The performance of BUMPER is shown to be comparable with weighted average partial least squares (WAPLS) in each case. Additional artificial datasets are constructed with similar characteristics to the real data, and these are used to explore the reasons for the differing performances of the different training sets.

Seminar on Soviet Military Manpower: A Focus on the Soviet Military District, held at the University of Edinburgh, Edinburgh, Scotland, 5-7 April 1978.

DTIC Science & Technology

1978-01-01

irrational uses of labor inputs, improvement of training and skills of cadres, and providing more amenitiesi 6 the Siberian and Far Eastern regions of the... Siberian Military Districts, geography and nature impel the local military authorities to devote much manpower for provision of essential food supplies...awarded to the Belorussian, Kiev, Odessa, North Caucasus and Turkestan Military Districts in 1968; to the Baltic, Carpathian, Volga, Urals, Siberian

[The medical support of resettlement of peasants in Siberia during the Stolypin reform].

PubMed

Yegorysheva, I V; Gontcharova, S G

2013-01-01

The article considers the organization of medical care of settlers en route and in places of their settlement beyond the Ural during the Stolypin agrarian reform. The role of P.A. Stolypin, the Chairman of Council of ministers is demonstrated concerning the application of urgent measures on improvement of functioning of departments, controlling the resettlement and arrangement of peasants at new places. The development of resettlement medicine patterned after zemstvo medicine enhanced the penetration of scientific medicine into inaccessible regions of country.

Retrospective dosimetry related to chronic environmental exposure

NASA Technical Reports Server (NTRS)

Degteva, M. O.; Kozheurov, V. P.; Tolstykh, E. I.; Neta, R. (Principal Investigator)

1998-01-01

Radioactive contamination of the environment occurred in the early fifties as a result of the releases from the Mayak plutonium production complex (Southern Urals, Russia). The releases of liquid wastes into the Techa river resulted in chronic exposure of 30,000 residents of the riverside communities. Since 1951 90Sr body burdens have been measured for over half of this cohort. This paper presents the analysis of data on 90Sr in humans and describes the reconstruction of internal doses for these people.

Analysis of Chronic Radiation Sickness Cases in the Population of the Southern Urals

DTIC Science & Technology

1994-08-01

manufacturing plant. She usually felt very tired by the end of her work- day. Her medical history included flu, parotitis, measles, scarlet fever , and...childhood. He had typhoid fever at the berg et al. [271, external radiation at the patient’s age of 17 and malaria at the age of 22. The onset of...introduced for natural 40K radioactivity. With the ena ( petechial skin eruption, hemorihages into the deduction of this value, the net activity of beta

USSR Report Agriculture No. 1399.

DTIC Science & Technology

1983-09-15

from inflammation of the udder. It is easy to estimate that for an average milk yield of 2,054 kilograms, the loss for one mastitis cow is 400...important and vital one. Thus it is apparent that milk losses in the Urals caused by injury to the udders, the cow going dry and mastitis amount to...the cow from drying up and eliminate mastitis and if we maintain the cows at the required state of nourishment, then each year we should be able to

New Light-Time Curve of Eclipsing Binary AM Leo

NASA Astrophysics Data System (ADS)

Gorda, S. Yu.; Matveeva, E. A.

2017-12-01

We present 72 photoelectric and CCD times of minima of eclipsing binary AM Leo obtained mainly during at Kourovka Astronomical Observatory of the Ural Federal University in Russia. We obtained new values of period of 50.5 years and eccentricity of 0.28 of the orbit of the eclipsing pair around the mass center of the system AM Leo with the third body. These results have been received taking into account the times of minima taken from literature and obtained from to .

Retrospective dosimetry related to chronic environmental exposure.

PubMed

Degteva, M O; Kozheurov, V P; Tolstykh, E I

1998-01-01

Radioactive contamination of the environment occurred in the early fifties as a result of the releases from the Mayak plutonium production complex (Southern Urals, Russia). The releases of liquid wastes into the Techa river resulted in chronic exposure of 30,000 residents of the riverside communities. Since 1951 90Sr body burdens have been measured for over half of this cohort. This paper presents the analysis of data on 90Sr in humans and describes the reconstruction of internal doses for these people.

Ural-Tweed Bighorn Sheep Wildlife Mitigation Project, 1984-1990 Final Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, Lewis R.; Yde, Chris A.

The results of habitat improvement project activities accomplished under contract No.84-38 for bighorn sheep mitigation along Koocanusa Reservoir from September 1, 1984, through June 30, 1990, are reported here. Habitat treatments were applied to ten areas and covered 1100 acres. Treatments used were prescribed fire, slashing combined with prescribed fire, and fertilization. Several variations in season or intensity were used within the slashing and prescribed fire treatments. This project was coordinated with and complemented concurrent Kootenai National Forest habitat improvement activities.

[Mathematic analysis of risk factors influence on occupational respiratory diseases development].

PubMed

Budkar', L N; Bugaeva, I V; Obukhova, T Iu; Tereshina, L G; Karpova, E A; Shmonina, O G

2010-01-01

Analysis covered 1348 case histories of workers exposed to industrial dust in Urals region. The analysis applied mathematical processing of survival theory and correlation analysis. The authors studied influence of various factors: dust concentration, connective tissue dysplasia, smoking habits--on duration for diseases caused by dust to appear. Findings are that occupational diseases develop reliably faster with higher ambient dust concentrations and with connective tissue dysplasia syndrome. Smoking habits do not alter duration of pneumoconiosis development, but reliably increases development of occupational dust bronchitis.

Palaeopolyploidy, spatial structure and conservation genetics of the narrow steppe plant Vella pseudocytisus subsp. paui (Vellinae, Cruciferae).

PubMed

Pérez-Collazos, Ernesto; Catalán, Pilar

2006-04-01

Vella pseudocytisus subsp. paui (Cruciferae) is a narrow endemic plant to the Teruel province (eastern Spain), which is listed in the National Catalogue of Endangered Species. Two distinct ploidy levels (diploid, 2n = 34, and tetraploid, 2n = 68) have been reported for this taxon that belongs to the core subtribe Vellinae, a western Mediterranean group of shrubby taxa with a chromosome base number of x = 17. Allozyme and AFLP analyses were conducted (a) to test for the ploidy and putative palaeo-allopolyploid origin of this taxon, (b) to explore levels of genetic diversity and spatial structure of its populations, and (c) to address in-situ and ex-situ strategies for its conservation. Six populations that covered the entire geographical range of this taxon were sampled and examined for 19 allozyme loci and three AFLP primer pair combinations. In addition, the gametic progenies of five individuals were analysed for two allozyme loci that showed fixed heterozygosity. Multiple banded allozyme profiles for most of the surveyed loci indicated the polyploidy of this taxon. Co-inherited fixed heterozygous patterns were exhibited by the gametophytic tissues of the mother plants. Both allozyme and AFLP markers detected high levels of genetic diversity, and a strong micro-spatial genetic structure was recovered from AFLP phenetic analyses and Mantel correlograms. Allozyme data support the hypothesis of an allotetraploid origin of Vella pseudocytisus subsp. paui that could be representative of other taxa of the core Vellinae group. AFLP data distinguished three geographically distinct groups with no genetic interaction among them. Allotetraploidy and outcrossing reproduction have probably contributed to maintenance of high levels of genetic variability of the populations, whereas habitat fragmentation may have enhanced the high genetic isolation observed among groups. In-situ microgenetic reserves and a selective sampling of germplasm stocks for ex-situ conservation of this taxon are proposed.

Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

PubMed

Höhna, Sebastian

2014-01-01

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

Genotypic relationships among strains classified under the (Pasteurella) haemolytica-complex as indicated by ribotyping and multilocus enzyme electrophoresis.

PubMed

Angen, O; Caugant, D A; Olsen, J E; Bisgaard, M

1997-10-01

Two-hundred and one strains classified under the (Pasteurella) haemolytica-complex isolated from cattle, sheep, deer, pigs, hares and rabbits were investigated by ribotyping. Fifty-nine of these strains were selected for further studies using multilocus enzyme electrophoresis (MEE). A correlation between the clusters identified by ribotyping and MEE was demonstrated and the results furthermore indicated that a genetic basis exists for most clusters previously outlined by the use of quantitative evaluation of phenotypic data. The taxonomic relevance of ornithine decarboxylase and fermentation of L-arabinose, D-sorbitol and glucosides for taxonomic delineation within the (P.) haemolytica-complex was supported. A taxonomic importance was further indicated for ONPG, ONPX, ONPF, meso-inositol, D-xylose, maltose, dextrine and NPG in relation to some of the taxa. Within the porcine taxon 15, however, differences in ornithine decarboxylase did not correspond to genetic clusters. Six lineages were revealed by MEE. Lineage A contained electrophoretic types (ETs) representing biogroups 1, 3A-3H, 8A and 9, indicating a genetic relationship between these groups--an observation which was supported by ribotyping. Lineage B included biogroup 8D, 3 strains from biogroup 10 and a single strain from biogroup 1 and taxon 18/biovar 1. Lineage C contained strains allocated to biogroup 6 from ruminants and the porcine taxon 15. The similarity between these two groups was accentuated by ribotyping. Lineage D and the single isolate in lineage E contained strains allocated to biogroups 7, 10, 8B and 8C, in addition to single strains from biogroups 6 and 9. The same strains were found in the heterogenous ribotype cluster 17. Lineage F contained strains representing the leprine taxon 20 and the ruminant (P.) granulomatis. Ribotyping indicated that the ruminant biogroup 3J was affiliated with both taxon 20 and (P.) granulomatis.

Marine benthic ecological functioning over decreasing taxonomic richness

NASA Astrophysics Data System (ADS)

Törnroos, Anna; Bonsdorff, Erik; Bremner, Julie; Blomqvist, Mats; Josefson, Alf B.; Garcia, Clement; Warzocha, Jan

2015-04-01

Alterations to ecosystem function due to reductions in species richness are predicted to increase as humans continue to affect the marine environment, especially in coastal areas, which serve as the interface between land and sea. The potential functional consequences due to reductions in species diversity have attracted considerable attention recently but little is known about the consequence of such loss in natural communities. We examined how the potential for function is affected by natural reductions in taxon richness using empirical (non-simulated) coastal marine benthic macrofaunal data from the Skagerrak-Baltic Sea region (N. Europe), where taxon richness decreases 25-fold, from 151 to 6 taxa. To estimate functional changes we defined multiple traits (10 traits and 51 categories) on which trait category richness, functional diversity (FD) and number of taxa per trait category were calculated. Our results show that decrease in taxon richness leads to an overall reduction in function but functional richness remains comparatively high even at the lowest level of taxon richness. Although the taxonomic reduction was sharp, up to 96% of total taxon richness, we identified both potential thresholds in functioning and subtler changes where function was maintained along the gradient. The functional changes were not only caused by reductions in taxa per trait category, some categories were maintained or even increased. Primarily, the reduction in species richness altered trait categories related to feeding, living and movement and thus potentially could have an effect on various ecosystem processes. This highlights the importance of recognising ecosystem multifunctionality, especially at low taxonomic richness. We also found that in this system rare species (singletons) did not stand for the functional complexities and changes. Our findings were consistent with theoretical and experimental predictions and suggest that a large proportion of the information about alterations of function is found in measures such as functional diversity and number of taxa per trait category.

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

PubMed Central

Kilian, Norbert; Henning, Tilo; Plitzner, Patrick; Müller, Andreas; Güntsch, Anton; Stöver, Ben C.; Müller, Kai F.; Berendsohn, Walter G.; Borsch, Thomas

2015-01-01

We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work. Database URL: http://campanula.e-taxonomy.net/ PMID:26424081

Palaeopolyploidy, Spatial Structure and Conservation Genetics of the Narrow Steppe Plant Vella pseudocytisus subsp. paui (Vellinae, Cruciferae)

PubMed Central

PÉREZ-COLLAZOS, ERNESTO; CATALÁN, PILAR

2006-01-01

• Background and Aims Vella pseudocytisus subsp. paui (Cruciferae) is a narrow endemic plant to the Teruel province (eastern Spain), which is listed in the National Catalogue of Endangered Species. Two distinct ploidy levels (diploid, 2n = 34, and tetraploid, 2n = 68) have been reported for this taxon that belongs to the core subtribe Vellinae, a western Mediterranean group of shrubby taxa with a chromosome base number of x = 17. Allozyme and AFLP analyses were conducted (a) to test for the ploidy and putative palaeo-allopolyploid origin of this taxon, (b) to explore levels of genetic diversity and spatial structure of its populations, and (c) to address in-situ and ex-situ strategies for its conservation. • Methods Six populations that covered the entire geographical range of this taxon were sampled and examined for 19 allozyme loci and three AFLP primer pair combinations. In addition, the gametic progenies of five individuals were analysed for two allozyme loci that showed fixed heterozygosity. • Key Results Multiple banded allozyme profiles for most of the surveyed loci indicated the polyploidy of this taxon. Co-inherited fixed heterozygous patterns were exhibited by the gametophytic tissues of the mother plants. Both allozyme and AFLP markers detected high levels of genetic diversity, and a strong micro-spatial genetic structure was recovered from AFLP phenetic analyses and Mantel correlograms. • Conclusions Allozyme data support the hypothesis of an allotetraploid origin of Vella pseudocytisus subsp. paui that could be representative of other taxa of the core Vellinae group. AFLP data distinguished three geographically distinct groups with no genetic interaction among them. Allotetraploidy and outcrossing reproduction have probably contributed to maintenance of high levels of genetic variability of the populations, whereas habitat fragmentation may have enhanced the high genetic isolation observed among groups. In-situ microgenetic reserves and a selective sampling of germplasm stocks for ex-situ conservation of this taxon are proposed. PMID:16495317

Temporal, spatial and ecological dynamics of speciation among amphi-Beringian small mammals

USGS Publications Warehouse

Hope, Andrew G.; Takebayashi, Naoki; Galbreath, Kurt E.; Talbot, Sandra L.; Cook, Joseph A.

2013-01-01

Quaternary climate cycles played an important role in promoting diversification across the Northern Hemisphere, although details of the mechanisms driving evolutionary change are still poorly resolved. In a comparative phylogeographical framework, we investigate temporal, spatial and ecological components of evolution within a suite of Holarctic small mammals. We test a hypothesis of simultaneous divergence among multiple taxon pairs, investigating time to coalescence and demographic change for each taxon in response to a combination of climate and geography.

A surface-associated activity trap for capturing water surface and aquatic invertebrates in wetlands

USGS Publications Warehouse

Hanson, Mark A.; Roy, Christiane C.; Euliss, Ned H.; Zimmer, Kyle D.; Riggs, Michael R.; Butler, Malcolm G.

2000-01-01

We developed a surface-associated activity trap (SAT) for sampling aquatic invertebrates in wetlands. We compared performance of this trap with that of a conventional activity trap (AT) based on non-detection rates and relative abundance estimates for 13 taxa of common wetland invertebrates and for taxon richness using data from experiments in constructed wetlands. Taxon-specific non-detection rates for ATs generally exceeded those of SATs, and largest improvements using SATs were for Chironomidae and Gastropoda. SATs were efficient at capturing cladocera, Chironomidae, Gastropoda, total Crustacea, and multiple taxa (taxon richness) but were only slightly better than ATs at capturing Dytiscidae. Temporal differences in capture rates were observed only for cladocera, Chironomidae, Dytiscidae, and total Crustacea, with capture efficiencies of SATs usually decreasing from mid-June through mid-July for these taxa. We believe that SATs may be useful for characterizing wetland invertebrate communities and for developing improved measures of prey available to foraging waterfowl and other aquatic birds.

A surface-associated activity trap for capturing water-surface and aquatic invertebrates in wetlands

USGS Publications Warehouse

Hanson, M.A.; Roy, C.C.; Euliss, N.H.; Zimmer, K.D.; Riggs, M.R.; Butler, Malcolm G.

2000-01-01

We developed a surface-associated activity trap (SAT) for sampling aquatic invertebrates in wetlands. We compared performance of this trap with that of a conventional activity trap (AT) based on non-detection rates and relative abundance estimates for 13 taxa of common wetland invertebrates and for taxon richness using data from experiments in constructed wetlands. Taxon-specific non-detection rates for ATs generally exceeded those of SATs, and largest improvements using SATs were for Chironomidae and Gastropoda. SATs were efficient at capturing cladocera, Chironomidae, Gastropoda, total Crustacea, and multiple taxa (taxon richness) but were only slightly better than ATs at capturing Dytiscidae. Temporal differences in capture rates were observed only for cladocera, Chironomidae, Dytiscidae, and total Crustacea, with capture efficiencies of SATs usually decreasing from mid-June through mid-July for these taxa. We believe that SATs may be useful for characterizing wetland invertebrate communities and for developing improved measures of prey available to foraging waterfowl and other aquatic birds.

Development, optimization, and single laboratory validation of an event-specific real-time PCR method for the detection and quantification of Golden Rice 2 using a novel taxon-specific assay.

PubMed

Jacchia, Sara; Nardini, Elena; Savini, Christian; Petrillo, Mauro; Angers-Loustau, Alexandre; Shim, Jung-Hyun; Trijatmiko, Kurniawan; Kreysa, Joachim; Mazzara, Marco

2015-02-18

In this study, we developed, optimized, and in-house validated a real-time PCR method for the event-specific detection and quantification of Golden Rice 2, a genetically modified rice with provitamin A in the grain. We optimized and evaluated the performance of the taxon (targeting rice Phospholipase D α2 gene)- and event (targeting the 3' insert-to-plant DNA junction)-specific assays that compose the method as independent modules, using haploid genome equivalents as unit of measurement. We verified the specificity of the two real-time PCR assays and determined their dynamic range, limit of quantification, limit of detection, and robustness. We also confirmed that the taxon-specific DNA sequence is present in single copy in the rice genome and verified its stability of amplification across 132 rice varieties. A relative quantification experiment evidenced the correct performance of the two assays when used in combination.

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

PubMed

Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J

2017-06-01

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

The girdles of the oldest fossil turtle, Proterochersis robusta, and the age of the turtle crown

PubMed Central

2013-01-01

Background Proterochersis robusta from the Late Triassic (Middle Norian) of Germany is the oldest known fossil turtle (i.e. amniote with a fully formed turtle shell), but little is known about its anatomy. A newly prepared, historic specimen provides novel insights into the morphology of the girdles and vertebral column of this taxon and the opportunity to reassess its phylogenetic position. Results The anatomy of the pectoral girdle of P. robusta is similar to that of other primitive turtles, including the Late Triassic (Carnian) Proganochelys quenstedti, in having a vertically oriented scapula, a large coracoid foramen, a short acromion process, and bony ridges that connect the acromion process with the dorsal process, glenoid, and coracoid, and by being able to rotate along a vertical axis. The pelvic elements are expanded distally and suturally attached to the shell, but in contrast to modern pleurodiran turtles the pelvis is associated with the sacral ribs. Conclusions The primary homology of the character “sutured pelvis” is unproblematic between P. robusta and extant pleurodires. However, integration of all new observations into the most complete phylogenetic analysis that support the pleurodiran nature of P. robusta reveals that this taxon is more parsimoniously placed along the phylogenetic stem of crown Testudines. All current phylogenetic hypotheses therefore support the basal placement of this taxon, imply that the sutured pelvis of this taxon developed independently from that of pleurodires, and conclude that the age of the turtle crown is Middle Jurassic. PMID:24314094

Reach-scale stream restoration in agricultural streams of southern Minnesota alters structural and functional responses of macroinvertebrates

USGS Publications Warehouse

Dolph, Christine L.; Eggert, Susan L.; Magner, Joe; Ferrington, Leonard C.; Vondracek, Bruce C.

2015-01-01

Recent studies suggest that stream restoration at the reach scale may not increase stream biodiversity, raising concerns about the utility of this conservation practice. We examined whether reach-scale restoration in disturbed agricultural streams was associated with changes in macroinvertebrate community structure (total macroinvertebrate taxon richness, total macroinvertebrate density, Ephemeroptera, Plecoptera, Trichoptera [EPT] taxon richness, % abundance of EPT taxa) or secondary production (macroinvertebrate biomass over time). We collected macroinvertebrate samples over the course of 1 y from restored and unrestored reaches of 3 streams in southern Minnesota and used generalized least-square (GLS) models to assess whether measures of community structure were related to reach type, stream site, or sampling month. After accounting for effects of stream site and time, we found no significant difference in total taxon richness or % abundance of EPT taxa between restored and unrestored reaches. However, the number of EPT taxa and macroinvertebrate density were significantly higher in restored than in unrestored reaches. We compared secondary production estimates among study reaches based on 95th-percentile confidence intervals generated via bootstrapping. In each study stream, secondary production was significantly (2–3×) higher in the restored than in the unrestored reach. Higher productivity in the restored reaches was largely a result of the disproportionate success of a few dominant, tolerant taxa. Our findings suggest that reach-scale restoration may have ecological effects that are not detected by measures of total taxon richness alone.

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

PubMed Central

Little, Damon P.

2011-01-01

For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple–sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple–sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are unable to accurately differentiate between highly similar sequences and are not designed to cope with hierarchic phylogenetic relationships or within taxon variability. Here, I present a novel alignment–free sequence identification algorithm–BRONX–that accounts for observed within taxon variability and hierarchic relationships among taxa. BRONX identifies short variable segments and corresponding invariant flanking regions in reference sequences. These flanking regions are used to score variable regions in the query sequence without the production of a global multiple–sequence alignment. By incorporating observed within taxon variability into the scoring procedure, misidentifications arising from shared alleles/haplotypes are minimized. An explicit treatment of more inclusive terminals allows for separate identifications to be made for each taxonomic level and/or for user–defined terminals. BRONX performs better than all other methods when there is imperfect overlap between query and reference sequences (e.g. mini–barcode queries against a full–length barcode database). BRONX consistently produced better identifications at the genus–level for all query types. PMID:21857897

Ecohydrologic Changes due to Tree Expansion into Tundra in the Polar Urals, Russia

NASA Astrophysics Data System (ADS)

Ivanov, V. Y.; Wang, J.; El Sharif, H. A.; Liu, D.; Sheshukov, A. Y.; Mazepa, V.; Shiyatov, S.; Sokolov, A.

2017-12-01

The Arctic has been warming at an accelerating rate over the last several decades and the changing climate has caused the invasion of trees and shrubs into tundra across the polar regions of Alaska, Canada, and Russia. These vegetation changes may have the potential to impact regional hydrology and climate. This study aims to develop mechanistic and quantitative understanding of implications of forest encroachment into tundra. Specifically, for several areas with well-documented larch and spruce expansion in the Polar Urals and southern Yamal Peninsula of Russia over 1960-2010s, we hypothesize that the encroachment process alters the seasonality of energy budget characterized by enhanced total evapotranspiration and concomitant subsurface warming. We are collecting a comprehensive set of field observational data on micrometeorology, snow conditions, radiative fluxes, tree sap flows, soil temperature, moisture, and heat fluxes, and active layer thickness. A novel model of maximum entropy production (MEP) is used to derive the surface energy budgets as the partition of radiative fluxes into turbulent and conductive heat fluxes across the ecotone interface. We are presenting preliminary findings that illustrate the identified differences of seasonal snow and heat budget regimes for two contrasting sites: one of which has experienced a recent tree encroachment, while for the other this process has not yet occurred. Observed and modeled heat fluxes are used to inform a comprehensive physical model to study the impact of vegetation encroachment process on the permafrost dynamics.

Chemical and boron isotopic composition of tourmaline from the Mariinsky emerald deposit, Central Urals, Russia

NASA Astrophysics Data System (ADS)

Baksheev, Ivan A.; Trumbull, Robert B.; Popov, Mikhail P.; Erokhin, Yuri V.; Kudryavtseva, Olesya E.; Yapaskurt, Vasily O.; Khiller, Vera V.; Vovna, Galina M.; Kiselev, Vladimir I.

2018-04-01

Tourmaline is abundant at the Mariinsky schist-hosted emerald deposit in the Central Urals, Russia, both in emerald-bearing phlogopite veins (type 1) and later, emerald-free pockets, lenses, and veinlets cutting the phlogopite veins (type 2). The Ca content in tourmaline is influenced by the host rocks (ultramafic and mafic rocks), associated minerals, and minerals crystallized before tourmaline (amphibole, fluorite, margarite). The Na concentration in tourmaline depends on the presence or absence of paragonite, and the association with micas also strongly influences the contents of Li, Zn, Ni, and Co in tourmaline. Type 1 tourmalines associated with phlogopite are relatively depleted in these elements, whereas type 2 tourmalines associated with margarite or paragonite are enriched. Some differences in isomorphic substitutions along with the trace element composition (Zn, V, Sr, Co, REE) may have value in exploration of emerald-bearing and emerald-free veins in schist-hosted emerald deposits. The δ11B values in tourmaline of all types fall in a narrow total range from -11.3 to -8.4‰. These values, combined with a mineralization temperature of 420-360 °C, yield an estimated δ11B fluid composition of -7.4 to -6.8‰ suggesting a mixed source of boron, likely dominated from the granitic rocks surrounding the emerald belt. The narrow range of B-isotope compositions in tourmaline from throughout the Mariinsky deposit suggests a well-mixed hydrothermal system.

Chronic radioisotope effects on residents of the Techa River (Russia) region: cytogenetic analysis more than 50 years after onset of exposure.

PubMed

Vozilova, A V; Shagina, N B; Degteva, M O; Akleyev, A V

2013-08-30

This paper presents the results of a cytogenetic study conducted among residents of the Techa Riverside communities (Southern Urals, Russia) exposed in the early 1950s as a result of releases of liquid radioactive wastes from the Mayak plutonium-production facility. The study was performed 50-60 years after the beginning of the exposure for those individuals who were predominantly exposed to strontium radioisotopes ((89,90)Sr) through drinking contaminated river water and consumption of local foodstuff. Standard cytogenetic methods were used for evaluation of the frequency of unstable chromosome aberrations in exposed persons as well as in persons from the control group who were of similar age and sex, living in similar socio-economic conditions in non-contaminated territories of the Southern Urals. The exposure doses were reconstructed for the studied donors using the Techa River Dosimetry System developed in 2009. The doses of internal exposure from ingested radionuclides were evaluated using individual or family in vivo measurements of (90)Sr-body burden. Individual cumulative absorbed doses in red bone marrow (RBM) in the studied persons varied in the range of 0.01-4.4Gy. A significantly higher level of unstable chromosome aberrations (UCA) in T-cells was observed in the group of exposed individuals as compared to control group. The highest UCA level was detected in the individuals who were suspected of having chronic radiation syndrome. Copyright © 2013 Elsevier B.V. All rights reserved.

Detection of damaged areas caused by the oil extraction in a steppe region using winter landsat imagery

NASA Astrophysics Data System (ADS)

Mjachina, Ksenya; Hu, Zhiyong; Chibilyev, Alexander

2018-01-01

Oil production in a steppe region disturbs the landscape and damages the steppe ecosystem. The objective of this research was to detect areas damaged by oil production in an oil field within the Russian Volga-Ural steppe region using winter Landsat imagery. We developed a practicable and effective approach using winter snow season multispectral Landsat satellite imagery. To this end, we applied seven algorithms of spectral or texture-based transformation: K-means, maximum likelihood estimation, topsoil grain size index, soil brightness, normalized differential snow index, tasselled cap, and co-occurrence measures. The co-occurrence texture measure variance shows the optimal result of identifying damaged areas. The unique feature of our method is that it can differentiate damaged areas from the bare soil of cropland within a cold steppe region where the area damaged by oil production is mixed with bare (fallow) croplands that have a polygonal shape similar to well pads. Such similarities can lead to confusion in object-based classification. Using the co-occurrence measures, we found that from 1988 to 2015, damaged area is nearly three times as big in the peak period of the oil field development (2001 and 2009) as in 1988. Landscape fragmentation also peaked in 2001 and 2009. Our approach for this project is useful and cost effective regular monitoring of damages from oil production for both the Volga-Ural steppe region and other cold steppe regions.

Management and recovery options for Ural river beluga sturgeon.

PubMed

Doukakis, Phaedra; Babcock, Elizabeth A; Pikitch, Ellen K; Sharov, Alexei R; Baimukhanov, Mirgaly; Erbulekov, Sagiden; Bokova, Yelena; Nimatov, Akhat

2010-06-01

Management of declining fisheries of anadromous species sometimes relies heavily on supplementation of populations with captive breeding, despite evidence that captive breeding can have negative consequences and may not address the root cause of decline. The beluga sturgeon (Huso huso), a species threatened by the market for black caviar and reductions in habitat quality, is managed through harvest control and hatchery supplementation, with an emphasis on the latter. We used yield per recruit and elasticity analyses to evaluate the population status and current levels of fishing and to identify the life-history stages that are the best targets for conservation of beluga of the Ural River. Harvest rates in recent years were four to five times higher than rates that would sustain population abundance. Sustainable rates of fishing mortality are similar to those for other long-lived marine species such as sharks and mammals. Yield per recruit, which is maximized if fish are first harvested at age 31 years, would be greatly enhanced by raising minimum size limits or reducing illegal take of subadults. Improving the survival of subadult and adult females would increase population productivity by 10 times that achieved by improving fecundity and survival from egg to age 1 year (i.e., hatchery supplementation). These results suggest that reducing mortality of subadults and adult wild fish is a more effective conservation strategy than hatchery supplementation. Because genetics is not factored into hatchery management practices, supplementation may even reduce the viability of the beluga sturgeon.

Climate-driven shift of the tree-line ecotone in the Polar Urals and impacts on land-surface properties

NASA Astrophysics Data System (ADS)

Ivanov, V. Y.; Shiyatov, S.; Mazepa, V.

2013-12-01

Warming of the Arctic climate has triggered a number of changes in terrestrial physical and biogeochemical systems. One of the eloquent expressions of such changes is an expansion of trees and shrubs into tundra areas. There is an emerging need to understand how changes of land-surface thermal, hydrological, and biogeochemical regimes will impact ecosystems in future as well as the associated feedback mechanisms. This study focuses on the area that has undergone one of the rapidest changes in the forest-tundra alpine areas of the Polar Urals, Russia (66.7N, 65.4E). The prevailing species of this forest-tundra ecotone underlain by continuous permafrost is larch (L. sibirica), a predominant species of the Russian Arctic. Open larch and mixed forests with Siberian spruce (P. obovata) and birch (B. tortuosa) are abundant in the downslope, valley areas. Average frost-free period is 64 days with growing season lasting between mid-June to early August. Based on meteorological record at a station in Salekhard, over the period of 1920-2004, the mean summer temperatures have increased by 0.9 deg. and the mean winter temperatures by 1.2 deg., as compared to the 1883-1920 period. The mean summer precipitation has increased from 146 to 178 mm, while as winter precipitation has grown from 67 to 113 mm. This has resulted in 80-100 m altitudinal expansion of single trees and forest that was accompanied by a marked increase in the vertical and radial tree growth, crown density, and productivity of tree stands. Eleven altitudinal transects 300-1100 m long and 20-80 m wide have been developed for long-term monitoring of spatiotemporal dynamics of communities starting in early 1960s. In order to quantitatively assess changes in the composition, structure, and spatial distribution of the forest-tundra communities, census campaigns of 1960-62, 1999, and 2011 produced detailed mappings of locations of all alive and dead trees, and measurements of their essential allometric characteristics. In total, of 1494, 1851, and 1985 trees were observed during the three respective census periods. Analyses of the temporal change of land-surface conditions at the tree scale are presented. Changes of effective surface albedo, shading factors, and radiative characteristics of the area are estimated. Current instrumentation program of the site will inform a physically-based model that will investigate heat-moisture dynamics of the changed land-surface. Expansion of dense and open larch forests on banks of the Kerdomanshor River, Polar Urals, Russia, 1962-2004.

Comparative glacio-climatological analysis of mass balance variability along the geographical margin of Europe

NASA Astrophysics Data System (ADS)

Lehoczky, Annamária; Kern, Zoltán; Pongrácz, Rita

2014-05-01

Glacio-climatological studies recognise glacier mass balance changes as high-confident climate indicators. The climatic sensitivity of a glacier does not simply depend on regional climate variability but also influenced via large- and mesoscale atmospheric circulation patterns. This study focuses on recent changes in the mass balance using records from three border regions of Europe, and investigates the relationships between the seasonal mass balance components, regional climatic conditions, and distant atmospheric forcing. Since glaciers in different macro-climatological conditions (i.e., mid-latitudes or high-latitudes, dry-continental or maritime regions) may present strongly diverse mass balance characteristics, the three analysed regions were selected from different glacierised macroregions (using the database of the World Glacier Monitoring Service). These regions belong to the Caucasus Mountains (Central Europe macroregion), the Polar Ural (Northern Asia macroregion), and Svalbard (Arctic Islands macroregion). The analysis focuses on winter, summer, and annual mass balance series of eight glaciers. The climatic variables (atmospheric pressure, air temperature, precipitation) and indices of teleconnection patterns (e.g., North Atlantic Oscillation, Pacific Decadal Oscillation) are used from the gridded databases of the University of East Anglia, Climatic Research Unit and the National Oceanic and Atmospheric Administration, National Center for Environmental Prediction. However, the period and length of available mass balance data in the selected regions vary greatly (the first full record is in 1958, Polar Ural; the last is in 2010, Caucasus Mountains), a comparative analysis can be carried out for the period of 1968-1981. Since glaciers from different regions respond to large- and mesoscale climatic forcings differently, and because the mass balance of glaciers within a region often co-vary, our specific objectives are (i) to examine the variability and the integrative climatic signal in the averaged mass balance records of the selected regions; (ii) to analyse the possible coupling between the mass balance and climatic variables, including the dominant patterns of Northern Hemisphere climate variability; and (iii) to compare the main characteristics of the three regions. Furthermore, (iv) a short discussion is given considering the significant decreasing trend of the cumulative annual mass balances in every region under the detected climatic changes in the second half of the 20th century. Preliminary results suggest that the strongest teleconnection links could be between winter mass balance and winter NAO for the Polar Ural (r=0.46, p<0.05), and between annual mass balance and PDO for Svalbard (r=-0.43, p<0.05). Neither seasonal, nor annual mass balance records showed significant correlation with any of the examined circulation indices for the Caucasus.

[Testate amoebae inhabiting middle taiga bogs in Western Siberia].

PubMed

Kur'ina, I V; Preĭs, Iu I; Bobrov, A A

2010-01-01

The population of testate amoebae from the most typical middle taiga bogs of Western Siberia have been studied. More than one hundred (103) species and intraspecific taxons of testate amoebae have been revealed in recent surface samples. The relation between ecological characteristics of habitats and the composition of a Protozoa population has been demonstrated. The ecological preferences of species concerning the index of wetness, ash level, and acidity have been revealed. Using the correspondence analysis, the ecological optimums and the tolerance of species and intraspecific taxons of testate amoebae have been established.

Typification and taxonomic status re-evaluation of 15 taxon names within the species complex Cymbella affinis/tumidula/turgidula (Cymbellaceae, Bacillariophyta)

PubMed Central

da Silva, Weliton José; Jahn, Regine; Ludwig, Thelma Alvim Veiga; Hinz, Friedel; Menezes, Mariângela

2015-01-01

Abstract Specimens belonging to the Cymbella affinis / Cymbella tumidula / Cymbella turgidula species complex have many taxonomic problems, due to their high morphological variability and lack of type designations. Fifteen taxon names of this complex, distributed in five species, were re-evaluated concerning their taxonomic status, and lectotypified based on original material. In addition to light microscopy, some material was analyzed by electron microscopy. Four new combinations are proposed in order to reposition infraspecific taxa. PMID:26312038

Software development for teleroentgenogram analysis

NASA Astrophysics Data System (ADS)

Goshkoderov, A. A.; Khlebnikov, N. A.; Obabkov, I. N.; Serkov, K. V.; Gajniyarov, I. M.; Aliev, A. A.

2017-09-01

A framework for the analysis and calculation of teleroentgenograms was developed. Software development was carried out in the Department of Children's Dentistry and Orthodontics in Ural State Medical University. The software calculates the teleroentgenogram by the original method which was developed in this medical department. Program allows designing its own methods for calculating the teleroentgenograms by new methods. It is planned to use the technology of machine learning (Neural networks) in the software. This will help to make the process of calculating the teleroentgenograms easier because methodological points will be placed automatically.

Colloidal Dynamics Simulations of Rheology and Stability of Concentrated Fuel Slurries.

DTIC Science & Technology

1987-04-10

Weals potential as the adsorbed polymer concentration and Hamaker con- stant are changed. These calculations provide quantitative evidence for the...derived by Hamaker : 3 6 U (r) A d 2 2 +2Ln( 2- d2(3 A T2 2 2 2 2 A value of 5.0 x 10" 2 0 j was used for the Hamaker constant, A. A plot of Eq. (31) is...parameter controlling the strength of the repulsive steric potential. The Hamaker constant A (Eq. (33)) is the nat- ural choice for the attractive

Earth observations taken from shuttle orbiter Atlantis during STS-84 mission

NASA Image and Video Library

1997-05-21

STS084-701-026 (15-24 May 1997) --- The Volga River enters the Caspian, the world's largest inland sea, from the north in this high oblique view. The Volga, the principle waterway of western Russian, is considered the historic cradle of Russia. The Ural River, east of the Volga, also enters the northern part of the Caspian. The dimensions of the Caspian are 1,200 kilometers (750 miles) from north to south, but averages 320 kilometers (200 miles) in width. Oil and natural gas are this regions most important resources.

Historical phytoplankton data from Helgoland Roads: Can they be linked to modern time series data?

NASA Astrophysics Data System (ADS)

Kraberg, Alexandra C.; Rodriguez, Natalia; Salewski, Christian R.

2015-07-01

The Helgoland Roads phytoplankton data set is one of the longest and most detailed phytoplankton time series data sets in the world. The time series has been initiated in 1962 and based on the resulting counts a taxon list of 261 taxa has been assembled, 93 of which are diatoms. However, plankton research has been carried out at the site since the 19th century although many old records were lost during the World War II. Here we describe a small historic data set that was recovered from the Wadden Sea Station Sylt and placed in the AWI's own archive, the Archive for German Polar Research (Archiv für deutsche Polarforschung - AdP). This data set is unique in that it contains species specific diatom data from the period 1906-1908. As the data set itself contained only little direct metadata linking it to the phytoplankton monitoring site Helgoland Roads ('Helgoland Reede' in German), further research of the available literature and additional searches of material in the AWI archive were carried out before it could be ascertained that the documents recovered from Sylt really contained data from the Biological Institute on the island of Helgoland. Following this the data in the original data set underwent taxonomic checks to establish that all species were valid species or older synonyms of currently accepted taxon names. The resulting data set was then compared to the Helgoland Roads taxon list and the most current published checklist for Helgoland Roads. Of the 6 pennate and 59 centric diatoms recorded between 1906 and 1908 most are also found in the current taxon lists, only 7 were not found in either the checklist or Helgoland Roads taxon list. However, there are exceptions, most notably the centric diatom Pseudosolenia calcar-avis, which only occurred in the historic records of 1906-1908 and has not been reported from the North Sea in any modern records. While only semi-quantitative, these data are nevertheless an important complement to the Helgoland Roads phytoplankton data set, providing a historic basis for documenting long-term changes in the diatom community at Helgoland Roads.

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions

NASA Astrophysics Data System (ADS)

Schopf, J. William; Kitajima, Kouki; Spicuzza, Michael J.; Kudryavtsev, Anatoliy B.; Valley, John W.

2018-01-01

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ˜3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ13C compositions to vary systematically taxon to taxon from ‑31‰ to ‑39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ13C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (‑27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (‑27.6‰), and those typical of modern prokaryotic phototrophs (‑25 ± 10‰). The SIMS data for the two highest δ13C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ13C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ13C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions.

PubMed

Schopf, J William; Kitajima, Kouki; Spicuzza, Michael J; Kudryavtsev, Anatoliy B; Valley, John W

2018-01-02

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ∼3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ 13 C compositions to vary systematically taxon to taxon from -31‰ to -39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ 13 C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (-27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (-27.6‰), and those typical of modern prokaryotic phototrophs (-25 ± 10‰). The SIMS data for the two highest δ 13 C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ 13 C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ 13 C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

Ingroup relationships of Lagerpetidae (Avemetatarsalia: Dinosauromorpha): a further phylogenetic investigation on the understanding of dinosaur relatives.

