High‐resolution conodont biostratigraphy from the Darriwilian Stage (Middle Ordovician) of the Argentine Precordillera and biodiversity analyses: a CONOP9 approach

Ordovician conodonts have been extensively documented in the Argentine Precordillera, providing a robust database for a diverse set of palaeontological studies. Despite the numerous studies, the published taxonomy and stratigraphical ranges, data remain contradictory for particular time intervals. Data from a new conodont collection from the Gualcamayo Formation exposed at the Cerro La Chilca section, and new information on the occurrence and ranges of species from the Las Chacritas and Las Aguaditas sections are presented herein. We used a computer‐assisted numerical sequencing program (CONOP9) to construct a composite stratigraphical range chart from data of 57 conodont species in four sections from the Argentine Precordillera. The identified zones of Lenodus variabilis, Yangtzeplacognathus crassus, Eoplacognathus pseudoplanus and Eoplacognathus suecicus allowed us to verify and adjust the biostratigraphical scheme for the Darriwilian of the Central Precordillera. Additionally, species of the genera Histiodella, namely Histiodella sinuosa, Histiodella holodentata, Histiodella kristinae and Histiodella bellburnenisis, enable a reasonable correlation between the Histiodella‐based zonation and the Baltoscandian zonation. Conodont diversity is evaluated using conventional measures (total diversity and normalized diversity) and an interval‐free approach with CONOP9 software. Our data show a positive pattern in conodont diversification, increasing rapidly through the L. variabilis to the Y. crassus zones and reaching a peak in the E. pseudoplanus Zone. When analysing diversity fluctuations with respect to the environmental changes within the depositional basin, migrations in and out of the basin related to local sea level fluctuations appear to be an important process driving the conodont diversity pattern in the Precordillera.     

Pea-derived vaccines demonstrate high immunogenicity and protection in rabbits against rabbit haemorrhagic disease virus

Vaccines against rabbit haemorrhagic disease virus (RHDV) are commercially produced in experimentally infected rabbits. A genetically engineered and manufactured version of the major structural protein of RHDV (VP60) is considered to be an alternative approach for vaccine production. Plants have the potential to become an excellent recombinant production system, but the low expression level and insufficient immunogenic potency of plant‐derived VP60 still hamper its practical use. In this study, we analysed the expression of a novel multimeric VP60‐based antigen in four different plant species, including Nicotiana tabacum L., Solanum tuberosum L., Brassica napus L. and Pisum sativum L. Significant differences were detected in the expression patterns of the novel fusion antigen cholera toxin B subunit (CTB)::VP60 (ctbvp60_SEKDEL) at the mRNA and protein levels. Pentameric CTB::VP60 molecules were only detected in N. tabacum and P. sativum, and displayed equal levels of CTB, at approximately 0.01% of total soluble protein (TSP), and traces of detectable VP60. However, strong enhancement of the CTB protein content via self‐fertilization was only observed in P. sativum, where it reached up to 0.7% of TSP. In rabbits, a strong decrease in the protective vaccine dose required from 48–400 µg potato‐derived VP60 [ Castanon, S., Marin, M.S., Martin‐Alonso, J.M., Boga, J.A., Casais, R., Humara, J.M., Ordas, R.J. and Parra, F. (1999) Immunization with potato plants expressing VP60 protein protects against rabbit hemorrhagic disease virus. J. Virol. 73 , 4452–4455; Castanon, S., Martin‐Alonso, J.M., Marin, M.S., Boga, J.A., Alonso, P., Parra, F. and Ordas, R.J. (2002) The effect of the promoter on expression of VP60 gene from rabbit hemorrhagic disease virus in potato plants. Plant Sci. 162 , 87–95] to 0.56–0.28 µg antigenic VP60 (measured with VP60 enzyme‐linked immunosorbent assay) of crude CTB::VP60 pea extracts was demonstrated. Rabbits immunized with pea‐derived CTB::VP60 showed anti‐VP60‐specific antibodies, similar to RikaVacc^®‐immunized rabbits, and survived RHDV challenge.     

