Late Wenlock (Middle Silurian) global Bioevent: Possible chemical cause for mass graptolite mortalities

Graptolites nearly became extinct in the latest Wenlock in all preserved stratigraphic sequences of this age. Graptolite mortalities occurred along the western coast of Laurentia and at sites that surrounded the Proto‐Tethys. Graptolite mass mortalities took place among deep‐water, open ocean dwelling organisms. After the mass mortalities, only the Pristiograptus dubius group and retiolids surface or near‐surface dwellers, survived. For a period of time, little speciation or diversification occurred. The base of the Ludlow is marked by diversification, with appearances of S. colonus, M. nilssoni and other groups which occur in near surface waters. None of the extensive plate movements postulated for the Silurian readily explain the mass extinctions that occurred. During the Silurian, global temperatures were warmer than present and atmospheric oxygen concentrations were lower, creating extensive oceanic anoxia. Below the oxygenated surface layers of the ocean, was an anoxic, non‐sulfidic zone (i.e. nitrate‐reducing) above a sulfidic zone. Graptolites lived over a range of depth from the oxygenated zone to either near or in the nitrate‐reducing zones. As the oxygen concentration declined through the Silurian, the depth of the oxic zone would have become shoaler with expanding anoxia. Late Wenlock graptolites that were unable to migrate to shallower depths, living in borderline oxygen conditions, could have been killed, resulting in the mortalities of the late Wenlock. Only those graptolites that were surface dwellers survived, adapted and reradiated.     

A refined graptolite biostratigraphy for the late Ordovician–early Silurian of central Wales

Morphometric analysis of graptolites from the persculptus and acuminatus biozones of central Wales identifies four successive morphospecies of normalograptids. These graptolites can be used for biostratigraphical subdivision of these strata as follows: (i) an early persculptus Biozone interval containing broad forms with geniculate thecae that have the morphology of Persculptograptus persculptus with an early insertion point for the full median septum (theca 1¹); (ii) a supra‐adjacent level of early persculptus Biozone age, with narrower, parallel‐sided forms, that have been referred to as Normalograptus? aff. parvulus and have a slightly later insertion point for the full median septum (theca 1²); (iii) a third interval, encompassing the later part of the persculptus Biozone to the early acuminatus Biozone, with Normalograptus? cf. parvulus, which has the full median septum delayed to the level of theca 3–7; and (iv) a younger interval, in the mid‐acuminatus Biozone with Persculptograptus cf. persculptus specimens that do not display the median septum on its reverse side. These taxa can be used for refined biostratigraphy and correlation in the late Ordovician and early Silurian of central Wales. The progressive delay in the insertion of the median septum in these taxa may have wider application for the correlation of the interval immediately after the Hirnantian glacial maximum.     

Evaluation of jackknife and bootstrap for defining confidence intervals for pairwise agreement measures

Several research fields frequently deal with the analysis of diverse classification results of the same entities. This should imply an objective detection of overlaps and divergences between the formed clusters. The congruence between classifications can be quantified by clustering agreement measures, including pairwise agreement measures. Several measures have been proposed and the importance of obtaining confidence intervals for the point estimate in the comparison of these measures has been highlighted. A broad range of methods can be used for the estimation of confidence intervals. However, evidence is lacking about what are the appropriate methods for the calculation of confidence intervals for most clustering agreement measures. Here we evaluate the resampling techniques of bootstrap and jackknife for the calculation of the confidence intervals for clustering agreement measures. Contrary to what has been shown for some statistics, simulations showed that the jackknife performs better than the bootstrap at accurately estimating confidence intervals for pairwise agreement measures, especially when the agreement between partitions is low. The coverage of the jackknife confidence interval is robust to changes in cluster number and cluster size distribution.     

Rapid global change: implications for defining natives and aliens

The ability to ascribe native or alien status to species in a rapidly changing world underpins diverse research fields that overlap with global change and biological invasions via biodiversity. Current definitions generally link alien status to anthropogenic dispersal events, but this can create conflicts for active management and global change adaptation strategies, such as managed relocation and restoration ecology. Here we propose a unifying approach that allows for the incorporation of rapid global change into biological invasion terminology. We introduce the concept of a projected dispersal envelope (PDE) to define the region where a species is or could be native, irrespective of human involvement. The PDE integrates biogeography and niche theory with existing invasion terminology to place a spatial and temporal context on species movements. We draw on a diverse suite of topical organism movements to illustrate these concepts. Our restructured definitions allow for native species to move into or with rapidly shifting climatic regions, as well as identifying the inappropriate introduction of alien species to new areas. Moreover, our definitions framework forms a timely and essential component of adaptation policies and responses for invasive species management and the enhancement of biodiversity in a rapidly changing world.     

Stepwise confidence intervals for monotone dose-response studies

Summary .   In dose–response studies, one of the most important issues is the identification of the minimum effective dose (MED), where the MED is defined as the lowest dose such that the mean response is better than the mean response of a zero-dose control by a clinically significant difference. Dose–response curves are sometimes monotonic in nature. To find the MED, various authors have proposed step-down test procedures based on contrasts among the sample means. In this article, we improve upon the method of Marcus and Peritz (1976, Journal of the Royal Statistical Society, Series B 38 , 157–165) and implement the dose–response method of Hsu and Berger (1999, Journal of the American Statistical Association 94 , 468–482) to construct the lower confidence bound for the difference between the mean response of any nonzero-dose level and that of the control under the monotonicity assumption to identify the MED. The proposed method is illustrated by numerical examples, and simulation studies on power comparisons are presented.     