PubMed

MÜller, Rodrigo Temp; Langer, Max Cardoso; Dias-da-Silva, SÉrgio

2018-03-07

Despite representing a key-taxon in dinosauromorph phylogeny, Lagerpertidae is one of the most obscure and enigmatic branches from the stem that leads to the dinosaurs. Recent new findings have greatly increased our knowledge about lagerpetids, but no phylogenetic analysis has so far included all known members of this group. Here, we present the most inclusive phylogenetic study so far conducted for Lagerpetidae. Phylogenetic analyses were performed based on three independent data matrixes. In two of them, Lagerpeton chanarensis Romer, 1971 is the sister taxon to all other known Lagerpetidae, whereas Ixalerpeton polesinensis Cabreira et al., 2016 is in a sister group relationship with a clade that includes PVSJ 883 and Dromomeron. Conversely, the other analysis supports an alternative topology, where I. polesinensis is the sister taxon to either L. chanarensis or all other Lagerpetidae. Although coeval and geographically close, I. polesinensis and PVSJ 883 do not form a clade exclusive of other lagerpetids. As previously suggested D. gigas Martínez, Apaldetti, Correa Abelín, 2016 is the sister taxon of D. romeri Irmis et al., 2007. The phylogenetic analyses also indicate that the earliest lagerpetids are restricted to southwestern Pangea, whereas later forms spread across the entire western portion of the supercontinent. Finally, quantification of the codified characters of our analysis reveals that Lagerpetidae is one of the poorest known among the Triassic dinosauromorph groups in terms of their anatomy, so that new discoveries of more complete specimens are awaited to establish a more robust phylogeny.

Rediscovery and reclassification of the dipteran taxon Nothomicrodon Wheeler, an exclusive endoparasitoid of gyne ant larvae.

PubMed

Pérez-Lachaud, Gabriela; Jahyny, Benoit J B; Ståhls, Gunilla; Rotheray, Graham; Delabie, Jacques H C; Lachaud, Jean-Paul

2017-03-31

The myrmecophile larva of the dipteran taxon Nothomicrodon Wheeler is rediscovered, almost a century after its original description and unique report. The systematic position of this dipteran has remained enigmatic due to the absence of reared imagos to confirm indentity. We also failed to rear imagos, but we scrutinized entire nests of the Brazilian arboreal dolichoderine ant Azteca chartifex which, combined with morphological and molecular studies, enabled us to establish beyond doubt that Nothomicrodon belongs to the Phoridae (Insecta: Diptera), not the Syrphidae where it was first placed, and that the species we studied is an endoparasitoid of the larvae of A. chartifex, exclusively attacking sexual female (gyne) larvae. Northomicrodon parasitism can exert high fitness costs to a host colony. Our discovery adds one more case to the growing number of phorid taxa known to parasitize ant larvae and suggests that many others remain to be discovered. Our findings and literature review confirm that the Phoridae is the only taxon known that parasitizes both adults and the immature stages of different castes of ants, thus threatening ants on all fronts.

Rediscovery and reclassification of the dipteran taxon Nothomicrodon Wheeler, an exclusive endoparasitoid of gyne ant larvae

PubMed Central

Pérez-Lachaud, Gabriela; Jahyny, Benoit J. B.; Ståhls, Gunilla; Rotheray, Graham; Delabie, Jacques H. C.; Lachaud, Jean-Paul

2017-01-01

The myrmecophile larva of the dipteran taxon Nothomicrodon Wheeler is rediscovered, almost a century after its original description and unique report. The systematic position of this dipteran has remained enigmatic due to the absence of reared imagos to confirm indentity. We also failed to rear imagos, but we scrutinized entire nests of the Brazilian arboreal dolichoderine ant Azteca chartifex which, combined with morphological and molecular studies, enabled us to establish beyond doubt that Nothomicrodon belongs to the Phoridae (Insecta: Diptera), not the Syrphidae where it was first placed, and that the species we studied is an endoparasitoid of the larvae of A. chartifex, exclusively attacking sexual female (gyne) larvae. Northomicrodon parasitism can exert high fitness costs to a host colony. Our discovery adds one more case to the growing number of phorid taxa known to parasitize ant larvae and suggests that many others remain to be discovered. Our findings and literature review confirm that the Phoridae is the only taxon known that parasitizes both adults and the immature stages of different castes of ants, thus threatening ants on all fronts. PMID:28361946

An acercostracan marrellomorph (Euarthropoda) from the Lower Ordovician of Morocco.

PubMed

Legg, David A

2016-04-01

Enosiaspis hrungnir gen. et sp. nov., a new species of marrellomorph arthropod from the Lower Ordovician (Tremadocian) Fezouata biota of Morocco, is described. This taxon is characterised by the possession of a cordiform dorsal carapace with an anterior notch and a doublure-like structure formed from fused marginal spines, covering the entire body. The head comprises at least five segments which bear an anterior pair of antenna, followed by three pairs of potentially biramous, geniculate appendages. The trunk possesses around 25 pairs of delicate, almost filamentous appendages, which decrease in size posteriorly. Similar features are also found in Xylokorys chledophilia from the Silurian of England, and Vachonisia rogeri from the Devonian of Germany, indicating acercostracan affinities for E. hrungnir. This was tested using a phylogenetic analysis which resolved this taxon as sister taxon to a group composed of the formerly mentioned taxa. The similarities between the ventral spinose carapace doublure of E. hrungnir and the mediolateral spines of marrellid marrellomorphs further support claims that the dorsal shield of acercostracans evolved from the fusion of spinose anlagen, akin to the formation of the carapace of crustaceans.

A New Azhdarchid Pterosaur from the Late Cretaceous of the Transylvanian Basin, Romania: Implications for Azhdarchid Diversity and Distribution

PubMed Central

Vremir, Mátyás; Kellner, Alexander W. A.; Naish, Darren; Dyke, Gareth J.

2013-01-01

We describe a new taxon of medium-sized (wing span ca. 3 m) azhdarchid pterosaur from the Upper Cretaceous Transylvanian Basin (Sebeş Formation) of Romania. This specimen is the most complete European azhdarchid yet reported, comprising a partially articulated series of vertebrae and associated forelimb bones. The new taxon is most similar to the Central Asian Azhdarcho lancicollis Nessov but possesses a suite of autapomorphies in its vertebrae that include the relative proportions of cervicals three and four and the presence of elongated prezygapophyseal pedicles. The new taxon is interesting in that it lived contemporaneously with gigantic forms, comparable in size to the famous Romanian Hatzegopteryx thambema. The presence of two distinct azhdarchid size classes in a continental depositional environment further strengthens suggestions that these pterosaurs were strongly linked to terrestrial floodplain and wooded environments. To support this discussion, we outline the geological context and taphonomy of our new specimen and place it in context with other known records for this widespread and important Late Cretaceous pterosaurian lineage. PMID:23382886

An acercostracan marrellomorph (Euarthropoda) from the Lower Ordovician of Morocco

NASA Astrophysics Data System (ADS)

Legg, David A.

2016-04-01

Enosiaspis hrungnir gen. et sp. nov., a new species of marrellomorph arthropod from the Lower Ordovician (Tremadocian) Fezouata biota of Morocco, is described. This taxon is characterised by the possession of a cordiform dorsal carapace with an anterior notch and a doublure-like structure formed from fused marginal spines, covering the entire body. The head comprises at least five segments which bear an anterior pair of antenna, followed by three pairs of potentially biramous, geniculate appendages. The trunk possesses around 25 pairs of delicate, almost filamentous appendages, which decrease in size posteriorly. Similar features are also found in Xylokorys chledophilia from the Silurian of England, and Vachonisia rogeri from the Devonian of Germany, indicating acercostracan affinities for E. hrungnir. This was tested using a phylogenetic analysis which resolved this taxon as sister taxon to a group composed of the formerly mentioned taxa. The similarities between the ventral spinose carapace doublure of E. hrungnir and the mediolateral spines of marrellid marrellomorphs further support claims that the dorsal shield of acercostracans evolved from the fusion of spinose anlagen, akin to the formation of the carapace of crustaceans.

A primitive therizinosauroid dinosaur from the Early Cretaceous of Utah

USGS Publications Warehouse

Kirkland, J.I.; Zanno, L.E.; Sampson, S.D.; Clark, J.M.; DeBlieux, D.D.

2005-01-01

Therizinosauroids are an enigmatic group of dinosaurs known mostly from the Cretaceous period of Asia, whose derived members are characterized by elongate necks, laterally expanded pelves, small, leaf-shaped teeth, edentulous rostra and mandibular symphyses that probably bore keratinized beaks. Although more than a dozen therizinosauroid taxa are known, their relationships within Dinosauria have remained controversial because of fragmentary remains and an unusual suite of characters. The recently discovered 'feathered' therizinosauroid Beipiaosaurus from the Early Cretaceous of China helped to clarify the theropod affinities of the group. However, Beipiaosaurus is also poorly represented. Here we describe a new, primitive therizinosauroid from an extensive paucispecific bonebed at the base of the Cedar Mountain Formation (Early Cretaceous) of east-central Utah. This new taxon represents the most complete and most basal therizinosauroid yet discovered. Phylogenetic analysis of coelurosaurian theropods incorporating this taxon places it at the base of the clade Therizinosauroiden, indicating that this species documents the earliest known stage in the poorly understood transition from carnivory to herbivory within Therizinosauroidea. The taxon provides the first documentation, to our knowledge, of therizinosauroids in North America during the Early Cretaceous.

The French Atlantic littoral and the Massif Armoricain, part 1. [Island of Jersey, Fromentine, Loire Estuary, and Mont Saint-Michel Bay

NASA Technical Reports Server (NTRS)

Verger, F. (Principal Investigator); Monget, J. M.; Guerin, O.; Poisson, R. M.; Thomas, Y.

1977-01-01

The author has identified the following significant results. For interpretation of Isle of Jersey imagery, two types of taxons were defined according to their variability in time. On the whole, taxons with a similar spectral signature were opposed to those with strongly varying spectral signature. The taxon types were low diachronic variations and strong diachronic variation. Imagery interpretation was restricted to the landward part of the Fromentine area, including the sand beaches which were often difficult to spectrally separate from the barren coastal dunes in the southern part of Noirmoutier Island as well as along the Breton marsh. From 1972 to 1976, sandbanks reduced in area. Two high river discharge images showed over a two year period an identical outline for the Bilho bank to seaward, whereas upstream, the bank has receeded in the same time to a line joining Paimboeuf to Montoir. The Brillantes bank has receeded at both ends, partly due to dredging operations in the access channel to Donges harbor.

Eoalosa janvieri gen. et sp. nov., a new clupeid fish (Teleostei, Clupeiformes) from the Eocene of Monte Bolca, Italy.

PubMed

Marramà, Giuseppe; Carnevale, Giorgio

2018-01-01

Fishes of the family Clupeidae are extremely abundant in the Eocene fossiliferous limestone of Monte Bolca representing the most common group from this celebrated locality. A new clupeid from the Pesciara site, Eoalosa janvieri gen. et sp. nov., is described. The new taxon exhibits a unique combination of characters supporting its recognition as a new genus and species of clupeid fish that is tentatively placed in the subfamily Alosinae. The description of this new taxon improves our knowledge of the diversity of clupeoid fishes in the Eocene of Monte Bolca.

Invertebrate colonization rates in the tailwater of a Kentucky flood-control reservoir

USGS Publications Warehouse

Swink, W.D.; Novotny, J.F.

1985-01-01

Invertebrate colonization on newly introduced rock substrates was examined from July through October 1982 in the tailwater of Barren River Lake, Kentucky. Chironomidae, the dominant taxon of benthic insects, reached full colonization by day 14. Colonization by Oligochaeta, the other major invertebrate taxon, was not completed by the end of the 95-day period of observation. It may have been delayed because insufficient food (periphyton and detritus) had accumulated on the clean rocks. Rapid recolonization of dewatered substrates may be especially critical for maintaining adequate fish food in tailwaters of flood-control reservoir.

Some Free-Living Heterotrophic Flagellates from Marine Sediments of Tropical Australia

NASA Astrophysics Data System (ADS)

Je Lee, Won

2006-06-01

The diversity of heterotrophic flagellates was examined at marine sediments around Cape Tribulation, Australia. The species described belong to the Alveolates, Apusomonadidae, Cercomonadida, Choanoflagellida, Cry ptomonadida, Diplomonadida, Euglenozoa incertae sedis, Kathablepharidae, Kinetoplastida, Pedinellids, Stephanopogonidae, Stramenopiles, Stramenopiles incertae sedis, Thaumatomonadidae and Protista incertae sedis. Among the 51 species from 38 genera encountered in this study is one new taxon: Glissandra similis n. sp., and two new names are introduced: Goniomonas abrupta (Skvortzov 1924) nomen nodum and Cercomonas skvortzovi (Skvortzov 1977) nomen nodum. There was little evidence for endemism because most flagellates including one new taxon described here have been reported.

Crustal structure of mountain belts and basins: Industry and academic collaboration at Cornell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allmendinger, R.; Barazangi, M.; Brown, L.

1995-08-01

Interdisciplinary investigations of the large-scale structure and evolution of key basins and orogenic belts around the world are the focal point of academic-industry interaction at Cornell. Ongoing and new initiatives with significant industry involvement include: Project INDEPTH (Interdisciplinary Deep Profiling of Tibet and the Himalayas), a multinational effort to delineate deep structure across the type example of active continent-continent collision. 300 km of deep reflection profiling was collected across the Himalaya: and southern Tibet Plateau in 1992 and 1994. CAP (Cornell Andes Project), a long-standing interdisciplinary effort to understand the structure and evolution of the Andes, with a focus onmore » Argentina, Chile and Bolivia. A deep reflection profile is tentatively planned for 1997. Intra-plate Orogeny in the Middle East and North Africa is the focus of multidisciplinary regional syntheses of existing seismic reflection and other databases in Syria (Palmyrides)and Morocco (Atlas), with an emphasis on reactivation and inversion tectonics. Project URSEIS (Urals Reflection Seismic Experiment and Integrated Studies) is a collaboration with EUROPROBE to collect 500 km of vibroseis and dynamite deep reflection profiling across the southern Urals in 1995. Project CRATON, an element in COCORP`s systematic exploration of the continental US, is a nascent multi-disciplinary effort to understand the buried craton of the central US and the basins built upon it. Global Basins Research Network (GBRN) is a diversified observational and computational effort to image and model the movement of pore fluids in detail and on a regional scale for a producing oil structure in the Gulf of Mexico.« less

Representative Doses to Members of the Public from Atmospheric Releases of 131I at the Mayak Production Association Facilities from 1948 through 1972

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eslinger, Paul W.; Napier, Bruce A.; Anspaugh, Lynn R.

Scoping epidemiologic studies performed by researchers from the Southern Urals Biophysics Institute revealed an excess prevalence of thyroid nodules and an increased incidence of thyroid cancer among residents of Ozersk, Russia, who were born in the early 1950s. Ozersk is located about 5 km from the facilities where the Mayak Production Association produced nuclear materials for the Russian weapons program. Reactor operations began in June 1948 and chemical separation of plutonium from irradiated fuel began in February 1949. The U.S.–Russia Joint Coordinating Committee on Radiation Effects Research conducted a series of projects over a 10-year period to assess the radiationmore » risks in the Southern Urals. This paper uses data collected under Committee projects to reconstruct individual time-dependent thyroid doses to reference individuals living in Ozersk from 131I released to the atmosphere. Between 3.22×1016 and 4.31×1016 Bq of 131I released may have been released during the 1948–1972 time period, and a best estimate is 3.76×1016 Bq. A child born in 1947 is estimated to have received a cumulative thyroid dose of 2.3 Gy for 1948–1972, with a 95% confidence interval of 0.51–7.3 Gy. Annual doses were the highest in 1949 and a child who was 5 years old in 1949 is estimated to have a received an annual thyroid dose of 0.93 Gy with a 95% confidence interval of 0.19–3.5 Gy.« less

Acanthocephalans of the genus Centrorhynchus (Palaeacanthocephala: Centrorhynchidae) of birds of prey (Falconiformes) and owls (Strigiformes) in Slovakia.

PubMed

Komorová, P; Špakulová, M; Hurníková, Z; Uhrín, M

2015-06-01

Three species of thorny-headed worms of the genus Centrorhynchus were found to parasitize birds of prey and owls in the territory of the Slovakia during the years 2012-2014. Out of 286 examined bird individuals belonging to 23 species, only Buteo buteo, Buteo rufinus, Falco tinnunculus (Falconiformes), Asio otus, Strix aluco, Strix uralensis and Tyto alba (Strigiformes) were infected by acanthocephalans. All the bird species except for S. aluco represent new host records for Slovakia. The most prevalent acanthocephalan Centrorhynchus aluconis was detected in all 15 examined birds of non-migratory Ural owl S. uralensis (P = 100%); however, it was found occasionally also in two individuals of the tawny owl S. aluco (P = 20%), one long-eared owl A. otus (P = 7.7%), one barn owl T. alba (P = 33.3%) and the common buzzard B. buteo (P = 0.8%). Two other thorny-headed worms occurred exclusively in Falconiformes in raw or mixed infections: Centrorhynchus buteonis was found in 11 individuals of B. buteo (P = 9.2%), and two birds (B. buteo and B. rufinus) were parasitized simultaneously by C. buteonis and the species Centrorhynchus globocaudatus. Moreover, the latest, relatively rare acanthocephalan was found alone in two common kestrels F. tinnunculus (P = 2.7%). Regarding intensity of infection, it ranged from a single female of C. buteonis, C. globocaudatus or C. aluconis per host (four cases) to a maximum of 82 C. aluconis per an Ural owl. The difference in acanthocephalan species spectrum between birds of prey and owls in Slovakia was apparent.

Predation risk landscape modifies flying and red squirrel nest site occupancy independently of habitat amount

PubMed Central

Korpimäki, Erkki; Villers, Alexandre; Selonen, Vesa

2018-01-01

Habitat choice often entails trade-offs between food availability and predation risk. Understanding the distribution of individuals in space thus requires that both habitat characteristics and predation risk are considered simultaneously. Here, we studied the nest box use of two arboreal squirrels who share preferred habitat with their main predators. Nocturnal Ural owls (Strix uralensis) decreased occurrence of night-active flying squirrels (Pteromys volans) and diurnal goshawks (Accipiter gentilis) that of day-active red squirrels (Sciurus vulgaris). Unexpectedly, the amount of preferred habitat had no effect on nest box use, but, surprisingly, both squirrel species seemed to benefit from close proximity to agricultural fields and red squirrels to urban areas. We found no evidence of trade-off between settling in a high-quality habitat and avoiding predators. However, the amount of poor-quality young pine forests was lower in occupied sites where goshawks were present, possibly indicating habitat specific predation on red squirrels. The results suggest that erecting nest boxes for Ural owls should be avoided in the vicinity of flying squirrel territories in order to conserve the near threatened flying squirrels. Our results also suggest that flying squirrels do not always need continuous old forests, and hence the currently insufficient conservation practices could be improved with reasonable increases in the areas left untouched around their nests. The results of this study demonstrate the importance of taking into account both habitat requirements and predation risk as well as their interactive effects when modeling the occupancy of threatened animal species and planning their conservation. PMID:29596438

Reconstruction of climate, soil, and vegetation conditions of the Srubnaya cultural epoch on the basis of kurgan studies in the Cis-Ural forest-steppe of the Republic of Bashkortostan

NASA Astrophysics Data System (ADS)

Prikhod'ko, V. E.; Rohozin, Ye. P.; Chaplygin, M. S.

2016-09-01

The reconstruction of soil, vegetation, and climatic conditions for the Srubnaya cultural epoch (3660 ± 40 (date wood), 3860 ± 120 (bones date) was performed on the basis of palynological and paleosol studies with radiocarbon dating of bones and wood fragments from two kurgans in the Cis-Ural forest-steppe of the Republic of Bashkortostan. Morphological features and chemical properties of the modern background soils, the soils formed on the surface of burial mounds (kurgans), and the soils buried under them were characterized. According to palynological data, the climate of this territory in the period of construction of these kurgans was more humid than the modern climate. The paleovegetation of the Srubnaya epoch was represented by mesophilic herbaceous steppes with a lower participation of xerophytic species as compared to the modern steppe and by small forest groves composed of birch and pine trees with some admixture of lime trees. The temperature conditions were close to those at present, or somewhat cooler, which is evidenced by the lower content of pollen of the broadleaved trees. The modern background soils and the soils buried under the kurgans are classified as thin light loamy typical calcareous chernozems; they have similar morphologies and physicochemical properties. However, the reconstructed organic matter content in the upper 50 cm of the buried paleosols is higher than that in the modern soils. This attests to more favorable climatic conditions during the Srubnaya epoch and is in agreement with palynological data.

[Factors of anxiety and autonomic tonus in senior preschool children from Magnitogorsk].

PubMed

Ingel', F I; Stepanova, A A; Stepanova, O P; Legostaeva, T B; Koganova, Z I; Kozlova, O B

2013-01-01

In the paper there are presented the results of a study of anxiety and balance ofparts of autonomous nervous system in healthy children 5-7 years old, residing in different parts of Magnitogorsk. It is shown that state of heightened and high alert was shown to be more common among children living on the left bank of the Urals river around the Magnitogorsk Metallurgical Integrated Plant. In these children an imbalance in the work of the parts of the autonomic nervous system was detected more frequently, at that shifts were observed mainly in the direction to ergotropic tone. At the same time balanced work of the parts of the autonomic nervous system was observed more frequently in children living on the right bank of the Urals river. Discovered psychosomatic features of examined children turned out to be associated with both the social characteristics of family lifestyle and the emotional stress of parents, and the contents of some organic compounds in total snow samples collected in the territories of kindergartens which they attended. One ofthe most significant results ofthe work we consider the detection of a correlation relationship between emotional stress of parents and activity of key enzymes in their children, reflecting the protective and adaptive reactions of the organism. On the basis of these and previously obtained data, we suggest that social and psychological factors of the family are not only a potential source of maladaptation of the child, but, probably, can have an impact on the stability and sensitivity of the genome of children.

Petroleum geology and resources of the North Caspian Basin, Kazakhstan and Russia

USGS Publications Warehouse

Ulmishek, Gregory F.

2001-01-01

The North Caspian basin is a petroleum-rich but lightly explored basin located in Kazakhstan and Russia. It occupies the shallow northern portion of the Caspian Sea and a large plain to the north of the sea between the Volga and Ural Rivers and farther east to the Mugodzhary Highland, which is the southern continuation of the Ural foldbelt. The basin is bounded by the Paleozoic carbonate platform of the Volga-Ural province to the north and west and by the Ural, South Emba, and Karpinsky Hercynian foldbelts to the east and south. The basin was originated by pre-Late Devonian rifting and subsequent spreading that opened the oceanic crust, but the precise time of these tectonic events is not known. The sedimentary succession of the basin is more than 20 km thick in the central areas. The drilled Upper Devonian to Tertiary part of this succession includes a prominent thick Kungurian (uppermost Lower Permian) salt formation that separates strata into the subsalt and suprasalt sequences and played an important role in the formation of oil and gas fields. Shallow-shelf carbonate formations that contain various reefs and alternate with clastic wedges compose the subsalt sequence on the 1 basin margins. Basinward, these rocks grade into deep-water anoxic black shales and turbidites. The Kungurian salt formation is strongly deformed into domes and intervening depressions. The most active halokinesis occurred during Late Permian?Triassic time, but growth of salt domes continued later and some of them are exposed on the present-day surface. The suprasalt sequence is mostly composed of clastic rocks that are several kilometers thick in depressions between salt domes. A single total petroleum system is defined in the North Caspian basin. Discovered reserves are about 19.7 billion barrels of oil and natural gas liquids and 157 trillion cubic feet of gas. Much of the reserves are concentrated in the supergiant Tengiz, Karachaganak, and Astrakhan fields. A recent new oil discovery on the Kashagan structure offshore in the Caspian Sea is probably also of the supergiant status. Major oil and gas reserves are located in carbonate reservoirs in reefs and structural traps of the subsalt sequence. Substantially smaller reserves are located in numerous fields in the suprasalt sequence. These suprasalt fields are largely in shallow Jurassic and Cretaceous clastic reservoirs in salt dome-related traps. Petroleum source rocks are poorly identified by geochemical methods. However, geologic data indicate that the principal source rocks are Upper Devonian to Lower Permian deep-water black-shale facies stratigraphically correlative to shallow-shelf carbonate platforms on the basin margins. The main stage of hydrocarbon generation was probably in Late Permian and Triassic time, during deposition of thick orogenic clastics. Generated hydrocarbons migrated laterally into adjacent subsalt reservoirs and vertically, through depressions between Kungurian salt domes where the salt is thin or absent, into suprasalt clastic reservoirs. Six assessment units have been identified in the North Caspian basin. Four of them include Paleozoic subsalt rocks of the basin margins, and a fifth unit, which encompasses the entire total petroleum system area, includes the suprasalt sequence. All five of these assessment units are underexplored and have significant potential for new discoveries. Most undiscovered petroleum resources are expected in Paleozoic subsalt carbonate rocks. The assessment unit in subsalt rocks with the greatest undiscovered potential occupies the south basin margin. Petroleum potential of suprasalt rocks is lower; however, discoveries of many small to medium size fields are expected. The sixth identified assessment unit embraces subsalt rocks of the central basin areas. The top of subsalt rocks in these areas occurs at depths ranging from 7 to 10 kilometers and has not been reached by wells. Undiscovered resources of this unit did not rec

Application of Spaceborne Differential Radar Interferometry to Rockbursts, Mining Subsidence and Shallow Moderate Earthquakes

NASA Astrophysics Data System (ADS)

Eneva, M.; Baker, E.

2002-12-01

We have processed ERS SAR scenes for several sites of rockbursts and mining subsidence, including South Africa (gold), Colorado (coal), the state of New York (salt), Germany (potash), and Poland (copper). We are also looking at JERS-1 scenes from a potash mine in the Ural mountains (Russia) for which no suitable ERS data exist. Sizeable mining-induced events have occurred at most of these sites: mb5.1 in April 1999, S. Africa; ML3.6 in March 1994, New York; ML4.8 in September 1996, Germany; mb4.9 in April 2000, Poland; and mb4.7 in January 1995, Urals. It is reasonable to expect detectable surface displacements from rockbursts, as they are rather shallow compared with tectonic earthquakes of similar size. Indeed, in the case of the 1999 S. African event differential InSAR detects up to 9-cm displacement away from the satellite, while the 1995 collapse in the Urals has resulted in up to 4.5-m surface subsidence. Some of the study rockbursts have occurred on the background of ongoing mining subsidence (e. g., Poland, Urals, New York), adding a detectable boost to the existing subsidence rate. In other cases, mining subsidence is planned and intermittent, without unexpected collapse (e.g., long-wall coal mining in Colorado). We have applied deformation modeling using a 3D finite-difference code, focusing on the April 1999 event that was associated with a normal slip along the Dagbreek fault. Seismic events in this area (Welkom, S. Africa) are commonly associated with collapse of mined out volumes around west-dipping normal faults, but it is not clear how these faults contribute to the seismic and static displacements. The 1999 event provides an opportunity to address this ambiguity, as our InSAR measurements of surface displacements are complemented by local, regional, and teleseismic waveform records, as well as by measurements of displacements in the mine tunnels intersecting the Dagbreek fault. We are using these data to constrain the source and are investigating the use of 3D modeling methods in resolving discrepancies between seismically and geodetically based models. Other than contributing to the mining practice, our InSAR results are relevant to the identification of ground truth to be compared with seismically determined epicenters. The 1999 S. African event is our best example in this respect, with an interferogram showing a clear fringe pattern that is easy to compare with existing seismic locations. For the purpose of ground truth, we have also examined ERS SAR scenes over sites of moderate tectonic earthquakes in Algeria (northern Africa). Due to the configuration of the existing seismic networks, these events are commonly located much too to the north. So far we have identified a possible signal (~ 2 cm LOS) in the differential interferograms from descending and ascending interferometric pairs over the site of a December 1999 Mw5.6 earthquake, and are in the process of looking at additional SAR scenes over a site of a November 2000 Mw5.7 event. Our results show that differential InSAR can be effective in providing detailed spatial coverage of surface changes associated with mining activities, as well as in establishing ground truth for the seismic locations of moderate tectonic earthquakes. The main limitation of the technique for such purposes is the insufficient temporal coverage of sites of interest by the ERS satellites, resulting in extensive decorrelation in some of the study cases. ENVISAT data are likely to be more effective in the future, especially if regular data collection is supplemented with ordering of data acquisitions on as-needed basis.

Can Global Weed Assemblages Be Used to Predict Future Weeds?

PubMed Central

Morin, Louise; Paini, Dean R.; Randall, Roderick P.

2013-01-01

Predicting which plant taxa are more likely to become weeds in a region presents significant challenges to both researchers and government agencies. Often it is done in a qualitative or semi-quantitative way. In this study, we explored the potential of using the quantitative self-organising map (SOM) approach to analyse global weed assemblages and estimate likelihoods of plant taxa becoming weeds before and after they have been moved to a new region. The SOM approach examines plant taxa associations by analysing where a taxon is recorded as a weed and what other taxa are recorded as weeds in those regions. The dataset analysed was extracted from a pre-existing, extensive worldwide database of plant taxa recorded as weeds or other related status and, following reformatting, included 187 regions and 6690 plant taxa. To assess the value of the SOM approach we selected Australia as a case study. We found that the key and most important limitation in using such analytical approach lies with the dataset used. The classification of a taxon as a weed in the literature is not often based on actual data that document the economic, environmental and/or social impact of the taxon, but mostly based on human perceptions that the taxon is troublesome or simply not wanted in a particular situation. The adoption of consistent and objective criteria that incorporate a standardized approach for impact assessment of plant taxa will be necessary to develop a new global database suitable to make predictions regarding weediness using methods like SOM. It may however, be more realistic to opt for a classification system that focuses on the invasive characteristics of plant taxa without any inference to impacts, which to be defined would require some level of research to avoid bias from human perceptions and value systems. PMID:23393591

Evaluating and interpreting cross-taxon congruence: Potential pitfalls and solutions

NASA Astrophysics Data System (ADS)

Gioria, Margherita; Bacaro, Giovanni; Feehan, John

2011-05-01

Characterizing the relationship between different taxonomic groups is critical to identify potential surrogates for biodiversity. Previous studies have shown that cross-taxa relationships are generally weak and/or inconsistent. The difficulties in finding predictive patterns have often been attributed to the spatial and temporal scales of these studies and on the differences in the measure used to evaluate such relationships (species richness versus composition). However, the choice of the analytical approach used to evaluate cross-taxon congruence inevitably represents a major source of variation. Here, we described the use of a range of methods that can be used to comprehensively assess cross-taxa relationships. To do so, we used data for two taxonomic groups, wetland plants and water beetles, collected from 54 farmland ponds in Ireland. Specifically, we used the Pearson correlation and rarefaction curves to analyse patterns in species richness, while Mantel tests, Procrustes analysis, and co-correspondence analysis were used to evaluate congruence in species composition. We compared the results of these analyses and we described some of the potential pitfalls associated with the use of each of these statistical approaches. Cross-taxon congruence was moderate to strong, depending on the choice of the analytical approach, on the nature of the response variable, and on local and environmental conditions. Our findings indicate that multiple approaches and measures of community structure are required for a comprehensive assessment of cross-taxa relationships. In particular, we showed that selection of surrogate taxa in conservation planning should not be based on a single statistic expressing the degree of correlation in species richness or composition. Potential solutions to the analytical issues associated with the assessment of cross-taxon congruence are provided and the implications of our findings in the selection of surrogates for biodiversity are discussed.

The impact of pesticides on the macroinvertebrate community in the water channels of the Río Negro and Neuquén Valley, North Patagonia (Argentina).

PubMed

Macchi, Pablo; Loewy, Ruth Miriam; Lares, Betsabé; Latini, Lorena; Monza, Liliana; Guiñazú, Natalia; Montagna, Cristina Mónica

2018-04-01

Agriculture represents the second most important economic activity in the North Patagonian Region of Argentina and non-selective insecticides are still being used with significant implications to the quality of the environment. The range of concentrations (μg/L) determined for azinphosmethyl, chlorpyrifos, and carbaryl in drainage channels were from non-detected to 1.02, 1.45, and 11.21, respectively. Macroinvertebrate abundance and taxon richness in drainage channels were significantly lower in November compared to the other sampling months (October, February). The decrease in taxon richness observed in November was associated with chlorpyrifos and azinphosmethyl peak concentrations. The most remarkable changes were the decrease in sensitive taxa such as Baetidae and the increase in some tolerant taxa such as Chironomidae and Gastropoda.For all three pesticides, the acute hazard quotient exceeded the risk criteria for invertebrates. The effects of the three pesticides on aquatic organisms, characterized by joint probability curves, showed that the LC 50 of 10% of the species were exceeded five and three times by the concentrations of azinphosmethyl and chlorpyrifos during the study period, respectively. However, the correlation between the pesticide concentrations and both taxon richness and abundance of macroinvertebrates at each site (irrigation and drainage channels) was indicative that only chlorpyrifos was negatively correlated with both parameters (Spearman r 2 - 0.61, p = 0.0051 and Spearman r 2 - 0.59, p = 0.0068 for taxon richness and abundance correlation, respectively). We conclude that macroinvertebrate assemblages in drainage channels were highly affected by chlorpyrifos levels.

Morphological Variations within the Ontogeny of Deinonychus antirrhopus (Theropoda, Dromaeosauridae)

PubMed Central

Parsons, William L.; Parsons, Kristen M.

2015-01-01

This research resulted from the determination that MCZ 8791 is a specimen of Deinonychus antirrhopus between one and two years of age and that the morphological variations within particular growth stages of this taxon have yet to be described. The primary goal of the research is to identify ontogenetic variations in this taxon. Histological analyses determined that the Deinonychus specimens AMNH 3015 and MOR 1178 were adults. Comparisons are made between MCZ 8791 and these adult specimens. The holotype, YPM 5205, and the other associated specimens of this taxon within the YPM collection are similar in size and morphology to AMNH 3015. Further comparisons were made with the three partial specimens OMNH 50268, MCZ 4371, and MOR 1182. Although these specimens represent only a partial ontogenetic series, a number of morphological variations can be described. One secondary goal of this research is to compare the known pattern of variable, informative, ontogenetic characters in MCZ 8791 to a similar pattern of morphological characters in the sub-adult dromaeosaurid specimen Bambiraptor feinbergorum, AMNH FR: 30556. If the characters that have been determined to represent variable juvenile morphology in the ontogeny of Deinonychus are exhibited in Bambiraptor, this study will begin the process of determining whether a similar, conservative, ontogenetic pattern exists throughout the rest of Dromaeosauridae. If defensible, it may reduce the number of sympatric taxa within this clade. The other secondary goal relates to the forelimb function. The approximate body size, forelimb length, wrist development, and the presence of a more prominent olecranon on the ulna of MCZ 8791 support the hypothesis that juveniles of this taxon possessed some form of flight capability. PMID:25875499

Bryozoans are returning home: recolonization of freshwater ecosystems inferred from phylogenetic relationships.

PubMed

Koletić, Nikola; Novosel, Maja; Rajević, Nives; Franjević, Damjan

2015-01-01

Bryozoans are aquatic invertebrates that inhabit all types of aquatic ecosystems. They are small animals that form large colonies by asexual budding. Colonies can reach the size of several tens of centimeters, while individual units within a colony are the size of a few millimeters. Each individual within a colony works as a separate zooid and is genetically identical to each other individual within the same colony. Most freshwater species of bryozoans belong to the Phylactolaemata class, while several species that tolerate brackish water belong to the Gymnolaemata class. Tissue samples for this study were collected in the rivers of Adriatic and Danube basin and in the wetland areas in the continental part of Croatia (Europe). Freshwater and brackish taxons of bryozoans were genetically analyzed for the purpose of creating phylogenetic relationships between freshwater and brackish taxons of the Phylactolaemata and Gymnolaemata classes and determining the role of brackish species in colonizing freshwater and marine ecosystems. Phylogenetic relationships inferred on the genes for 18S rRNA, 28S rRNA, COI, and ITS2 region confirmed Phylactolaemata bryozoans as radix bryozoan group. Phylogenetic analysis proved Phylactolaemata bryozoan's close relations with taxons from Phoronida phylum as well as the separation of the Lophopodidae family from other families within the Plumatellida genus. Comparative analysis of existing knowledge about the phylogeny of bryozoans and the expansion of known evolutionary hypotheses is proposed with the model of settlement of marine and freshwater ecosystems by the bryozoans group during their evolutionary past. In this case study, brackish bryozoan taxons represent a link for this ecological phylogenetic hypothesis. Comparison of brackish bryozoan species Lophopus crystallinus and Conopeum seurati confirmed a dual colonization of freshwater ecosystems throughout evolution of this group of animals.

Assessing Conservation Values: Biodiversity and Endemicity in Tropical Land Use Systems

PubMed Central

Waltert, Matthias; Bobo, Kadiri Serge; Kaupa, Stefanie; Montoya, Marcela Leija; Nsanyi, Moses Sainge; Fermon, Heleen

2011-01-01

Despite an increasing amount of data on the effects of tropical land use on continental forest fauna and flora, it is debatable whether the choice of the indicator variables allows for a proper evaluation of the role of modified habitats in mitigating the global biodiversity crisis. While many single-taxon studies have highlighted that species with narrow geographic ranges especially suffer from habitat modification, there is no multi-taxa study available which consistently focuses on geographic range composition of the studied indicator groups. We compiled geographic range data for 180 bird, 119 butterfly, 204 tree and 219 understorey plant species sampled along a gradient of habitat modification ranging from near-primary forest through young secondary forest and agroforestry systems to annual crops in the southwestern lowlands of Cameroon. We found very similar patterns of declining species richness with increasing habitat modification between taxon-specific groups of similar geographic range categories. At the 8 km2 spatial level, estimated richness of endemic species declined in all groups by 21% (birds) to 91% (trees) from forests to annual crops, while estimated richness of widespread species increased by +101% (trees) to +275% (understorey plants), or remained stable (- 2%, butterflies). Even traditional agroforestry systems lost estimated endemic species richness by - 18% (birds) to - 90% (understorey plants). Endemic species richness of one taxon explained between 37% and 57% of others (positive correlations) and taxon-specific richness in widespread species explained up to 76% of variation in richness of endemic species (negative correlations). The key implication of this study is that the range size aspect is fundamental in assessments of conservation value via species inventory data from modified habitats. The study also suggests that even ecologically friendly agricultural matrices may be of much lower value for tropical conservation than indicated by mere biodiversity value. PMID:21298054

'Candidatus Phytoplasma noviguineense', a novel taxon associated with Bogia coconut syndrome and banana wilt disease on the island of New Guinea.

PubMed

Miyazaki, Akio; Shigaki, Toshiro; Koinuma, Hiroaki; Iwabuchi, Nozomu; Rauka, Gou Bue; Kembu, Alfred; Saul, Josephine; Watanabe, Kiyoto; Nijo, Takamichi; Maejima, Kensaku; Yamaji, Yasuyuki; Namba, Shigetou

2018-01-01

Bogia coconut syndrome (BCS) is one of the lethal yellowing (LY)-type diseases associated with phytoplasma presence that are seriously threatening coconut cultivation worldwide. It has recently emerged, and is rapidly spreading in northern parts of the island of New Guinea. BCS-associated phytoplasmas collected in different regions were compared in terms of 16S rRNA gene sequences, revealing high identity among them represented by strain BCS-Bo R . Comparative analysis of the 16S rRNA gene sequences revealed that BCS-Bo R shared less than a 97.5 % similarity with other species of 'Candidatus Phytoplasma', with a maximum value of 96.08 % (with strain LY; GenBank accession no. U18747). This result indicates the necessity and propriety of a novel taxon for BCS phytoplasmas according to the recommendations of the IRPCM. Phylogenetic analysis was also conducted on 16S rRNA gene sequences, resulting in a monophyletic cluster composed of BCS-Bo R and other LY-associated phytoplasmas. Other phytoplasmas on the island of New Guinea associated with banana wilt and arecanut yellow leaf diseases showed high similarities to BCS-Bo R and were closely related to BCS phytoplasmas. Based on the uniqueness of their 16S rRNA gene sequences, a novel taxon 'Ca.Phytoplasma noviguineense' is proposed for these phytoplasmas found on the island of New Guinea, with strain BCS-Bo R (GenBank accession no. LC228755) as the reference strain. The novel taxon is described in detail, including information on the symptoms of associated diseases and additional genetic features of the secY gene and rp operon.