The non‐hierarchical,non‐uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X‐ray microtomography

Hammel, J.U., Filatov, M.V., Herzen, J, Beckmann, F., Kaandorp, J.A. and Nickel M. 2011. The non‐hierarchical, non‐uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X‐ray microtomography. —Acta Zoologica (Stockholm) 00 :1–12. As sessile filter feeders, sponges rely on a highly efficient fluid transport system. Their physiology depends on efficient water exchange, which is performed by the aquiferous system. This prominent poriferan anatomical character represents a dense network of incurrent and excurrent canals on which we lack detailed 3D models. To overcome this, we investigated the complex leucon‐type architecture in the demosponge Tethya wilhelma using corrosion casting, microtomography, and 3D reconstructions. Our integrative qualitative and quantitative approach allowed us to create, for the first time, high‐resolution 3D representations of entire canal systems which were used for detailed geometric and morphometric measurements. Canal diameters lack distinct size classes, and bifurcations are non‐uniformly ramified. A relatively high number of bifurcations show previously unknown and atypical cross‐sectional area ratios. Scaling properties and topological patterns of the canals indicate a more complex overall architecture than previously assumed. As a consequence, it might be more convenient to group canals into functional units rather than hierarchical clusters. Our data qualify the leucon canal system architecture of T. wilhelma as a highly efficient fluid transport system adapted toward minimal flow resistance. Our results and approach are relevant for a better understanding of sponge biology and cultivation techniques.     

Comparative analysis of core collection sampling methods for mandarin germplasm based on molecular and phenotypic data

Gene banks have been established to conserve the genetic diversity of crop species. Large germplasm collections lead to management problems (space, maintenance costs, etc.), especially in collections involving species with recalcitrant seeds that must be maintained as growing plants. Core collections (CCs) are thus developed to reduce the size of large germplasm collections while keeping the maximum variability. This also facilitates fine phenotypic evaluation. In this study, several software packages (DARwin, PowerMarker and MSTRAT) and methods (Max length subtree, M strategy, simulated annealing and MinSD) were compared to define a mandarin (Citrus reticulata) CC. One hundred and sixty‐seven accessions were sampled from two germplasm collections, which were genotyped with 50 SSR, 24 InDel and 68 single nucleotide polymorphism markers. All the CC obtained were tested for the maintenance of the genetic variability parameters (Ho and He) of the initial collection, the level of linkage disequilibrium (LD) and the phenotypic diversity retention. The Max length subtree function from DARWin seemed to be the most appropriate method for establishing a CC in C. reticulata. It maintained 96.82% of the allelic richness and 17.96% of the size of the initial collection with only 30 accessions. Besides it did not increase the LD (r² value) of the initial collection and retained the vast majority of the phenotypic variability. However, a CC with 70 accessions would be more helpful for genetic association studies.     

A collection of enhancer trap insertional mutants for functional genomics in tomato

With the completion of genome sequencing projects, the next challenge is to close the gap between gene annotation and gene functional assignment. Genomic tools to identify gene functions are based on the analysis of phenotypic variations between a wild type and its mutant; hence, mutant collections are a valuable resource. In this sense, T‐DNA collections allow for an easy and straightforward identification of the tagged gene, serving as the basis of both forward and reverse genetic strategies. This study reports on the phenotypic and molecular characterization of an enhancer trap T‐DNA collection in tomato (Solanum lycopersicum L.), which has been produced by Agrobacterium‐mediated transformation using a binary vector bearing a minimal promoter fused to the uidA reporter gene. Two genes have been isolated from different T‐DNA mutants, one of these genes codes for a UTP‐glucose‐1‐phosphate uridylyltransferase involved in programmed cell death and leaf development, which means a novel gene function reported in tomato. Together, our results support that enhancer trapping is a powerful tool to identify novel genes and regulatory elements in tomato and that this T‐DNA mutant collection represents a highly valuable resource for functional analyses in this fleshy‐fruited model species.     