Invasion of European pine stands by a North American forest pathogen and its hybridization with a native interfertile taxon.

PubMed

Gonthier, P; Nicolotti, G; Linzer, R; Guglielmo, F; Garbelotto, M

2007-04-01

It was recently reported that North American (NA) individuals of the forest pathogen Heterobasidion annosum were found in a single pine stand near Rome, in association with the movement of US troops during World War II. Here, we report on some aspects of the invasion biology of this pathogen in Italian coastal pinewoods, and on its interaction with native (EU) Heterobasidion populations. Spores of Heterobasidion were sampled using woody traps in pine stands along 280 km of coast around Rome. DNA of single-spore colonies was characterized by two sets of nuclear and one set of mitochondrial taxon-specific polymerase chain reaction primers. NA spores were found not only in a single site, but in many locations over a wide geographic area. Invasion occurred at an estimated rate of 1.3 km/year through invasion corridors provided by single trees, and not necessarily by sizable patches of forests. Within the 100-km long range of expansion, the NA taxon was dominant in all pure pine stands. Because abundance of the EU taxon is low and identical among stands within and outside the area invaded by NA individuals, we infer that the exotic population has invaded habitats mostly unoccupied by the native species. Discrepancy between a mitochondrial and a nuclear marker occurred in 3.8% of spores from one site, a mixed oak-pine forest where both taxa were equally represented. Combined phylogenetic analyses on nuclear and mitochondrial loci confirmed these isolates were recombinant. The finding of hybrids indicates that genetic interaction between NA and EU Heterobasidion taxa is occurring as a result of their current sympatry.

Distinct features of intraspecific and intrapopulation variability of the skull size in the red fox.

PubMed

Gos'kov, A M; Bol'shakov, V N; Korytin, N S

2017-05-01

The range of chronographic variability of the average size of the skull in the red fox (data collected by the authors) from a compact area in the Middle Urals has been assessed for a 30-year period, and the results obtained have been compared with the published data on the geographical variability within the vast species range. The range of changes of the average dimensions of the skull over time spanned almost the entire range of geographical variability. Therefore, the problem of search for factors that determine the morphological diversity arises.

Metallographic examination of the structure of the metal of cold arms of the nineteenth-early twentieth centuries made at the Zlatoust arms factory

NASA Astrophysics Data System (ADS)

Schastlivtsev, V. M.; Rodionov, D. P.; Gerasimov, V. Yu.; Khlebnikova, Yu. V.

2010-11-01

Data are given concerning the structure and the chemical composition of carbon steel used for making cold arms, which was produced at the Zlatoust arms factory in the nineteenth and early twentieth centuries. The results of the analysis of the structure of metal demonstrates the general trend of the development of metallurgy both at the Ural plants and in the world: from the creation of the crucible methods of production of cast steel to the mass production of cast steel by the Bessemer and Martin methods.

Preface

NASA Astrophysics Data System (ADS)

Rodionova, Valeria V.; Kurlyandskaya, Galina V.

2016-10-01

This special issue of Journal of Magnetism and Magnetic Materials contains selected peer-reviewed papers from the International Baltic Conference on Magnetism: focus on biomedical aspects (IBCM-2015) held in Svetlogorsk, Kaliningrad region, Russia on the base of Immanuel Kant Baltic Federal University (IKBFU, Kaliningrad, Russia) during August 30-September 03, 2015. Ural Federal University named after the first President of Russia B.N. Yeltsin (UrFU, Yekaterinburg, Russia) acted as a co-organizer of the IBCM-2015. IKBFU and UrFU vice-rectors for science - Prof. Artyom V. Yurov and Prof. Vladimir V. Kruzhaev - took a special care for the IBCM-2015.

Vojnovskytesidae - a new family of Mississippian Rugosa (Anthozoa)

NASA Astrophysics Data System (ADS)

Fedorowski, Jerzy; Kullmann, Jürgen

2013-12-01

Fedorowski, J. and Kullmann, J. 2013. Vojnovskytesidae - a new family of Mississippian Rugosa (Anthozoa). Acta Geologica Polonica, 63(4), 657-679. Warszawa. Two new species of the genus Vojnovskytes Fedorowski, 2009, namely V. marcinowskii and V. arcuatus, and a new genus, Vojnimitor, based on the new species V. proiectus, all from Mississippian strata of northern Spain, are described. Vojnovskytes variabilis (Vojnovsky-Krieger, 1934), the type species for the genus from the lowermost Visean strata of southern Urals, also is discussed and illustrated. Characters displayed by the taxa mentioned permit introduction of a new family Vojnovskytesidae.

Ural-Tweed Bighorn Sheep Investigation.

DTIC Science & Technology

1979-01-01

use of Isouth, southwe-st, and west el)-Osed overs -teepenod terrain alonr~ the east escarpment of Lirke KoocanusQ. Five habitat types, PSME/ SYAL ...8217 SYAL PSIM, PHIiA PS:: , L7 a b Jan. a2/7b -,4/47 14/47 Feb. 9/31 9 ,𔄁 1’ , Mar. 12/43 1/4 10/36 3/11/ A, r. 9/50 2/12 7/3, May 3/1i 12/71 2/11 Ji...of the sheep use Table 13). In order of apparent decreasing importance, these habitat types were- 1) PSME/ SYAL , 2) PSME/CARU, 3) PSME/PHMA, 4) PSME

A new genus and species of winter stoneflies (Plecoptera: Capniidae) from Southwest China, with a commented checklist of the family in the Oriental Realm.

PubMed

Murányi, Dávid; Li, Weihai; Yang, Ding

2015-12-22

A new genus and species of the family Capniidae (Plecoptera), Sinocapnia kuankuoshui gen. n., sp. n. is described from the adult male and a female collected in Guizhou Province of southwest China. The new taxon is distinguished from all extant Capniidae genera and the assemblage of species currently included in Capnia sensu lato by combination of unique genitalic, wing, and thoracic sclerites characters. No closely related taxon is indicated on the basis of morphological characters. An annotated checklist of the family Capniidae from the Oriental Realm is given.

Pseudomonas mesophilica and an unnamed taxon, clinical isolates of pink-pigmented oxidative bacteria.

PubMed

Gilardi, G L; Faur, Y C

1984-10-01

Twenty-one strains of pink-pigmented bacteria, isolated from human clinical specimens and an environmental source, were compared with Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. These isolates were gram-negative, oxidative rods which were motile by means of a single polar flagellum; gave positive catalase, indophenol oxidase, urease, and amylase reactions; and grew slowly at 30 degrees C. Fourteen isolates conformed to the designated type strains Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. The remaining seven strains represented an undescribed taxon. These pink bacteria appear to be invaders of debilitated patients with an underlying chronic disease.

Pseudomonas mesophilica and an unnamed taxon, clinical isolates of pink-pigmented oxidative bacteria.

PubMed Central

Gilardi, G L; Faur, Y C

1984-01-01

Twenty-one strains of pink-pigmented bacteria, isolated from human clinical specimens and an environmental source, were compared with Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. These isolates were gram-negative, oxidative rods which were motile by means of a single polar flagellum; gave positive catalase, indophenol oxidase, urease, and amylase reactions; and grew slowly at 30 degrees C. Fourteen isolates conformed to the designated type strains Pseudomonas mesophilica ATCC 29983 and Protaminobacter ruber ATCC 8457. The remaining seven strains represented an undescribed taxon. These pink bacteria appear to be invaders of debilitated patients with an underlying chronic disease. PMID:6490848

Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration.

PubMed

Benjamino, Jacquelynn; Lincoln, Stephen; Srivastava, Ranjan; Graf, Joerg

2018-05-10

As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions. Shifts in the termite gut microbiota after diet change in each colony were observed using 16S rRNA gene sequencing and beta diversity analyses. The artificial neural network accurately predicted the relative abundances of taxa at random points in the temporal study and showed that low-abundant taxa maintain community driving correlations in the hindgut. This combinatorial approach utilizing 16S rRNA gene sequencing and deep learning revealed that low-abundant bacteria that often do not belong to the core community are drivers of the termite hindgut bacterial community composition.

Evolutionary history of Leishmania killicki (synonymous Leishmania tropica) and taxonomic implications.

PubMed

Chaara, Dhekra; Ravel, Christophe; Bañuls, Anne- Laure; Haouas, Najoua; Lami, Patrick; Talignani, Loïc; El Baidouri, Fouad; Jaouadi, Kaouther; Harrat, Zoubir; Dedet, Jean-Pierre; Babba, Hamouda; Pratlong, Francine

2015-04-01

The taxonomic status of Leishmania (L.) killicki, a parasite that causes chronic cutaneous leishmaniasis, is not well defined yet. Indeed, some researchers suggested that this taxon could be included in the L. tropica complex, whereas others considered it as a distinct phylogenetic complex. To try to solve this taxonomic issue we carried out a detailed study on the evolutionary history of L. killicki relative to L. tropica. Thirty-five L. killicki and 25 L. tropica strains isolated from humans and originating from several countries were characterized using the MultiLocus Enzyme Electrophoresis (MLEE) and the MultiLocus Sequence Typing (MLST) approaches. The results of the genetic and phylogenetic analyses strongly support the hypothesis that L. killicki belongs to the L. tropica complex. Our data suggest that L. killicki emerged from a single founder event and that it evolved independently from L. tropica. However, they do not validate the hypothesis that L. killicki is a distinct complex. Therefore, we suggest naming this taxon L. killicki (synonymous L. tropica) until further epidemiological and phylogenetic studies justify the L. killicki denomination. This study provides taxonomic and phylogenetic information on L. killicki and improves our knowledge on the evolutionary history of this taxon.

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

PubMed Central

Aberer, Andre J.; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

Abstract The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees. PMID:22962004

Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice.

PubMed

Aberer, Andre J; Krompass, Denis; Stamatakis, Alexandros

2013-01-01

The presence of rogue taxa (rogues) in a set of trees can frequently have a negative impact on the results of a bootstrap analysis (e.g., the overall support in consensus trees). We introduce an efficient graph-based algorithm for rogue taxon identification as well as an interactive webservice implementing this algorithm. Compared with our previous method, the new algorithm is up to 4 orders of magnitude faster, while returning qualitatively identical results. Because of this significant improvement in scalability, the new algorithm can now identify substantially more complex and compute-intensive rogue taxon constellations. On a large and diverse collection of real-world data sets, we show that our method yields better supported reduced/pruned consensus trees than any competing rogue taxon identification method. Using the parallel version of our open-source code, we successfully identified rogue taxa in a set of 100 trees with 116 334 taxa each. For simulated data sets, we show that when removing/pruning rogue taxa with our method from a tree set, we consistently obtain bootstrap consensus trees as well as maximum-likelihood trees that are topologically closer to the respective true trees.

Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses.

PubMed

Bào, Yīmíng; Amarasinghe, Gaya K; Basler, Christopher F; Bavari, Sina; Bukreyev, Alexander; Chandran, Kartik; Dolnik, Olga; Dye, John M; Ebihara, Hideki; Formenty, Pierre; Hewson, Roger; Kobinger, Gary P; Leroy, Eric M; Mühlberger, Elke; Netesov, Sergey V; Patterson, Jean L; Paweska, Janusz T; Smither, Sophie J; Takada, Ayato; Towner, Jonathan S; Volchkov, Viktor E; Wahl-Jensen, Victoria; Kuhn, Jens H

2017-05-11

The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel "filovirus." Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

BUMPER: the Bayesian User-friendly Model for Palaeo-Environmental Reconstruction

NASA Astrophysics Data System (ADS)

Holden, Phil; Birks, John; Brooks, Steve; Bush, Mark; Hwang, Grace; Matthews-Bird, Frazer; Valencia, Bryan; van Woesik, Robert

2017-04-01

We describe the Bayesian User-friendly Model for Palaeo-Environmental Reconstruction (BUMPER), a Bayesian transfer function for inferring past climate and other environmental variables from microfossil assemblages. The principal motivation for a Bayesian approach is that the palaeoenvironment is treated probabilistically, and can be updated as additional data become available. Bayesian approaches therefore provide a reconstruction-specific quantification of the uncertainty in the data and in the model parameters. BUMPER is fully self-calibrating, straightforward to apply, and computationally fast, requiring 2 seconds to build a 100-taxon model from a 100-site training-set on a standard personal computer. We apply the model's probabilistic framework to generate thousands of artificial training-sets under ideal assumptions. We then use these to demonstrate both the general applicability of the model and the sensitivity of reconstructions to the characteristics of the training-set, considering assemblage richness, taxon tolerances, and the number of training sites. We demonstrate general applicability to real data, considering three different organism types (chironomids, diatoms, pollen) and different reconstructed variables. In all of these applications an identically configured model is used, the only change being the input files that provide the training-set environment and taxon-count data.

Niltavinae, a new taxon of Old World flycatchers (Aves: Muscicapidae).

PubMed

Sangster, George; Alström, Per; Forsmark, Emma; Olsson, Urban

2016-11-23

The relationships among Old World chats and flycatchers (Muscicapidae) have recently been clarified in two independent molecular phylogenetic studies (Sangster et al. 2010, Zuccon & Ericson 2010). Both studies recovered a well-supported clade of predominantly blue flycatchers of the genera Niltava, Cyornis, Eumyias and Cyanoptila, some species traditionally included in the genus Rhinomyias and one species traditionally included in Ficedula (F. monileger). The family-group name Niltavinae Sangster, Alström, Forsmark & Olsson, 2010, was introduced for this clade (Sangster et al. 2010). Unfortunately, our description of the new taxon Niltavinae did not include a diagnosis (sensu ICZN article 13.1.1) and thus inadvertently made this name unavailable for nomenclatural purposes (Zuccon 2011). The supplementary data associated with our original paper included evidence by which the taxon Niltavinae can be diagnosed: a 1 base pair (bp) deletion in the ornithine decarboxylase gene, as shown in Figure S1 in the online version (doi:10.1016/j.ympev.2010.07.008), but this was not mentioned in the printed version of our paper. Given that Niltavinae Sangster, Alström, Forsmark & Olsson, 2010 represents a nomen nudum, and the clade for which this name was intended thus remains unnamed, we here provide the following description.

A taxonomic review of white grubs and leaf chafers (Coleoptera: Scarabaeidae: Melolonthinae) recorded from forestry and agricultural crops in Sub-Saharan Africa.

PubMed

Harrison, J du G; Wingfield, M J

2016-04-01

Integrated pest management (IPM) is difficult to implement when one knows little about the pest complex or species causing the damage in an agricultural system. To implement IPM on Sub-Saharan African melolonthine pests access to taxon specific knowledge (their identity) and what is known (their biology) of potential pest species is a crucial step. What is known about Sub-Saharan African melolonthine white grubs and chafers has not yet been amalgamated, and this review thus synthesizes all available literature for the Region. The comprehensive nature of the review highlights pest taxon trends within African melolonthines. To facilitate the retrieval of this information for IPM purposes, all relevant taxonomic and biological information is provided for the taxa covered including an on-line supplementary annotated-checklist of taxon, crop, locality and reference(s). Based on the literature reviewed, recommendations are made to promote effective and efficient management of African melolonthine scarab pests. An on-line supplementary appendix provides a list of specialists, useful internet resources, keys, catalogues and sampling methods for the larvae and adults of melolonthine scarab beetles for subsequent morphological or molecular work.

Representative doses to members of the public from atmospheric releases of (131)I at the Mayak Production Association facilities from 1948 through 1972.

PubMed

Eslinger, Paul W; Napier, Bruce A; Anspaugh, Lynn R

2014-09-01

Scoping epidemiology studies performed by researchers from the Southern Urals Biophysics Institute revealed an excess prevalence of thyroid nodules and an increased incidence of thyroid cancer among residents of Ozersk, Russia, who were born in the early 1950s. Ozersk is located about 5 km from the facilities where the Mayak Production Association produced nuclear materials for the Russian weapons program. Reactor operations began in June 1948 and chemical separation of plutonium from irradiated fuel began in February 1949. The U.S.-Russia Joint Coordinating Committee on Radiation Effects Research conducted a series of projects over a 10-year period to assess the radiation risks in the Southern Urals. This paper uses data collected under Committee projects to present examples of reconstructed time-dependent thyroid doses to reference individuals living in Ozersk from (131)I released to the atmosphere for all relevant exposure pathways. Between 3.22 × 10(16) and 4.31 × 10(16) Bq of (131)I may have been released during the 1948-1972 time period, and a best estimate is 3.76 × 10(16) Bq. In general, younger children incur greater thyroid doses from (131)I than adults. A child born in 1947 is estimated to have received a cumulative thyroid dose of 2.3 Gy for 1948-1972, with a 95% confidence interval of 0.51-7.3 Gy. Annual doses were the highest in 1949 and a child who was 5 years old in 1949 is estimated to have a received an annual thyroid dose of 0.93 Gy with a 95% confidence interval of 0.19-3.5 Gy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recent Rapid Decline of the Arctic Winter Sea Ice in the Barents-Kara Seas Owing to Combined Effects of the Ural Blocking and SST

NASA Astrophysics Data System (ADS)

Luo, Binhe; Yao, Yao

2018-04-01

This study investigates why the Arctic winter sea ice loss over the Barents-Kara Seas (BKS) is accelerated in the recent decade. We first divide 1979-2013 into two time periods: 1979-2000 (P1) and 2001-13 (P2), with a focus on P2 and the difference between P1 and P2. The results show that during P2, the rapid decline of the sea ice over the BKS is related not only to the high sea surface temperature (SST) over the BKS, but also to the increased frequency, duration, and quasi-stationarity of the Ural blocking (UB) events. Observational analysis reveals that during P2, the UB tends to become quasi stationary and its frequency tends to increase due to the weakening (strengthening) of zonal winds over the Eurasia (North Atlantic) when the surface air temperature (SAT) anomaly over the BKS is positive probably because of the high SST. Strong downward infrared (IR) radiation is seen to occur together with the quasi-stationary and persistent UB because of the accumulation of more water vapor over the BKS. Such downward IR favors the sea ice decline over the BKS, although the high SST over the BKS plays a major role. But for P1, the UB becomes westward traveling due to the opposite distribution of zonal winds relative to P2, resulting in weak downward IR over the BKS. This may lead to a weak decline of the sea ice over the BKS. Thus, it is likely that the rapid decline of the sea ice over the BKS during P2 is attributed to the joint effects of the high SST over the BKS and the quasi-stationary and long-lived UB events.

South Ural State University Campus: Architectural Development Concept in Accordance with International Standards

NASA Astrophysics Data System (ADS)

Shabiev, S. G.

2017-11-01

The article deals with the vital problem of the implementation of the Program to enhance the competitiveness of the South Ural State University (SUSU) among other scientific and educational centers, which defines the main objective - to form a world-class university. According to the set objective, the most important task is to build a landscaped campus, which can be efficiently solved by the architectural means. The solution of this task is based on the scientific methods of the territorial and architectural improvement of the main university building complex development in the northern academic area and the architectural and aesthetic improvement of the space structural arrangement of the buildings. The author analyzes the global practice of modern campuses in Russia and abroad based on the Internet resources. The author carried out some additional on-site surveys of foreign campuses in Australia, Canada and China. The essence of the architectural concept of the first university campus development stage lies in the science-based achievement of a harmonious architectural and space unity of solid and plane elements of the site development, landscape arrangement of the main building’s courtyard and the adjacent territories with an efficient use of the relief, water areas and planting, allotment of additional spaces for landscaped areas due to a split-level arrangement, including a landscaped platform, increase of the underground space utilization share with the arrangement of an underground car parking and an underground walkway considering the environmental requirements. Further, it is planned to use the author’s methodological approach for the southern academic and the northern residential university areas, which will allow to create a duly completed landscaped SUSU campus with a developed infrastructure according to the international standards.

Effect of rainfall intensity and slope steepness on the development of soil erosion in the Southern Cis-Ural region (A model experiment)

NASA Astrophysics Data System (ADS)

Sobol, N. V.; Gabbasova, I. M.; Komissarov, M. A.

2017-09-01

The effect of rainfall intensity on the erosion of residual calcareous agrogray soils and clay-illuvial agrochernozems in the Southern Cis-Ural region on slopes of different inclination and vegetation type has been studied by simulating with a small-size sprinkler. It has been shown that soil loss linearly depends on rainfall intensity (2, 4, and 6 mm/min) and slope inclination (3° and 7°). When the rainfall intensity and duration, and the slope inclination increase, soil loss by erosion from agrogray soils increases higher than from agrochernozems. On the plowland with a slope of 3°, runoff begins 12, 10, and 5 min, on the average, after the beginning of rains at these intensities. When the slope increases to 7°, runoff begins earlier by 7, 6, and 4 min, respectively. After the beginning of runoff and with its increase by 1 mm, the soil loss from slopes of 3° and 7° reaches 4.2 and 25.7 t/ha on agrogray soils and 1.4 and 4.7 t/ha on agrochernozems, respectively. Fallow soils have higher erosion resistance, and the soil loss little depends on the slope gradient: it gradually increases to 0.3-1.0 t/ha per 1 mm of runoff with increasing rainfall intensity and duration. The content of physical clay in eroded material is higher than in the original soils. Fine fractions prevail in this material, which increases their humus content. The increase in rainfall intensity and duration to 4 and 6 mm/min results in the entrapment of coarse silt and sand by runoff.

Impact of northern Eurasian snow cover in autumn on the warm Arctic-cold Eurasia pattern during the following January and its linkage to stationary planetary waves

NASA Astrophysics Data System (ADS)

Xu, Xinping; He, Shengping; Li, Fei; Wang, Huijun

2018-03-01

The connection between Eurasian snow cover (SC) in autumn and Eurasian winter mean surface air temperature (SAT) has been identified by many studies. However, some recent observations indicate that early and late winter climate sometimes shows an out-of-phase relationship, suggesting that the winter mean situation might obscure the important relationships that are relevant for scientific research and applications. This study investigates the relationship between October northern Eurasian SC (NESC; 58°-68°N, 30°-90°E) and Eurasian SAT during the winter months and finds a significant relationship only exists in January. Generally, following reduced October NESC, the East Asian trough and Ural high are intensified in January, and anomalous northeasterly winds prevail in mid-latitudes, causing cold anomalies over Eurasia. Meanwhile, anomalous southwesterly winds along the northern fringe of the Ural high favor warm anomalies in the Arctic. The dynamical mechanism for the connection between NESC in October and the warm Arctic-cold Eurasia (WACE) anomaly in January is further investigated from the perspective of quasi-stationary planetary wave activity. It is found that planetary waves with zonal wavenumber-1 (ZWN1) play a dominant role in this process. Specifically, the ZWN1 pattern of planetary-scale waves concurrent with October NESC anomaly extends from the surface to the upper-stratosphere. It persists in the stratosphere through November-December and propagates downward to the surface by the following January, making the connection between October NESC and January climate possible. Additionally, the influence of October NESC on the January WACE pattern has intensified since the early-2000s.

New insights into Arctic paleogeography and tectonics from U-Pb detrital zircon geochronology

USGS Publications Warehouse

Miller, E.L.; Toro, J.; Gehrels, G.; Amato, J.M.; Prokopiev, A.; Tuchkova, M.I.; Akinin, V.V.; Dumitru, T.A.; Moore, Thomas E.; Cecile, M.P.

2006-01-01

To test existing models for the formation of the Amerasian Basin, detrital zircon suites from 12 samples of Triassic sandstone from the circum-Arctic region were dated by laser ablation-inductively coupled plasma-mass spectrometry (ICP-MS). The northern Verkhoyansk (NE Russia) has Permo-Carboniferous (265-320 Ma) and Cambro-Silurian (410-505 Ma) zircon populations derived via river systems from the active Baikal Mountain region along the southern Siberian craton. Chukotka, Wrangel Island (Russia), and the Lisburne Hills (western Alaska) also have Permo-Carboniferous (280-330 Ma) and late Precambrian-Silurian (420-580 Ma) zircons in addition to Permo-Triassic (235-265 Ma), Devonian (340-390 Ma), and late Precambrian (1000-1300 Ma) zircons. These ages suggest at least partial derivation from the Taimyr, Siberian Trap, and/ or east Urals regions of Arctic Russia. The northerly derived Ivishak Formation (Sadlerochit Mountains, Alaska) and Pat Bay Formation (Sverdrup Basin, Canada) are dominated by Cambrian-latest Precambrian (500-600 Ma) and 445-490 Ma zircons. Permo-Carboniferous and Permo-Triassic zircons are absent. The Bjorne Formation (Sverdrup Basin), derived from the south, differs from other samples studied with mostly 1130-1240 Ma and older Precambrian zircons in addition to 430-470 Ma zircons. The most popular tectonic model for the origin of the Amerasian Basin involves counterclockwise rotation of the Arctic Alaska-Chukotka microplate away from the Canadian Arctic margin. The detrital zircon data suggest that the Chukotka part of the microplate originated closer to the Taimyr and Verkhoyansk, east of the Polar Urals of Russia, and not from the Canadian Arctic. Copyright 2006 by the American Geophysical Union.

Tetrapod localities from the Triassic of the SE of European Russia

NASA Astrophysics Data System (ADS)

Tverdokhlebov, Valentin P.; Tverdokhlebova, Galina I.; Surkov, Mikhail V.; Benton, Michael J.

2003-01-01

Fossil tetrapods (amphibians and reptiles) have been discovered at 206 localities in the Lower and Middle Triassic of the southern Urals area of European Russia. The first sites were found in the 1940s, and subsequent surveys, from the 1960s to the present day, have revealed many more. Broad-scale stratigraphic schemes have been published, but full documentation of the rich tetrapod faunas has not been presented before. The area of richest deposits covers some 900,000 km 2 of territory between Samara on the River Volga in the NW, and Orenburg and Sakmara in the SW. Continental sedimentary deposits, consisting of mudstones, siltstones, sandstones, and conglomerates deposited by rivers flowing off the Ural Mountain chain, span much of the Lower and Middle Triassic (Induan, Olenekian, Anisian, Ladinian). The succession is divided into seven successive svitas, or assemblages: Kopanskaya (Induan), Staritskaya, Kzylsaiskaya, Gostevskaya, and Petropavlovskaya (all Olenekian), Donguz (Anisian), and Bukobay (Ladinian). This succession, comprising up to 3.5 km of fluvial and lacustrine sediments, documents major climatic changes. At the beginning of the Early Triassic, arid-zone facies were widely developed, aeolian, piedmont and proluvium. These were replaced by fluvial facies, with some features indicating aridity. At the end of the Middle Triassic, deltaic and lacustrine-marsh formations were dominant, indicating more humid conditions. The succession of Early to Mid Triassic tetrapod faunas documents the recovery of life after the end-Permian mass extinction. The earliest faunas consist only of small, aquatic tetrapods, in low-diversity, low-abundance assemblages. Climbing the succession through the Early Triassic, more terrestrially adapted tetrapods appear, and larger herbivorous and carnivorous reptiles come to dominate in the Mid Triassic as ecosystems were rebuilt.

Does the cortical bone resorption rate change due to 90Sr-radiation exposure? Analysis of data from Techa Riverside residents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tolstykh, E I; Shagina, N B; Degteva, M O

2011-08-01

The Mayak Production Association released large amounts of 90Sr into the Techa River (Southern Urals, Russia) with peak amounts in 1950-1951. Techa Riverside residents ingested an average of about 3,000 kBq of 90Sr. The 90Sr-body burden of approximately 15,000 individuals has been measured in the Urals Research Center for Radiation Medicine in 1974-1997 with use of a special whole-body counter (WBC). Strontium-90 had mainly deposited in the cortical part of the skeleton by 25 years following intake, and 90Sr elimination occurs as a result of cortical bone resorption. The effect of 90Sr-radiation exposure on the rate of cortical bone resorptionmore » was studied. Data on 2,022 WBC measurements were selected for 207 adult persons, who were measured three or more times before they were 50-55 years old. The individual-resorption rates were calculated with the rate of strontium recirculation evaluated as 0.0018 year -1. Individual absorbed doses in red bone marrow (RBM) and bone surface (BS) were also calculated. Statistically significant negative relationships of cortical bone resorption rate were discovered related to 90Sr-body burden and dose absorbed in the RBM or the BS. The response appears to have a threshold of about 1.5-Gy RBM dose. The radiation induced decrease in bone resorption rate may not be significant in terms of health. However, a decrease in bone remodeling rate can be among several causes of an increased level of degenerative dystrophic bone pathology in exposed persons.« less

Increase in accumulation of strontium-90 in the maternal skeleton during pregnancy and lactation: analysis of the Techa River data.

PubMed

Tolstykh, Evgenia I; Shagina, Natalia B; Degteva, Marina O

2014-08-01

The unique contamination of the Techa River (Southern Urals, Russia) in the 1950s by long-lived (90)Sr allows investigation of the accumulation of bone-seeking elements in humans. This study is based on information compiled at the Urals Research Center for Radiation Medicine (Chelyabinsk, Russia) over a long period of time. It includes the results of in vivo measurements of (90)Sr-body burden with a whole body counter (WBC), data on personal medical examinations and residence and family histories. Data on 185 women from two Techa riverside villages Muslyumovo and Brodokalmak were selected. The settlements differ in terms of (90)Sr diet intake (higher in Muslyumovo than in Brodokalmak) and ethnicity (residents were mainly Slavs in Brodokalmak and Turkic in Muslyumovo). Results of a total of 555 WBC measurements performed in 1974-1997 were available for the women studied; maximum measured values reached 40 kBq/body. The women from each settlement were subdivided into three groups according to their childbearing history: pregnancy and lactation occurred (1) during the period of maximal (90)Sr intake (1950-1951); (2) after the period of maximal intake and (3) before this period or women who were childless. An increase was found in accumulation of (90)Sr in maternal skeleton during pregnancy and lactation (group 1) by a factor of 1.5-2 in comparison with non-pregnant, non-lactating women. This result was found in both Muslyumovo and Brodokalmak samples. An increase in accumulation of toxic elements in pregnant/lactating women is associated with increased radiation/toxic doses and risk for the women's health.

The taxonomic status of Petropedetes newtonii (Amphibia, Anura, Petropedetidae).

PubMed

Sánchez-Vialas, Alberto; Calvo-Revuelta, Marta; Castroviejo-Fisher, Santiago; la Riva, Ignacio De

2018-01-01

The taxon Petropedetes newtonii was described in 1895 by Bocage, from Bioko Island (Equatorial Guinea). This taxon, whose holotype is lost, has been misidentified since Boulenger's revision of the genus in 1900 and its relationships with other taxa ( P. vulpiae and P. johnstoni ) is confusing. Currently, P. newtonii is considered a synonym of P. johnstoni . In this work, by revising morphological characters of non-webbed Petropedetes of Bioko, we demonstrate the morphological singularity of these specimens with respect to P. johnstoni and P. vulpiae and their association with the name Petropedetes newtonii . Consequently, we provide the subsequent designation of a neotype of P. newtonii and revalidate this species from its synonym with P. johnstoni .

[South] Korea.

PubMed

1987-04-01

The Republic of Korea occupies approximately 38,000 square miles in the southern position of a mountaineous peninsula. It shares a land boundary with North Korea. With a population of more than 40 million people, South Korea has 1 of the highest population densities in the world. The language spoken is a Uralic language, closely akin to Japanese, Hungarian, Finnish, and Mongolian, and the traditional religions are Shamanism and Buddhism. Over the course of time, South Korea has been invaded and fought over by its neighbors. The US and the Soviet Union have never been able to reach a unification agreement for North and South Korea. The 3rd Republic era, begun in 1963, saw a time of rapid industrialization and a great deal of economic growth. The 5th Republic began with a new constitution and new elections brought about the election of a president to a 7-year term of office beginning in 1981. Economic growth has been remarkable over the last 25 years despite the fact that North Korea possesses most of the mineral and hydroelectric resources and the existing heavy industrial base built by the Japanese while South Korea has the limited agricultural resources and had, initially, a large unskilled labor pool. Serious industrial growth began in South Korea in the early 1960s and the GNP grew at an annual rate of 10% during the period 1963-78. Current GNP is now, at $2000, well beyond that of its neighbors to the north. The outlook for longterm growth is good; however, the military threat posed by North Korea and the absence of foreign economic assistance has resulted in Korea spending 1/3 of its budget on defense. South Korea is active in international affairs and in the UN. Economic realities have forced Korea to give economics priority in their foreign policy. There has been an on-again, off-again quality to dialogue between the 2 nations. However, the US is committed to maintaining peace on the Korean peninsula. In order to do so, they have supplied manpower and support to supplement Korea's efforts to deter aggression. The US also believes that talks between governments are essential if reunification will ultimately occur. South Korea is now the US' largest commercial partner and Korea seems to understand that they can benefit greatly by having increased US private sector involvement in Korea's development.

The equivalence of two phylogenetic biodiversity measures: the Shapley value and Fair Proportion index.

PubMed

Hartmann, Klaas

2013-11-01

Most biodiversity conservation programs are forced to prioritise species in order to allocate their funding. This paper contains a mathematical proof that provides biological support for one common approach based on phylogenetic indices. Phylogenetic trees describe the evolutionary relationships between a group of taxa. Two indices for computing the distinctiveness of each taxon in a phylogenetic tree are considered here-the Shapley value and the Fair Proportion index. These indices provide a measure of the importance of each taxon for overall biodiversity and have been used to prioritise taxa for conservation. The Shapley value is the biodiversity contribution a taxon is expected to make if all taxa are equally likely to become extinct. This interpretation makes it appealing to use the Shapley value in biodiversity conservation applications. The Fair Proportion index lacks a convenient interpretation, however it is significantly easier to calculate and understand. It has been empirically observed that there is a high correlation between the two indices. This paper shows the mathematical basis for this correlation and proves that as the number of taxa increases, the indices become equivalent. Consequently in biodiversity prioritisation the simpler Fair Proportion index can be used whilst retaining the appealing interpretation of the Shapley value.

Nymphal development and lerp construction of Glycaspis sp. (Hemiptera: Psylloidea) on Eucalyptus sideroxylon (Myrtaceae) in central-west New South Wales, Australia.

PubMed

Sharma, Anamika; Raman, Anantanarayanan; Taylor, Gary; Fletcher, Murray

2013-11-01

The ability to form lerps is common in Australian Psylloidea. Various species of Glycaspis Taylor (Aphalaridae) form conical lerps on different species of Eucalyptus. Lerps, being a rich sugar source, are preferentially fed by bell miners (Aves: Meliphagidae). In this paper we report the process of lerp construction by a purported new species of Glycaspis living on Eucalyptus sideroxylon. This taxon constructs lerps with anal sugary exudates first building the ribs of the lerps and later filling the space between the polymerized ribs with horizontal tractions of the same sugary substance. Developmental events in this taxon do not follow Dyar's rule strictly. Oviposition induces a non-lethal hypersensitive response in the host leaf. Population trends assessed in 2011-2012 and 2012-2013 showed distinct variations, which have been related to environmental factors. In the 2012-2013 sampling, oviposition occurred preferentially proximally to leaf cracks (possibly induced by intense frost events); we infer that this could be a strategy of this taxon to establish an 'easier' access to moisture. Sensillar designs vary between the nymphal instars and adults. The trichoid sensilla and sensillar cavities on the antennae perform mechanosensory and olfactory functions. The mouthpart complex includes a relatively long stylet bundle. Copyright © 2013 Elsevier Ltd. All rights reserved.

TipMT: Identification of PCR-based taxon-specific markers.

PubMed

Rodrigues-Luiz, Gabriela F; Cardoso, Mariana S; Valdivia, Hugo O; Ayala, Edward V; Gontijo, Célia M F; Rodrigues, Thiago de S; Fujiwara, Ricardo T; Lopes, Robson S; Bartholomeu, Daniella C

2017-02-11

Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity. Here, we report the development of a Tool for Identification of Primers for Multiple Taxa (TipMT), which is a web application to search and design primers for genotyping based on genomic data. The tool identifies and targets single sequence repeats (SSR) or orthologous/taxa-specific genes for genotyping using Multiplex PCR. This pipeline was applied to the genomes of four species of Leishmania (L. amazonensis, L. braziliensis, L. infantum and L. major) and validated by PCR using artificial genomic DNA mixtures of the Leishmania species as templates. This experimental validation demonstrates the reliability of TipMT because amplification profiles showed discrimination of genomic DNA samples from Leishmania species. The TipMT web tool allows for large-scale identification and design of taxon-specific primers and is freely available to the scientific community at http://200.131.37.155/tipMT/ .

Phylogeny of the Haplosporidia (Eukaryota: Alveolata) based on small subunit ribosomal RNA gene sequence.

PubMed

Flores, B S; Siddall, M E; Burreson, E M

1996-08-01

The phylogenetic position of the phylum Haplosporidia was investigated with the complete small subunit rRNA gene sequences from 5 species in the phylum: Haplosporidium nelsoni and Haplosporidium costale, parasites of the eastern oyster Crassostrea virginica; Haplosporidium louisiana, a parasite of the mudcrab Panopeus herbstii; Minchinia teredinis, a parasite of shipworms (Teredo spp.) and Urosporidium crescens, a hyperparasite found in metacercariae of the trematode Megalophallus sp. in the blue crab, Callinectes sapidus. Multiple alignments of small subunit rRNA gene sequences included the 5 haplosporidian taxa and 14 taxa in the alveolate phyla Ciliophora, Dinoflagellida, and Apicomplexa. Maximum parsimony analysis placed the phylum Haplosporidia as a monophyletic group within the alveolate clade, as a taxon of equal rank with the other 3 alveolate phyla, and as a sister taxon to the clade composed of the phyla Dinoflagellida and Apicomplexa. Transversionally weighted parsimony placed the haplosporidians as a sister taxon to the ciliates. A separate analysis focused on the relationships of species in the genus Haplosporidium. Analyses were conducted with the haplosporidians as a functional ingroup, using each of the alveolate phyla individually as functional outgroups. The results indicated that species in the genus Haplosporidium do not form a monophyletic assemblage. As such, the present morphological criteria for distinguishing the genera Haplosporidium and Minchinia are insufficient.

Effects of land use on arbuscular mycorrhizal fungal communities in Estonia.

PubMed

Sepp, Siim-Kaarel; Jairus, Teele; Vasar, Martti; Zobel, Martin; Öpik, Maarja

2018-04-01

Arbuscular mycorrhizal (AM) fungal communities vary across habitat types, as well as across different land use types. Most relevant research, however, has focused on agricultural or other severely human-impacted ecosystems. Here, we compared AM fungal communities across six habitat types: calcareous grassland, overgrown ungrazed calcareous grassland, wooded meadow, farmyard lawn, boreonemoral forest, and boreonemoral forest clear-cut, exhibiting contrasting modes of land use. AM fungi in the roots of a single host plant species, Prunella vulgaris, and in its rhizosphere soil were identified using 454-sequencing from a total of 103 samples from 12 sites in Estonia. Mean AM fungal taxon richness per sample did not differ among habitats. AM fungal community composition, however, was significantly different among habitat types. Both abandonment and land use intensification (clearcutting; trampling combined with frequent mowing) changed AM fungal community composition. The AM fungal communities in different habitat types were most similar in the roots of the single host plant species and most distinct in soil samples, suggesting a non-random pattern in host-fungal taxon interactions. The results show that AM fungal taxon composition is driven by habitat type and land use intensity, while the plant host may act as an additional filter between the available and realized AM fungal species pool.

How and why to achieve greater objectivity in taxonomy, exemplified by a fossil ostracod (Amplocypris abscissa) from the Miocene Lake Pannon

PubMed Central

Danielopol, Dan L.; Gross, Martin; Harzhauser, Mathias; Minati, Klaus; Piller, Werner E.

2017-01-01

A project on fossil ostracods from Hennersdorf (Vienna Basin, Middle Pannonian “E” stage) documents the non-marine ostracod Amplocypris abscissa (Reuss 1850) as a polymorphic taxon. The high morphological variability of the valves belonging to this species and its geographic distribution in the Lake Pannon point to a widely spread fossil taxon. This traditional view emerges from the fact that A. abscissa displays few homologous “landmarks” (morphological reference points) which makes it difficult to compare morphotypes within and among populations. The present contribution offers arguments for the need of objective criteria when describing ostracods with few visible morphological traits. It is demonstrated that using a composite algorithmic approach which combines information implemented in the computer programme MORPHOMATICA for different variables, measured on interval and ratio scales, is able to define morphological traits objectively. The data analysed with multivariate statistics are further used for diagnostic profiles of clearly delineated morphotypes. The potential taxonomic value of three morphotypes here identified for Amplocypris abscissa is discussed. It is argued that this taxon represents a phylogenetic lineage within which a cluster of species with discrete morphological traits exists. Finally, it is proposed to apply similar algorithms for the necessary revision of the whole group of Amplocypris species from Lake Pannon. PMID:28090196

Development and application of a general plasmid reference material for GMO screening.

PubMed

Wu, Yuhua; Li, Jun; Wang, Yulei; Li, Xiaofei; Li, Yunjing; Zhu, Li; Li, Jun; Wu, Gang

The use of analytical controls is essential when performing GMO detection through screening tests. Additionally, the presence of taxon-specific sequences is analyzed mostly for quality control during GMO detection. In this study, 11 commonly used genetic elements involving three promoters (P-35S, P-FMV35S and P-NOS), four marker genes (Bar, NPTII, HPT and Pmi), and four terminators (T-NOS, T-35S, T-g7 and T-e9), together with the reference gene fragments from six major crops of maize, soybean, rapeseed, rice, cotton and wheat, were co-integrated into the same single plasmid to construct a general reference plasmid pBI121-Screening. The suitability test of pBI121-Screening plasmid as reference material indicated that the non-target sequence on the pBI121-Screening plasmid did not affect the PCR amplification efficiencies of screening methods and taxon-specific methods. The sensitivity of screening and taxon-specific assays ranged from 5 to 10 copies of pBI121-Screening plasmid, meeting the sensitivity requirement of GMO detection. The construction of pBI121-Screening solves the lack of a general positive control for screening tests, thereby reducing the workload and cost of preparing a plurality of the positive control. Copyright © 2016 Elsevier B.V. All rights reserved.

A unique Middle Miocene European hominoid and the origins of the great ape and human clade

PubMed Central

Moyà-Solà, Salvador; Alba, David M.; Almécija, Sergio; Casanovas-Vilar, Isaac; Köhler, Meike; De Esteban-Trivigno, Soledad; Robles, Josep M.; Galindo, Jordi; Fortuny, Josep

2009-01-01

The great ape and human clade (Primates: Hominidae) currently includes orangutans, gorillas, chimpanzees, bonobos, and humans. When, where, and from which taxon hominids evolved are among the most exciting questions yet to be resolved. Within the Afropithecidae, the Kenyapithecinae (Kenyapithecini + Equatorini) have been proposed as the sister taxon of hominids, but thus far the fragmentary and scarce Middle Miocene fossil record has hampered testing this hypothesis. Here we describe a male partial face with mandible of a previously undescribed fossil hominid, Anoiapithecus brevirostris gen. et sp. nov., from the Middle Miocene (11.9 Ma) of Spain, which enables testing this hypothesis. Morphological and geometric morphometrics analyses of this material show a unique facial pattern for hominoids. This taxon combines autapomorphic features—such as a strongly reduced facial prognathism—with kenyapithecine (more specifically, kenyapithecin) and hominid synapomorphies. This combination supports a sister-group relationship between kenyapithecins (Griphopithecus + Kenyapithecus) and hominids. The presence of both groups in Eurasia during the Middle Miocene and the retention in kenyapithecins of a primitive hominoid postcranial body plan support a Eurasian origin of the Hominidae. Alternatively, the two extant hominid clades (Homininae and Ponginae) might have independently evolved in Africa and Eurasia from an ancestral, Middle Miocene stock, so that the supposed crown-hominid synapomorphies might be homoplastic. PMID:19487676

Age of zircons from the xenolith of metapelite in granitoids of the Verkhisetsk massif (Middle Urals): Evidence for granite-related stages of metamorphism

NASA Astrophysics Data System (ADS)

Zinkova, E. A.; Pribavkin, S. V.

2016-02-01

Two age stages in the formation of high-aluminous gneisses related to the major stages of granite formation of the Uralian mobile belt were revealed in this study. The first stage (372 ± 2 Ma) corresponds to the age of metamorphism of the amphibolite facies and is controlled by intrusion of the tonalite-trondhjemite series under the environment of the continental margin. At the second stage (307 ± 3 Ma), gneiss underwent contact metamorphism under the influence of plutons of the adamellite-granite composition formed during the early episodes of collisional metamorphism.

Mineral Composition and Structure of the Sverdlovsk Meteorite (H4-5)

NASA Astrophysics Data System (ADS)

Berzin, S. V.; Koroteev, V. A.; Ivanov, K. S.; Kleimenov, D. A.; Kiseleva, D. V.; Cherednichenko, N. V.

2018-03-01

A fragment of the Sverdlovsk Meteorite, which was found in 1985 in the Central Urals, is studied by modern analytical methods. It belongs to H chondrites of petrologic type 4-5; shock stage of meteorite is S1-2, terrestrial weathering is W1. The composition of minerals of the meteorite is studied. It is found for the first time that the metal and sulfides are concentrated in fine veinlets of the recrystallized matrix of the chondrite and are accompanied by segregations of metal and troilite inside these veinlets. The distribution of trace elements of the metal phase of the meteorite is studied.

Selenium, tellurium and precious metal mineralogy in Uchalinsk copper-zinc-pyritic district, the Urals

NASA Astrophysics Data System (ADS)

Vikentev, I.

2016-04-01

During processing the most of Au, Ag, Se, Te, Pb, Bi, Sb, Hg as well as notable part of Cu, Zn and Cd fail for tailings and became heavy metal pollutants. Modes of occurrence of Au, Ag, Te and Se covers two giant VMS deposits: Uchaly (intensively deformed) and Uzelginsk (altered by late hydrothermal processes) as well as middle-sized Molodezn and West Ozern deposits (nondeformed) have been studied. Mineral forms of these elements as well as their presence in disperse mode in common ore minerals (pyrite, chalcopyrite, sphalerite) have been studied using SEM, EPMA, INAA, ICP-MS and LA-ICP-MS.

Skeleton of an unusual, cat-sized marsupial relative (Metatheria: Marsupialiformes) from the middle Eocene (Lutetian: 44-43 million years ago) of Turkey

PubMed Central

Maga, A. Murat

2017-01-01

We describe a near-complete, three-dimensionally preserved skeleton of a metatherian (relative of modern marsupials) from the middle Eocene (Lutetian: 44–43 million years ago) Lülük member of the Uzunçarşıdere Formation, central Turkey. With an estimated body mass of 3–4 kg, about the size of a domestic cat (Felis catus) or spotted quoll (Dasyurus maculatus), it is an order of magnitude larger than the largest fossil metatherians previously known from the Cenozoic of the northern hemisphere. This new taxon is characterised by large, broad third premolars that probably represent adaptations for hard object feeding (durophagy), and its craniodental morphology suggests the capacity to generate high bite forces. Qualitative and quantitative functional analyses of its postcranial skeleton indicate that it was probably scansorial and relatively agile, perhaps broadly similar in locomotor mode to the spotted quoll, but with a greater capacity for climbing and grasping. Bayesian phylogenetic analysis of a total evidence dataset comprising 259 morphological characters and 9kb of DNA sequence data from five nuclear protein-coding genes, using both undated and “tip-and-node dating” approaches, place the new taxon outside the marsupial crown-clade, but within the clade Marsupialiformes. It demonstrates that at least one metatherian lineage evolved to occupy the small-medium, meso- or hypo-carnivore niche in the northern hemisphere during the early Cenozoic, at a time when there were numerous eutherians (placentals and their fossil relatives) filling similar niches. However, the known mammal fauna from Uzunçarşıdere Formation appears highly endemic, and geological evidence suggests that this region of Turkey was an island for at least part of the early Cenozoic, and so the new taxon may have evolved in isolation from potential eutherian competitors. Nevertheless, the new taxon reveals previously unsuspected ecomorphological disparity among northern hemisphere metatherians during the first half of the Cenozoic. PMID:28813431

New Specimens of the Rare Taeniodont Wortmania (Mammalia: Eutheria) from the San Juan Basin of New Mexico and Comments on the Phylogeny and Functional Morphology of “Archaic” Mammals

PubMed Central

Williamson, Thomas E.; Brusatte, Stephen L.

2013-01-01

Background Taeniodonta is a clade of Late Cretaceous – Paleogene mammals remarkable for their relatively extreme cranial, dental, and postcranial adaptations and notable for being among the first mammals to achieve relatively large size following the Cretaceous-Paleogene mass extinction. Previous workers have hypothesized that taeniodonts can be divided into two clades: Conoryctidae, a group of small-bodied taeniodonts with supposedly “generalized” postcranial skeletons, and Stylinodontidae, a group of large-bodied, robust animals with massive forelimbs and claws adapted for scratch-digging. However, many taeniodont taxa are poorly known and few are represented by postcranial material, leaving many details about their anatomy, biology, and evolution ambiguous. Methodology/Principal Findings In this paper, we describe three new specimens of the rare taxon Wortmaniaotariidens from the early Paleocene (Puercan) of New Mexico. Among these specimens is one that includes remarkably complete cranial and dental material, including associated upper and lower teeth, and another that consists of partial forelimbs. These specimens allow for an updated anatomical description of this unusual taxon, supply new data for phylogenetic analyses, and enable a more constrained discussion of taeniodont biology and functional morphology. Conclusions/Significance The new specimen of Wortmania that includes associated upper and lower teeth indicates that previous interpretations of the upper dentition of this taxon were not accurate and the taxon Robertschochiasullivani is a junior synonym of W . otariidens . New specimens that include partial forelimbs indicate that Wortmania is very similar to later, large-bodied taeniodonts, with marked and distinctive adaptations for scratch-digging. Comparisons with other taeniodont taxa that include postcranial material suggest that all taeniodonts may have had scratch-digging adaptations. A phylogenetic analysis shows that Schowalteria and Onychodectes are basal taeniodonts, Stylinodontidae (including Wortmania) is monophyletic, and a monophyletic Conoryctidae (but not including Onychodectes) is only recovered when certain characters are ordered. PMID:24098738

Charting taxonomic knowledge through ontologies and ranking algorithms

NASA Astrophysics Data System (ADS)

Huber, Robert; Klump, Jens

2009-04-01

Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute to the preservation our scientific heritage.

Echinoid associations with coral habitats differ with taxon in the deep sea and the influence of other echinoids, depth, and fishing history on their distribution

NASA Astrophysics Data System (ADS)

Stevenson, Angela; Davies, Jaime S.; Williams, Alan; Althaus, Franziska; Rowden, Ashley A.; Bowden, David A.; Clark, Malcolm R.; Mitchell, Fraser J. G.

2018-03-01

Patterns of habitat use by animals and knowledge of the environmental factors affecting these spatial patterns are important for understanding the structure and dynamics of ecological communities. Both aspects are poorly known for deep-sea habitats. The present study investigates echinoid distributions within cold water coral (CWC) habitats on continental margins off France, Australia, and New Zealand. It further examines the influence of habitat-related variables that might help explain the observed distribution of echinoid taxa. Six echinoid taxa were examined from video and photographic transects to reveal taxon-specific distribution patterns and habitat-related influences. The Echinoidea were found in all habitats studied, but tended to aggregate in architecturally complex habitats associated with living cold-water corals. However, a taxon-specific investigation found that such associations were largely an artefact of the dominant taxa observed in a specific region. Despite the food and shelter resources offered to echinoids by matrix-forming coral habitats, not all taxa were associated with these habitats, and some had a random association with the habitats examined, while others displayed non-random associations. Echinoid distribution was correlated with several variables; the presence of other echinoids, depth, and fishing history were the most influential factors. This study indicates that image data can be a useful tool to detect trends in echinoid habitat associations. It also suggests that refinement of the methods, in particular with studies conducted at a more precise taxon and habitat scale, would facilitate better quantitative analyses of habitat associations and paint a more realistic picture of a population's ecology. Most deep-sea ecological studies to date have been conducted at a relatively coarse taxonomic and habitat resolution, and lack sufficient resolution to provide useful information for the conservation of vulnerable deep-sea habitats.

Eco-engineered rock pools: a concrete solution to biodiversity loss and urban sprawl in the marine environment

NASA Astrophysics Data System (ADS)

Firth, Louise B.; Browne, Keith A.; Knights, Antony M.; Hawkins, Stephen J.; Nash, Róisín

2016-09-01

In coastal habitats artificial structures typically support lower biodiversity and can support greater numbers of non-native and opportunistic species than natural rocky reefs. Eco-engineering experiments are typically trialed to succeed; but arguably as much is learnt from failure than from success. Our goal was to trial a generic, cost effective, eco-engineering technique that could be incorporated into rock armouring anywhere in the world. Artificial rock pools were created from manipulated concrete between boulders on the exposed and sheltered sides of a causeway. Experimental treatments were installed in locations where they were expected to fail and compared to controls installed in locations in which they were expected to succeed. Control pools were created lower on the structure where they were immersed on every tidal cycle; experimental pools were created above mean high water spring tide which were only immersed on spring tides. We hypothesised that lower and exposed pools would support significantly higher taxon and functional diversity than upper and sheltered pools. The concrete pools survived the severe winter storms of 2013/14. After 12 months, non-destructive sampling revealed significantly higher mean taxon and functional richness in lower pools than upper pools on the exposed side only. After 24 months the sheltered pools had become inundated with sediments, thus failing to function as rock pools as intended. Destructive sampling on the exposed side revealed significantly higher mean functional richness in lower than upper pools. However, a surprisingly high number of taxa colonised the upper pools leading to no significant difference in mean taxon richness among shore heights. A high number of rare taxa in the lower pools led to total taxon richness being almost twice that of upper pools. These findings highlight that even when expected to fail concrete pools supported diverse assemblages, thus representing an affordable, replicable means of enhancing biodiversity on a variety of artificial structures.

New specimens of the rare taeniodont Wortmania (Mammalia: Eutheria) from the San Juan Basin of New Mexico and comments on the phylogeny and functional morphology of "archaic" mammals.

PubMed

Williamson, Thomas E; Brusatte, Stephen L

2013-01-01

Taeniodonta is a clade of Late Cretaceous-Paleogene mammals remarkable for their relatively extreme cranial, dental, and postcranial adaptations and notable for being among the first mammals to achieve relatively large size following the Cretaceous-Paleogene mass extinction. Previous workers have hypothesized that taeniodonts can be divided into two clades: Conoryctidae, a group of small-bodied taeniodonts with supposedly "generalized" postcranial skeletons, and Stylinodontidae, a group of large-bodied, robust animals with massive forelimbs and claws adapted for scratch-digging. However, many taeniodont taxa are poorly known and few are represented by postcranial material, leaving many details about their anatomy, biology, and evolution ambiguous. In this paper, we describe three new specimens of the rare taxon Wortmania otariidens from the early Paleocene (Puercan) of New Mexico. Among these specimens is one that includes remarkably complete cranial and dental material, including associated upper and lower teeth, and another that consists of partial forelimbs. These specimens allow for an updated anatomical description of this unusual taxon, supply new data for phylogenetic analyses, and enable a more constrained discussion of taeniodont biology and functional morphology. The new specimen of Wortmania that includes associated upper and lower teeth indicates that previous interpretations of the upper dentition of this taxon were not accurate and the taxon Robertschochia sullivani is a junior synonym of W. otariidens. New specimens that include partial forelimbs indicate that Wortmania is very similar to later, large-bodied taeniodonts, with marked and distinctive adaptations for scratch-digging. Comparisons with other taeniodont taxa that include postcranial material suggest that all taeniodonts may have had scratch-digging adaptations. A phylogenetic analysis shows that Schowalteria and Onychodectes are basal taeniodonts, Stylinodontidae (including Wortmania) is monophyletic, and a monophyletic Conoryctidae (but not including Onychodectes) is only recovered when certain characters are ordered.

Accessory and rock forming minerals monitoring the evolution of zoned mafic ultramafic complexes in the Central Ural Mountains

NASA Astrophysics Data System (ADS)

Krause, J.; Brügmann, G. E.; Pushkarev, E. V.

2007-04-01

This study describes major and trace element compositions of accessory and rock forming minerals from three Uralian-Alaskan-type complexes in the Ural Mountains (Kytlym, Svetley Bor, Nizhnii Tagil) for the purpose of constraining the origin, evolution and composition of their parental melts. The mafic-ultramafic complexes in the Urals are aligned along a narrow, 900 km long belt. They consist of a central dunite body grading outward into clinopyroxenite and gabbro lithologies. Several of these dunite bodies have chromitites with platinum group element mineralization. High Fo contents in olivine (Fo 92-93) and high Cr/(Cr + Al) in spinel (0.67-0.84) suggest a MgO-rich (> 15 wt.%) and Al 2O 3-poor ultramafic parental magma. During its early stages the magma crystallized dominantly olivine, spinel and clinopyroxene forming cumulates of dunite, wehrlite and clinopyroxenite. This stage is monitored by a common decrease in the MgO content in olivine (Fo 93-86) and the Cr/(Cr + Al) value of coexisting accessory chromite (0.81-0.70). Subsequently, at subsolidus conditions, the chromite equilibrated with the surrounding silicates producing Fe-rich spinel while Al-rich spinel exsolved chromian picotite and chromian titanomagnetite. This generated the wide compositional ranges typical for spinel from Uralian-Alaskan-type complexes world wide. Laser ablation analyses (LA-ICPMS) reveal that clinopyroxene from dunites and clinopyroxenite from all three complexes have similar REE patterns with an enrichment of LREE (0.5-5.2 prim. mantle) and other highly incompatible elements (U, Th, Ba, Rb) relative to the HREE (0.25-2.0 prim. mantle). This large concentration range implies the extensive crystallization of olivine and clinopyroxene together with spinel from a continuously replenished, tapped and crystallizing magma chamber. Final crystallization of the melt in the pore spaces of the cooling cumulate pile explains the large variation in REE concentrations on the scale of a thin section, the REE-rich rims on zoned clinopyroxene phenocrysts (e.g. La Rim/La Core ˜ 2), and the formation of interstitial clinopyroxene with similar REE enrichment. Trace element patterns of the parental melt inferred from clinopyroxene analyses show negative anomalies for Ti, Zr, Hf, and a positive anomaly for Sr. These imply a subduction related geotectonic setting for the Uralian zoned mafic-ultramafic complexes. Ankaramites share many petrological and geochemical features with these complexes and could represent the parental melts of this class of mafic-ultramafic intrusions. Diopside from chromitites and cross cutting diopside veins in dunite has similar trace element patterns with LREE/HREE ratios (e.g. La/Lu = 5-60) much higher than those in diopside from all other lithologies. We suggest that the chromitites formed at high temperatures (800-900 °C) during the waning stages of solidification as a result of the interaction of an incompatible element-rich melt or fluid with the dunite cumulates.

Devonian paleomagnetism of the North Tien Shan: Implications for the middle-Late Paleozoic paleogeography of Eurasia

NASA Astrophysics Data System (ADS)

Levashova, Natalia M.; Mikolaichuk, Alexander V.; McCausland, Philip J. A.; Bazhenov, Mikhail L.; Van der Voo, Rob

2007-05-01

The Ural-Mongol belt (UMB), between Siberia, Baltica and Tarim, is widely recognized as the locus of Asia's main growth during the Paleozoic, but its evolution remains highly controversial, as illustrated by the disparate paleogeographic models published in the last decade. One of the largest tectonic units of the UMB is the Kokchetav-North Tien Shan Domain (KNTD) that stretches from Tarim in the south nearly to the West Siberian Basin. The KNTD comprises several Precambrian microcontinents and numerous remnants of Early Paleozoic island arcs, marginal basins and accretionary complexes. In Late Ordovician time, all these structures had amalgamated into a single contiguous domain. Its paleogeographic position is of crucial importance for elucidating the Paleozoic evolution of the UMB in general and of the Urals in particular. The Aral Formation, located in Kyrgyzstan in the southern part of the KNTD, consists of a thick Upper Devonian (Frasnian) basalt-andesite sequence. Paleomagnetic data show a dual-polarity characteristic component (Dec/Inc = 286° / + 56°, α95 = 9°, k = 21, N = 15 sites). The primary origin of this magnetization is confirmed by a positive test on intraformational conglomerates. We combine this result with other Paleozoic data from the KNTD and show its latitudinal motion from the Late Ordovician to the end of the Paleozoic. The observed paleolatitudes are found to agree well with the values extrapolated from Baltica to a common reference point (42.5°N, 73°E) in our sampling area for the entire interval; hence coherent motion of the KNTD and Baltica is strongly indicated for most of the Paleozoic. This finding contradicts most published models of the UMB evolution, where the KNTD is separated from Baltica by a rather wide Ural Ocean containing one or more major plate boundaries. An exception is the model of Şengör and Natal'in [A.M.C. Şengör, B.A. Natal'in, Paleotectonics of Asia: fragments of a synthesis, in: A. Yin and M. Harrison (eds.), The tectonic evolution of Asia, Cambridge University Press, Cambridge (1996) 486-640], in which coherent paleolatitudinal motion of Baltica and the KNTD is hypothesized — the latter as part of the Kipchak Arc. We suggest a parallel hypothesis, which explains coherent motion of the KNTD and Baltica. In particular, we argue that if a basin with oceanic crust ever existed between the KNTD and Baltica, it was a narrow one without (significant) active spreading in Middle to Late Paleozoic time. Notably, the paleogeographic position of Siberia during the Middle Paleozoic and hence, the width of the Khanty-Mansi Ocean between Siberia, on the one hand, and Baltica-KNTD, on the other hand, remains largely unconstrained, because of the paucity of high-quality Silurian, Devonian and Carboniferous paleomagnetic results from Siberia.

Mechanisms of formation of mantle section pyroxenites of Voykar Ophiolite, Polar Urals, Russia

NASA Astrophysics Data System (ADS)

Belousov, Ivan; Batanova, Valentina; Sobolev, Alexander; Savelieva, Galina

2010-05-01

Ural Mountains mark a major mid Paleozoic collision event, which resulted in the closure of an ocean basin separating the Siberian and European plates. Voykar Ophiolite is located in the Northern part of Uralian Ophiolite Belt. Ophiolitic sequence rocks of Polar Urals are usually considered as giant fragments of mantle and MORB-type crust formed in back-arc settings (e.g. Savelieva et al., 1987). Mantle section of Voykar Ophiolite comprises most of the ophiolitic sequence. It is up to 8 km thick and consists mostly of spinel harzburgites with multiple dunitic bodies and pyroxenitic veins representing pathways for different melts/fluids. While it is generally accepted that dunites in mantle sections are formed by melt-rock reaction and mark melt pathways (e.g. Kelemen et al., 1995), formation of pyroxenites is a subject of debate. Often pyroxenites from mantle sections of ophiolites (Varfalvy et al., 1997), as well as pyroxenites from mantle wedge xenoliths (Arai et al., 2006, Bali et al., 2007, Gregoire et al., 2008) are interpreted as interaction products between high-SiO2 melts and mantle peridotites. Such melts are believed to be widespread in SSZ mantle: boninites, high-MgO andesites and adakites. However, some researchers (e.g. Berly et al., 2006, Halama et al., 2009) propose pyroxenite formation in metasomatic reaction with fluid from subducting plate. Moreover, some pyroxenites could be formed by the melt crystallization in hydrous conditions (Muntener et al., 2001). We present comprehensive study of mineral major and trace element compositions from the mantle section rocks of Voykar Ophiolite in order to determine mechanism of formation of pyroxenites in ophiolitic mantle sections. Compositions of clinopyroxene and olivine from pyroxenites were compared to their compositions in harzburgites and dunites. Furthermore, compositions of clinopyroxene and magmatic amphibole from mantle section pyroxenites were used to calculate equilibrium melts. Geochemical data (enrichment of clinopyroxenes and amphiboles in LREE and LILE (Rb, Ba, Sr) relative to HFSE (Nb, Zr)) together with structural data suggests that pyroxenites display clear suprasubduction signatures and refer to the last stage of Voykar Ophiolite mantle section formation. All minerals from pyroxenites tend to have lower Mg-numbers and, therefore, high-Si meltsfluids have played major role in their formation. Depletion of clinopyroxenes in HREE and enrichment in Sr and LREE across the harzburgite-pyroxenite contacts suggests that this high-Si melts most probably refer to depleted SSZ melts, such as boninites. One group of magmatic amphibole in pyroxenites refers to such melts. However, another group of magmatic amphiboles probably refers to high-Si fluid depleted in REE and enriched in LILE (Rb, Ba, Sr) and Pb. Therefore, the variety of pyroxenite segregations, veins, and dikes reflects progressive stages of melt/fluid migration through harzburgite and dunite at various P-T conditions. For some pyroxenites (such as zoned websterite dikes) formation by fractional crystallization of hydrous magmas couldn't be excluded.

Development of EST-SSR markers for Elaeocarpus photiniifolia (Elaeocarpaceae), an endemic taxon of the Bonin Islands.

PubMed

Sugai, Kyoko; Setsuko, Suzuki; Uchiyama, Kentaro; Murakami, Noriaki; Kato, Hidetoshi; Yoshimaru, Hiroshi

2012-02-01

Expressed sequence tag (EST)-derived microsatellite markers were developed for Elaeocarpus photiniifolia, an endemic taxon of the Bonin Islands. Initially, a complementary DNA (cDNA) library was constructed by de novo pyrosequencing of total RNA extracted from a seedling. A total of 267 primer pairs were designed from the library. Of the 48 tested loci, 25 loci were polymorphic among 41 individuals representing the entire geographical range of the species, with the number of alleles per locus and expected heterozygosity ranging from two to 14 and 0.09 to 0.86, respectively. Most loci were transferable to a related species, E. sylvestris. The developed markers will be useful for evaluating the genetic structure of E. photiniifolia.

A new species of small-eared shrew from Colombia and Venezuela (Mammalia: Soricomorpha: Soricidae: Genus Cryptotis)

USGS Publications Warehouse

Woodman, N.

2002-01-01

Populations of small-eared shrews inhabiting the northern Cordillera Oriental of Colombia and adjoining Venezuelan highlands in the vicinity of Paramo de Tama have been referred alternatively to Cryptotis thomssi or Cryptotis meridensis. Morphological and morphometrical study of this population indicates that it belongs to neither taxon, but represents a distinct, previously unrecognized species. I describe this new species as Cryptotis tamensis and redescribe C. meridensis. Recognition of the population at Paramo de Tama as a separate taxon calls into question the identities of populations of shrews currently represented only by single specimens from Cerro Pintado in the Sierra de Perija, Colombia, and near El Junquito in the coastal highlands of Venezuela.

Annotated type catalogue of the Amphibulimidae (Mollusca, Gastropoda, Orthalicoidea) in the Natural History Museum, London

PubMed Central

Breure, Abraham S.H.; Ablett, Jonathan D.

2011-01-01

Abstract The type status is described of 39 taxa classified within the family Amphibulimidae (superfamily Orthalicoidea) and kept in the London museum. One taxon, Bulimus elaeodes Pfeiffer, 1853, is removed to the Strophocheilidae. Lectotypes are designated for Bulimus adoptus Reeve, 1849; Bulimus (Eurytus) eros Angas, 1878; Helix onca d'Orbigny, 1835; Amphibulima pardalina Guppy, 1868. The type status of the following taxon is changed to lectotype in accordance with Art. 74.6 ICZN: Strophocheilus (Dryptus) jubeus Fulton, 1908. As general introduction to this and following papers on Orthalicoid types in the Natural History Museum, a brief history of the London collection is given and several examples of handwriting from different authors are presented. PMID:22144852

A new Trimerocephalus species (Trilobita, Phacopidae) from the Late Devonian (Early Famennian) of Poland.

PubMed

Kin, Adrian; Błażejowski, Błażej

2013-01-01

This study presents a detailed morphological analysis of a new species belonging to the blind trilobite Trimerocephalus McCoy, 1849, T. chopini n. sp., based on exceptionally well preserved articulated specimens from the Late Devonian (Early Famennian) of the Holy Cross Mountains in central Poland. The occurrence of this taxon in Kowala Quarry near Kielce has been reported previously, with specimens often found in single-file queues representing migratory behaviour that was followed by a mass mortality event that preserved these assemblages. The new taxon is compared with other species of Trimerocephalus and is interpreted as being most closely related to a clade consisting of T. caecus, T. lelievrei, T, inimbi, T. shotoriensis and T. tardispinosus.

The endangered Florida pondweed (Potamogeton floridanus) is a hybrid: Why we need to understand biodiversity thoroughly.

PubMed

Kaplan, Zdeněk; Fehrer, Judith; Bambasová, Veronika; Hellquist, C Barre

2018-01-01

Thorough understanding of biodiversity is a fundamental prerequisite for biological research. A lack of taxonomic knowledge and species misidentifications are particularly critical for conservation. Here we present an example of Potamogeton floridanus, the Florida Pondweed, an endangered taxon endemic to a small area in the Florida panhandle, whose taxonomic status remained controversial for more than a century, and all previous attempts to elucidate its identity have failed. We applied molecular approaches to tackle the origin of the mysterious taxon and supplemented them with morphological and anatomical investigations of both historical herbarium collections and plants recently collected in the type area for a comprehensive taxonomic reassessment. Sequencing of two nuclear ribosomal markers and one chloroplast non-coding spacer resulted in the surprising discovery that P. floridanus is a hybrid of P. pulcher and P. oakesianus, with the former being the maternal parent. The hybrid colony is currently geographically isolated from the distribution range of P. oakesianus. We show that previous molecular analyses have failed to reveal its hybrid identity due to inadequate nuclear DNA sequence editing. This is an example how the uncritical use of automized sequence reads can hamper molecular species identifications and also affect phylogenetic tree construction and interpretation. This unique hybrid taxon, P. ×floridanus, adds another case study to the debate on hybrid protection; consequences for its conservation are discussed.

Phytophthora parsiana sp. nov., a new high-temperature tolerant species.

PubMed

Mostowfizadeh-Ghalamfarsa, R; Cooke, D E L; Banihashemi, Z

2008-07-01

As part of a study to examine the phylogenetic history of the taxonomically challenging species Phytophthora cryptogea and P. drechsleri, a distinct monophyletic group of isolates, previously described as P. drechsleri or P. cryptogea, were characterised. Analysis of their rDNA ITS sequences indicated that these isolates were distinct from P. drechsleri, P. cryptogea, and all members of Phytophthora ITS clades 1-8, clustering instead alongside basal groups previously described as clades 9 and 10. This group comprised six isolates all of which were isolated from woody plants, such as pistachio (Pistacia vera, Iran and USA), fig (Ficus carica, Iran), and almond (Prunus dulcis, Greece). Analysis of sequence data from nuclear (beta-tubulin and translation elongation factor 1alpha) and mitochondrial (cytochrome c oxidase subunit I) genes confirmed the ITS-based analysis as these isolates formed a distinct monophyletic group in all NJ trees. The isolates were fast growing with a relatively high optimum growth temperature of 30 degrees C and, in most cases, rapid colony growth even at 37 degrees C. The isolates produced complex colony patterns on almost all media, especially corn meal agar (CMA). Phylogenetic analysis and examination of all the other morphological and physiological data lead us to infer that this taxon has not been described previously. As this taxon was first isolated and described from Iran we propose that this taxon be formally designated as Phytophthora parsiana.

The endangered Florida pondweed (Potamogeton floridanus) is a hybrid: Why we need to understand biodiversity thoroughly

PubMed Central

Fehrer, Judith; Bambasová, Veronika; Hellquist, C. Barre

2018-01-01

Thorough understanding of biodiversity is a fundamental prerequisite for biological research. A lack of taxonomic knowledge and species misidentifications are particularly critical for conservation. Here we present an example of Potamogeton floridanus, the Florida Pondweed, an endangered taxon endemic to a small area in the Florida panhandle, whose taxonomic status remained controversial for more than a century, and all previous attempts to elucidate its identity have failed. We applied molecular approaches to tackle the origin of the mysterious taxon and supplemented them with morphological and anatomical investigations of both historical herbarium collections and plants recently collected in the type area for a comprehensive taxonomic reassessment. Sequencing of two nuclear ribosomal markers and one chloroplast non-coding spacer resulted in the surprising discovery that P. floridanus is a hybrid of P. pulcher and P. oakesianus, with the former being the maternal parent. The hybrid colony is currently geographically isolated from the distribution range of P. oakesianus. We show that previous molecular analyses have failed to reveal its hybrid identity due to inadequate nuclear DNA sequence editing. This is an example how the uncritical use of automized sequence reads can hamper molecular species identifications and also affect phylogenetic tree construction and interpretation. This unique hybrid taxon, P. ×floridanus, adds another case study to the debate on hybrid protection; consequences for its conservation are discussed. PMID:29608584

Redescription of Calyptosuchus (Stagonolepis) wellesi (Archosauria: Pseudosuchia: Aetosauria) from the Late Triassic of the Southwestern United States with a discussion of genera in vertebrate paleontology.

PubMed

Parker, William G

2018-01-01

Calyptosuchus wellesi is a medium-sized desmatosuchian aetosaur common in Adamanian (early to middle Norian) age rocks from the Chinle Formation and Dockum Group of the Western United States. Known chiefly from osteoderms, this taxon has never been fully described and non-osteoderm material assigned to Calyptosuchus has been done so based on questionable criteria. Mapping of aetosaurian elements from the Placerias Quarry allows for the recognition of associated material providing support for referrals of non-osteoderm material. Furthermore, another previously undescribed specimen from the Chinle Formation of Arizona provides more details about this taxon. Presently Calyptosuchus lacks discrete autapomorphies, but can be distinguished from other aetosaurs based on a unique combination of characters supported by a phylogenetic analysis. Calyptosuchus is one of the most common aetosaurians in the Western United States and an index taxon of the early Adamanian biozone. The name Calyptosuchus is retained and encouraged as the applicable genus name for the species wellesi rather than the often used Stagonolepis because assignments of taxa to multi-species genus names are problematic and in this case provides a proposed taxonomic relationship that cannot be unambiguously supported, even by phylogenetic analyses. Because of the inherent limitations of the fossil record, referral of specimens and species to species and genera respectively is an epistemological problem in vertebrate paleontology.

The nasal and paranasal architecture of the Middle Miocene ape Pierolapithecus catalaunicus (primates: Hominidae): phylogenetic implications.

PubMed

Pérez de Los Ríos, Miriam; Moyà-Solà, Salvador; Alba, David M

2012-09-01

The internal (nasal and paranasal) cranial anatomy of the Middle Miocene (11.9 Ma [millions of years ago]) great ape Pierolapithecus catalaunicus (Hominidae: Dryopithecini) is described on the basis of computed-tomography scans of the holotype specimen (IPS21350), with particular emphasis on its phylogenetic implications. Pierolapithecus displays the following characters: an anteriorly-restricted maxillary sinus that posteriorly spreads towards the ethmoidal area (thus resembling the pongine condition), although being situated well above the molar roots (as in kenyapithecins, other dryopithecins and pongines); lack of frontal sinus (a synapomorphy of derived pongines, independently acquired by both cercopithecoids and hylobatids); posteriorly-situated turbinals (as in Pongo); anteriorly-projecting nasolacrimal canal (as in Pongo); and probably stepped nasal floor with non-overlapping premaxillary-maxillary contact (as in dryopithecines and stem hominoids, although it cannot be conclusively shown due to bone damage). Overall, Pierolapithecus displays a mosaic of primitive hominid and derived pongine features that are inconsistent with this taxon being a hominine (as previously suggested). Two alternative phylogenetic interpretations are possible: Pierolapithecus may be a stem member of the Hominidae as previously suggested in its original description, or alternatively this taxon may be a stem member of the Ponginae s.l. (with the European dryopithecines being the sister taxon to the Asian pongines). Copyright © 2012 Elsevier Ltd. All rights reserved.

Defining operational taxonomic units using DNA barcode data.

PubMed

Blaxter, Mark; Mann, Jenna; Chapman, Tom; Thomas, Fran; Whitton, Claire; Floyd, Robin; Abebe, Eyualem

2005-10-29

The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.

Taxonomic revision of the moss salamander Nototriton barbouri (Schmidt (Caudata: Plethodontidae), with description of two new species from the Cordillera Nombre de Dios, Honduras.

PubMed

Townsend, Josiah H

2016-11-24

Moss salamanders (genus Nototriton) are represented in northern Central America by nine putative species: N. barbouri, N. brodiei, N. lignicola, N. limnospectator, N. mime, N. picucha, N. saslaya, N. stuarti, and N. tomamorum. I estimate the phylogenetic relationships for these species based on data from three mitochondrial gene fragments (16S, cytochrome b, and COI), and compare morphological variation among putative taxa. As evidenced here and in previous studies, the taxon N. barbouri is paraphyletic with respect to populations from the Cordillera Nombre de Dios in northern Honduras. I restrict this taxon to populations from the Sierra de Sulaco in central Yoro, Honduras, and describe two new species from the Cordillera Nombre de Dios.

Genetic analysis reveals the diversity of larval Gobiidae in a temperate estuary.

PubMed

Ojaveer, H; Gross, R; Laur, K; Arula, T; Klais, R

2017-10-01

Using molecular tools to examine Gobiidae, the second most abundant taxon in ichthyoplankton samples in the Gulf of Riga (Baltic Sea), the sand goby Pomatoschistus minutus was the most abundant taxon (82% of all individuals analysed), the common goby Pomatoschistus microps constituted 12% and the black goby Gobius niger 6%. The spatiotemporal distribution of P. microps and G. niger indicated a preference for habitats closer to the river inlet and their abundances increased slightly towards the end of the sampling period in summer. The species composition was interpreted in the context of the prevailing habitat conditions, characterized by extremely low water transparency, low salinity, limited spread of vegetated area and dominance of sandy-muddy substrata. © 2017 The Fisheries Society of the British Isles.

The Basal Nodosaurid Ankylosaur Europelta carbonensis n. gen., n. sp. from the Lower Cretaceous (Lower Albian) Escucha Formation of Northeastern Spain

PubMed Central

Kirkland, James I.; Alcalá, Luis; Loewen, Mark A.; Espílez, Eduardo; Mampel, Luis; Wiersma, Jelle P.

2013-01-01

Nodosaurids are poorly known from the Lower Cretaceous of Europe. Two associated ankylosaur skeletons excavated from the lower Albian carbonaceous member of the Escucha Formation near Ariño in northeastern Teruel, Spain reveal nearly all the diagnostic recognized character that define nodosaurid ankylosaurs. These new specimens comprise a new genus and species of nodosaurid ankylosaur and represent the single most complete taxon of ankylosaur from the Cretaceous of Europe. These two specimens were examined and compared to all other known ankylosaurs. Comparisons of these specimens document that Europelta carbonensis n. gen., n. sp. is a nodosaur and is the sister taxon to the Late Cretaceous nodosaurids Anoplosaurus, Hungarosaurus, and Struthiosaurus, defining a monophyletic clade of European nodosaurids– the Struthiosaurinae. PMID:24312471

Dancing with the Muses: dissociation and flow.

PubMed

Thomson, Paula; Jaque, S Victoria

2012-01-01

This study investigated dissociative psychological processes and flow (dispositional and state) in a group of professional and pre-professional dancers (n=74). In this study, high scores for global (Mdn=4.14) and autotelic (Mdn=4.50) flow suggest that dancing was inherently integrating and rewarding, although 17.6% of the dancers were identified as possibly having clinical levels of dissociation (Dissociative Experiences Scale-Taxon cutoff score≥20). The results of the multivariate analysis of variance indicated that subjects with high levels of dissociation had significantly lower levels of global flow (p<.05). Stepwise linear regression analyses demonstrated that dispositional flow negatively predicted the dissociative constructs of depersonalization and taxon (p<.05) but did not significantly predict the variance in absorption/imagination (p>.05). As hypothesized, dissociation and flow seem to operate as different mental processes.

Digital preparation and osteology of the skull of Lesothosaurus diagnosticus (Ornithischia: Dinosauria).