Evolution of Paleocene to Early Eocene larger benthic foraminifer assemblages of the Indus Basin,Pakistan

Afzal, J., Williams, M., Leng, M.J., Aldridge, R.J. & Stephenson, M.H. 2011: Evolution of Paleocene to Early Eocene larger benthic foraminifer assemblages of the Indus Basin, Pakistan. Lethaia, Vol. 44, pp. 299–320. The Paleocene–Early Eocene carbonate successions of the Indus Basin in Pakistan formed on the northwestern continental shelf margin of the Indian Plate in the eastern Tethys Ocean. Based on larger benthic foraminifera (LBF), eight Tethyan foraminiferal biozones (SBZ1–SBZ8) spanning the Paleocene to Early Eocene interval are identified. The base of the Eocene is identified by the first appearance of Alveolina sp. Other stratigraphically important LBFs that are characteristic of the earliest Eocene are Ranikothalia nuttalli, Discocyclina dispansa and Assilina dandotica. Stable isotope analysis through the Paleocene–Eocene (P–E) boundary interval identifies more positive δ¹³C values for the Late Paleocene (+3.4‰ to +3.0‰) and lower values (+2.7‰ to +1.6‰) for the earliest Eocene. However, there is insufficient sampling resolution to identify the maximum negative δ¹³C excursion of the Paleocene–Eocene Thermal Maximum. During Late Paleocene times LBF assemblages in the Indus Basin were taxonomically close to those of west Tethys, facilitating biostratigraphic correlation. However, this faunal continuity is lost at the P–E boundary and the earliest Eocene succession lacks typical west Tethys Nummulites, while Alveolina are rare; LBFs such as Miscellanea and Ranikothalia continue to dominate in the Indus Basin. The absence of Nummulites from the earliest Eocene of Pakistan and rarity of Alveolina, elsewhere used as the prime marker for the base of the Eocene, may imply biogeographical barriers between east and west Tethys, perhaps caused by the initial stages of India‐Asia collision. Later, at the level of the Eocene SBZ8 Biozone, faunal links were re‐established and many foraminifera with west Tethys affinities appeared in east Tethys, suggesting the barriers to migration ceased. □Biostratigraphy, Eocene, India‐Asia collision, larger benthic foraminifera, palaeoecology, Paleocene.     

An in vitro system for the rapid functional characterization of genes involved in carotenoid biosynthesis and accumulation

We have developed an assay based on rice embryogenic callus for rapid functional characterization of metabolic genes. We validated the assay using a selection of well‐characterized genes with known functions in the carotenoid biosynthesis pathway, allowing rapid visual screening of callus phenotypes based on tissue color. We then used the system to identify the functions of two uncharacterized genes: a chemically synthesized β–carotene ketolase gene optimized for maize codon usage, and a wild‐type Arabidopsis thaliana ortholog of the cauliflower Orange gene. In contrast to previous reports (Lopez, A.B., Van Eck, J., Conlin, B.J., Paolillo, D.J., O'Neill, J. and Li, L. ( 2008 ) J. Exp. Bot. 59, 213–223; Lu, S., Van Eck, J., Zhou, X., Lopez, A.B., O'Halloran, D.M., Cosman, K.M., Conlin, B.J., Paolillo, D.J., Garvin, D.F., Vrebalov, J., Kochian, L.V., Küpper, H., Earle, E.D., Cao, J. and Li, L. ( 2006 ) Plant Cell 18, 3594–3605), we found that the wild‐type Orange allele was sufficient to induce chromoplast differentiation. We also found that chromoplast differentiation was induced by increasing the availability of precursors and thus driving flux through the pathway, even in the absence of Orange. Remarkably, we found that diverse endosperm‐specific promoters were highly active in rice callus despite their restricted activity in mature plants. Our callus system provides a unique opportunity to predict the effect of metabolic engineering in complex pathways, and provides a starting point for quantitative modeling and the rational design of engineering strategies using synthetic biology. We discuss the impact of our data on analysis and engineering of the carotenoid biosynthesis pathway.     