PubMed

Porro, Laura B; Witmer, Lawrence M; Barrett, Paul M

2015-01-01

Several skulls of the ornithischian dinosaur Lesothosaurus diagnosticus (Lower Jurassic, southern Africa) are known, but all are either incomplete, deformed, or incompletely prepared. This has hampered attempts to provide a comprehensive description of skull osteology in this crucial early dinosaurian taxon. Using visualization software, computed tomographic scans of the Lesothosaurus syntypes were digitally segmented to remove matrix, and identify and separate individual cranial and mandibular bones, revealing new anatomical details such as sutural morphology and the presence of several previously undescribed elements. Together with visual inspection of exposed skull bones, these CT data enable a complete description of skull anatomy in this taxon. Comparisons with our new data suggest that two specimens previously identified as Lesothosaurus sp. (MNHN LES 17 and MNHN LES 18) probably represent additional individuals of Lesothosaurus diagnosticus.

Hitting the sweet spot-glycans as targets of fungal defense effector proteins.

PubMed

Künzler, Markus

2015-05-06

Organisms which rely solely on innate defense systems must combat a large number of antagonists with a comparably low number of defense effector molecules. As one solution of this problem, these organisms have evolved effector molecules targeting epitopes that are conserved between different antagonists of a specific taxon or, if possible, even of different taxa. In order to restrict the activity of the defense effector molecules to physiologically relevant taxa, these target epitopes should, on the other hand, be taxon-specific and easily accessible. Glycans fulfill all these requirements and are therefore a preferred target of defense effector molecules, in particular defense proteins. Here, we review this defense strategy using the example of the defense system of multicellular (filamentous) fungi against microbial competitors and animal predators.

Using of Synchrotron radiation for study of multielement composition of the small mammals diet and tissues

NASA Astrophysics Data System (ADS)

Bezel, V. S.; Koutzenogii, K. P.; Mukhacheva, S. V.; Chankina, O. V.; Savchenko, T. I.

2007-05-01

The Synchrotron radiation X-ray Fluorescence analysis (SRXRF) was used for estimation of "geochemical selection" of elements by small mammals, which belong to different trophic groups and inhabit polluted and background areas (the Middle Ural). The concentrations of K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Br, Rb, Sr, Y, Cd, Pb in the diet and into hepar of a herbivorous ( bank vole) and carnivorous ( Laxmann's shrew) small mammals were compared. Herbivores play a particular role in chemical elements translocation between trophic levels, limiting element transition to consumers of the consequent levels. Whereas, insectivores concentrate most elements in their tissues under the same conditions.

[The planning of resource support of secondary medical care in hospital].

PubMed

Kungurov, N V; Zil'berberg, N V

2010-01-01

The Ural Institute of dermatovenerology and immunopathology developed and implemented the software concerning the personalized total recording of medical services and pharmaceuticals. The Institute also presents such software as listing of medical services, software module of calculation of financial costs of implementing full standards of secondary medical care in case of chronic dermatopathy, reference book of standards of direct specific costs on laboratory and physiotherapy services, reference book of pharmaceuticals, testing systems and consumables. The unified information system of management recording is a good technique to substantiate the costs of the implementation of standards of medical care, including high-tech care with taking into account the results of total calculation of provided medical services.

Methodology for cloud-based design of robots

NASA Astrophysics Data System (ADS)

Ogorodnikova, O. M.; Vaganov, K. A.; Putimtsev, I. D.

2017-09-01

This paper presents some important results for cloud-based designing a robot arm by a group of students. Methodology for the cloud-based design was developed and used to initiate interdisciplinary project about research and development of a specific manipulator. The whole project data files were hosted by Ural Federal University data center. The 3D (three-dimensional) model of the robot arm was created using Siemens PLM software (Product Lifecycle Management) and structured as a complex mechatronics product by means of Siemens Teamcenter thin client; all processes were performed in the clouds. The robot arm was designed in purpose to load blanks up to 1 kg into the work space of the milling machine for performing student's researches.

Cyanobacterial-algal cenoses in ordinary chernozems under the impact of different phytoameliorants

NASA Astrophysics Data System (ADS)

Dubovik, I. E.; Suyundukov, Ya. T.; Khasanova, R. F.; Shalygina, R. R.

2016-04-01

General ecological and taxonomic characteristics of cyanobacterial-algal cenoses in ordinary chernozems under different ameliorative plants (phytoameliorants) were studied in the Trans-Ural region of the Republic of Bashkortostan. A comparative analysis of the taxa of studied cenoses in the soils under leguminous herbs and grasses was performed. The phytoameliorative effect of different herbs and their relationships with cyanobacterial-algal cenoses were examined. Overall, 134 cyanoprokaryotic and algal species belonging to 70 genera, 36 families, 15 orders, and 9 classes were identified. Cyanobacterial-algal cenoses included the divisions of Chlorophyta, Cyanoprokaryota, Xanthophyta, Bacillariophyta, and Euglenophyta. Representatives of Ch-, X-, CF-, and P-forms were the leading ecobiomorphs in the studied cenoses.

Is Homo heidelbergensis a distinct species? New insight on the Mauer mandible.

PubMed

Mounier, Aurélien; Marchal, François; Condemi, Silvana

2009-03-01

The discovery of new fossils in Africa, Asia, and Europe, and the recognition of a greater diversity in the middle Pleistocene fossil record, has led to a reconsideration of the species Homo heidelbergensis. This nomen, formulated by Schoetensack in 1908 to describe the Mauer jaw (Germany), was almost forgotten during most of the past century. Numerous fossils have been attributed to it but no consensus has arisen concerning their classification. The holotype anatomical traits are still poorly understood, and numerous fossils with no mandibular remains have been placed in the taxon. Some researchers propose H. heidelbergensis as an Afro-European taxon that is ancestral to both modern humans and Neandertals whereas others think it is a strictly European species that is part of the Neandertal lineage. We focus on the validity of H. heidelbergensis, using the traditional basis of species recognition: anatomical description. We provide a comparative morphological analysis using 47 anatomical traits of 36 Pleistocene fossils from Africa, Asia, and Europe and 35 extant human mandibles. We re-examine the mandibular features of Mauer and discuss the specimen's inclusion in H. heidelbergensis, as well as alternative evolutionary theories. To lend objectivity to specimen grouping, we use multiple correspondence analysis associated with hierarchical classification that creates clusters corresponding to phenetic similarities between jaws. Our phenetic and comparative morphological analyses support the validity of H. heidelbergensis as a taxon. A set of morphological features can be statistically identified for the definition of the species. Some traits can be used to delimit H. heidelbergensis in an evolutionary framework (e.g., foramina mentale posteriorly positioned, horizontal retromolar surface). Those traits are also present on African (e.g., Tighenif) and European (e.g., Sima de los Huesos) specimens that show a close relationship with the Mauer mandible. Therefore, the definition of H. heidelbergensis is more precise and mainly supports the theory of an Afro-European taxon, which is the last common ancestor of H. neanderthalensis and H. sapiens. However, the results of this study fail to entirely discount the hypothesis that considers H. heidelbergensis as a chronospecies leading to the Neandertals.

The prevalence of terraced treescapes in analyses of phylogenetic data sets.

PubMed

Dobrin, Barbara H; Zwickl, Derrick J; Sanderson, Michael J

2018-04-04

The pattern of data availability in a phylogenetic data set may lead to the formation of terraces, collections of equally optimal trees. Terraces can arise in tree space if trees are scored with parsimony or with partitioned, edge-unlinked maximum likelihood. Theory predicts that terraces can be large, but their prevalence in contemporary data sets has never been surveyed. We selected 26 data sets and phylogenetic trees reported in recent literature and investigated the terraces to which the trees would belong, under a common set of inference assumptions. We examined terrace size as a function of the sampling properties of the data sets, including taxon coverage density (the proportion of taxon-by-gene positions with any data present) and a measure of gene sampling "sufficiency". We evaluated each data set in relation to the theoretical minimum gene sampling depth needed to reduce terrace size to a single tree, and explored the impact of the terraces found in replicate trees in bootstrap methods. Terraces were identified in nearly all data sets with taxon coverage densities < 0.90. They were not found, however, in high-coverage-density (i.e., ≥ 0.94) transcriptomic and genomic data sets. The terraces could be very large, and size varied inversely with taxon coverage density and with gene sampling sufficiency. Few data sets achieved a theoretical minimum gene sampling depth needed to reduce terrace size to a single tree. Terraces found during bootstrap resampling reduced overall support. If certain inference assumptions apply, trees estimated from empirical data sets often belong to large terraces of equally optimal trees. Terrace size correlates to data set sampling properties. Data sets seldom include enough genes to reduce terrace size to one tree. When bootstrap replicate trees lie on a terrace, statistical support for phylogenetic hypotheses may be reduced. Although some of the published analyses surveyed were conducted with edge-linked inference models (which do not induce terraces), unlinked models have been used and advocated. The present study describes the potential impact of that inference assumption on phylogenetic inference in the context of the kinds of multigene data sets now widely assembled for large-scale tree construction.

Morphology meets molecules: a new genus and two new species of diphyllidean cestodes from the Yellowspotted skate, Leucoraja wallacei, from South Africa.

PubMed

Abbott, Lauren McKenna; Caira, Janine N

2014-06-01

Two morphologically disparate undescribed species of diphyllidean cestodes from the Yellowspotted skate, Leucoraja wallacei , from South Africa were included in a recent molecular phylogenetic study aimed at revising diphyllidean classification. From a molecular standpoint, these species were determined to be only distantly related to one another. One (originally referred to as Echinobothrium n. sp. 2) showed affinities with species of the batoid-parasitizing Echinobothrium sensu stricto and is described here as Echinobothrium marquesi n. sp. This species most closely resembles Echinobothrium joshuai, an affinity supported by the previous molecular study, but differs in the form of its "B" hooks and degree of overlap between bothria and cephalic peduncle. The other species (originally referred to as New genus n. sp. 1), although exhibiting the full complement of scolex armature, grouped among primarily shark-hosted genera, most of which lack or exhibit reduced scolex armatures. That unexpected result suggested that erection of a novel genus might be warranted, but morphological grounds supporting the action were not apparent at that time. The present study aimed to explore the morphology of this taxon in more detail. Light and scanning electron microscopy revealed this taxon to be exceptional in that its lateral hooklets, which are arranged in 2 clusters like those of Echinobothrium and Coronocestus, are unique in being arranged in anterior and posterior rows, rather than in a single row. Andocadoncum n. gen. is erected, with Andocadoncum meganae n. sp. as its type, to accommodate this taxon. A minor adjustment to the existing hook formula by presenting counts for the anterior hooklets (a) separately from the posterior hooklets (b) readily accommodates this new form. Leucoraja wallacei is distinctive among skates in hosting 2 different genera of diphyllideans. In the context of the previous molecular phylogenetic analyses, it appears that the presence of Andocadoncum n. gen. in this skate species may be the result of a host-switching event involving a weakly or unarmed shark-hosted taxon moving to a batoid-a shift that was likely accompanied by a return to the fully armed condition seen, for example, in other batoid-parasitizing members of the order.

Ribosomes in the sea: a window on taxon-specific lysis

NASA Astrophysics Data System (ADS)

Suttle, C.; Zhong, X.; Wirth, J.

2016-02-01

Microbes are estimated to comprise more than 90% of the biomass in the world's oceans, are major drivers of biogeochemical cycles, and have turnover rates ranging from hours to days. Despite the central role that microbes play in marine ecosystems, there is no robust method to evaluate taxon-specific mortality rates. Here, we report a method that employs extracellular free-ribosomes as a proxy to evaluate taxon-specific microbial lysis. The method was validated with laboratory cultures of the marine heterotrophic bacterium Vibrio natriegens strain PWH3a and the photoautotroph Synechococcus strain DC2, with and without grazers or viruses, to identify the origin and fate of the extracellular free-ribosomes. Our results showed both viral lysis and programmed-cell-death (PCD) contribute to free-ribosome production. Ribosomes were not released when cells were grazed, but grazers could consume free-ribosomes. We show that extracellular free-ribosomes can be used to evaluate microbial mortality caused by viral lysis and PCD. This approach was applied to environmental samples by examining the taxonomic composition and relative abundance of free 16S-ribosomes in seawater samples collected from the Strait of Georgia and Saanich Inlet, British Columbia, Canada. Based on the presence of free ribosomes, lysis was detected in 2198 out of 4013 prokaryotic taxa, representing 22 bacterial and three archaeal phyla. Of these, lysis of 140 taxa could be detected in all nine samples. Based on the ratio of free ribosomes to cellular ribosomes, some taxa associated with specific ecological niches appeared to be subject to high rates of lysis, including the genera Achromobacter, Chryseobacterium, Clostridium, Delftia, Ferruginibacter, Lactobacillus, Marinomonas, Massilia, Microbacterium, Ochrobactrum, Paenibacillus, Phyllobacterium, Pseudomonas, Rhodobacter, and Stenotrophomonas. Our results showed high-lysis coupled with low-abundance, suggesting that taxa in lower abundance are subject to higher relative rates of cell lysis, consistent with previous suggestions. The ability to estimate taxon-specific mortality as the result of cell lysis adds an important tool in our quest to explain the distribution and abundance of specific microbial taxa in nature.

Pathogenic properties of enterohepatic Helicobacter spp. isolated from rhesus macaques with intestinal adenocarcinoma

PubMed Central

Lertpiriyapong, Kvin; Handt, Laurence; Feng, Yan; Mitchell, Thomas W.; Lodge, Kenneth E.; Shen, Zeli; Dewhirst, Floyd E.; Muthupalani, Sureshkumar

2014-01-01

Considerable progress has been made in understanding the roles of Helicobacter pylori in inflammation and gastric cancer; however, far less is known about the roles of enterohepatic Helicobacter species (EHS) in carcinogenesis and their zoonotic or pathogenic potential. We determined the prevalence of EHS infection in a cohort of geriatric rhesus monkeys in which intestinal adenocarcinoma (IAC) is common and investigated the association between EHS infection and IAC. The cohort consisted of 36 animals, 14 of which (age 26–35 years) had IAC. Of the 36 rhesus, 35 (97 %) were positive for EHS using PCR or bacterial isolation from faeces, colonic or tumour tissues. Only a single rhesus, which had IAC, was negative for EHS by all detection methods. The EHS identified by 16S rRNA sequencing in this study were from three Helicobacter taxa: Helicobacter macacae (previously rhesus monkey taxon 1), Helicobacter sp. rhesus monkey taxon 2, previously described from strain MIT 99-5507, and Helicobacter sp. rhesus monkey taxon 4, related to Helicobacter fennelliae. Thirteen of 14 monkeys with IAC were positive for either H. macacae (7/13, 54 %), EHS rhesus monkey taxon 4 (4/13, 31 %) or a mixture of the two EHS (2/13, 15 %). These results indicate that EHS are prevalent among aged rhesus macaques with IAC. Using Helicobacter genus-specific florescent in situ hybridization, EHS were detected on the surface of colonic epithelia of infected monkeys. All Helicobacter isolates, including H. macacae, effectively adhered to, invaded, and significantly induced proinflammatory genes, including IL-8, IL-6, TNF-α and iNOS, while downregulating genes involved in the function of inflammasomes, particularly IL-1β, CASPASE-1, NRLP3, NLRP6 and NLRC4 in the human colonic T84 cell line (P<0.0001). These results suggest that EHS may represent an aetiological agent mediating diarrhoea, chronic inflammation, and possibly intestinal cancer in non-human primates, and may play a role in similar disease syndromes in humans. Downregulation of inflammasome function may represent an EHS strategy for long-term persistence in the host and play a role in inducing pathological changes in the host’s lower bowel. PMID:24696515

Preface: Proceedings of the 13th Conference on Liquid and Amorphous Metals (LAM13) (Ekaterinburg, Russia, 8 14 July 2007)

NASA Astrophysics Data System (ADS)

Popel, Pjotr; Gelchinskii, Boris; Sidorov, Valeriy

2008-03-01

The most recent developments in the field of liquid and amorphous metals and alloys are regularly updated through two complementary international conferences: the liquid and amorphous metals conference (LAM) and the rapidly quenched materials (RQ) conference. The first series of conferences started as LM1 in 1966 at Brookhaven for the basic understanding of liquid metals. The subsequent LM conferences were held in Tokyo (1972) and Bristol (1976). The conference was renewed in Grenoble (1980) as a LAM conference including amorphous metals and continued in Los Angeles (1983), Garmisch-Partenkirchen (1986), Kyoto (1989), Vienna (1992), Chicago (1995), Dortmund (1998), Yokohama (2001) and Metz (2004). The conferences are mainly devoted to liquid and amorphous metals and alloys. However, communications on some non-metallic systems such as semiconductors, quasicrystals etc, are also accepted. The conference tradition strongly encourages participation from junior researchers and graduate students. The 13th conference of the LAM series was organized in Ekaterinburg, Russia, by the Institute of Metallurgy of the Ural Branch of the Russian Academy of Sciences (IMet UB RAS) and the Ural State Pedagogical University (USPU), and held from 8-14 July 2007 under the chairmanship of Professors Pjotr Popel (USPU) and Boris Gelchinskii (IMet UB RAS). Two hundred and forty two active participants and about 60 guest participants from 20 countries attended the conference. There were no parallel sessions and all oral reports were separated into three groups: invited talks (40 min), full-scale oral reports (25 min), and brief oral reports (15 min). The program included ten sessions, ranging from purely theoretical subjects to the technological application of molten and amorphous alloys. The following sessions took place: A: Electronic structure and transport, magnetic properties; B: Phase transitions; C: Structure; D: Atomic dynamics and transport; E: Thermodynamics; F: Modelling, simulation; G: Surface and interface; H: Mechanical properties and new materials; I: Quasicrystals; J: Industrial applications. The largest sessions were E, C, D and F with 53, 47, 43 and 40 reports, respectively. Posters were exhibited during the first (sessions A-E) or last (sessions F-J) three days of the conference. As usual, each oral session started with an invited talk. In accordance with contemporary tendencies the first invited talk of M Yao (Kyoto University) was devoted to interrelations between liquid metal studies and nanoscience. He pointed out that the physics of disordered matter, especially liquid metals, has provided nanoscience with basic ideas and theoretical tools such as ab initio molecular dynamics (MD) simulation. K Tamura (Kyoto University) reported experimental investigation results of expanded liquid rubidium, showing that observed structural features are originated from the instability of low-density electron gas. Modern theory has predicted that interacting electron gas suffers negative compressibility and the static dielectric function (DF) becomes negative when electron density is sufficiently reduced. Negative DF is of special interest when considering the possibility of new types of superconductors. In the next invited lecture, M I Mendelev and J R Morris (USA) described how MD simulations were performed to study phase transformations in supercooled liquid Al. The authors found that the widely used EAM potential for Al enables vitrification for cooling rates achievable in classical MD simulation, while other Al potentials enable crystallization under the same conditions. The reason for this difference was discussed, as well as features of vitrification in the EA Al. P Häussler (Chemnitz Univeristy) spoke about fundamental structure-forming processes in liquid and amorphous materials. He proposed the resonance model as an autonomous missing link between the microscopic description of atoms/molecules of Schrödinger's equation, and crystals, where global concepts such as planar resonances exist and Bloch's theorem is applied. D Holland-Moritz (Institut für Materialphysik, Köln) presented the first results of the quasielastic neutron scattering experiments on electromagnetically levitated metallic melts. The studies were indicative of Arrhenius behavior of the diffusion constants over the whole temperature regime investigated, ranging from temperatures above the melting temperature up to the metastable regime of an undercooled liquid. L Son (USPU) discussed the existing analytical theories of liquid-liquid phase transitions that have been assumed for a wide variety of liquids, but are poorly understood analytically. The application of these theories to liquid metal systems was also demonstrated. An approach to the study of dynamics and kinetics of cavitation in stretched liquid metals by the classical MD method was presented in the talk of G E Norman (Institute for High Temperatures, Moscow). Both quantitative and qualitative disagreements with the classic theory of homogeneous nucleation were found. Analytic extentions of MD results beyond the space and temporal limits accessible for the MD method were also discussed. G Wilde (University of Muenster) spoke about the experimental investigation into the impact of interface properties and, more specifically, of interface morphology in matrix-encased metallic nanoparticles on macroscopic properties, such as melting transition by a combination of microscopic, microanalytical and calorimetric measurements. The results were discussed with respect to the underlying mechanisms that lead to size dependent phase equilibria. In the invited talk of V Keryvin (University of Rennes) the indentation ability was proposed as a probe for pressure sensitivity in metallic glasses. The main conclusion was that the indentation test provides a good means to study the elasto-plastic behavior of these materials as well as being a relevant tool to subject metallic glasses to multiaxial loadings. The influence of changes in local ordering of precursor melt on the formation of the amorphous state and subsequent crystallization was the subject of a report presented by P Śvec (Institute of Physics, Bratislava). The effect was shown for a rapidly quenched Fe-Mo-B system with addition of Cu and substitution of Fe by Co prepared under varying conditions of planar flow casting and using master alloys with specific melt treatment. Approximately 320 abstracts were received and 180 manuscripts were finally submitted for publication. Papers from invited lectures and full-scale oral reports are published in Journal of Physics: Condensed Matter for this special issue. All papers from brief oral reports and posters were collected for an issue of Journal of Physics: Conference Series. All were edited by staff from Ekaterinburg. It was decided during the joint meeting of both the International Advisory Board and International Program Committee that the next conference in the LAM series, LAM14, will be arranged by the groups of A Di Cicco (Camerino University) and T Scopigno (University of Rome 'La Sapienza'), and will take place in Rome, Italy, in 2010. It is no easy task to outline new scientific tendencies in the field of liquid and amorphous alloys just after the LAM conference. It takes one or two years to estimate the significance of the event. Only one conclusion is obvious: the LAM13 conference has opened a door between the global scientific community and Russian scientists, who have special expertise in the field but could not actively participate at the LAM conferences before because of the economic situation in Russia. We are grateful to the Advisory and Program Committees of the LAM12 conference in Metz and especially to Dr Monique Calvo-Dahlborg for the opportunity to manage such an event in Russia. In addition we would like to give our sincere thanks to: the authorities of the Ural Branch of the Russian Academy of Sciences and the Ural State Pedagogical University who did their best to help us with all our problems, especially to Boris Igoshev and Nikolay Vatolin; all the sponsors who supported the conference: the Russian Foundation for Basic Research, the Ural Mining and Metallurgical Company headed by Andrey Kozicyn, the Open Joint Stock Company 'Uralsvjazinform' (Alexey Ufimkin), the A A Baikov Institute of Metallurgy and Materials Science, RAS (July Kovneristii), the Institute for Physics and Power Engineering (Alexandre Ephanov), the Nuclear Power Plant 'Beloyarskaya' (Nikolay Oshkanov), the South Ural State University (German Vjatkin), Ural Technical Institute of Communications and Informatics (Evgeny Subbotin), Physical-Technical Institute UB RAS (Vladimir Lad'yanov), Metallurgical Department of the Ural State Technical University (Victor Shimov), Academy of Sciences of Chechen Republic (Raikom Dadashev) and NETZSCH-Gerätebau GmbH; the invited lecturers who immediately answered positively to the invitation and contributed to the high level of success of LAM13; the colleagues who acted as chairmen in the various sessions; Graham Douglas and Richard Palmer who kindly answered our queries and tried to satisfy our requirements; the seniors of the LAM series who could not participate at the 13th conference but helped us to manage it in the best way, namely J Dupuy, M Silbert, F Sommer, W C Pilgrim, W Freyland, K Lu, J Brmejo and F Hensel. We dedicate the LAM13 conference to the 80 year jubilee of Professor Nikolay Vatolin who is one of the leaders of Russian investigation in the field of liquid and amorphous metals, and who managed 12 similar conferences in our country. One of us (PP) commemorates his father, Professor Stanislav Popel, who was a known specialist in high temperature capillarity and sadly left us six months before the event.

Paleohydrology of the Polar Urals from the Last Glacial Maximum Through the Holocene

NASA Astrophysics Data System (ADS)

Cowling, O.; Thomas, E.; Svendsen, J. I.; Haflidason, H.

2017-12-01

Paleohydrologic records provide important information concerning the past response of local hydrology to abrupt temperature changes. Arctic hydrology is particularly sensitive to temperature due to feedbacks involving sea ice and ice sheets. The most recent deglacial interval contains multiple abrupt temperature changes, which provide opportunities to study the relationship between temperature, ice sheets, and hydrology. We present a lacustrine δ2Hwax record from Bolshoye Schuchye, in the Polar Ural Mountains, spanning 24.5- 1.3 ka, and interpret hydroclimate conditions at a multi-centennial scale from the Last Glacial Maximum (LGM) through the Holocene. Bolshoye Schuchye's position beyond the reach of local glaciers during the LGM makes it a unique site, since lacustrine paleoclimate records from the Arctic rarely span this entire interval, so Bolshoye Schuchye helps to cover a gap in understanding of paleoclimate. Compound specific analysis of leaf wax hydrogen isotopes (δ2Hwax) is a hydroclimate proxy that can be used to infer moisture source area, transport history, and local aridity. Inferences based on δ2Hwax rely on mechanistic understanding of the process by which hydrogen from meteoric water is incorporated into waxes, and subsequently deposited in lake sediments. The δ2Hwax value of a sample reflects the isotopic composition of precipitation, while also incorporating fractionation that occurs between precipitation and uptake by plants, and biosynthetic fractionation during wax synthesis. Comparisons between different chain length waxes can be used to infer the isotopic composition of terrestrial and aquatic waxes, as terrestrial plants tend to produce longer chain lengths than aquatic macrophytes. The offset between terrestrial and aquatic δ2Hwax, expressed as ɛt-a, indicates differences between the precipitation used by terrestrial plants, and the lake water used by aquatic plants. Significant changes in ɛt-a can represent shifts in local aridity or precipitation seasonality. The record we present from Bolshoye Schuchye gives insights into terrestrial hydrologic changes resulting from rapid temperature shifts since the LGM.

Alteration and chemical U-Th-total Pb dating of heterogeneous high-uranium zircon from a pegmatite from the Aduiskii massif, middle Urals, Russia

NASA Astrophysics Data System (ADS)

Zamyatin, Dmitry A.; Shchapova, Yuliya V.; Votyakov, Sergey L.; Nasdala, Lutz; Lenz, Christoph

2017-09-01

The U-Th-Pb isotope system in the accessory mineral zircon may be disturbed, as for instance by the secondary loss of radiogenic lead. The recognition of such alteration is crucial for the sound interpretation of geochronology results, in particular for chemical dating by means of an electron probe micro-analyser (EPMA). Here we present the example of high-U zircon samples from a granite pegmatite from the Aduiskii Massif, Middle Urals, Russia. The structural and chemical heterogeneity of samples was characterised by EPMA, including joint probability distribution (JPD) analysis of back-scattered electrons (BSE), cathodoluminescence (CL) and U M β images, and by Raman and photoluminescence (PL) spectroscopy. We found a high-U interior region (U up to 11.4 wt%) without any obvious indication of alteration. This domain has stoichiometric composition, and its Raman spectrum is similar to that of amorphous ZrSiO4. In addition, altered lower-U regions are present that are non-stoichiometric and contain non-formula elements such as Ca, Al, Fe, and water up to several wt%. Their Raman spectra yielded a band near 760-810 cm-1 which is not related to any ZrSiO4 vibration; we assign it tentatively to the symmetric stretching of (UO2)2+ groups. This assignment is supported by the observation of a fairly intense PL phenomenon whose spectral position and vibrational-coupling structure strongly indicates a uranyl-related emission. Altered zones were formed by both fluid-driven diffusion reaction and coupled dissolution-reprecipitation processes. The variation of BSE and CL intensities in amorphous high-U zircon is controlled by its chemical composition and the presence of water and uranyl groups. We have determined a weighted mean EPMA age of 246 ± 2 Ma, which agrees reasonably well with previous dating results for the Aduiskii Massif.

Tuberculous spondylitis in Russia and prominent role of multidrug-resistant clone Mycobacterium tuberculosis Beijing B0/W148.

PubMed

Vyazovaya, Anna; Mokrousov, Igor; Solovieva, Natalia; Mushkin, Alexander; Manicheva, Olga; Vishnevsky, Boris; Zhuravlev, Viacheslav; Narvskaya, Olga

2015-04-01

Extrapulmonary and, in particular, spinal tuberculosis (TB) constitutes a minor but significant part of the total TB incidence. In spite of this, almost no studies on the genetic diversity and drug resistance of Mycobacterium tuberculosis isolates from spinal TB patients have been published to date. Here, we report results of the first Russian and globally largest molecular study of M. tuberculosis isolates recovered from patients with tuberculous spondylitis (TBS). The majority of 107 isolates were assigned to the Beijing genotype (n = 80); the other main families were T (n = 11), Ural (n = 7), and LAM (n = 4). Multidrug resistance (MDR) was more frequently found among Beijing (90.5%) and, intriguingly, Ural (71.4%) isolates than other genotypes (5%; P < 0.001). The extremely drug-resistant (XDR) phenotype was exclusively found in the Beijing isolates (n = 7). A notable prevalence of the rpoB531 and katG315 mutations in Beijing strains that were similarly high in both TBS (this study) and published pulmonary TB (PTB) samples from Russia shows that TBS and PTB Beijing strains follow the same paradigm of acquisition of rifampin (RIF) and isoniazid (INH) resistance. The 24-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) subtyping of 80 Beijing isolates further discriminated them into 24 types (Hunter Gaston index [HGI] = 0.83); types 100-32 and 94-32 represented the largest groups. A genotype of Russian successful clone B0/W148 was identified in 30 of 80 Beijing isolates. In conclusion, this study highlighted a crucial impact of the Beijing genotype and the especially prominent role of its MDR-associated successful clone B0/W148 cluster in the development of spinal MDR-TB in Russian patients. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Earth Observations

NASA Image and Video Library

2010-09-11

ISS024-E-014233 (11 Sept. 2010) --- A smoke plume near the northern Caspian Sea, Kazakhstan is featured in this image photographed by an Expedition 24 crew member on the International Space Station. This broad view of the north coast of the Caspian Sea shows a smoke plume (left) and two river deltas (bottom and lower right). The larger delta is that of the Volga River which appears prominently here in sunglint (light reflected off a water surface back towards the observer), and the smaller less prominent delta is that of the Ural River. Wide angle, oblique views ? taken looking outward at an angle, rather than straight down towards Earth ? such as this give an excellent impression of how crew members onboard the space station view Earth. For a sense of scale, the Caucasus Mts. (across the Caspian, top right) are approximately 1,100 kilometers to the southwest of the International Space Station?s nadir point location ? the point on Earth directly underneath the spacecraft ? at the time this image was taken. The smoke plume appears to be sourced in the dark-toned coastal marsh vegetation along the outer fringe of the Ural River delta, rather than in a city or at some oil storage facility. Although even small fires produce plumes that are long and bright and thus easily visible from space, the density of the smoke in this plume, and its 350-kilometer length across the entire north lobe of the Caspian Sea, suggest it was a significant fire. The smoke was thick enough nearer the source to cast shadows on the sea surface below. Lines mark three separate pulses of smoke, the most recent, nearest the source, extending directly south away from the coastline (lower left). With time, plumes become progressively more diffuse. The oldest pulse appears to be the thinnest, casting no obvious shadows (center left).

Model testing of radioactive contamination by 90Sr, 137Cs and 239,240Pu of water and bottom sediments in the Techa River (Southern Urals, Russia).

PubMed

Kryshev, I I; Boyer, P; Monte, L; Brittain, J E; Dzyuba, N N; Krylov, A L; Kryshev, A I; Nosov, A V; Sanina, K D; Zheleznyak, M I

2009-03-15

This paper presents results of testing models for the radioactive contamination of river water and bottom sediments by (90)Sr, (137)Cs and (239,240)Pu. The scenario for the model testing was based on data from the Techa River (Southern Urals, Russia), which was contaminated as a result of discharges of liquid radioactive waste into the river. The endpoints of the scenario were model predictions of the activity concentrations of (90)Sr, (137)Cs and (239,240)Pu in water and bottom sediments along the Techa River in 1996. Calculations for the Techa scenario were performed by six participant teams from France (model CASTEAUR), Italy (model MARTE), Russia (models TRANSFER-2, CASSANDRA, GIDRO-W) and Ukraine (model RIVTOX), all using different models. As a whole, the radionuclide predictions for (90)Sr in water for all considered models, (137)Cs for MARTE and TRANSFER-2, and (239,240)Pu for TRANSFER-2 and CASSANDRA can be considered sufficiently reliable, whereas the prediction for sediments should be considered cautiously. At the same time the CASTEAUR and RIVTOX models estimate the activity concentrations of (137)Cs and (239,240)Pu in water more reliably than in bottom sediments. The models MARTE ((239,240)Pu) and CASSANDRA ((137)Cs) evaluated the activity concentrations of radionuclides in sediments with about the same agreement with observations as for water. For (90)Sr and (137)Cs the agreement between empirical data and model predictions was good, but not for all the observations of (239,240)Pu in the river water-bottom sediment system. The modelling of (239,240)Pu distribution proved difficult because, in contrast to (137)Cs and (90)Sr, most of models have not been previously tested or validated for plutonium.

Testing Central and Inner Asian admixture among contemporary Hungarians.

PubMed

Bíró, András; Fehér, Tibor; Bárány, Gusztáv; Pamjav, Horolma

2015-03-01

Historically, the Carpathian Basin was the final destination for many nomadic peoples who migrated westward from Inner and Central Asia towards Europe. Proto-Hungarians (Steppe Magyars) were among those who came from the East, the Eurasian Steppe in the early middle ages. In order to detect the paternal genetic contribution from nomadic Steppe tribes, we tested 966 samples from Central Asian (Uzbekistan, Kazakhstan), Inner Asian (Mongolians and Buryats in Mongolia) and Hungarian-speaking European (Hungarian, Sekler and Csango) populations. We constructed median-joining networks of certain haplogroups in Hungarian-speaking European, and Altaic-speaking Central and Inner Asian populations. We estimated that the possible paternal genetic contribution from the above described populations among contemporary Hungarian speaking populations ranged between 5% and 7.4%. It is lowest among Hungarians from Hungary (5.1%), while higher among Hungarian-speaking groups in Romania, notably Sekler (7.4%) and Csango (6.3%). However, these results represent only an upper limit. Actual Central/Inner Asian admixture might be somewhat lower as some of the related lineages may have come from a common third source. The main haplogroups responsible for the Central/Inner Asian admixture among Hungarians are J2*-M172 (xM47, M67, M12), J2-L24, R1a-Z93; Q-M242 and E-M78. Earlier studies showed very limited Uralic genetic influence among Hungarians, and based on the present study, Altaic/Turkic genetic contribution is also not significant, although significantly higher than the Uralic one. The conclusion of this study is that present-day Hungarian speakers are genetically very similar to neighbouring populations, isolated Hungarian speaking groups having relatively higher presence of Central and Inner Asian genetic elements. At the same time, the reliable historical and genetic conclusions require an extension of the study to a significantly larger database with deep haplogroup resolution, including ancient DNA data. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Metamorphism of eclogites from the UHP Maksyutov Complex, south Ural Mountains, Russia

NASA Astrophysics Data System (ADS)

Burlick, T. D.; Leech, M. L.

2013-12-01

The Maksyutov Complex is a mid- to late Paleozoic ultrahigh-pressure (UHP) subduction terrane in the south Ural Mountains of Russia. Radial fractures around quartz inclusions in garnet, omphacite, and glaucophane interpreted as pre-existing coesite; and microdiamond aggregates in garnet identified by Raman spectroscopy demonstrate Maksyutov rocks were subducted to UHP conditions (>2.8 GPa for coesite and >3.0 GPa for diamond at 600°C). Peak UHP eclogite-facies metamorphism (Grt+Omp+Ph+Coe+Rt ×Ttn) took place at c. 385 M and Maksyutov rocks were exhumed through retrograde blueschist-facies metamorphism (Grt+Gln+Ph+Qz×Chl×Ep) by 360 Ma. Pseudosections were constructed to constrain the P-T conditions recorded by the equilibrium mineral assemblanges in eclogites and their retrograded equivalents using bulk rock XRF analysis in the system Na2O-CaO-K2O-FeO-MgO-Al2O3-SiO2-H2O-TiO2 and the suite of free energy minimization programs, Perple_X 6.6.8 [Connolly 2009] with the internally consistent end-member thermodynamic database from Holland and Powell [1998] (mod 2004); solution models for omphacite (Holland and Powell, 1996), clinoamphibole (Dale et al. 2005), white mica (Coggon & Holland 2002, Auzanneau et al 2010), chlorite and garnet (Holland and Powell 1998; Powell and Holland 1999), and feldspar (Thompson and Hovis 1979; Newton et al. 1980) were used with H2O as a saturated component. Both conventional thermometry, using microprobe analyses and Grt-Cpx cation exchange as well as pseudosection modeling result in higher peak equilibrium temperatures than has been previously been reported in the Maksyutov. Pseudosection modeling gives minimum P-T conditions of 625°-675°C and 2.8-3.1 GPa for peak assemblages from the least retrogressed eclogites, while Fe-Mg exchange thermometry yields temperatures of 775°C × 25°C for pressures ranging from 2.5 to 3.5 GPa.

Boletus durhamensis sp. nov. from North Carolina

Treesearch

Beatriz Ortiz-Santana; Alan E. Bessette; Owen L. McConnell

2016-01-01

A new bolete with cinnamon-brown pores, Boletus durhamensis, is described. Collected in northern North Carolina, it is possibly mycorrhizal with Quercus spp. Morphological and molecular characters support this taxon as a new species.

Note on the paleobiogeography of Compsognathidae (Dinosauria: Theropoda) and its paleoecological implications.

PubMed

Sales, Marcos A F; Cascon, Paulo; Schultz, Cesar L

2014-03-01

The paleobiogeography of the theropod clade Compsognathidae is here reaccessed in order to test the hypothesis of this taxon being adapted specifically to inhabit semi-arid environments. Data about localities where these fossils were collected and their paleoenvironments were gathered from the literature. Compsognathids seem to be found especially in sedimentary deposits known as Fossil Lagerstätten, which were formed under a set of specific conditions that allowed the preservation of the fragile bone remains of these animals. This bias limits an accurate analysis of the historical and/or ecological paleobiogeography of this taxon. Actually, it is possible that compsognathids had an almost worldwide distribution during the Mesozoic Era. Their occurrence in Lower Cretaceous rocks of China suggests that they also inhabited environments with moist conditions instead of being restricted to semi-arid to arid environments.

Osteological evidence for sister group relationship between pseudo-toothed birds (Aves: Odontopterygiformes) and waterfowls (Anseriformes)

NASA Astrophysics Data System (ADS)

Bourdon, Estelle

2005-12-01

The phylogenetic affinities of the extinct pseudo-toothed birds have remained controversial. Some authors noted that they resemble both pelicans and allies (Pelecaniformes) and tube-nosed birds (Procellariiformes), but assigned them to a distinct taxon, the Odontopterygiformes. In most recent studies, the pseudo-toothed birds are referred to the family Pelagornithidae inside the Pelecaniformes. Here, I perform a cladistic analysis with five taxa of the pseudo-toothed birds including two undescribed new species from the Early Tertiary of Morocco. The present hypothesis strongly supports a sister group relationship of pseudo-toothed birds (Odontopterygiformes) and waterfowls (Anseriformes). The Odontoanserae (Odontopterygiformes plus Anseriformes) are the sister group of Neoaves. The placement of the landfowls (Galliformes) as the sister taxon of all other neognathous birds does not support the consensus view that the Galloanserae (Galliformes plus Anseriformes) are monophyletic.

Generic redescription, two new species, and a key to the species of the cicada genus Ariasa Distant, 1905 with the description of a new genus (Hemiptera: Cicadidae: Cicadinae: Fidicinini).

PubMed

Sanborn, Allen F

2016-07-13

The cicada genus Ariasa Distant, 1905 is redescribed.  Ariasa albimaculosa n. sp. is described from Colombia and A. bartletti n. sp. is described from Peru.  The current 14 species of Ariasa are listed along with their synonymies, known distribution of each species, and a key to the species is provided.  The first records of Ariasa bilaqueata (Uhler, 1903) for Peru and French Guiana are provided. Cracenpsaltria brasiliorum (Kirkaldy, 1909) rev. stat., n. comb. is determined to be the correct name for the taxon Cicada marginata Olivier, 1790 and the new genus Cracenpsaltria n. gen. is erected for the taxon.  The distribution of C. brasiliorum rev. stat., n. comb. is expanded to include Bolivia and Peru.

Defining operational taxonomic units using DNA barcode data

PubMed Central

Blaxter, Mark; Mann, Jenna; Chapman, Tom; Thomas, Fran; Whitton, Claire; Floyd, Robin; Abebe, Eyualem

2005-01-01

Abstract The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene ‘for’ speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to ‘species’, and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data. PMID:16214751

Review of taxonomy, geographic distribution, and paleoenvironments of Azhdarchidae (Pterosauria)

PubMed Central

Averianov, Alexander

2014-01-01

Abstract The taxonomy, geographic distribution, and paleoenvironmental context of azhdarchid pterosaurs are reviewed. All purported pteranodontid, tapejarid, and azhdarchid specimens from the Cenomanian Kem Kem beds of Morocco are referred to a single azhdarchid taxon, Alanqa saharica. The four proposed autapomorphies of Eurazhdarcho langendorfensis from the lower Maastrichtian Sebeş Formation of Romania are based on misinterpretations of material and this taxon is likely a subjective junior synonym of Hatzegopteryx thambema. Among 54 currently reported azhdarchid occurrences (51 skeletal remains and 3 tracks) 13% are from lacustrine deposits, 17% from fluvial plain deposits, 17% from coastal plain deposits, 18% from estuarine and lagoonal deposits, and 35% from costal marine deposits. Azhdarchids likely inhabited a variety of environments, but were abundant near large lakes and rivers and most common in nearshore marine paleoenvironments. PMID:25152671

Of Paleo-Genes and Perch: What if an “Alien” Is Actually a Native?

PubMed Central

Stager, J. Curt; Sporn, Lee Ann; Johnson, Melanie; Regalado, Sean

2015-01-01

Documenting whether a biotic taxon is native or alien to an ecosystem has theoretical value for ecological and evolutionary studies, and has practical value because it can potentially identify a taxon as a desirable component of an ecosystem or target it for removal. In some cases, however, such background information is inadequate or unavailable. Here we use paleo-DNA to re-evaluate the historical status of yellow perch in the 6 million acre Adirondack State Park of northern New York. Yellow perch DNA in a 2200-year sediment record reveals a long-term native status for these supposedly alien fish and challenges assumptions that they necessarily exclude native trout from upland lakes. Similar approaches could be applied to other species with uncertain historical distributions and could help to identify unrecognized pockets of biodiversity. PMID:25751263

Three new species of Grouvellinus Champion, 1923 from Maliau Basin, Sabah, Borneo, discovered by citizen scientists during the first Taxon Expedition (Insecta, Coleoptera, Elmidae)

PubMed Central

Freitag, Hendrik; Pangantihon, Clister V.; Njunjić, Iva

2018-01-01

Abstract Further results are presented of the first field course at Maliau Basin, Malaysian Borneo organized by Taxon Expeditions, an organization which enables citizen scientists to be directly involved in taxonomic discoveries. Three new species of the aquatic beetle genus Grouvellinus Champion, 1923, namely G. leonardodicaprioi sp. n., G. andrekuipersi sp. n., and G. quest sp. n. were collected jointly by the citizen scientists and taxonomists during the fieldwork in Maliau Basin. Material was mainly sampled from sandstone bottom rocks of blackwater streams at altitudes between 900 m and 1,000 m using fine-meshed hand-nets. The genus is widely distributed in the Oriental and Palearctic regions, but these are the first records from the island of Borneo. PMID:29740222

Sedum tarokoense (Crassulaceae), a new species from a limestone area in Taiwan.

PubMed

Lu, Chang-Tse; Lin, Hung-Wen; Liou, Wei-Ting; Wang, Jenn-Che

2013-12-01

An unknown Sedum was found from the limestone region in Taiwan. After a detailed comparison with other congeners in Taiwan and neighboring countries, we identified this plant as a new species. This new taxon resembles S. nokoense Yamamoto, S. alfredii Hance, and S. uniflorum Hook. & Arn. subsp. oryzifolium (Makino) H. Ohba, but differs in leaf shape, sepal morphology, and seed testa micro-morphology. Ecologically, this new taxon occurs exclusively on limestone, while S. nokoense and S. alfredii grow in non-limestone areas and S. uniflorum subsp. oryzifolium is only found on sandy seashores. Sedum tarokoense H.W. Lin & J.C. Wang is described as a new species. We provide a description, line drawing, and distribution map, as well as photograph, a key and a table to distinguish S. tarokoense from its related species.

Real-Time PCR-Based Quantitation Method for the Genetically Modified Soybean Line GTS 40-3-2.

PubMed

Kitta, Kazumi; Takabatake, Reona; Mano, Junichi

2016-01-01

This chapter describes a real-time PCR-based method for quantitation of the relative amount of genetically modified (GM) soybean line GTS 40-3-2 [Roundup Ready(®) soybean (RRS)] contained in a batch. The method targets a taxon-specific soybean gene (lectin gene, Le1) and the specific DNA construct junction region between the Petunia hybrida chloroplast transit peptide sequence and the Agrobacterium 5-enolpyruvylshikimate-3-phosphate synthase gene (epsps) sequence present in GTS 40-3-2. The method employs plasmid pMulSL2 as a reference material in order to quantify the relative amount of GTS 40-3-2 in soybean samples using a conversion factor (Cf) equal to the ratio of the RRS-specific DNA to the taxon-specific DNA in representative genuine GTS 40-3-2 seeds.

Do Patterns of Bacterial Diversity along Salinity Gradients Differ from Those Observed for Macroorganisms?

PubMed Central

Zhang, Yong; Shen, Ji; van der Gast, Christopher; Hahn, Martin W.; Wu, Qinglong

2011-01-01

It is widely accepted that biodiversity is lower in more extreme environments. In this study, we sought to determine whether this trend, well documented for macroorganisms, also holds at the microbial level for bacteria. We used denaturing gradient gel electrophoresis (DGGE) with phylum-specific primers to quantify the taxon richness (i.e., the DGGE band numbers) of the bacterioplankton communities of 32 pristine Tibetan lakes that represent a broad salinity range (freshwater to hypersaline). For the lakes investigated, salinity was found to be the environmental variable with the strongest influence on the bacterial community composition. We found that the bacterial taxon richness in freshwater habitats increased with increasing salinity up to a value of 1‰. In saline systems (systems with >1‰ salinity), the expected decrease of taxon richness along a gradient of further increasing salinity was not observed. These patterns were consistently observed for two sets of samples taken in two different years. A comparison of 16S rRNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in the freshwater lake. These results suggest that different evolutionary forces may act on bacterial populations in freshwater and hypersaline lakes on the Tibetan Plateau, potentially resulting in different community structures and diversity patterns. PMID:22125616

A sequential approach using genetic and morphological analyses to test species status: the case of United States federally endangered Agalinis acuta (Orobanchaceae).

PubMed

Pettengill, James B; Neel, Maile C

2011-05-01

Given that inaccurate taxonomy can have negative consequences for species of conservation concern and result in erroneous conclusions regarding macroecological patterns, efficient methods for resolving taxonomic uncertainty are essential. The primary objective of this study was to assess the evolutionary distinctiveness of the federally endangered plant species Agalinis acuta (Orobanchaceae) to ensure it represents a distinct taxon warranting protection under the United States Endangered Species Act. We describe and implement a sequential approach that begins with the most restrictive criteria of genealogical exclusivity within which we first conducted a phylogenetic analysis based on six chloroplast DNA loci assayed from multiple representatives of five putative species. Because of the possibility that incomplete lineage sorting is responsible for the lack of genealogical exclusivity among A. acuta individuals, we then conducted intensive population level analyses based on 21 microsatellite loci and 61 morphological traits. The distinctiveness of A. acuta from Agalinis decemloba and Agalinis tenella was not supported under the genealogical species concept. The results from the analyses of microsatellite loci and morphological characters evaluated under alternative species concepts also did not support the distinctiveness of A. acuta from A. decemloba . Through this successive approach, we found insufficient evidence to support the evolutionary distinctiveness of the listed taxon A. acuta . We recommend that it be synonymized under A. decemloba and also conclude that the taxon that would now include A. acuta is deserving of protection under the Endangered Species Act.

Delineating Species with DNA Barcodes: A Case of Taxon Dependent Method Performance in Moths

PubMed Central

Kekkonen, Mari; Mutanen, Marko; Kaila, Lauri; Nieminen, Marko; Hebert, Paul D. N.

2015-01-01

The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work. PMID:25849083

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

PubMed Central

Parks, Matthew B; Wickett, Norman J; Alverson, Andrew J

2018-01-01

Abstract Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available. PMID:29040712

New species of Rotundomys (Cricetinae) from the Late Miocene of Spain and its bearing on the phylogeny of Cricetulodon and Rotundomys.

PubMed

López-Antoñanzas, Raquel; Peláez-Campomanes, Pablo; Álvarez-Sierra, Ángeles

2014-01-01

The material of Rotundomys (Rodentia, Cricetinae) from the Late Miocene fossiliferous complex of Cerro de los Batallones (Madrid, Spain) is described and compared with all species currently placed in the genera Rotundomys and Cricetulodon. Both the morphology and size variation encompassed in the collection of specimens from Batallones suggest they belong to a single taxon different from the other known species of these genera. A new species Rotundomys intimus sp. nov. is, therefore, named for it. A cladistic analysis, which is the first ever published concernig these taxa, has been conducted to clear up the phylogenetic position of the new species. Our results suggest that Rotundomys intimus sp. nov. inserts between R. mundi and R. sabatieri as a relatively primitive taxon inside the clade Rotundomys. The new taxon is more derived than R. mundi in having a transversal connection between the metalophulid and the anterolophulid on some m1 but more primitive than R. sabatieri and the most evolved species of Rotundomys (R. montisrotuni +R.bressanus) in its less developed lophodonty showing distinct cusps, shallower valleys, and the presence of a subdivided anteroloph on the M1. The species of Cricetulodon do not form a monophyletic group. As a member of Rotundomys, Rotundomys intimus sp. nov. is more derived than all of these taxa in its greater lophodonty and the complete loss of the anterior protolophule, mesolophs, and mesolophids.

Assessment of DNA degradation induced by thermal and UV radiation processing: implications for quantification of genetically modified organisms.

PubMed

Ballari, Rajashekhar V; Martin, Asha

2013-12-01

DNA quality is an important parameter for the detection and quantification of genetically modified organisms (GMO's) using the polymerase chain reaction (PCR). Food processing leads to degradation of DNA, which may impair GMO detection and quantification. This study evaluated the effect of various processing treatments such as heating, baking, microwaving, autoclaving and ultraviolet (UV) irradiation on the relative transgenic content of MON 810 maize using pRSETMON-02, a dual target plasmid as a model system. Amongst all the processing treatments examined, autoclaving and UV irradiation resulted in the least recovery of the transgenic (CaMV 35S promoter) and taxon-specific (zein) target DNA sequences. Although a profound impact on DNA degradation was seen during the processing, DNA could still be reliably quantified by Real-time PCR. The measured mean DNA copy number ratios of the processed samples were in agreement with the expected values. Our study confirms the premise that the final analytical value assigned to a particular sample is independent of the degree of DNA degradation since the transgenic and the taxon-specific target sequences possessing approximately similar lengths degrade in parallel. The results of our study demonstrate that food processing does not alter the relative quantification of the transgenic content provided the quantitative assays target shorter amplicons and the difference in the amplicon size between the transgenic and taxon-specific genes is minimal. Copyright © 2013 Elsevier Ltd. All rights reserved.

New Species of Rotundomys (Cricetinae) from the Late Miocene of Spain and Its Bearing on the Phylogeny of Cricetulodon and Rotundomys

PubMed Central

López-Antoñanzas, Raquel; Peláez-Campomanes, Pablo; Álvarez-Sierra, Ángeles

2014-01-01

The material of Rotundomys (Rodentia, Cricetinae) from the Late Miocene fossiliferous complex of Cerro de los Batallones (Madrid, Spain) is described and compared with all species currently placed in the genera Rotundomys and Cricetulodon. Both the morphology and size variation encompassed in the collection of specimens from Batallones suggest they belong to a single taxon different from the other known species of these genera. A new species Rotundomys intimus sp. nov. is, therefore, named for it. A cladistic analysis, which is the first ever published concernig these taxa, has been conducted to clear up the phylogenetic position of the new species. Our results suggest that Rotundomys intimus sp. nov. inserts between R. mundi and R. sabatieri as a relatively primitive taxon inside the clade Rotundomys. The new taxon is more derived than R. mundi in having a transversal connection between the metalophulid and the anterolophulid on some m1 but more primitive than R. sabatieri and the most evolved species of Rotundomys (R. montisrotuni +R.bressanus) in its less developed lophodonty showing distinct cusps, shallower valleys, and the presence of a subdivided anteroloph on the M1. The species of Cricetulodon do not form a monophyletic group. As a member of Rotundomys, Rotundomys intimus sp. nov. is more derived than all of these taxa in its greater lophodonty and the complete loss of the anterior protolophule, mesolophs, and mesolophids. PMID:25389967

Joint US/Russian Studies of Population Exposures Resulting from Nuclear Production Activities in the Southern Urals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Napier, Bruce A.

2014-01-01

Beginning in 1948, the Soviet Union initiated a program for production of nuclear materials for a weapons program. The first facility for production of plutonium was constructed in the central portion of the country east of the southern Ural Mountains, about halfway between the major industrial cities of Ekaterinburg and Chelyabinsk. The facility now known as the Mayak Production Association and its associated town, now known as Ozersk, were built to irradiate uranium in reactors, separate the resulting plutonium in reprocessing plants, and prepare plutonium metal. The rush to production, coupled with inexperience in handling radioactive materials, lead to largemore » radiation exposures, not only to the workers in the facilities, but also to the surrounding public. Fuel processing started with no controls on releases, and fuel dissolution and accidents in reactors resulted in release of about 37 PBq (1015 Bq) of 131I between 1948 and 1967. Designed disposals of low- and intermediate-level liquid radioactive wastes, and accidental releases via cooling water from tank farms of high-level liquid radioactive wastes, into the small Techa River caused significant contamination and exposures to residents of numerous small riverside villages downstream of the site. Discovery of the magnitude of the aquatic contamination in late 1951 caused revisions to the waste handling regimes, but not before over 200 PBq of radionuclides (with large contributions of 90Sr and 137Cs) were released. Liquid wastes were diverted to tiny Lake Karachay (which today holds over 4 EBq); cooling water was stopped in the tank farms. In 1957, one of the tanks in the tank farm overheated and exploded; over 70 PBq, disproportionately 90Sr, was blown over a large area to the northeast of the site; a large area was contaminated and many villages evacuated. This area today is known as the East Urals Radioactive Trace (EURT). Each of these releases was significant; together they have created a group of cohorts unrivaled in the world for their chronic, low-dose-rate radiation exposure. The 26,000 workers at Mayak were highly exposed to external gamma and inhaled plutonium. A cohort of individuals raised as children in Ozersk is under evaluation for their exposures to radioiodine. The Techa River Cohort consists of over 30,000 people who were born before the start of exposure in 1949 and lived along the Techa River. The Techa River Offspring Cohort consists of about 21,000 persons born to one or more exposed parents of this group - many of whom also lived along the contaminated river. The EURT Cohort consists of about 18,000 people who were evacuated from the EURT soon after the 1957 explosion and another 8000 who remained. These groups together are the focus of dose reconstruction and epidemiological studies funded by the US, Russia, and the European Union to address the question “Are doses delivered at low dose rates as effective in producing health effects as the same doses delivered at high dose rates?”« less

43 CFR 11.72 - Quantification phase-baseline services determination.

Code of Federal Regulations, 2010 CFR

2010-10-01

... taxonomist or systematic biologist, who has access to a major systematic biology collection for that taxon... time it should be transferred to a major systematic biology collection; or (iii) In the case of a...

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2012 CFR

2012-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2014 CFR

2014-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2013 CFR

2013-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

Code of Federal Regulations, 2011 CFR

2011-01-01

... life history; (6) Native and world distribution; (7) Distribution in the United States, if any... impacts (e.g., impacts on ecosystem processes, natural community composition or structure, human health...

Order XIII. Pseudonocardineae ord.nov.

USDA-ARS?s Scientific Manuscript database

The formal description of the actinobacterial higher taxon, the suborder Pseudonocardineae, is presented. The differential morphological and chemotaxonomic characteristics and diagnostic signature nucleotides from the 16S rRNA gene for the families Actinosynnemataceae and Pseudonocardiaceae in the ...

Accumulation of /sup 60/Co by freshwater plants under natural conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trapeznikov, A.V.; Trapeznikova, V.N.

1979-03-01

The study of /sup 60/Co accumulation by aquatic plants is of interest in finding effective bioindicators for radioactive pollution of nuclear power station cooling ponds. In this respect, /sup 60/Co accumulation was studied in four species of higher aquatic plants most commonly found in the Urals: water thyme (Elodea canadensis), hornwort (Ceratophyllum demersum), lesser duckweed (Lemna minor), and fennel pondweed (Potamogeton pectinatus). The /sup 60/Co accumulation coefficients in the plants studied reached considerable values. The data obtained demonstrate that plants such as hornwort and water thyme with /sup 60/Co accumulation coefficients of 33,500 and 21,500, respectively, may be recommended asmore » bioindicators for these radionuclides in the water bodies polluted with radioactive cobalt.« less

Monitoring of waste disposal in deep geological formations

NASA Astrophysics Data System (ADS)

German, V.; Mansurov, V.

2003-04-01

In the paper application of kinetic approach for description of rock failure process and waste disposal microseismic monitoring is advanced. On base of two-stage model of failure process the capability of rock fracture is proved. The requests to monitoring system such as real time mode of data registration and processing and its precision range are formulated. The method of failure nuclei delineation in a rock masses is presented. This method is implemented in a software program for strong seismic events forecasting. It is based on direct use of the fracture concentration criterion. The method is applied to the database of microseismic events of the North Ural Bauxite Mine. The results of this application, such as: efficiency, stability, possibility of forecasting rockburst are discussed.

Fauna Europaea: Neuropterida (Raphidioptera, Megaloptera, Neuroptera)

PubMed Central

2015-01-01

Abstract Fauna Europaea provides a public web-service with an index of scientific names of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. For Neuropterida, data from three Insect orders (Raphidioptera, Megaloptera, Neuroptera), comprising 15 families and 397 species, are included. PMID:25941450

Discovery of KPS-1b, a Transiting Hot-Jupiter, with an Amateur Telescope Setup (Abstract)

NASA Astrophysics Data System (ADS)

Benni, P.; Burdanov, A.; Krushinsky, V.; Sokov, E.

2018-06-01

(Abstract only) Using readily available amateur equipment, a wide-field telescope (Celestron RASA, 279 mm f/2.2) coupled with a SBIG ST-8300M camera was set up at a private residence in a fairly light polluted suburban town thirty miles outside of Boston, Massachusetts. This telescope participated in the Kourovka Planet Search (KPS) prototype survey, along with a MASTER-II Ural wide field telescope near Yekaterinburg, Russia. One goal was to determine if higher resolution imaging ( 2 arcsec/pixel) with much lower sky coverage can practically detect exoplanet transits compared to the successful very wide-field exoplanet surveys (KELT, XO, WASP, HATnet, TrES, Qatar, etc.) which used an array of small aperture telescopes coupled to CCDs.

Polychronous Zirconology of Navysh Volcanics of the Ai Formation (Southern Urals)

NASA Astrophysics Data System (ADS)

Krasnobaev, A. A.; Puchkov, V. N.; Sergeeva, N. D.

2018-01-01

In order to resolve the age of Navysh volcanics (NV), which is usually attributed to the Lower Riphean of the Ai Formation, we have used geochronological, petrologic, and mineralogical methods of zirconology, apart from the SHRIMP isotopic data of single zircon grains. Moreover, TIMS isotope age analyses have been conducted, the results of which can be regarded as both controlling and providing the most correct information. The TIMS and SHRIMP data make it possible to suggest a polychronous character of the NV, which include not only Riphean, but also Paleozoic groups of volcanics. In this situation, an assessment of the scales of such polychroneity of NV and, correspondingly, of the Ai Formation as a whole becomes urgent.

Aquatic Life Benchmarks and Ecological Risk Assessments for Registered Pesticides

EPA Pesticide Factsheets

Each Aquatic Life Benchmark is based on the most sensitive, scientifically acceptable toxicity endpoint available to EPA for a given taxon (for example, freshwater fish) of all scientifically acceptable toxicity data available to EPA.

COMPARISON OF ECOLOGICAL COMMUNITIES: THE PROBLEM OF SAMPLE REPRESENTATIVENESS

EPA Science Inventory

Obtaining an adequate, representative sample of ecological communities to make taxon richness (TR) or compositional comparisons among sites is a continuing challenge. Sample representativeness literally means the similarity in species composition and relative abundance between a ...

Examining ethnic differences in self-reported psychopathic traits among Portuguese male juvenile offenders.

PubMed

Pechorro, Pedro; Poiares, Carlos; Barroso, Ricardo; Nunes, Cristina; Jesus, Saul Neves

2015-01-01

The aim of the present study was to analyze differences regarding psychopathic traits and related constructs in male youths of diverse ethnic backgrounds. The participants were 216 male youths from the Juvenile Detention Centers of the Portuguese Ministry of Justice (White Europeans group: n = 108; ethnic minorities group: n = 108). Psychopathy was measured by the Antisocial Process Screening Device and the Child and Adolescent Taxon Scale. The results showed that no differences were found between ethnic groups regarding psychopathic traits and psychopathy taxon. Independent of ethnic group membership, psychopathic trait scores were significantly associated with behavioral problems, conduct disorder, self-reported delinquency, seriousness of criminal activity, age of criminal activity onset, and age at first trouble with the law. The present study adds support to the literature regarding youth psychopathic traits and supports the psychopathy construct as universally and interculturally consistent. © The Author(s) 2013.

First Miocene rodent from Lebanon provides the 'missing link' between Asian and African gundis (Rodentia: Ctenodactylidae).

PubMed

López-Antoñanzas, Raquel; Knoll, Fabien; Maksoud, Sibelle; Azar, Dany

2015-08-07

Ctenodactylinae (gundis) is a clade of rodents that experienced, in Miocene time, their greatest diversification and widest distribution. They expanded from the Far East, their area of origin, to Africa, which they entered from what would become the Arabian Peninsula. Questions concerning the origin of African Ctenodactylinae persist essentially because of a poor fossil record from the Miocene of Afro-Arabia. However, recent excavations in the Late Miocene of Lebanon have yielded a key taxon for our understanding of these issues. Proafricanomys libanensis nov. gen. nov. sp. shares a variety of dental characters with both the most primitive and derived members of the subfamily. A cladistic analysis demonstrates that this species is the sister taxon to a clade encompassing all but one of the African ctenodactylines, plus a southern European species of obvious African extraction. As such, Proafricanomys provides the 'missing link' between the Asian and African gundis.

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium

PubMed Central

Chase, Alexander B.; Arevalo, Philip; Polz, Martin F.; Berlemont, Renaud; Martiny, Jennifer B. H.

2016-01-01

Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus Curtobacterium, as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominantly associates it as the causal pathogen in the agricultural crops of dry beans. Therefore, we sought to investigate whether the abundance of this genus was because of its role as a plant pathogen or another ecological role. By collating >24,000 16S rRNA sequences with 120 genomes across the Microbacteriaceae family, we show that Curtobacterium has a global distribution with a predominant presence in soil ecosystems. Moreover, this genus harbors a high diversity of genomic potential for the degradation of carbohydrates, specifically with regards to structural polysaccharides. We conclude that Curtobacterium may be responsible for the degradation of organic matter within litter communities. PMID:27920771

Coryneform bacteria in infectious diseases: clinical and laboratory aspects.

PubMed Central

Coyle, M B; Lipsky, B A

1990-01-01

Coryneform isolates from clinical specimens frequently cannot be identified by either reference laboratories or research laboratories. Many of these organisms are skin flora that belong to a large number of taxonomic groups, only 40% of which are in the genus Corynebacterium. This review provides an update on clinical presentations, microbiological features, and pathogenic mechanisms of infections with nondiphtheria Corynebacterium species and other pleomorphic gram-positive rods. The early literature is also reviewed for a few coryneforms, especially those whose roles as pathogens are controversial. Recognition of newly emerging opportunistic coryneforms is dependent on sound identification schemes which cannot be developed until cell wall analyses and nucleic acid studies have defined the taxonomic groups and all of the reference strains within each taxon have been shown by molecular methods to be authentic members. Only then can reliable batteries of biochemical tests be selected for distinguishing each taxon. PMID:2116939

An enigmatic aquatic snake from the Cenomanian of Northern South America

PubMed Central

Carrillo-Briceño, Jorge D.; Neenan, James M.

2016-01-01

We report the first record of a snake from the Cretaceous of northern South America. The remains come from the La Luna Formation (La Aguada Member, Cenomanian of Venezuela) and consist of several vertebrae, which belong to the precloacal region of the vertebral column. Comparisons to extant and extinct snakes show that the remains represent a new taxon, Lunaophis aquaticus gen. et sp nov. An aquatic mode of life is supported by the ventral position of the ribs, indicating a laterally compressed body. The systematic relationships of this new taxon are difficult to determine due to the scarcity of fossil material; it is, however, a representative of an early lineage of snakes that exploited tropical marine pelagic environments, as reflected by the depositional conditions of the La Aguada Member. Lunaophis is also the first aquatic snake from the Cenomanian found outside of the African and European Tethyan and Boreal Zones. PMID:27257536

First Miocene rodent from Lebanon provides the 'missing link' between Asian and African gundis (Rodentia: Ctenodactylidae)

PubMed Central

López-Antoñanzas, Raquel; Knoll, Fabien; Maksoud, Sibelle; Azar, Dany

2015-01-01

Ctenodactylinae (gundis) is a clade of rodents that experienced, in Miocene time, their greatest diversification and widest distribution. They expanded from the Far East, their area of origin, to Africa, which they entered from what would become the Arabian Peninsula. Questions concerning the origin of African Ctenodactylinae persist essentially because of a poor fossil record from the Miocene of Afro-Arabia. However, recent excavations in the Late Miocene of Lebanon have yielded a key taxon for our understanding of these issues. Proafricanomys libanensis nov. gen. nov. sp. shares a variety of dental characters with both the most primitive and derived members of the subfamily. A cladistic analysis demonstrates that this species is the sister taxon to a clade encompassing all but one of the African ctenodactylines, plus a southern European species of obvious African extraction. As such, Proafricanomys provides the 'missing link' between the Asian and African gundis. PMID:26250050

A new South American Miocene species of 'one-holed' sand dollar (Echinoidea: Clypeasteroida: Monophorasteridae).

PubMed

Mooi, Rich; Martínez, Sergio A; Río, Claudia J Del

2016-10-02

A new species of monophorasterid sand dollar, Monophoraster telfordi n. sp., is described from the Early Miocene basal horizons of the Chenque Formation of Patagonia, Santa Cruz Province, in southern Argentina. The new taxon raises the number of known species in the family to six, and represents first unequivocal record of the genus for the Early Miocene of South America. It is therefore also the oldest member of the genus. M. telfordi is characterized by its test width to length ratio, which is much higher than for the other two described species in the genus, but less than that known for the extremely wide members of the sister taxon, Amplaster. M. telfordi is also unusual among monophorasterids in lacking broad continuity between basicoronal and post-basicoronal plates in the oral interambulacra. A key is provided to all the known species of Monophorasteridae.

Forecasting model of Corylus, Alnus, and Betula pollen concentration levels using spatiotemporal correlation properties of pollen count.

PubMed

Nowosad, Jakub; Stach, Alfred; Kasprzyk, Idalia; Weryszko-Chmielewska, Elżbieta; Piotrowska-Weryszko, Krystyna; Puc, Małgorzata; Grewling, Łukasz; Pędziszewska, Anna; Uruska, Agnieszka; Myszkowska, Dorota; Chłopek, Kazimiera; Majkowska-Wojciechowska, Barbara

The aim of the study was to create and evaluate models for predicting high levels of daily pollen concentration of Corylus , Alnus , and Betula using a spatiotemporal correlation of pollen count. For each taxon, a high pollen count level was established according to the first allergy symptoms during exposure. The dataset was divided into a training set and a test set, using a stratified random split. For each taxon and city, the model was built using a random forest method. Corylus models performed poorly. However, the study revealed the possibility of predicting with substantial accuracy the occurrence of days with high pollen concentrations of Alnus and Betula using past pollen count data from monitoring sites. These results can be used for building (1) simpler models, which require data only from aerobiological monitoring sites, and (2) combined meteorological and aerobiological models for predicting high levels of pollen concentration.

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium.

PubMed

Chase, Alexander B; Arevalo, Philip; Polz, Martin F; Berlemont, Renaud; Martiny, Jennifer B H

2016-01-01

Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus Curtobacterium , as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominantly associates it as the causal pathogen in the agricultural crops of dry beans. Therefore, we sought to investigate whether the abundance of this genus was because of its role as a plant pathogen or another ecological role. By collating >24,000 16S rRNA sequences with 120 genomes across the Microbacteriaceae family, we show that Curtobacterium has a global distribution with a predominant presence in soil ecosystems. Moreover, this genus harbors a high diversity of genomic potential for the degradation of carbohydrates, specifically with regards to structural polysaccharides. We conclude that Curtobacterium may be responsible for the degradation of organic matter within litter communities.

Serendipity at the Smithsonian: The 107-year journey of Rhipidocyrtus muiri Falin & Engel, new genus and species (Ripidiinae, Ripidiini), from jungle beast to valid taxon

PubMed Central

Falin, Zachary H.; Engel, Michael S.

2014-01-01

Abstract The long and tortuous history of an enigmatic and rare new genus and species of ripidiine wedge beetle (Ripiphoridae: Ripidiinae: Ripidiini) from Borneo is discussed and the taxon described and figured as Rhipidocyrtus muiri Falin & Engel, gen. n. and sp. n. The holotype male, and only known specimen, was collected 107 years ago in Borneo but subsequent to this it was transferred among early researchers in the early 1900s. The specimen was dissected and many portions slide mounted, but these were disassociated from the pinned body for more than a generation. A happenstance encounter led to the rediscovery and reassociation of the body and slide-mounted abdomen and other sclerites in 2011, and to its eventual description herein. Ripidiine diversity is briefly discussed and comparisons made between Rhipidocyrtus and other members of the subfamily. PMID:25061398

Taxometric analyses of pedophilia utilizing self-report, behavioral, and sexual arousal indicators.

PubMed

Stephens, Skye; Leroux, Elisabeth; Skilling, Tracey; Cantor, James M; Seto, Michael C

2017-11-01

Pedophilia refers to the recurrent, intense sexual interest in prepubescent children who, by definition, have not developed any secondary sex characteristics. Researchers have begun to investigate whether persons with pedophilia are qualitatively different from those without pedophilia (pedophilia is a taxon) or if people vary in their level of sexual interest toward children (pedophilia is dimensional). Two relatively small studies have previously attempted to address this question, but produced conflicting results. The present study built on these studies with a substantially larger sample of 2,227 men who committed sexual offenses and were assessed at a sexual behavior clinic. The present study also examined a broader range of measures more closely approximating the diagnostic criteria for pedophilic disorder, including phallometric assessment of sexual arousal patterns. The results of 3 taxometric analyses did not find support for the assertion that pedophilia is a taxon. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Serendipity at the Smithsonian: The 107-year journey of Rhipidocyrtus muiri Falin & Engel, new genus and species (Ripidiinae, Ripidiini), from jungle beast to valid taxon.

PubMed

Falin, Zachary H; Engel, Michael S

2014-01-01

THE LONG AND TORTUOUS HISTORY OF AN ENIGMATIC AND RARE NEW GENUS AND SPECIES OF RIPIDIINE WEDGE BEETLE (RIPIPHORIDAE: Ripidiinae: Ripidiini) from Borneo is discussed and the taxon described and figured as Rhipidocyrtus muiri Falin & Engel, gen. n. and sp. n. The holotype male, and only known specimen, was collected 107 years ago in Borneo but subsequent to this it was transferred among early researchers in the early 1900s. The specimen was dissected and many portions slide mounted, but these were disassociated from the pinned body for more than a generation. A happenstance encounter led to the rediscovery and reassociation of the body and slide-mounted abdomen and other sclerites in 2011, and to its eventual description herein. Ripidiine diversity is briefly discussed and comparisons made between Rhipidocyrtus and other members of the subfamily.

An expanded nuclear phylogenomic PCR toolkit for Sapindales1

PubMed Central

Collins, Elizabeth S.; Gostel, Morgan R.; Weeks, Andrea

2016-01-01

Premise of the study: We tested PCR amplification of 91 low-copy nuclear gene loci in taxa from Sapindales using primers developed for Bursera simaruba (Burseraceae). Methods and Results: Cross-amplification of these markers among 10 taxa tested was related to their phylogenetic distance from B. simaruba. On average, each Sapindalean taxon yielded product for 53 gene regions (range: 16–90). Arabidopsis thaliana (Brassicales), by contrast, yielded product for two. Single representatives of Anacardiaceae and Rutacaeae yielded 34 and 26 products, respectively. Twenty-six primer pairs worked for all Burseraceae species tested if highly divergent Aucoumea klaineana is excluded, and eight of these amplified product in every Sapindalean taxon. Conclusions: Our study demonstrates that customized primers for Bursera can amplify product in a range of Sapindalean taxa. This collection of primer pairs, therefore, is a valuable addition to the toolkit for nuclear phylogenomic analyses of Sapindales and warrants further investigation. PMID:28101434

Evolution and Functional Morphology of the Proboscis in Kalyptorhynchia (Platyhelminthes).

PubMed

Smith, Julian P S; Litvaitis, Marian K; Gobert, Stefan; Uyeno, Theodore; Artois, Tom

2015-08-01

Predatory flatworms belonging to the taxon Kalyptorhynchia are characterized by an anterior muscular proboscis that they use to seize prey. In many cases, the proboscis is armed with hooks, derived either from the extracellular matrix that surrounds the muscles or from intracellular deposits in the epithelium covering the proboscis. Glands associated with the proboscis reportedly are venomous; however, there are few direct tests of this hypothesis. This article reviews the structure and current knowledge of the function of the proboscis in the Kalyptorhynchia, points to areas in which the current understanding of phylogenetic relationships within this taxon is incongruent with our hypothesis of how the proboscis evolved, and addresses areas in need of further research, especially as regards functional morphology and biomechanics. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Global meta-analysis reveals low consistency of biodiversity congruence relationships.

PubMed

Westgate, Martin J; Barton, Philip S; Lane, Peter W; Lindenmayer, David B

2014-05-21

Knowledge of the number and distribution of species is fundamental to biodiversity conservation efforts, but this information is lacking for the majority of species on earth. Consequently, subsets of taxa are often used as proxies for biodiversity; but this assumes that different taxa display congruent distribution patterns. Here we use a global meta-analysis to show that studies of cross-taxon congruence rarely give consistent results. Instead, species richness congruence is highest at extreme spatial scales and close to the equator, while congruence in species composition is highest at large extents and grain sizes. Studies display highest variance in cross-taxon congruence when conducted in areas with dissimilar areal extents (for species richness) or latitudes (for species composition). These results undermine the assumption that a subset of taxa can be representative of biodiversity. Therefore, researchers whose goal is to prioritize locations or actions for conservation should use data from a range of taxa.

The latent structure of alcohol misuse in young adults: Do taxometric results differ as a function of prior criminal history?

PubMed

Walters, Glenn D

2015-12-01

The purpose of this study was to determine whether the latent structure of alcohol misuse is categorical or continuous in male and female adults with and without a history of prior criminal offending. Data from 3452 (1530 male, 1922 female) 27-to-32 year old members of the National Longitudinal Study of Adolescent to Adult Health (Add Health) were subjected to taxometric analysis using three nonredundant taxometric procedures--mean above minus below a cut (MAMBAC), maximum covariance (MAXCOV), and latent mode factor analysis (L-Mode). Analyses produced results consistent with categorical latent structure in males with a previous history of criminal offending but not in males without a previous history of criminal offending or females with or without a history of criminal offending. The findings from the other groups were indeterminate for the most part (i.e., neither categorical nor continuous). The presumptive taxon was validated by testing differences in age of onset and frequency of criminal arrest and drunkenness between the putative taxon and the upper portion of the complement. As predicted, all four validation outcomes were significantly worse in the taxon group. On the basis of these results it is concluded that alcohol misuse in young adults may have features of both categorical and continuous latent structure and that the categorical aspects are more prominent in males with a history of offending behavior. Additional research is required to determine which aspects and features of alcohol misuse are categorical and which aspects and features are continuous. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Macrochaete gen. nov. (Nostocales, Cyanobacteria), a taxon morphologically and molecularly distinct from Calothrix.

PubMed

Berrendero Gómez, Esther; Johansen, Jeffrey R; Kaštovský, Jan; Bohunická, Markéta; Čapková, Kateřina

2016-08-01

Historically, the genus Calothrix included all noncolonial, tapered, heterocytous filaments within the cyanobacteria. However, recent molecular phylogenies show that "Calothrix" defined in this sense represents five distinct clades. The type species of Calothrix is marine, with solitary basal heterocytes, no akinetes, and distal ends tapering abruptly into short hairs. We examined the morphology and phylogeny of 45 tapering cyanobacteria in the Rivulariaceae, including freshwater and marine representatives of both Calothrix (35 strains) and its sister taxon Rivularia (10 strains). The marine Calothrix fall into two lineages, but we lack the generitype and so cannot identify the clade corresponding to the type species. The freshwater and soil Calothrix fall into the C. parietina clade and are characterized by having a basal heterocyte, no akinetes, and gradual tapering-but not into a long hyaline hair. Macrochaete gen. nov. is a freshwater taxon sister to the Calothrix lineages but clearly separated from Rivularia. The species in this genus differ morphologically from Calothrix by their ability to produce two heteromorphic basal heterocytes and specific secondary structures of the 16S-23S ITS. An additional feature present in most species is the presence of a distal, long hyaline hair, but this character has incomplete penetrance due to its expression only under specific environmental conditions (low phosphate), and in one species appears to be lost. We recognize three species: M. psychrophila (type species) from cold environments (high mountains, Antarctica), M. santannae from wet walls of subtropical South America, and M. lichenoides, a phycobiont of lichens from Europe. © 2016 Phycological Society of America.

The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes).

PubMed

Hardman, Michael

2005-12-01

The relationships among families of catfishes are poorly understood and have yet to be the subject of a comprehensive investigation with molecular data. Existing phylogenetic hypotheses are based on morphological data and incompletely resolved. This study analyzed complete sequences of mitochondrial gene cytochrome b for 170 species from 29 of 33 extant families, and focused on the relationships of Ictaluridae to other catfishes. In addition to previous phylogenetic studies, the fossil record, paleogeography, biogeography, and distribution of extant catfish families collectively suggest the location (if extant) of the ictalurid sister taxon to be Northern or Eastern Asia. Of the extant catfishes currently native to this area and included in this analysis, parsimony and Bayesian likelihood analyses recovered Cranoglanis bouderius as the most proximal sister taxon of Ictaluridae. Seemingly, ictalurids and cranoglanidids represent another biogeographic component linking freshwater fishes of North America and eastern Asia, e.g., catostomids and paddlefishes. The results coupled with present-day catfish distributions and inferences from the fossil record collectively suggest the ancestor of Ictaluridae to have invaded freshwaters of North America at the close of the Cretaceous through northeastern Asia and northwestern North America. Other superfamilial nodes supported the results of previous phylogenetic studies of narrower taxonomic scope. Several novel relationships were recovered (including a clade composed of Pimelodidae, Pseudopimelodidae, and Heptapteridae) and these along with sources of systematic error are discussed. A broad sampling of Bagridae permitted an examination of intergeneric relationships within this family and in light of recent morphological and molecular studies.

Ecological equivalency as a tool for endangered species management.