An optimized microsatellite marker set for detection of Metarhizium anisopliae genotype diversity on field and regional scales

Thirty-three Metarhizium anisopliae isolates sampled across Switzerland as well as 35 and 36 M. anisopliae isolates sampled from two field sites were assembled in three isolate collections. All isolates were analyzed using 27 newly developed and 14 previously published microsatellite markers. The 41 markers allowed for detection of 25 genotypes in the Swiss collection while 30 and 11 genotypes were detected in the two field collections. This indicated high genetic diversity on a regional as well as on a field scale. In order to improve genotyping efficiency, an optimized marker set, which allows discrimination of a large number of genotypes with as few markers as possible was developed. The optimized marker set consisted of 16 common markers, which provided resolution close to maximal resolution in all three collections (91–93 %). The results demonstrated that optimized marker sets have to be validated before large scale application to previously unassessed collections in order to avoid suboptimal resolution. This genetic tool will be valuable for analyses of genetic population structure of M. anisopliae in different habitats on a regional as well as on a field scale.     

Investigating human responses to political and environmental change through paleodiet and paleomobility

Bioarchaeological approaches are well suited for examining past responses to political and environmental changes. In the Andes, we hypothesized that political and environmental changes around AD 1100 resulted in behavioral changes, visible as shifts in paleodiet and paleomobility, among individuals in the San Pedro de Atacama oases and Loa River Valley. To investigate this hypothesis, we generated carbon and oxygen isotope data from cemeteries dating to the early Middle Horizon (Larache, Quitor‐5, Solor‐3), late Middle Horizon (Casa Parroquial, Coyo Oriental, Coyo‐3, Solcor‐Plaza, Solcor‐3, Tchecar), and Late Intermediate Period (Caspana, Quitor‐6 Tardío, Toconce, Yaye‐1, Yaye‐2, Yaye‐3, Yaye‐4). Carbon isotope data demonstrate a greater range of carbon sources during the late Middle Horizon compared with the Late Intermediate Period; while most individuals consumed largely C₃ sources, some late Middle Horizon individuals consumed more C₄ sources. Oxygen isotope data demonstrate greater diversity in drinking water sources during the late Middle Horizon compared with the Late Intermediate Period. Water samples were analyzed to provide baseline data on oxygen isotope variability within the Atacama Desert, and demonstrated that oxygen isotope values are indistinguishable in the San Pedro and Loa Rivers. However, oxygen isotope values in water sources in the high‐altitude altiplano and coast are distinct from those in the San Pedro and Loa Rivers. In conclusion, instead of utilizing a wider variety of resources after environmental and political changes, individuals exhibited a wider range of paleodietary and paleomobility strategies during the Middle Horizon, a period of environmental and political stability. Am J Phys Anthropol 157:179–201, 2015. © 2015 Wiley Periodicals, Inc.     

Revised correlation of Silurian Provincial Series of North America with global and regional chronostratigraphic units and δ13Ccarb chemostratigraphy

Cramer, B.D., Brett, C.E., Melchin, M.J., Männik, P., Kleffner, M.A., McLaughlin, P.I., Loydell, D.K., Munnecke, A., Jeppsson, L., Corradini, C., Brunton, F.R. & Saltzman, M.R. 2011: Revised correlation of Silurian Provincial Series of North America with global and regional chronostratigraphic units and δ¹³C_carb chemostratigraphy. Lethaia, Vol. 44, pp. 185–202. Recent revisions to the biostratigraphic and chronostratigraphic assignment of strata from the type area of the Niagaran Provincial Series (a regional chronostratigraphic unit) have demonstrated the need to revise the chronostratigraphic correlation of the Silurian System of North America. Recently, the working group to restudy the base of the Wenlock Series has developed an extremely high‐resolution global chronostratigraphy for the Telychian and Sheinwoodian stages by integrating graptolite and conodont biostratigraphy with carbonate carbon isotope (δ¹³C_carb) chemostratigraphy. This improved global chronostratigraphy has required such significant chronostratigraphic revisions to the North American succession that much of the Silurian System in North America is currently in a state of flux and needs further refinement. This report serves as an update of the progress on recalibrating the global chronostratigraphic correlation of North American Provincial Series and Stage boundaries in their type area. The revised North American classification is correlated with global series and stages as well as regional classifications used in the United Kingdom, the East Baltic, Australia, China, the Barrandian, and Altaj. Twenty‐four potential stage slices, based primarily on graptolite and conodont zones and correlated to the global series and stages, are illustrated alongside a new composite δ¹³C_carb curve for the Silurian. Conodont, graptolite, isotope, New York, Ontario, series, Silurian, stage.     

Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

Modern plant breeding can benefit from the allelic variation that exists in natural populations of crop wild relatives that evolved under natural selection in varying pedoclimatic conditions. In this study, next‐generation sequencing was used to generate 1.3 million genome‐wide single nucleotide polymorphisms (SNPs) on ex situ collections of Triticum urartu L., the wild donor of the A^u subgenome of modern wheat. A set of 75 511 high‐quality SNPs were retained to describe 298 T. urartu accessions collected throughout the Fertile Crescent. Triticum urartu showed a complex pattern of genetic diversity, with two main genetic groups distributed sequentially from west to east. The incorporation of geographical information on sampling points showed that genetic diversity was correlated to the geographical distance (R² = 0.19) separating samples from Jordan and Lebanon, from Syria and southern Turkey, and from eastern Turkey, Iran and Iraq. The wild emmer genome was used to derive the physical positions of SNPs on the seven chromosomes of the A^u subgenome, allowing us to describe a relatively slow decay of linkage disequilibrium in the collection. Outlier loci were described on the basis of the geographic distribution of the T. urartu accessions, identifying a hotspot of directional selection on chromosome 4A. Bioclimatic variation was derived from grid data and related to allelic variation using a genome‐wide association approach, identifying several marker–environment associations (MEAs). Fifty‐seven MEAs were associated with altitude and temperature measures while 358 were associated with rainfall measures. The most significant MEAs and outlier loci were used to identify genomic loci with adaptive potential (some already reported in wheat), including dormancy and frost resistance loci. We advocate the application of genomics and landscape genomics on ex situ collections of crop wild relatives to efficiently identify promising alleles and genetic materials for incorporation into modern crop breeding.     

Phylogenetic analysis of the north‐east Atlantic and Mediterranean species of the genus Stenosoma (Isopoda,Valvifera, Idoteidae)

Xavier, R., Santos, A. M., Harris, D. J., Sezgin, M., Machado, M., Branco, M. (2012). Phylogenetic analysis of the north‐east Atlantic and Mediterranean species of the genus Stenosoma (Isopoda, Valvifera, Idoteidae). —Zoologica Scripta, 41, 386–399. The marine isopod genus Stenosoma is widespread in the northern hemisphere. However, 12 of its 14 known species are found within the Mediterranean basin and adjacent regions of the north‐east Atlantic and the Black Sea. Such a high level of diversity confined to a limited region of a much larger circumglobal distribution suggests that the Mediterranean region may have played a crucial role in the evolutionary history of this genus. In the present work, the phylogeny of the genus Stenosoma was investigated on the basis of DNA sequencing data from one nuclear (28SrRNA) and two mitochondrial (COI, ND4) gene fragments obtained for nine of 12 Atlantic–Mediterranean species. Divergence time estimates point to a Tethyan origin of Stenosoma and suggest that the speciation events from which stem most of the extant species took place well before the Messinian Salinity Crisis. Stenosoma spinosum and Stenosoma appendiculatum are the only exceptions, as they apparently arose within the Mediterranean during the Pleistocene. Phylogenetic reconstruction agrees with current taxonomic status of most species. However, Stenosoma capito clustered in two distinct and well‐supported clades, one composed of eastern Mediterranean and Black Sea specimens and the other by western Mediterranean and Atlantic ones. Such polyphyly suggests the existence of a previously unrecognized species, Stenosoma sp., which so far has been confounded with S. capito.     