PubMed

Searcy, Christopher A; Rollins, Hilary B; Shaffer, H Bradley

2016-01-01

The use of taxon substitutes for extinct or endangered species is a controversial conservation measure. We use the example of the endangered California tiger salamander (Ambystoma californiense; CTS), which is being replaced by hybrids with the invasive barred tiger salamander (Ambystoma mavortium), to illustrate a strategy for evaluating taxon substitutes based on their position in a multivariate community space. Approximately one-quarter of CTS's range is currently occupied by "full hybrids" with 70% nonnative genes, while another one-quarter is occupied by "superinvasives" where a specific set of 3/68 genes comprising 4% of the surveyed genome is nonnative. Based on previous surveys of natural CTS breeding ponds, we stocked experimental mesocosms with field-verified, realistic densities of tiger salamander larvae and their prey, and used these mesocosms to evaluate ecological equivalency between pure CTS, full hybrids, and superinvasives in experimental pond communities. We also included a fourth treatment with no salamanders present to evaluate the community effects of eliminating Ambystoma larvae altogether. We found that pure CTS and superinvasive larvae were ecologically equivalent, because their positions in the multivariate community space were statistically indistinguishable and they did not differ significantly along any univariate community axes. Full hybrids were ecologically similar, but not equivalent, to the other two genotypes, and the no-Ambystoma treatment was by far the most divergent. We conclude that, at least for the larval stage, superinvasives are adequate taxon substitutes for pure CTS and should probably be afforded protection under the Endangered Species Act. The proper conservation status for full hybrids remains debatable.

Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes.

PubMed

Bruder, Lena M; Dörkes, Marcel; Fuchs, Bernhard M; Ludwig, Wolfgang; Liebl, Wolfgang

2016-10-01

The gut microbiome represents a key contributor to human physiology, metabolism, immune function, and nutrition. Elucidating the composition and genetics of the gut microbiota under various conditions is essential to understand how microbes function individually and as a community. Metagenomic analyses are increasingly used to study intestinal microbiota. However, for certain scientific questions it is sufficient to examine taxon-specific submetagenomes, covering selected bacterial genera in a targeted manner. Here we established a new variant of fluorescence in situ hybridization (FISH) combined with fluorescence-activated cell sorting (FACS), providing access to the genomes of specific taxa belonging to the complex community of the intestinal microbiota. In contrast to standard oligonucleotide probes, the RNA polynucleotide probe used here, which targets domain III of the 23S rRNA gene, extends the resolution power in environmental samples by increasing signal intensity. Furthermore, cells hybridized with the polynucleotide probe are not subjected to harsh pretreatments, and their genetic information remains intact. The protocol described here was tested on genus-specifically labeled cells in various samples, including complex fecal samples from different laboratory mouse types that harbor diverse intestinal microbiota. Specifically, as an example for the protocol described here, RNA polynucleotide probes could be used to label Enterococcus cells for subsequent sorting by flow cytometry. To detect and quantify enterococci in fecal samples prior to enrichment, taxon-specific PCR and qPCR detection systems have been developed. The accessibility of the genomes from taxon-specifically sorted cells for subsequent molecular analyses was demonstrated by amplification of functional genes. Copyright © 2016 Elsevier GmbH. All rights reserved.

A New Baurusuchid (Crocodyliformes, Mesoeucrocodylia) from the Late Cretaceous of Brazil and the Phylogeny of Baurusuchidae

PubMed Central

Montefeltro, Felipe C.; Larsson, Hans C. E.; Langer, Max C.

2011-01-01

Background Baurusuchidae is a group of extinct Crocodyliformes with peculiar, dog-faced skulls, hypertrophied canines, and terrestrial, cursorial limb morphologies. Their importance for crocodyliform evolution and biogeography is widely recognized, and many new taxa have been recently described. In most phylogenetic analyses of Mesoeucrocodylia, the entire clade is represented only by Baurusuchus pachecoi, and no work has attempted to study the internal relationships of the group or diagnose the clade and its members. Methodology/Principal Findings Based on a nearly complete skull and a referred partial skull and lower jaw, we describe a new baurusuchid from the Vale do Rio do Peixe Formation (Bauru Group), Late Cretaceous of Brazil. The taxon is diagnosed by a suite of characters that include: four maxillary teeth, supratemporal fenestra with equally developed medial and anterior rims, four laterally visible quadrate fenestrae, lateral Eustachian foramina larger than medial Eustachian foramen, deep depression on the dorsal surface of pterygoid wing. The new taxon was compared to all other baurusuchids and their internal relationships were examined based on the maximum parsimony analysis of a discrete morphological data matrix. Conclusion The monophyly of Baurusuchidae is supported by a large number of unique characters implying an equally large morphological gap between the clade and its immediate outgroups. A complex phylogeny of baurusuchids was recovered. The internal branch pattern suggests two main lineages, one with a relatively broad geographical range between Argentina and Brazil (Pissarrachampsinae), which includes the new taxon, and an endemic clade of the Bauru Group in Brazil (Baurusuchinae). PMID:21765925

Vertebrate biochronology of late Triassic red beds in New Mexico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunt, A.P.

1989-09-01

Four vertebrate biochrons can be recognized in Late Triassic strata of New Mexico: (A) Metoposaurus-Rutiodon-Desmatosuchus-Calyptosuchus-Placerias occurs in the Los Esteros member of the Santa Rosa formation near Lamy and is less well known from the lower Petrified Forest Member of the Chinle Formation near San Ysidro, at Mesa del Oro, near Fort Wingate, at Ojo Huelos, and in the Joyita hills. (B) Anaschisma-Belodon-Typothorax-Desmatosuchus-Paratypothorax occurs in the lower Bull Canyon formation in Bull Canyon and near Tucumcari, in the Trujillo Formation near Tucumcari, and possibly in the Travesser Formation of the Dry Cimarron valley, the Petrified Forest Member near Carthage, andmore » the Garita Creek formation near Lamy and Conchas Lake. (C) Anaschisma-Belodon-Typothorax occurs in the upper Bull Canyon formation in Bull Canyon, in the upper Petrified Forest Member near San Ysidro, at Ghost Ranch, near Albuquerque (Correo Sandstone Bed), and possibly in the Sloan Canyon Formation of the Dry Cimarron valley. (D) Anaschisma-new phytosaur, cf. Typothorax-new sphenosuchian, occurs in the Redonda Formation near Tucumcari. The biochronologic ranges of significant vertebrate taxa within New Mexico follow: metoposaurs - Metoposaurus (A-B ), Anaschisma (B-D); phytosuars - Rutiodon (A), Belodon (B-C), new taxon (D); aetosaurs - Calyptosuchus (A), Desmatosuchus (A-B), Paratypothorax (B), Typothorax (B-D ); rauisuchians - Postosuchus (A-B), Chatterjeea (B-C); sphenosuchians - new taxon 1 (A), Hesperosuchus (B), new taxon 2 (D); dinosaurs - ornithischians (B), Coelophysis (C), other theropods (B-C); therapsids - Placerias (A), Pseudotriconodon (C). Biochron A may be Carnian in age, whereas biochrons B-D are probably early to middle ( ) Norian.« less

A new rhynchocephalian from the late jurassic of Germany with a dentition that is unique amongst tetrapods.

PubMed

Rauhut, Oliver W M; Heyng, Alexander M; López-Arbarello, Adriana; Hecker, Andreas

2012-01-01

Rhynchocephalians, the sister group of squamates (lizards and snakes), are only represented by the single genus Sphenodon today. This taxon is often considered to represent a very conservative lineage. However, rhynchocephalians were common during the late Triassic to latest Jurassic periods, but rapidly declined afterwards, which is generally attributed to their supposedly adaptive inferiority to squamates and/or Mesozoic mammals, which radiated at that time. New finds of Mesozoic rhynchocephalians can thus provide important new information on the evolutionary history of the group. A new fossil relative of Sphenodon from the latest Jurassic of southern Germany, Oenosaurus muehlheimensis gen. et sp. nov., presents a dentition that is unique amongst tetrapods. The dentition of this taxon consists of massive, continuously growing tooth plates, probably indicating a crushing dentition, thus representing a previously unknown trophic adaptation in rhynchocephalians. The evolution of the extraordinary dentition of Oenosaurus from the already highly specialized Zahnanlage generally present in derived rhynchocephalians demonstrates an unexpected evolutionary plasticity of these animals. Together with other lines of evidence, this seriously casts doubts on the assumption that rhynchocephalians are a conservative and adaptively inferior lineage. Furthermore, the new taxon underlines the high morphological and ecological diversity of rhynchocephalians in the latest Jurassic of Europe, just before the decline of this lineage on this continent. Thus, selection pressure by radiating squamates or Mesozoic mammals alone might not be sufficient to explain the demise of the clade in the Late Mesozoic, and climate change in the course of the fragmentation of the supercontinent of Pangaea might have played a major role.

Morphology, biometry, and taxonomy of freshwater and marine interstitial cyphoderia (cercozoa: euglyphida).

PubMed

Todorov, Milcho; Golemansky, Vassil; Mitchell, Edward A D; Heger, Thierry J

2009-01-01

Good taxonomy is essential for ecological, biogeographical, and evolutionary studies of any group of organisms. Therefore, we performed detailed light- and scanning electron microscopy investigations on the shell ultrastructure and biometric analyses of the morphometric variability of five freshwater and marine interstitial testate amoebae of the genus Cyphoderia (C. trochus var. amphoralis, C. ampulla, C. margaritacea var. major, C. compressa, and C. littoralis), isolated from different populations in Bulgaria and Switzerland. Our aims were (1) to clarify the morphological characteristics of these taxa, and (2) to compare the morphology of a given taxon (C. ampulla) among different locations in Bulgaria and Switzerland as a first step towards an assessment of the geographical variation within a supposedly cosmopolitan taxon. Four of the studied taxa are characterized by a well-expressed main-size class and by a small size range of all the characters and can be defined as size-monomorphic species. Based on these results, the following systematic changes are proposed: C. major (Penard, 1891) n. comb. (Syn.: C. margaritacea var. major (Penard, 1891) and C. amphoralis (Wailes & Penard, 1911) n. comb. (Syn.: C. trochus var. amphoralis (Wailes & Penard, 1911)). However, we also show significant morphological variability between the Swiss and Bulgarian populations of C. ampulla, suggesting the possible existence of more than one taxon within this species. Further studies are required to assess (1) if these two morphologically different taxa represent individual species, (2) if so, if more species exist, and if this diversity is due to limited distribution ranges (endemism) or if several closely related taxa occur together in different geographical areas.

An introduction to loricifera, cycliophora, and micrognathozoa.

PubMed

Kristensen, Reinhardt Møbjerg

2002-07-01

Loriciferans, cycliophorans and micrognathozoans are amongst the latest groups of animals to be discovered. Other than all being microscopic, they have very different body plans and are not closely related. Loriciferans were originally assigned to the Aschelminthes. However, both new molecular and ultrastructural researches have shown that Aschelminthes consist of two unrelated groups, Cycloneuralia and Gnathifera. Cycloneuralia may be included in the Ecdysozoa, including all molting invertebrates, and Gnathifera are more closely related to Platyhelminthes. The phylum Loricifera shares many apomorphic characters (e.g., scalids on the introvert) with both Priapulida and Kinorhyncha, and can be included in the taxon Scalidophora, a subgroup of Cycloneuralia. Cycliophora was originally allied to the Entoprocta and Ectoprocta (Bryozoa) based on ultrastructual research. Subsequent molecular data show they may be related to Rotifera and Acanthocephala, within the taxon Gnathifera. The phylogenetic position of Cycliophora is therefore not settled, and more ultrastructural and molecular data are needed. Micrognathozoa is the most recent major group of animals to be described. They show strong affinities with both Rotifera and Gnathostomulida (within the taxon Gnathifera), especially in the fine structure of the pharyngeal apparatus, where the jaw elements have cuticular rods with osmiophilic cores. Furthermore the micrognathozoans have two rows of multiciliated cells that form a locomotory organ, similar to that seen in some gastrotrichs and interstitial annelids. This character is never seen in Rotifera or in the monociliated Gnathostomulida. Rotifera and Acanthocephala always have a syncytial epidermis (Syndermata). Micrognathozoa lack this characteristic feature. Therefore, they are postulated to be placed basally in the Gnathifera, either as a sister-group to Gnathostomulida or as a sister-group to Rotifera + Acanthocephala.

The phylogenetic position of poroid Hymenochaetaceae (Hymenochaetales, Basidiomycota) from Patagonia, Argentina.

PubMed

Rajchenberg, Mario; Pildain, María Belén; Bianchinotti, María V; Barroetaveña, Carolina

2015-01-01

Six poroid Hymenochaetaceae from Patagonia, Argentina, were studied phylogenetically with nuc rDNA internal transcribed spacer (ITS) and partial 28S rDNA sequences, together with morphological data. Two new genera and a new species are introduced as well as two new combinations proposed. Arambarria destruens gen. et sp. nov. is proposed for a taxon fruiting on fallen or standing, dead Diostea juncea and Lomatia hirsuta and previously recorded erroneously as Inocutis jamaicensis; it is distinguished by annual, effused to effused-reflexed basidiomes forming pilei, a monomitic hyphal system, thick-walled and yellowish basidiospores (brownish chestnut in potassium hydroxide solution), lack of a granular core in the context and lack of setoid elements. Nothophellinus gen. nov. is proposed to accommodate Phellinus andinopatagonicus, the main white wood-rotting polypore of standing Nothofagus pumilio and also an important wood-decayer of other Nothofagus species from southern Argentina and Chile. It is morphologically similar to Phellopilus (type species P. nigrolimitatus) but differs by lacking setae. The new combinations Pseudoinonotus crustosus and Phellinopsis andina are proposed for Inonotus crustosus and Phellinus andinus, respectively. Phellinus livescens, which decays the sapwood of several standing Nothofagus species, is closely related to Phellinus uncisetus, a Neotropical species related to Fomitiporia; for the time being P. livescens is retained in Phellinus sensu lato. An unidentified taxon responsible for a white heart-rot in living Austrocedrus chilensis grouped with Phellinus caryophyllii and Fulvifomes inermis, but its generic affinities remain ambiguous. Transmission electron microscopy studies confirm this unidentified taxon has an imperforate parenthesome, which is typical of the Hymenochaetaceae. © 2015 by The Mycological Society of America.

The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird?

PubMed Central

2015-01-01

The exceptionally well-preserved Romanian dinosaur Balaur bondoc is the most complete theropod known to date from the Upper Cretaceous of Europe. Previous studies of this remarkable taxon have included its phylogenetic interpretation as an aberrant dromaeosaurid with velociraptorine affinities. However, Balaur displays a combination of both apparently plesiomorphic and derived bird-like characters. Here, we analyse those features in a phylogenetic revision and show how they challenge its referral to Dromaeosauridae. Our reanalysis of two distinct phylogenetic datasets focusing on basal paravian taxa supports the reinterpretation of Balaur as an avialan more crownward than Archaeopteryx but outside of Pygostylia, and as a flightless taxon within a paraphyletic assemblage of long-tailed birds. Our placement of Balaur within Avialae is not biased by character weighting. The placement among dromaeosaurids resulted in a suboptimal alternative that cannot be rejected based on the data to hand. Interpreted as a dromaeosaurid, Balaur has been assumed to be hypercarnivorous and predatory, exhibiting a peculiar morphology influenced by island endemism. However, a dromaeosaurid-like ecology is contradicted by several details of Balaur’s morphology, including the loss of a third functional manual digit, the non-ginglymoid distal end of metatarsal II, and a non-falciform ungual on the second pedal digit that lacks a prominent flexor tubercle. Conversely, an omnivorous ecology is better supported by Balaur’s morphology and is consistent with its phylogenetic placement within Avialae. Our reinterpretation of Balaur implies that a superficially dromaeosaurid-like taxon represents the enlarged, terrestrialised descendant of smaller and probably volant ancestors. PMID:26157616

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap.

PubMed

Gokul, Jarishma K; Hodson, Andrew J; Saetnan, Eli R; Irvine-Fynn, Tristram D L; Westall, Philippa J; Detheridge, Andrew P; Takeuchi, Nozomu; Bussell, Jennifer; Mur, Luis A J; Edwards, Arwyn

2016-08-01

Microbial colonization of glacial ice surfaces incurs feedbacks which affect the melting rate of the ice surface. Ecosystems formed as microbe-mineral aggregates termed cryoconite locally reduce ice surface albedo and represent foci of biodiversity and biogeochemical cycling. Consequently, greater understanding the ecological processes in the formation of functional cryoconite ecosystems upon glacier surfaces is sought. Here, we present the first bacterial biogeography of an ice cap, evaluating the respective roles of dispersal, environmental and biotic filtration occurring at local scales in the assembly of cryoconite microbiota. 16S rRNA gene amplicon semiconductor sequencing of cryoconite colonizing a Svalbard ice cap coupled with digital elevation modelling of physical parameters reveals the bacterial community is dominated by a ubiquitous core of generalist taxa, with evidence for a moderate pairwise distance-decay relationship. While geographic position and melt season duration are prominent among environmental predictors of community structure, the core population of taxa appears highly influential in structuring the bacterial community. Taxon co-occurrence network analysis reveals a highly modular community structured by positive interactions with bottleneck taxa, predominantly Actinobacteria affiliated to isolates from soil humus. In contrast, the filamentous cyanobacterial taxon (assigned to Leptolyngbya/Phormidesmis pristleyi) which dominates the community and binds together granular cryoconite are poorly connected to other taxa. While our study targeted one ice cap, the prominent role of generalist core taxa with close environmental relatives across the global cryosphere indicate discrete roles for cosmopolitan Actinobacteria and Cyanobacteria as respective keystone taxa and ecosystem engineers of cryoconite ecosystems colonizing ice caps. © 2016 John Wiley & Sons Ltd.

Through thick and thin: cryptic sympatric speciation in the submersed genus Najas (Hydrocharitaceae).

PubMed

Les, Donald H; Peredo, Elena L; King, Ursula M; Benoit, Lori K; Tippery, Nicholas P; Ball, Cassandra J; Shannon, Robynn K

2015-01-01

Cryptic sympatric species arise when reproductive isolation is established in sympatry, leading to genetically divergent lineages that are highly similar morphologically or virtually indistinguishable. Although cryptic sympatric species have been reported in various animals, fungi, and protists, there are few compelling examples for plants. This investigation presents a case for cryptic sympatric speciation in Najas flexilis, a widespread aquatic plant, which extends throughout northern North America and Eurasia. The taxon is noted for its variable seed morphology, which earlier research associated with cytotypes; i.e., diploids were characterized by thicker seeds and tetraploids by thinner seeds. However, cytotypes are not patterned geographically with diploid and tetraploid plants often found in close proximity within the same lake. Using digital image and DNA sequence analyses, we found that diploids and tetraploids are well-isolated and remain genetically distinct throughout their sympatric range, where sterile hybrids occur frequently. Incorporation of sequence data from the single-copy nuclear phytoene desaturase locus revealed further that the tetraploids are allopolyploid derivatives of N. flexilis and N. guadalupensis, the latter a closely related species with an overlapping distribution. We conclude that the taxon widely known as N. flexilis actually comprises two cryptic, sibling species, which diverged in sympatry by interspecific hybridization and subsequent chromosomal isolation. By comparing seed morphology of type specimens, we associated the names N. flexilis and N. canadensis to the diploids and tetraploids respectively. Additionally, the narrowly restricted taxon known formerly as N. muenscheri is shown via morphological and genetic evidence to be synonymous with N. canadensis. Copyright © 2014 Elsevier Inc. All rights reserved.

Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

PubMed

Swain, Timothy D

2018-01-01

The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

[The influence of Janicki cercomer theory on the development of platyhelminthes systematics and evolution investigations].

PubMed

Pojmańska, Teresa

2005-01-01

The aim of this article was to present the development of ideas about the provenience of parasitic helminths and the phylogenetical relationships within this taxon, since the publication of the "cercomer theory" just to nowadays. The following essentials of the Janicki theory are outlined: main differences between free-living Turbellaria and parasitic platyhelminths (ciliated epithelium in Turbellaria versus unciliated surface in the others); universality of the cercomer presence in Monogenea, Digenea and Cestoda; evolutionary changes in the morphology and function of the cercomer; homology of the caudal appendices of all parasitic helminths; the subsequent evolution of parasitic platyhelminthes from the ancestor to Monogena, Digenea and Cestoda; proposition to establish a new common taxon--Cercomerophora--for these three groups. In this background the evolution of evolutionary ideas is reviewed, divided into two periods: up to the eighties of the XX century, and up to date. The first period can be characterised by the criticism of some points of the "cercomer theory" and formulation of some new hypotheses; these are those of Fuhrmann, Bychovsky, Llewellyn, Price and Malmberg, which: questioned the homology of the cercarial tail with the caudal appendices of Monogenea and Cestoda; rejected Digenea from the common group; established the common taxon--Cercomeromorpha--comprising only Monogenea and Cestoda; opposed the idea of radial evolution of three main groups of Platyhelmithes (Turbellaria, Digenea and Cercomeromorpha) to the idea of subsequent evolution presented by Janicki. The differences between these last hypotheses are also underlined, arising mainly from the different ideas on the importance of particular features as the evolutionary indicators of affinities between and within the taxons. As to the hypotheses dealing with the evolution of particular groups of parasitic platyhelminths formulated at the same period, the publications of Freeman and Jarecka (Cestoda), Heynemann, Ginetsinskaja, Pearson, Cable, Rhode and Gibson (Trematoda), Bychovsky, Lambert and Malmberg (Monogenea) are referred, with special emphasises on the differences in the ideas presented by their authors. In the second period two points are underlined: a dynamic development of new techniques and methods (including molecular investigations) allowing to gather more and more different data on the parasites, and, as a consequence of this phenomenon, a new approach to the evolutionary problems--the birth of numeric and phylogenetic systematics. In this period "the cercomer theory", as well as supporting the group Cercomeromorphae generally are not accepted (exception: Brooks et al.). In contrast, the new taxon--Neodermata has been created by Ehlers. The importance of this publication for further evolutionary study is stressed. In this background some publications are quoted, especially those, presenting the results of searching for monophyletic groups and joining them in hieratic kladograms (Brooks and al., Rohde at al., Littlewood at al., and the others). It is stated, that in spite of some differences in the kladograms builded by various authors (resulting mainly from the set of features being analysed) the monophyly of big taxons of Neodermata (Trematoda, Monogenea, Cestoda) is fairly well documented. In conclusion several points connected with the "cercomer theory" are emphasized. It is now obvious, that the base of this theory--homology of caudal appendices of Janicki's Cercomerophora has to be rejected, as well as his concept of subsequent evolution of Platyhelminthes. But the base of his joining of Monogena, Trematoda (in his theory--Digenea) and Cestoda in one group (lack of cilia on the body surface), opposite to the Turbellaria (ciliary ephitelium) is maintained by the creation of Neodermata, undoubtedly documented better and in a different way. Also his idea (after many years of rejecting) on close affinity of Digenea and Cestoda seems to have returned due to the study of Lockyer at al., who write: "Among the Neodermata, the Cercomeromorphae (Cestoda + Monogenea) was not supported, whereas Cestoda + Trematoda was supported".

Pinus ponderosa : A checkered past obscured four species

Treesearch

Ann Willyard; David S. Gernandt; Kevin Potter; Valerie Hipkins; Paula E. Marquardt; Mary Frances Mahalovich; Stephen K. Langer; Frank W. Telewski; Blake Cooper; Connor Douglas; Kristen Finch; Hassani H. Karemera; Julia Lefler; Payton Lea; Austin Wofford

2016-01-01

PREMISE OF THE STUDY: Molecular genetic evidence can help delineate taxa in species complexes that lack diagnostic morphological characters. Pinus ponderosa (Pinaceae; subsection Ponderosae ) is recognized as a problematic taxon: plastid phylogenies of exemplars were paraphyletic, and mitochondrial phylogeography suggested at...

Permafrost and indigenous land use in the northern Urals: Komi and Nenets reindeer husbandry

NASA Astrophysics Data System (ADS)

Istomin, Kirill V.; Habeck, Joachim Otto

2016-09-01

Permafrost is an integral part of the environmental conditions that frame indigenous peoples' livelihoods in many parts of the circumpolar region. On the basis of their long-term ethnographic field researches, the authors describe the various ways in which permafrost dynamics influence the lives and economic activities of two groups of reindeer-herding nomads in North-Eastern Europe and Western Siberia: Komi and Nenets. Permafrost affects the herders directly, for the herders have to take into account the probability of thermokarst while choosing the campsite and performing certain herding procedures. It also affects the herders indirectly, through its influence on landscape and vegetation and thus on reindeer behavior. More rapid permafrost degradation will have a range of adverse effects on reindeer herding.

Mineralogy of parent rock and peaty-podzolic soil of Iremel Ridge, Southern Urals

NASA Astrophysics Data System (ADS)

Khalitov, R. M.; Perova, E. N.; Abakumov, E. V.; Suleimanov, R. R.

2017-08-01

The mineralogy of soils and parent rocks of the Iremel Ridge has been studied by the methods of micromorphology, laser diffraction, computed X-ray microtomography, and X-ray fluorescence analysis. In hard rock and soil, the major minerals have been identified: quartz, illite, and a chlorite-group mineral (Fe analogue of sudoite), as well as accessory minerals: monazite, xenotime, rutile, zircon, and florencite. It has been found that chlorite, illite, and quartz are present in all horizons of the studied peaty-podzolic soil. Insignificant amounts of mixed-layered mineral and kaolinite could be suggested in the T and EL horizons of peaty-podzolic soil. The mixed-layered mineral is most probably of soil origin, which is related to the transformation of illites inherited from the parent rock under acidic conditions.

Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus

USDA-ARS?s Scientific Manuscript database

Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new ...

Type studies of corticioid Hymenomycetes described by Bresadola

Treesearch

Karen K. Nakasone

2008-01-01

Twenty-six type specimens of corticioid basidiomycetes in the genera Corticium, Cytidia, Grandinia, Hydnum, Kneiffia, Merulius, Odontia, Peniophora and Radulum described by Bresadola, alone or with others, were examined. The new taxon, Phlebia cryptocystidiata, is described and illustrated, and an epitype for...

Species delimitation: A case study in a problematic ant taxon

USDA-ARS?s Scientific Manuscript database

Species delimitation has been invigorated as a discipline in systematics by an influx of new character sets, analytical methods, and conceptual advances. We use genetic data from 68 markers, combined with distributional, bioclimatic, and coloration information, to distinguish evolutionarily indepe...

The Phytophthora species known as "Pg chlamydo"

Treesearch

Everett Hansen; Paul Reeser; Wendy Sutton

2009-01-01

Phytophthora taxon Pg chlamydo is perhaps the second most abundant Phytophthora species in the world, after P. gonapodyides, although it is commonly misidentified. Pg chlamydo is frequently encountered in streams and rivers in western North America, Argentina, China, and Europe. It has occasionally been...

CONCORDANCE OF TAXONOMIC RICHNESS PATTERNS ACROSS MULTIPLE ASSEMBLAGES IN LAKES OF THE NORTHEASTERN UNITED STATES

EPA Science Inventory

We investigated the concordance of taxonomic richness patterns and their environmental correlates for assemblages of benthic macroinvertebrates, riparian birds, sedimentary diatoms, fish, planktonic crustaceans, and planktonic rotifers in 186 northeastern U.S. lakes. Taxon counts...

Lentil genetic and genomic resources

USDA-ARS?s Scientific Manuscript database

Lentil (Lens culinaris spp. culinaris) has a long history associated with the early civilizations 11,000 BP in southwestern Asia. The progenitor taxon is Lens culinaris spp. orientalis. The primary source of germplasm for lentil crop improvement is from the International Center for Agricultural Rese...

A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand

PubMed Central

Suwannapoom, Chatmongkon; Tunprasert, Jitthep; Ruangsuwan, Thiti; Pawangkhanant, Parinya; Korost, Dmitriy V.

2018-01-01

We report on a discovery of Siamophryne troglodytes Gen. et sp. nov., a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA–16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Gastrophrynoides, the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates that S. troglodytes Gen. et sp. nov. represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the “out of Indo-Eurasia” biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such, S. troglodytes Gen. et sp. nov. is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it. PMID:29497587

A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand.

PubMed

Suwannapoom, Chatmongkon; Sumontha, Montri; Tunprasert, Jitthep; Ruangsuwan, Thiti; Pawangkhanant, Parinya; Korost, Dmitriy V; Poyarkov, Nikolay A

2018-01-01

We report on a discovery of Siamophryne troglodytes Gen. et sp. nov., a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA-16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Gastrophrynoides , the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates that S. troglodytes Gen. et sp. nov. represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the "out of Indo-Eurasia" biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such, S. troglodytes Gen. et sp. nov. is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it.

Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Mollusca

PubMed Central

Wiklund, Helena; Taylor, John D.; Dahlgren, Thomas G.; Todt, Christiane; Ikebe, Chiho; Rabone, Muriel; Glover, Adrian G.

2017-01-01

Abstract We present the first DNA taxonomy publication on abyssal Mollusca from the Clarion-Clipperton Zone (CCZ), central Pacific ocean, using material collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise ‘AB01’ to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration area ‘UK-1’ in the eastern CCZ. This is the third paper in a series to provide regional taxonomic data for a region that is undergoing intense deep-sea mineral exploration for high-grade polymetallic nodules. Taxonomic data are presented for 21 species from 42 records identified by a combination of morphological and genetic data, including molecular phylogenetic analyses. These included 3 heterodont bivalves, 5 protobranch bivalves, 4 pteriomorph bivalves, 1 caudofoveate, 1 monoplacophoran, 1 polyplacophoran, 4 scaphopods and 2 solenogastres. Gastropoda were recovered but will be the subject of a future study. Seven taxa matched published morphological descriptions for species with deep Pacific type localities, and our sequences provide the first genetic data for these taxa. One taxon morphologically matched a known cosmopolitan species but with a type locality in a different ocean basin and was assigned the open nomenclature ‘cf’ as a precautionary approach in taxon assignments to avoid over-estimating species ranges. One taxon is here described as a new species, Ledella knudseni sp. n. For the remaining 12 taxa, we have determined them to be potentially new species, for which we make the raw data, imagery and vouchers available for future taxonomic study. The Clarion-Clipperton Zone is a region undergoing intense exploration for potential deep-sea mineral extraction. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections. PMID:29118626

Phylogenomic Study Indicates Widespread Lateral Gene Transfer in Entamoeba and Suggests a Past Intimate Relationship with Parabasalids

PubMed Central

Grant, Jessica R.; Katz, Laura A.

2014-01-01

Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence—a taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence—to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our approach, using an automated phylogenomic pipeline to build taxon-rich gene trees, suggests that LGT is more extensive than previously thought. Our analyses reveal that genes have frequently entered the Entamoeba genome via nonvertical events, including at least 116 genes acquired directly from bacteria or archaea, plus an additional 22 genes in which Entamoeba plus one other eukaryote are nested among bacteria and/or archaea. These genes may make good candidates for novel therapeutics, as drugs targeting these genes are less likely to impact the human host. Although we recognize the challenges of inferring intradomain transfers given systematic errors in gene trees, we find 109 genes supporting LGT from a eukaryote to Entamoeba spp., and 178 genes unique to Entamoeba spp. and one other eukaryotic taxon (i.e., presence/absence data). Inspection of these intradomain LGTs provide evidence of a common sister relationship between genes of Entamoeba (Amoebozoa) and parabasalids (Excavata). We speculate that this indicates a past close relationship (e.g., symbiosis) between ancestors of these extant lineages. PMID:25146649

On the complexity of the Saccharomyces bayanus taxon: hybridization and potential hybrid speciation.

PubMed

Pérez-Través, Laura; Lopes, Christian A; Querol, Amparo; Barrio, Eladio

2014-01-01

Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99-100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains.

On the Complexity of the Saccharomyces bayanus Taxon: Hybridization and Potential Hybrid Speciation

PubMed Central

Pérez-Través, Laura; Lopes, Christian A.; Querol, Amparo; Barrio, Eladio

2014-01-01

Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99–100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains. PMID:24705561

Identification of some ectomycorrhizal basidiomycetes by PCR amplification of their gpd (glyceraldehyde-3-phosphate dehydrogenase) genes.

PubMed Central

Kreuzinger, N; Podeu, R; Gruber, F; Göbl, F; Kubicek, C P

1996-01-01

Degenerated oligonucleotide primers designed to flank an approximately 1.2-kb fragment of the gene encoding glyceraldehyde-3-phosphate dehydrogenase (gpd) from ascomycetes and basidiomycetes were used to amplify the corresponding gpd fragments from several species of the ectomycorrhizal fungal taxa Boletus, Amanita, and Lactarius. Those from B. edulis, A. muscaria, and L. deterrimus were cloned and sequenced. The respective nucleotide sequences of these gene fragments showed a moderate degree of similarity (72 to 76%) in the protein-encoding regions and only a low degree of similarity in the introns (56 to 66%). Introns, where present, occurred at conserved positions, but the respective positions and numbers of introns in a given taxon varied. The amplified fragment from a given taxon could be distinguished from that of others by both restriction nuclease cleavage analysis and Southern hybridization. A procedure for labeling DNA probes with fluorescein-12-dUTP by PCR was developed. These probes were used in a nonradioactive hybridization assay, with which the gene could be detected in 2 ng of chromosomal DNA of L. deterrimus on slot blots. Taxon-specific amplification was achieved by the design of specific oligonucleotide primers. The application of the gpd gene for the identification of mycorrhizal fungi under field conditions was demonstrated, with Picea abies (spruce) mycorrhizal roots harvested from a northern alpine forest area as well as from a plant-breeding nursery. The interference by inhibitory substances, which sometimes occurred in the DNA extracted from the root-fungus mixture, could be overcome by using very diluted concentrations of template DNA for a first round of PCR amplification followed by a second round with nested oligonucleotide primers. We conclude that gpd can be used to detect ectomycorrhizal fungi during symbiotic interaction. PMID:8795234

Ecological Change in the Turkana Basin Over the Past 4 Ma

NASA Astrophysics Data System (ADS)

Cerling, T. E.

2014-12-01

The fossil record of C4 grasses is extremely sparse so that much speculation on their importance through time is based solely on stable carbon isotope ratios in derived materials, such as tooth enamel, soil carbonate, leaf waxes. I present stable isotope analyses of modern large mammals from different 25 sites in East and Central Africa, primarily from national parks and national reserves, that show patterns of dietary strategies in environments ranging from closed forests to open grasslands. This uses isotope values from each locality for each taxon to estimate diet, rather to assume a constant diet for a taxon across all localities. Each taxon can be represented on the dietary continuum from pure C3-browsing to pure C4-grazing. Fossil assemblages from the Turkana basin are evaluated in the same way over the past 4.2 million years. The fossil record shows patterns with no modern analogue in the national parks and reserves of East and Central Africa for significant periods of time. Significant patterns shifts occur between 2.0 and 2.5 million years ago, and also in the past million years. These dietary changes at the community level occur during the evolutionary backdrop of C4 grasses, which have gone from less than 1% Net Primary Productivity (NPP) at 10 million years ago to more than 50% NPP in the tropics today. It is likely that C4 plants have also undergone important changes in nutrient content, defense against herbivory, fire adaptation, and propagation strategies in the past 10 million years; such issues could signficantly influence dietary strategies at the community level through time.

A Phylogenomic Solution to the Origin of Insects by Resolving Crustacean-Hexapod Relationships.

PubMed

Schwentner, Martin; Combosch, David J; Pakes Nelson, Joey; Giribet, Gonzalo

2017-06-19

Insects, the most diverse group of organisms, are nested within crustaceans, arguably the most abundant group of marine animals. However, to date, no consensus has been reached as to which crustacean taxon is the closest relative of hexapods. A majority of studies have proposed that Branchiopoda (e.g., fairy shrimps) is the sister group of Hexapoda [1-7]. However, these investigations largely excluded two equally important taxa, Remipedia and Cephalocarida. Other studies suggested Remipedia [8-11] or Remipedia + Cephalocarida [12, 13] as potential sister groups of hexapods, but they either did not include Cephalocarida or used only Sanger sequence data and morphology [9, 12]. Here we present the first phylogenomic study specifically addressing the origins of hexapods, including transcriptomes for two species each of Cephalocarida and Remipedia. Phylogenetic analyses of selected matrices, ranging from 81 to 1,675 orthogroups and up to 510,982 amino acid positions, clearly reject a sister-group relationship between Hexapoda and Branchiopoda [1-7]. Nonetheless, support for a hexapod sister-group relationship to Remipedia or to Cephalocarida-Remipedia was highly dependent on the employed analytical methodology. Further analyses assessing the effects of gene evolutionary rate and targeted taxon exclusion support Remipedia as the sole sister taxon of Hexapoda and suggest that the prior grouping of Remipedia + Cephalocarida is an artifact, possibly due to long branch attraction and compositional heterogeneity. We further conclude that terrestrialization of Hexapoda probably occurred in the late Cambrian to early Ordovician, an estimate that is independent of their proposed sister group [4, 8, 12, 14]. Copyright © 2017 Elsevier Ltd. All rights reserved.

Non-destructive lichen biomass estimation in northwestern Alaska: a comparison of methods.

PubMed

Rosso, Abbey; Neitlich, Peter; Smith, Robert J

2014-01-01

Terrestrial lichen biomass is an important indicator of forage availability for caribou in northern regions, and can indicate vegetation shifts due to climate change, air pollution or changes in vascular plant community structure. Techniques for estimating lichen biomass have traditionally required destructive harvesting that is painstaking and impractical, so we developed models to estimate biomass from relatively simple cover and height measurements. We measured cover and height of forage lichens (including single-taxon and multi-taxa "community" samples, n = 144) at 73 sites on the Seward Peninsula of northwestern Alaska, and harvested lichen biomass from the same plots. We assessed biomass-to-volume relationships using zero-intercept regressions, and compared differences among two non-destructive cover estimation methods (ocular vs. point count), among four landcover types in two ecoregions, and among single-taxon vs. multi-taxa samples. Additionally, we explored the feasibility of using lichen height (instead of volume) as a predictor of stand-level biomass. Although lichen taxa exhibited unique biomass and bulk density responses that varied significantly by growth form, we found that single-taxon sampling consistently under-estimated true biomass and was constrained by the need for taxonomic experts. We also found that the point count method provided little to no improvement over ocular methods, despite increased effort. Estimated biomass of lichen-dominated communities (mean lichen cover: 84.9±1.4%) using multi-taxa, ocular methods differed only nominally among landcover types within ecoregions (range: 822 to 1418 g m-2). Height alone was a poor predictor of lichen biomass and should always be weighted by cover abundance. We conclude that the multi-taxa (whole-community) approach, when paired with ocular estimates, is the most reasonable and practical method for estimating lichen biomass at landscape scales in northwest Alaska.

Non-Destructive Lichen Biomass Estimation in Northwestern Alaska: A Comparison of Methods

PubMed Central

Rosso, Abbey; Neitlich, Peter; Smith, Robert J.

2014-01-01

Terrestrial lichen biomass is an important indicator of forage availability for caribou in northern regions, and can indicate vegetation shifts due to climate change, air pollution or changes in vascular plant community structure. Techniques for estimating lichen biomass have traditionally required destructive harvesting that is painstaking and impractical, so we developed models to estimate biomass from relatively simple cover and height measurements. We measured cover and height of forage lichens (including single-taxon and multi-taxa “community” samples, n = 144) at 73 sites on the Seward Peninsula of northwestern Alaska, and harvested lichen biomass from the same plots. We assessed biomass-to-volume relationships using zero-intercept regressions, and compared differences among two non-destructive cover estimation methods (ocular vs. point count), among four landcover types in two ecoregions, and among single-taxon vs. multi-taxa samples. Additionally, we explored the feasibility of using lichen height (instead of volume) as a predictor of stand-level biomass. Although lichen taxa exhibited unique biomass and bulk density responses that varied significantly by growth form, we found that single-taxon sampling consistently under-estimated true biomass and was constrained by the need for taxonomic experts. We also found that the point count method provided little to no improvement over ocular methods, despite increased effort. Estimated biomass of lichen-dominated communities (mean lichen cover: 84.9±1.4%) using multi-taxa, ocular methods differed only nominally among landcover types within ecoregions (range: 822 to 1418 g m−2). Height alone was a poor predictor of lichen biomass and should always be weighted by cover abundance. We conclude that the multi-taxa (whole-community) approach, when paired with ocular estimates, is the most reasonable and practical method for estimating lichen biomass at landscape scales in northwest Alaska. PMID:25079228

Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

PubMed Central

Jeffries, Thomas C.; Ijaz, Umer Z.; Hamonts, Kelly

2017-01-01

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients. PMID:29038749

The systematic position of the enigmatic thyreophoran dinosaur Paranthodon africanus, and the use of basal exemplifiers in phylogenetic analysis.