Analysis of the high- and low-spin Soret bands of horse-heart metmyoglobin complexes

Interest in the thermodynamics of the iron-binding site in hemoproteins has increased in recent years due to refinements in x-ray crystallographic studies of hemoproteins [see Deathage, J. F., Lee, R. S., Anderson, C. M. & Moffat, K. (1976) J. Mol. Biol. 104 , 687–706; Heidner, E. J., Ladner, R. C. & Perutz, M. F. (1976) J. Mol. Biol. 104 , 707–722; Deathage, J. F., Lee, R. S. & Moffat, K. (1976) J. Mol. Biol. 104 , 723–728; Ladner, R. C., Heidner, E. J. & Perutz, M. F. (1976) J. Mol. Biol. 114 , 385–414; Fermi, G. & Perutz, M. F. (1977) J. Mol. Biol. 114 , 421–431; Takano, T. (1977) J. Mol. Biol. 110 , 537–568 and 569–589], the synthesis and x-ray analysis of model heme compounds [see Scheidt, W. R. (1977) Acc. Chem. Res. 10 , 339–345; Kastner, M. E., Scheidt, W. R., Mashino, T. & Reed, C. A. (1978) J. Am. Chem. Soc. 100 , 666–667; Mashiko, T., Kastner, M. E., Spartalian, K., Scheidt, W. R. & Reed, C. A. (1978) J. Am. Chem. Soc. 100 , 6354–6362; Hill, H. A. O., Skite, P. P., Buchler, J. W., Luchr, H., Tonn, M., Gregson, A. K. & Pellizer, G. (1979) Chem. Commun. 4 , 151–152; and Scheidt, W. R., Cohen, I. A. & Kastner, M. E. (1979) Biochemistry 18 , 3546–3556], and the numerous data on heme–protein interactions that account for the differences observed in ligand binding between the various species of animals. Numerous probes have been used and provide information about the structure and thermodynamics of the binding site, but no single probe can provide the complete picture [see Iizuka, T. & Yonetani, T. (1970) Adv. Biophys. 1 , 157–182; Smith, D. W. & Williams, R. J. P. (1970) Struct. Bond. 7 , 1–45; and Spiro, T. G. (1975) Biochim. Biophys. Acta 416 , 169–189].     

Crystallization and preliminary X-ray analysis of Escherichia coli methionyl–tRNA formyltransferase

Methionyl–tRNA formyltransferase from Escherichia coli, a monomer of 34kDa, was overexpressed from its cloned gene fmt (Guillon, J.M., Mechulam, Y., Schmitter, J.M., Blanquet, S., and Fayat, G., J. Bacteriol. 174:4294–4301, 1992) and crystallized using ammonium sulphate as precipitant. The crystals are trigonal and have unit cell parameters a = b = 151.0Å, c = 81.8Å. They belong to space group P3₂21 and diffract to 2.0Å resolution. The structure is being solved by multiple isomorphous replacement. © 1996 Wiley-Liss, Inc.     

Vertical displacement and taphonomic filtering of nannofossils by bioturbation in the Cretaceous–Palaeogene boundary section at Caravaca,SE Spain

K?dzierski, M., Rodríguez‐Tovar, F.J. & Uchman, A. 2011: Vertical displacement and taphonomic filtering of nannofossils by bioturbation in the Cretaceous–Palaeogene boundary section at Caravaca, SE Spain. Lethaia, Vol. 44, pp. 321–328. At the Caravaca section, SE Spain, the position of the Cretaceous–Palaeogene (K–Pg) boundary is well‐defined, with multidisciplinary datasets from a thin rusty layer at the base of the 10 cm dark boundary layer. Nannoplankton assemblages containing the Danian taxon Neochiastozygus sp. and enriched in Thoracosphaera spp. are displaced below the K–Pg boundary into the trace fossils Zoophycos, Thalassinoides and Chondrites. These trace fossils are filled with dark‐coloured sediments of the dark boundary layer. The nannofossil assemblage from the 1‐cm thick interval below the boundary, enriched in Thoracosphaera spp. and Braarudosphaera spp., may have been displaced by Chondrites tracemakers, the traces of which are abundant in this interval. The downward transport of the Danian nannofossils into the Maastrichtian by the tracemakers seems to be one of the common mechanisms responsible for their apparent appearance below the K–Pg boundary. The dark boundary layer contains very rare Danian specimens and abundant Maastrichtian nannofossils. The Maastrichtian taxa were most likely conveyed up on to the seafloor by tracemakers during the Danian. The redistribution of nannoplankton down and up across the rusty layer (K–Pg), challenges the usefulness of nannofossils for high‐resolution stratigraphy of the K–Pg boundary. □Nannoplankton, Cretaceous–Palaeogene boundary event, biogenic mixing, trace fossils.     

Recovery and virulence phenotyping of the historic ‘Stubbs collection’ of the yellow rust fungus Puccinia striiformis from wheat

A unique collection of spore samples of Puccinia striiformis, often referred to as the ‘Stubbs collection’, has been stored in liquid nitrogen from 18 to 45 years. A subset of samples representing 35 countries and 28 years was investigated to assess recovery rate, race identity and previously undetected virulence. A new method for recovery using an airbrush sprayer and Novec? 7100 for inoculating the host plants was highly successful. Ninety‐six percent of 231 isolates were recovered. Virulence phenotyping was done using differential sets of wheat genotypes representing specific‐resistance genes. A total of 181 samples represented single genotypes (isolates), whereas 40 samples consisted of at least two genotypes. Race identity was confirmed for 102 of 181 single‐genotype isolates. The virulence phenotype was updated for additional 44 isolates based on improved resolution of results because of updated and more informative wheat‐differential sets. The remaining 35 isolates showed discrepancies for one or more virulences when compared with past results. Additional virulences corresponding to Yr17, Yr25 and Yr27, respectively, which were not assayed originally, were discovered. The value of biological collections for research and plant breeding is discussed along with the challenges of maintaining collections of biotrophic microorganisms.     

Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species‐level resolution is difficult to obtain. Next‐generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 “barcode” and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (southern England). Operational taxonomic unit (OTU) recovery was tested under 72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1, while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognized with morphological monitoring. The increase was due to the following: greater taxonomic resolution (e.g., splitting a single morphotaxon “Chironomidae” into 55 named OTUs); splitting of Linnaean binomials into multiple molecular OTUs; and the use of a filtration‐flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between “impacted” vs. “control” samples, detectable with each gene marker, for each major taxonomic group, and for meio‐ and macrofaunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional nonmolecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecology.     

New species of <Emphasis Type="Italic">Jakutoproductus</Emphasis> from the Lower Permian of Verkhoyansk Region

Two new brachiopod species of Jakutoproductus, J. lenensis sp. nov. and J. talchanensis sp. nov., are described. J. lenensis occurs in the upper part of the J. verkhoyanicus Zone of the Khorokytian Horizon (Asselian–Sakmarian deposits) of the lower reaches of the Lena River and in the Sobolokh-Mayan and Allara-Khadaryn’ya river basins. J. talchanensis is identified from the Khorokytian Horizon of the Talchan River (Baraiy River basin). A new subzone, the J. lenensis Subzone, is proposed for the upper part of the J. verkhoyanicus Zone of the Khorokytian Horizon of the Verkhoyansk Region.     

Assessment of the effects of transgenic Bt cotton Bollgard II on the abundance of nontarget arthropods in Burkina Faso

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Pollen use by Megalopta sweat bees in relation to resource availability in a tropical forest

1. Spatial and temporal availability of pollen helps shape bee foraging behaviour and productivity, which has been studied in great detail at the landscape level, but never in a diverse tropical forest. 2. To study the effect of spatio‐temporal variation in resource distribution on pollen use and productivity, we identified pollen from spatially explicit nest collections of two generalist sweat bees, Megalopta genalis Meade‐Waldo and M. centralis Friese, from Barro Colorado Island, Panama, a 50‐ha forest dynamics plot during the 2007 dry and early wet seasons. Pollen from nests collected in 1998–1999 without spatial information was also identified. 3. Bees used pollen of at least 64 species; many of these occurred in only one collection. The 2007 collections contained pollen of 35 different species, but were dominated by five species, especially Hura crepitans L. and Pseudobombax septenatum (Jacq.) Dugand. 4. Temporal availability, but not distance from nest, influenced flower use at a 50‐ha scale. 5. Body size was not associated with minimum flight distance as inferred from pollen collections. 6. Nest productivity and pollen diversity decreased from the dry to wet seasons, mirroring community‐level availability of floral resources. 7. Results suggest that on a scale of 50 ha, bees are choosing certain host plant species regardless of distance from the nest, but adjusting foraging behaviour opportunistically based on the temporal availability of host flowers.