PubMed

Raven, Thomas J; Maidment, Susannah C R

2018-01-01

The first African dinosaur to be discovered, Paranthodon africanus was found in 1845 in the Lower Cretaceous of South Africa. Taxonomically assigned to numerous groups since discovery, in 1981 it was described as a stegosaur, a group of armoured ornithischian dinosaurs characterised by bizarre plates and spines extending from the neck to the tail. This assignment has been subsequently accepted. The type material consists of a premaxilla, maxilla, a nasal, and a vertebra, and contains no synapomorphies of Stegosauria. Several features of the maxilla and dentition are reminiscent of Ankylosauria, the sister-taxon to Stegosauria, and the premaxilla appears superficially similar to that of some ornithopods. The vertebral material has never been described, and since the last description of the specimen, there have been numerous discoveries of thyreophoran material potentially pertinent to establishing the taxonomic assignment of the specimen. An investigation of the taxonomic and systematic position of Paranthodon is therefore warranted. This study provides a detailed re-description, including the first description of the vertebra. Numerous phylogenetic analyses demonstrate that the systematic position of Paranthodon is highly labile and subject to change depending on which exemplifier for the clade Stegosauria is used. The results indicate that the use of a basal exemplifier may not result in the correct phylogenetic position of a taxon being recovered if the taxon displays character states more derived than those of the basal exemplifier, and we recommend the use, minimally, of one basal and one derived exemplifier per clade. Paranthodon is most robustly recovered as a stegosaur in our analyses, meaning it is one of the youngest and southernmost stegosaurs.

Feeding biomechanics of Late Triassic metoposaurids (Amphibia: Temnospondyli): a 3D finite element analysis approach.

PubMed

Fortuny, Josep; Marcé-Nogué, Jordi; Konietzko-Meier, Dorota

2017-06-01

The Late Triassic freshwater ecosystems were occupied by different tetrapod groups including large-sized anamniotes, such as metoposaurids. Most members of this group of temnospondyls acquired gigantic sizes (up to 5 m long) with a nearly worldwide distribution. The paleoecology of metoposaurids is controversial; they have been historically considered passive, bottom-dwelling animals, waiting for prey on the bottom of rivers and lakes, or they have been suggested to be active mid-water feeders. The present study aims to expand upon the paleoecological interpretations of these animals using 3D finite element analyses (FEA). Skulls from two taxa, Metoposaurus krasiejowensis, a gigantic taxon from Europe, and Apachesaurus gregorii, a non-gigantic taxon from North America, were analyzed under different biomechanical scenarios. Both 3D models of the skulls were scaled to allow comparisons between them and reveal that the general stress distribution pattern found in both taxa is clearly similar in all scenarios. In light of our results, both previous hypotheses about the paleoecology of these animals can be partly merged: metoposaurids probably were ambush and active predators, but not the top predators of these aquatic environments. The FEA results demonstrate that they were particularly efficient at bilateral biting, and together with their characteristically anteropositioned orbits, optimal for an ambush strategy. Nonetheless, the results also show that these animals were capable of lateral strikes of the head, suggesting active hunting of prey. Regarding the important skull size differences between the taxa analyzed, our results suggest that the size reduction in the North American taxon could be related to drastic environmental changes or the increase of competitors. The size reduction might have helped them expand into new ecological niches, but they likely remained fully aquatic, as are all other metoposaurids. © 2017 Anatomical Society.

Transport of airborne pollen into the city of Thessaloniki: the effects of wind direction, speed and persistence

NASA Astrophysics Data System (ADS)

Damialis, Athanasios; Gioulekas, Dimitrios; Lazopoulou, Chariklia; Balafoutis, Christos; Vokou, Despina

2005-01-01

We examined the effect of the wind vector analyzed into its three components (direction, speed and persistence), on the circulation of pollen from differe nt plant taxa prominent in the Thessaloniki area for a 4-year period (1996- 1999). These plant taxa were Ambrosia spp., Artemisia spp., Chenopodiaceae, spp., Cupressaceae, Olea europaea, Pinaceae, Platanus spp., Poaceae, Populus spp., Quercus spp., and Urticaceae. Airborne pollen of Cupressaceae, Urticaceae, Quercus spp. and O. europaea make up approximately 70% of the total average annual pollen counts. The set of data that we worked with represented days without precipitation and time intervals during which winds blew from the same direction for at least 4 consecutive hours. We did this in order to study the effect of the different wind components independently of precipitation, and to avoid secondary effects produced by pollen resuspension phenomena. Factorial regression analysis among the summed bi-hourly pollen counts for each taxon and the values of wind speed and persistence per wind direction gave significant results in 22 cases (combinations of plant taxa and wind directions). The pollen concentrations of all taxa correlated significantly with at least one of the three wind components. In seven out of the 22 taxon-wind direction combinations, the pollen counts correlated positively with wind persistence, whereas this was the case for only two of the taxon-wind speed combinations. In seven cases, pollen counts correlated with the interaction effect of wind speed and persistence. This shows the importance of wind persistence in pollen transport, particularly when weak winds prevail for a considerable part of the year, as is the case for Thessaloniki. Medium/long-distance pollen transport was evidenced for Olea (NW, SW directions), Corylus (NW, SW), Poaceae (SW) and Populus (NW).

A new specimen of Manchurochelys manchoukuoensis from the Early Cretaceous Jehol Biota of Chifeng, Inner Mongolia, China and the phylogeny of Cretaceous basal eucryptodiran turtles

PubMed Central

2014-01-01

Background Manchurochelys manchoukuoensis is an emblematic turtle from the Cretaceous Yixian Formation of Liaoning, China, a geological rock unit that is famous for yielding perfectly preserved skeletons of fossil vertebrates, including that of feathered dinosaurs. Manchurochelys manchoukuoensis was one of the first vertebrates described from this fauna, also known as the Jehol Biota. The holotype was lost during World War II and only one additional specimen has been described since. Manchurochelys manchoukuoensis is a critical taxon for unraveling the phylogenetic relationships of Cretaceous pancryptodires from Asia, a group that is considered to be of key importance for the origin of crown-group hidden-neck turtles (Cryptodira). Results A new specimen of Manchurochelys manchoukuoensis is described here from the Jiufotang Formation of Qilinshan, Chifeng, Inner Mongolia, China. This is the third specimen described and expands the range of this taxon from the Yixian Formation of the Fuxin-Yixian Basin in Liaoning to the Jiufotang Formation of the Chifeng-Yuanbaoshan Basin. A possible temporal extension of the range is less certain. The new finding adds to our understanding of the morphology of this taxon and invites a thorough revision of the phylogeny of Macrobaenidae, Sinemydidae, and closely allied forms. Conclusions Our comprehensive phylogenetic analyses of Cretaceous Asian pancryptodires yielded two main competing hypotheses: in the first these taxa form a paraphyletic grade, whereas in the second they form a monophyletic clade. The inclusion of problematic tree changing taxa, such as Panpleurodires (stem + crown side-neck turtles) has a major influence on the phylogenetic relationships of Sinemydidae and closely allied forms. Manchurochelys manchoukuoensis nests within Sinemydidae together with Sinemys spp. and Dracochelys bicuspis in the majority of our analyses. PMID:24707892

A Standardized Reference Data Set for Vertebrate Taxon Name Resolution

PubMed Central

Zermoglio, Paula F.; Guralnick, Robert P.; Wieczorek, John R.

2016-01-01

Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only once during accessioning of specimens, or have a history of label changes without clear provenance. Before records are reliably usable in research, it is critical that these issues be addressed. However, still missing is an assessment of the scope of the problem, the effort needed to solve it, and a way to improve effectiveness of tools developed to aid the process. We present a carefully human-vetted analysis of 1000 verbatim scientific names taken at random from those published via the data aggregator VertNet, providing the first rigorously reviewed, reference validation data set. In addition to characterizing formatting problems, human vetting focused on detecting misspelling, synonymy, and the incorrect use of Darwin Core. Our results reveal a sobering view of the challenge ahead, as less than 47% of name strings were found to be currently valid. More optimistically, nearly 97% of name combinations could be resolved to a currently valid name, suggesting that computer-aided approaches may provide feasible means to improve digitized content. Finally, we associated names back to biocollections records and fit logistic models to test potential drivers of issues. A set of candidate variables (geographic region, year collected, higher-level clade, and the institutional digitally accessible data volume) and their 2-way interactions all predict the probability of records having taxon name issues, based on model selection approaches. We strongly encourage further experiments to use this reference data set as a means to compare automated or computer-aided taxon name tools for their ability to resolve and improve the existing wealth of legacy data. PMID:26760296

Multiplex electrochemical DNA platform for femtomolar-level quantification of genetically modified soybean.

PubMed

Manzanares-Palenzuela, C Lorena; de-Los-Santos-Álvarez, Noemí; Lobo-Castañón, María Jesús; López-Ruiz, Beatriz

2015-06-15

Current EU regulations on the mandatory labeling of genetically modified organisms (GMOs) with a minimum content of 0.9% would benefit from the availability of reliable and rapid methods to detect and quantify DNA sequences specific for GMOs. Different genosensors have been developed to this aim, mainly intended for GMO screening. A remaining challenge, however, is the development of genosensing platforms for GMO quantification, which should be expressed as the number of event-specific DNA sequences per taxon-specific sequences. Here we report a simple and sensitive multiplexed electrochemical approach for the quantification of Roundup-Ready Soybean (RRS). Two DNA sequences, taxon (lectin) and event-specific (RR), are targeted via hybridization onto magnetic beads. Both sequences are simultaneously detected by performing the immobilization, hybridization and labeling steps in a single tube and parallel electrochemical readout. Hybridization is performed in a sandwich format using signaling probes labeled with fluorescein isothiocyanate (FITC) or digoxigenin (Dig), followed by dual enzymatic labeling using Fab fragments of anti-Dig and anti-FITC conjugated to peroxidase or alkaline phosphatase, respectively. Electrochemical measurement of the enzyme activity is finally performed on screen-printed carbon electrodes. The assay gave a linear range of 2-250 pM for both targets, with LOD values of 650 fM (160 amol) and 190 fM (50 amol) for the event-specific and the taxon-specific targets, respectively. Results indicate that the method could be applied for GMO quantification below the European labeling threshold level (0.9%), offering a general approach for the rapid quantification of specific GMO events in foods. Copyright © 2015 Elsevier B.V. All rights reserved.

Evaluating β Diversity as a Surrogate for Species Representation at Fine Scale.

PubMed

Beier, Paul; Albuquerque, Fábio

2016-01-01

Species turnover or β diversity is a conceptually attractive surrogate for conservation planning. However, there has been only 1 attempt to determine how well sites selected to maximize β diversity represent species, and that test was done at a scale too coarse (2,500 km2 sites) to inform most conservation decisions. We used 8 plant datasets, 3 bird datasets, and 1 mammal dataset to evaluate whether sites selected to span β diversity will efficiently represent species at finer scale (sites sizes < 1 ha to 625 km2). We used ordinations to characterize dissimilarity in species assemblages (β diversity) among plots (inventory data) or among grid cells (atlas data). We then selected sites to maximize β diversity and used the Species Accumulation Index, SAI, to evaluate how efficiently the surrogate (selecting sites for maximum β diversity) represented species in the same taxon. Across all 12 datasets, sites selected for maximum β diversity represented species with a median efficiency of 24% (i.e., the surrogate was 24% more effective than random selection of sites), and an interquartile range of 4% to 41% efficiency. β diversity was a better surrogate for bird datasets than for plant datasets, and for atlas datasets with 10-km to 14-km grid cells than for atlas datasets with 25-km grid cells. We conclude that β diversity is more than a mere descriptor of how species are distributed on the landscape; in particular β diversity might be useful to maximize the complementarity of a set of sites. Because we tested only within-taxon surrogacy, our results do not prove that β diversity is useful for conservation planning. But our results do justify further investigation to identify the circumstances in which β diversity performs well, and to evaluate it as a cross-taxon surrogate.

Cyclestheria hislopi (Crustacea: Branchiopoda): a group of morphologically cryptic species with origins in the Cretaceous.

PubMed

Schwentner, Martin; Clavier, Simon; Fritsch, Martin; Olesen, Jørgen; Padhye, Sameer; Timms, Brian V; Richter, Stefan

2013-03-01

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI>13%, EF1α>3% and 28S>4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian-Australian lineage, with the latter diverging further in the Paleogene. Today's circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera. Copyright © 2012 Elsevier Inc. All rights reserved.

PREFACE: 13th International Conference on Liquid and Amorphous Metals

NASA Astrophysics Data System (ADS)

Popel, Pjotr; Gelchinskii, Boris; Sidorov, Valeriy; Son, Leonid; Sabirzjanov, Alexandre

2007-06-01

The state of the art in the field of liquid and amorphous metals and alloys is regularly updated through two series of complementary international conferences, the LAM (Liquid and Amorphous Metals) and the RQ (Rapidly Quenched Materials). The first series of the conferences started as LM-1 in 1966 at Brookhaven for the basic understanding of liquid metals. The subsequent LM conferences were held in Tokyo (1972) and Bristol (1976). The conference was renewed in Grenoble (1980) as a LAM conference including amorphous metals and continued in Los Angeles (1983), Garmisch-Partenkirchen (1986), Kyoto (1989), Vienna (1992), Chicago (1995), Dortmund (1998), Yokohama (2001) and Metz (2004). The conferences are mainly devoted to liquid and amorphous metals and alloys. However, communications on some non-metallic systems such as semi conductors, quasicrystals etc, were accepted as well. The conference tradition strongly encourages the participation of junior researchers and graduate students. The 13th conference of the LAM series was organized in Ekaterinburg, Russia, by the Institute of Metallurgy of the Ural Branch of the Russian Academy of Sciences (IMet UB RAS) and Ural State Pedagogical University (USPU) and held on 8-13 July 2007 under the chairmanship of Professors Pjotr Popel (USPU) and Boris Gelchinskii (IMet UB RAS). There were 242 active and about 60 guest participants from 20 countries who attended the conference. There were no parallel sessions and all oral reports were separated into three groups: invited talks (40 min), full-scale (25 min) and brief (15 min) oral reports. The program included 10 sessions, ranging from purely theoretical subjects to technological application of molten and amorphous alloys. The following sessions took place: A) Electronic structure and transport, magnetic properties; B) Phase transitions; C) Structure; D) Atomic dynamics and transport; E) Thermodynamics; F) Modelling, simulation; G) Surface and interface; H) Mechanical properties and new materials; I) Quasicrystals; J) Industrial applications. The most representative sessions were E (53 reports), C (47), D (43) and F (40). All posters were exhibited during the first (sections A-E) or the last (sections F-J) three days of the conference. All the sessions took place in the Government House of Sverdlovsk Region where, in addition, everyone was able to enjoy dishes of Russian cuisine during lunches and coffee breaks. As usual, each oral session started from an invited talk. Therefore, 10 invited lecturers presented their reports. In accordance with contemporary tendency the first invited talk of M Yao (Kyoto University) was devoted to interrelations between liquid metal studies and nano-science. He pointed out that physics of disordered matter, especially liquid metals, has provided nano-science with basic ideas and theoretical tools such as ab initio MD simulation. K Tamura (Kyoto University) reported results of experimental investigation of expanded liquid rubidium showing that observed structural features originate from the instability of the low-density electron gas. Modern theory has predicted that interacting electron gas suffers a negative compressibility and the static dielectric-function (DF) becomes negative when electron density is sufficiently reduced. The negative DF is of special interest in connection with the possibility of a new type of superconductor. In the invited lecture of M I Mendelev and J R Morris (USA) MD simulations were performed to study phase transformations in supercooled liquid Al. The authors found that widely used EAM potential for Al provides vitrification for the cooling rates achievable in classical MD simulation, while other Al potentials provide crystallization under the same conditions. The reason for this difference, as well as features of the vitrification in the EA Al, were discussed. P Häussler (Chemnitz University) spoke about fundamental structure-forming processes in liquid and amorphous materials. He had proposed the resonance model as an autonomous missing link between the microscopic description of atoms/molecules, described by Schrödinger's equation, and the crystals where global concepts as planar resonances exist and Bloch's theorem is applied. D Holland-Moritz (Institut für Materialphysik, Köln) presented results of the first quasielastic neutron scattering experiments on electromagnetically levitated metallic melts. The studies are indicative of Arrhenius behaviour of the diffusion constants in the whole investigated temperature regime ranging from temperatures above the melting temperature up to the metastable regime of an undercooled liquid. L Son (USPU) discussed the existing analytical theories of liquid-liquid phase transitions that have been supposed for a wide variety of liquids, but are rather poorly understood analytically. The application of these theories to liquid metal systems was also demonstrated. An approach to study dynamics and kinetics of cavitation in stretched liquid metals by the classical molecular dynamics (MD) method was presented in the talk of G E Norman (Institute for High Temperatures, Moscow). Both quantitative and qualitative disagreements with the classic theory of homogeneous nucleation were found. Analytic extentions of MD results beyond the space and temporal limits accessible for the MD method were discussed also. G Wilde (University of Münster) spoke about experimental investigation of the impact of interface properties and, more specifically, of the interface morphology in matrix-encased metallic nanoparticles on macroscopic properties, such as melting transition by a combination of microscopic, microanalytical and calorimetric measurements. These results are discussed with respect to the underlying mechanisms that leads to size dependent phase equilibria. In the invited talk of V Keryvin (University of Rennes) the indentation ability was proposed to be used as a probe for pressure-sensitivity in metallic glasses. The main conclusion was: the indentation test provides good means to study the elasto-plastic behaviour of these materials as well as a relevant tool to subject them to multiaxial loadings. The influence of changes in local ordering of precursor melt on the formation of amorphous state and subsequent crystallization was a subject of a report presented by P Švec (Institute of Physics, Bratislava). The effect was shown for rapidly quenched Fe-Mo-B system with addition of Cu and substitution of Fe by Co prepared under varying conditions of planar flow casting and using master alloys with specific melt treatment. About 320 abstracts were received and 180 manuscripts were finally submitted for publication. All the papers followed invited lectures and full-scale oral reports were sent to the Journal of Physics: Condensed Matter for publication in a special issue. These papers will be published according to the current standard practices, policies and procedures of the Journal. All the papers following brief oral reports and posters were collected for this volume of Journal of Physics: Conference Series. All of them were edited by editors from Ekaterinburg. The Journal will provide access to all of the accepted papers free of charge via its web server. Afterwards, to publish and ship hardcopies of both the journals (Journal of Physics: Condensed Matter and Journal of Physics: Conference Series) and CDs containing all Conference papers. It was decided during the joint meeting of both the International Advisory Board and International Program Committee that the next conference in the LAM series, LAM14, will be arranged by the groups of A Di Cicco, Camerino University, and T Scopigno, University Roma `La Sapienza', in Rome, Italy. It is not an easy task to comment on new scientific tendencies in the field of liquid and amorphous alloys just after the conference. It takes one or two years to estimate the significance of the event. Only one conclusion is obvious: the LAM13 Conference had opened a door between the world scientific community and Russian scientists who have high expertise in the field but could not actively participate in the conferences of the LAM series before because of the situation in Russian economics. We are thankful to the Advisory and Program Committees of previous LAM12 conference in Metz and especially to Dr Monique Calvo-Dahlborg for their trust and the opportunity to manage such an outstanding event in Russia. In addition we would like to give all our sincere thanks to:

A candidate for the Global Stratotype Section and Point at the base of the Serpukhovian in the South Urals, Russia

NASA Astrophysics Data System (ADS)

Richards, B. C.; Nikolaeva, S. V.; Kulagina, E. I.; Alekseev, A. S.; Gorozhanina, E. N.; Gorozhanin, V. M.; Konovalova, V. A.; Goreva, N. V.; Joachimski, M. M.; Gatovsky, Y. A.

2017-12-01

The Verkhnyaya Kardailovka section is one of the best candidates for the GSSP (Global Stratotype Section and Point) at the base of the Stage (Mississippian). For boundary definition, the first appearance of the conodont Lochriea ziegleri Nemirovskaya, Perret et Meischner, 1994 in the lineage Lochriea nodosa (Bischoff, 1957)- L. ziegleri is used. L. ziegleri appears in the Venevian Substage somewhat below the base of the Serpukhovian in the Moscow Basin. The position of the FAD of L. ziegleri within the Hypergoniatites- Ferganoceras Genozone is confirmed and lies between 19.53 and 19.63 m above the section's base. Before 2010, deep-water stylonodular limestone containing the boundary in unnamed formation C at Kardailovka was well exposed but only 3 m of Viséan strata cropped out immediately below. Recent trenching exposed another 10 m of underlying Viséan carbonates in formation C and older Viséan siliciclastics and volcanics in unnamed formation B. The contact between formation B and underlying crinoidal limestones in unnamed formation A representing the middle Viséan Zhukovian (Tulian) regional Substage was excavated. The boundary succession, situated in the Magnitogorsk tectonic zone above the Devonian Magnitogorsk arc and Mississippian magmatic and sedimentary rift succession, was deposited west of the Kazakhstanian continent during closure of the Ural Ocean. In the lower part of the section, Viséan tuffaceous siliciclastics and volcanics of formation B record rapid deepening after deposition of neritic middle Viséan crinoid lime grainstone of formation A and subsequent subaerial exposure. The overlying condensed upper Viséan to Serpukhovian succession in formation C comprises deep-water limestone deposited in a sediment-starved basin recording minor turbidite influx and carbonate-mound development. The δ13Ccarb plot shows a positive shift of 1‰ V-PDB (from +2 to +3‰) between 17.0 and 17.75 m (3.05 and 1.97 m below FAD L. ziegleri). The δ18Oapatite graph displays a prominent upward shift from 19.9 to 21.1‰ V-SMOW (at 19.15 to 19.51 m) in the nodosa Zone below FAD of Lochriea ziegleri.

Ural Eye and Medical Study: description of study design and methodology.

PubMed

Bikbov, Mukharram; Fayzrakhmanov, Rinat R; Kazakbaeva, Gyulli; Jonas, Jost B

2018-06-01

Since there is a scarcity on population-based health information available for Russia, we conducted this project to assess the prevalence of major ocular and systemic disorders and their associated risk factors. A population-based cross-sectional study (Ural Eye and Medical Study (UEMS)) was performed in Bashkortostan 1300 km east of Moscow. The sampling frame consisted of all inhabitants aged over 40 years and living in an urban study area in the capital city Ufa and a rural region at 65 km outside of Ufa. The target sample size was 2500 individuals for the urban region and 2500 persons for the rural region. The study participants underwent a detailed interview, a detailed ophthalmologic examination including biometry and optical coherence tomography, and clinical examination including assessment of electrocardiography, hearing test, blood sampling, spirometry, and hand grip dynamometry. After a first study period, the study population included 4254 individuals with a mean age of 60.3 ± 11.1 years (range: 40-94 years), mean body weight of 74.8 ± 14.4 kg (range: 31-170 kg), body height of 163.6 ± 8.9 cm (range: 112-196), body mass index of 28.0 ± 5.1 kg/m 2 (range: 13.96-60.96 kg/m 2 ), mean systolic blood pressure of 133.7 ± 21.0 mmHg (range: 84-232 mmHg), and mean diastolic blood pressure of 81.2 ± 10.6 mmHg (range: 40-134 mmHg). Mean refractive error was -0.21 ± 1.94 D and mean intraocular pressure was 13.6 ± 3.9 mmHg. The UEMS provides population-based normative data for a Russian region on the quantitative traits such as axial length, quality of life and lifestyle including smoking and alcohol consumption, and prevalence and risk factors of ocular and systemic diseases such as diabetes mellitus, arterial hypertension, chronic obstructive pulmonary disease, and depression.

Maastrichtian sedimentation and palaeoenvironments of the Saratov Volga region

NASA Astrophysics Data System (ADS)

Iakovishina, Elena; Blinova, Irina; Kopaevich, Ludmila; Vishnevskaya, Valentina; Bordunov, Sergey

2016-04-01

The Saratov Volga region was a shallow-marine epicontinental basin North-Eastern shelf zone of the Tethys Ocean in the Maastrichtian. The basis for the modeling conditions of sedimentation was the detection mineral composition of rocks, as well as the contents of various chemical elements in rocks in three reference sections: Lower Bannovka, quarries "Bolshevik" and "Kommunar". Rocks of quarries "Bolshevik" and "Kommunar" characterized by quartz-calcite mineral association. The main rock-forming mineral is calcite, small amounts in rocks contain quartz. Other mineral composition characterized section Lower Bannovka. At the base of the section in the rock marked the presence of the opal. The source of silica are radiolarians. Favorable conditions for the existence of which is cold deep water enriched with SiO2. Above the section marked authigenic glauconite, which are confined to zones of skip in sedimentation.Further up begins to dominate the accumulation of calcite with rich bentic foraminifera. Clay minerals in rocks of the section Lower Bannovka presented montmorillonite and illite. The relationship of chemical elements and their alkali modules allow to detail the conditions of sedimentation. The ratio of Fe/Mn in them varies from 44 to 5729. Higher values are characteristic of glauconite sandstones. Up the section marked decrease in the Ti/Zr, indicating that the increase in the distance from the source area to the place of deposition. The similarity values of the ratio Ti/Zr samples indicates a community source area. Sedimentation Model revealed the impact of the PreUral strait connecting Tethys and Paleoarktic. Through the Strait of deep cold water saturated with SiO2, penetrated into the of the Saratov Volga region, were accumulated clay. The closing of the PreUral Strait changed the conditions of sedimentation, the associated fall in sea levels due to global cooling reflected in the crisis of radiolarians, increase in the number of glauconite. Subsequent warming and warm-water transgression caused dominance of carbonates. The work was supported by grants 15-05-04990, 15-05-04700 Russian Foundation for Basic Research and IGCP project 609.

Nitrogen fixation activity in biological soil crusts dominated by cyanobacteria in the Subpolar Urals (European North-East Russia).

PubMed

Patova, Elena; Sivkov, Michail; Patova, Anna

2016-09-01

The nitrogen fixation by biological soil crusts with a dominance of cyanobacteria was studied using the acetylene reduction assay in the territory of the Subpolar Urals (65°11' N, 60°18' E), Russia. The field measurements of nitrogen fixation activity were conducted in situ for two different types of soil crusts dominated by Stigonema (V1 type) and Nostoc with Scytonema (V2 type). The nitrogen fixation process had similar dynamics in both crusts but nitrogen fixation rates were different. The crusts of the V2 type showed a significantly higher acetylene reduction activity, with ethylene production rate of 1.76 ± 0.49 g C2H4 m(-2) h(-1) at 15°C, compared with V1-type soil crusts, with a rate of 0.53 ± 0.21 mg C2H4 m(-2) h(-1) at 15°C. The daily value of acetylene reduction activity in V2-type soil crusts was 32.7 ± 6.2 mg C2H4 m(-2) d(-1) and in V1-type crusts, 12.3 ± 1.8 mg C2H4 m(-2) d(-1) After recalculation for N, the daily values of nitrogen fixation were in the range 3.3-22.3 mg N m(-2) d(-1), which is a few times higher than the values of N input from the precipitation to the soil in the studied regions. The dependence of nitrogen-fixation activity on temperature and light intensity of biological soil crusts was investigated. On the basis of temperature models obtained from the dependence, the nitrogen balance was calculated for the growing season (approximately 120 days). The crusts dominated by Stigonema species were fixing 0.3 g N m(-2) (ethylene production rate, 1.10 g C2H4 m(-2)) and crusts dominated by Nostoc and Scytonema were fixing 1.3 g N m(-2) (4.10 g C2H4 m(-2)). © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Shear waves in lithosphere studies on the territory of the U.S.S.R.

NASA Astrophysics Data System (ADS)

Alekseev, A. S.; Egorkin, A. V.; Pavlenkova, N. I.

1988-11-01

Thousands of kilometers of DSS profiles were compiled with three-component stations in the U.S.S.R. The results showed that the usual shots in holes or water basins normally create not only P-waves but shear waves as well. The most favourable condition for their generation is the presence of a sharp seismic boundary near the source, for example, the basement surface. The S-wave field, as a rule, contains all the types of reflected and refracted waves that are found in the P-field. The difference is in lower frequencies (they are lower by one third), somewhat higher intensity, and greater variability of amplitudes of shear waves. When recording the S-waves, the major information is obtained from the velocity relation VP/ VS = γ with depth and laterally. It reveals that three major factors are affecting this relation: the degree of rock fissuring, the composition of rocks and the temperatures at depth. Reduction of fissuring with depth i.e. with greater distances from the source, results in an overall drop of γ. As the composition of the uppermost crust changes (the Urals), γ increases in blocks composed of basic rocks. This value shows little changes on the Baltic and Ukrainian shields. On the Siberian platform, γ first increases with depth from 1.71 up to 1.76, probably, due to the dilatancy effect, and then it decreases to values less than 1.7 in the lower crust and upper mantle. In Western Siberia γ grows with depth reaching 1.79 in the lower crust; it is somewhat reduced in the mantle but still above 1.7. This can be ascribed apparently to a higher temperature regime of the lower crust in Western Siberia. In many regions a splitting of the shear waves of different polarization is observed due to velocity anisotropy. This was found for the first (refracted) waves in the Urals and for reflected waves from the M-boundary on the Siberian platform. In both cases anisotropy is associated with the crust. On the Ukrainian and Baltic shields the difference in the velocities of SH and SV-waves was not recorded.

CHIRONOMID EMERGENCE AND RELATIVE EMERGENT BIOMASS FROM TWO ALABAMA STREAMS

EPA Science Inventory

Chironomid pupal exuviae were sampled monthly using drift nets and hand sieves over an annual cycle from Hendrick Mill Branch (HMB; Blount County, AL) and Payne Creek (PC; Hale County, AL). Taxon richness, community composition, and emergence phonologies were similar despite mar...

A dinosaur missing-link? Chilesaurus and the early evolution of ornithischian dinosaurs.

PubMed

Baron, Matthew G; Barrett, Paul M

2017-08-01

The enigmatic dinosaur taxon Chilesaurus diegosuarezi was originally described as a tetanuran theropod, but this species possesses a highly unusual combination of features that could provide evidence of alternative phylogenetic positions within the clade. In order to test the relationships of Chilesaurus , we added it to a new dataset of early dinosaurs and other dinosauromorphs. Our analyses recover Chilesaurus in a novel position, as the earliest diverging member of Ornithischia, rather than a tetanuran theropod. The basal position of Chilesaurus within the clade and its suite of anatomical characters suggest that it might represent a 'transitional' taxon, bridging the morphological gap between Theropoda and Ornithischia, thereby offering potential insights into the earliest stages of ornithischian evolution, which were previously obscure. For example, our results suggest that pubic retroversion occurred prior to some of the craniodental and postcranial modifications that previously diagnosed the clade (e.g. the presence of a predentary bone and ossified tendons). © 2017 The Author(s).

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

PubMed Central

Anwar, Nadia; Hunt, Ela

2009-01-01

Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium

DOE PAGES

Chase, Alexander B.; Arevalo, Philip; Polz, Martin F.; ...

2016-11-22

Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus Curtobacterium, as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominantly associates it as the causal pathogen in the agricultural crops of dry beans. Therefore, we sought to investigate whether the abundance of this genus was because of its role as a plant pathogen or another ecological role. By collating >24,000 16S rRNA sequences with 120 genomes across the Microbacteriaceae family, wemore » show that Curtobacterium has a global distribution with a predominant presence in soil ecosystems. Moreover, this genus harbors a high diversity of genomic potential for the degradation of carbohydrates, specifically with regards to structural polysaccharides. We conclude that Curtobacterium may be responsible for the degradation of organic matter within litter communities.« less

A new miniaturized lizard from the late Eocene of France and Spain.

PubMed

Bolet, Arnau; Augé, Marc

2014-03-01

We report here a new lizard genus and species shared by two late Eocene localities situated at both versants of the present Pyrenees (South-Western Europe), one located in France (Escamps, MP19), and the other in Catalonia, Spain (Sossís, MP17a). The recovered specimens are remarkable because of their small size and peculiar morphology. Features of the dentary are interpreted as adaptations to a fossorial or semi-fossorial lifestyle, although such modifications obscure the exact phylogenetic relationships of the new taxon. We suggest that it might represent a further example of scincoid lizard that independently achieved adaptations for burrowing or surface-dwelling. This taxon reinforces the hypotheses that link the Southern Pyrenean assemblages to those from France rather than to those of the rest of the Iberian Peninsula, which are supposed to be somehow isolated and endemic to a certain degree during the middle and late Eocene, forming part of the so-called Western Iberian Bioprovince. Copyright © 2014 Wiley Periodicals, Inc.

A new species of Acanthodactylus Fitzinger 1834 (Sauria: Lacertidae) from southern Iran.

PubMed

Nastaran, Heidari; Nasrullah Rastegar, Pouyani; Eskandar, Rastegar-Pouyani; Mehdi, Rajabizadeh

2013-01-01

A new and distinctive species of lacertid genus Acanthodactylus Fitzinger, 1834 is described from 7 km east of Khamir Port, Hormozgan Province, southern Iran at an elevation of 30-40m above sea level (asl). Analyses of morphological characters and the comparison with other formerly known species of this genus have proven the status of this taxon as a new, distinct species. Combinations of scalation characters and distinct morphology, coloration and habitat peculiarities in calcareous mountains distinguish Acanthodactylus khamirensis sp.nov from all remaining species of the genus in the area. In order to show the validity of the new species, we carried out a comparative statistical analysis using 13 metric and six meristic morphological characters on all of the neighboring congeners of the new species using descriptive (one-way ANOVA) as well as multivariate analyses (PCA and DFA). The results confirm the specific status of the new taxon. Detailed information and an updated identification key for the genus A canthodactylus in Iran are presented.

Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus

PubMed Central

Nunes, Marcio R.T.; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C.; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P.; Carvalho, Valeria L.; da Silva, Sandro Patroca; Cardoso, Jedson F.; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G.; Widen, Steven G.; Vasconcelos, Pedro F.C.; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B.

2017-01-01

The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses. PMID:28193550

Genetic characterization, molecular epidemiology, and phylogenetic relationships of insect-specific viruses in the taxon Negevirus.

PubMed

Nunes, Marcio R T; Contreras-Gutierrez, María Angélica; Guzman, Hilda; Martins, Livia C; Barbirato, Mayla Feitoza; Savit, Chelsea; Balta, Victoria; Uribe, Sandra; Vivero, Rafael; Suaza, Juan David; Oliveira, Hamilton; Nunes Neto, Joaquin P; Carvalho, Valeria L; da Silva, Sandro Patroca; Cardoso, Jedson F; de Oliveira, Rodrigo Santo; da Silva Lemos, Poliana; Wood, Thomas G; Widen, Steven G; Vasconcelos, Pedro F C; Fish, Durland; Vasilakis, Nikos; Tesh, Robert B

2017-04-01

The recently described taxon Negevirus is comprised of a diverse group of insect-specific viruses isolated from mosquitoes and phlebotomine sandflies. In this study, a comprehensive genetic characterization, molecular, epidemiological and evolutionary analyses were conducted on nearly full-length sequences of 91 new negevirus isolates obtained in Brazil, Colombia, Peru, Panama, USA and Nepal. We demonstrated that these arthropod restricted viruses are clustered in two major phylogenetic groups with origins related to three plant virus genera (Cilevirus, Higrevirus and Blunevirus). Molecular analyses demonstrated that specific host correlations are not present with most negeviruses; instead, high genetic variability, wide host-range, and cross-species transmission were noted. The data presented here also revealed the existence of five novel insect-specific viruses falling into two arthropod-restrictive virus taxa, previously proposed as distinct genera, designated Nelorpivirus and Sandewavirus. Our results provide a better understanding of the molecular epidemiology, evolution, taxonomy and stability of this group of insect-restricted viruses. Copyright © 2017 Elsevier Inc. All rights reserved.

The Latent Structure of Attention Deficit/Hyperactivity Disorder in an Adult Sample

PubMed Central

Marcus, David K.; Norris, Alyssa L.; Coccaro, Emil F.

2012-01-01

The vast majority of studies that have examined the latent structure of attention deficit/hyperactivity disorder (ADHD) in children and adolescents have concluded that ADHD has a dimensional latent structure. In other words, ADHD symptomatology exists along a continuum and there is no natural boundary or qualitative distinction (i.e., taxon) separating youth with ADHD from those with subclinical inattention or hyperactivity/impulsivity problems. Although adult ADHD appears to be less prevalent than ADHD in youth (which could suggest a more severe adult ADHD taxon), researchers have yet to examine the latent structure of ADHD in adults. The present study used a sample (N = 600) of adults who completed a self-report measure of ADHD symptoms. The taxometric analyses revealed a dimensional latent structure for inattention, hyperactivity/impulsivity, and ADHD. These findings are consistent with previous taxometric studies that examined ADHD in children and adolescents, and with contemporary polygenic and multifactorial models of ADHD. PMID:22480749

The toxicity of arsenic(III), chromium(VI) and zinc to groundwater copepods.

PubMed

Hose, G C; Symington, K; Lott, M J; Lategan, M J

2016-09-01

Groundwater ecosystems globally are threatened by anthropogenic contamination, yet there are few ecotoxicological data using obligate groundwater biota on which to base risk assessments. Copepods are found inhabiting aquifers of different geologies around the world and so are a useful taxon for use in ecotoxicological studies of groundwater. The aim of this study was to test the sensitivity of obligate groundwater copepods to metal contaminants (arsenic(III), chromium(VI) and zinc) in groundwater in static 96 h, 14 days and 28 days exposure tests. The copepods were variably sensitive to As, Cr and Zn, with Cr being the most toxic across all taxa. No taxon was consistently most sensitive and there was no apparent relationship between the hardness, pH and organic carbon concentration of the diluent water and the sensitivity of biota. As expected, toxicity increased with exposure period and we encourage the use of longer exposure periods in future toxicity tests with groundwater organisms to reflect the greater exposure periods likely to be associated with groundwater contamination.

Morphogenia: a new genus of the Neotropical tribe Jubini (Coleoptera, Staphylinidae, Pselaphinae) from the Brazilian Amazon.

PubMed

Parker, Joseph

2014-01-01

A new genus and species of the large Neotropical pselaphine tribe Jubini is described from Manaus, Brazil, based on material preserved in the Natural History Museum, London. Morphogenia struhli gen. et sp. n. represents the possible sister taxon of the abundant and speciose genus Barrojuba Park, sharing with it the putatively derived condition of anterolaterally shifted vertexal foveae, producing a smoothly convex vertex devoid of fovea or sulci. However, unlike Barrojuba, Morphogenia retains a plesiomorphic antebasal sulcus on the pronotum in both sexes, and additionally lacks elaborate abdominal fovea-like pockets and teeth on the lateral margins of the pronotum that are typical of Barrojuba. The genus is also unusual among jubine genera in lacking the characteristic V- or Y-shaped gular carina. In contrast to the commonly-collected Barrojuba, specimens of Morphogenia are absent in extensive jubine collections housed in museums in the United States, indicating that the new taxon may be relatively scarce or localised.

Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice

PubMed Central

Shavit Grievink, Liat; Penny, David; Holland, Barbara R.

2013-01-01

Phylogenetic studies based on molecular sequence alignments are expected to become more accurate as the number of sites in the alignments increases. With the advent of genomic-scale data, where alignments have very large numbers of sites, bootstrap values close to 100% and posterior probabilities close to 1 are the norm, suggesting that the number of sites is now seldom a limiting factor on phylogenetic accuracy. This provokes the question, should we be fussy about the sites we choose to include in a genomic-scale phylogenetic analysis? If some sites contain missing data, ambiguous character states, or gaps, then why not just throw them away before conducting the phylogenetic analysis? Indeed, this is exactly the approach taken in many phylogenetic studies. Here, we present an example where the decision on how to treat sites with missing data is of equal importance to decisions on taxon sampling and model choice, and we introduce a graphical method for illustrating this. PMID:23471508