Confidence intervals of effect size for paired studies

To construct a confidence interval of effect size in paired studies, we propose four approximate methods--Wald method, variance-stabilizing transformation method, and signed and modified signed log-likelihood ratio methods. We compare these methods using simulation to determine those that have good performance in terms of coverage probability. In particular, simulations show that the modified signed log-likelihood ratio method produces a confidence interval with a nearly exact coverage probability and highly accurate and symmetric error probabilities even for very small samples. We apply the methods to data from an iron deficiency anemia study.     

Generalized affine gap costs for protein sequence alignment

Based on the observation that a single mutational event can delete or insert multiple residues, affine gap costs for sequence alignment charge a penalty for the existence of a gap, and a further length-dependent penalty. From structural or multiple alignments of distantly related proteins, it has been observed that conserved residues frequently fall into ungapped blocks separated by relatively nonconserved regions. To take advantage of this structure, a simple generalization of affine gap costs is proposed that allows nonconserved regions to be effectively ignored. The distribution of scores from local alignments using these generalized gap costs is shown empirically to follow an extreme value distribution. Examples are presented for which generalized affine gap costs yield superior alignments from the standpoints both of statistical significance and of alignment accuracy. Guidelines for selecting generalized affine gap costs are discussed, as is their possible application to multiple alignment. Proteins 32:88–96, 1998. Published 1998 Wiley-Liss, Inc.

1 This article is a US government work and, as such, is in the public domain in the United States of America.

     

Generalized prediction intervals for treatment effects in random‐effects models

This article derives generalized prediction intervals for random effects in linear random‐effects models. For balanced and unbalanced data in two‐way layouts, models are considered with and without interaction. Coverage of the proposed generalized prediction intervals was estimated in a simulation study based on an agricultural field experiment. Generalized prediction intervals were compared with prediction intervals based on the restricted maximum likelihood (REML) procedure and the approximate methods of Satterthwaite and Kenward and Roger. The simulation study showed that coverage of generalized prediction intervals was closer to the nominal level 0.95 than coverage of prediction intervals based on the REML procedure.     

Determining a unique defining DNA sequence for yeast species using hashing techniques

MOTIVATION: Yeasts are often still identified with physiological growth tests, which are both time consuming and unsuitable for detection of a mixture of organisms. Hence, there is a need for molecular methods to identify yeast species. RESULTS: A hashing technique has been developed to search for unique DNA sequences in 702 26S rRNA genes. A unique DNA sequence has been found for almost every yeast species described to date. The locations of the unique defining sequences are in accordance with the variability map of large subunit ribosomal RNA and provide detail of the evolution of the D1/D2 region. This approach will be applicable to the rapid identification of unique sequences in other DNA sequence sets. AVAILABILITY: Freely available upon request from the authors. Supplementary information: Results are available at http://www.sys.uea.ac.uk/~jjw/project/paper     

A simple method for global sequence comparison.

A simple method of sequence comparison, based on a correlation analysis of oligonucleotide frequency distributions, is here shown to be a reliable test of overall sequence similarity. The method does not involve sequence alignment procedures and permits the rapid screening of large amounts of sequence data. It identifies those sequences which deserve more careful analysis of sequence similarity at the level of resolution of the single nucleotide. It uses observed quantities only and does not involve the adoption of any theoretical model.     

Effects of monochromatic light on time sense for short intervals

We examined the effects of monochromatic light on the time sense and the central nervous system. Nine young adult volunteers participated in this study. They were exposed to red-light and blue-light environments (illuminance was kept at 310 lx). We evaluated the time sense by time-production tests of 90 s and 180 s and measured the P300 event-related potentials during an auditory oddball task. The 90-s time intervals produced by subjects in the two monochromatic light conditions were not significantly different. However, the 180-s time interval produced in the red-light condition (163.2+/-50.4 s) was significantly (p<0.05) shorter than that in the blue-light condition (199.0+/-54.4 s). The peak latency of P300 in the red light (322.2+/-26.6 ms) was found to be significantly (p<0.05) shorter also than that in the blue light (332.6+/-20.2 ms). The feelings measured by the visual analogue scales in the two light conditions were not significantly different. These results indicate that the time sense ran faster in the red-light than in the blue-light condition. We suggest that the higher activity in the central nervous system that is accounted for by the shorter latency of P300 is related to the acceleration of the time sense.     

Inverted central auditory hierarchies for encoding local intervals and global temporal patterns

1. Download : Download high-res image (241KB)
2. Download : Download full-size image

     

Potential global stratotype sections and points in China for defining Cambrian stages and series

Three stratigraphic sections in the Cambrian of China that contain complete successions across important biohorizons having chronostratigraphic value, and that may be useful for developing Cambrian stage or series boundaries, are reviewed. The Wuliu section (Guizhou, South China), contains the FAD of Oryctocephalus indicus at 58.2 m above the base of the Kaili Formation. The Wangcun North section (Hunan, South China), contains the FADs of Ptychagnostus (or Acidusus) atavus, Ptychagnostus punctuosus, and Lejopyge laevigata at 1.2 m, 56.7 m, and 111.3 m, respectively, above the base of the Huaqiao Formation. The Xiaoyangqiao section (Jilin, Northeast China), contains the FAD of Cordylodus proavus in the Fengshan Formation at 10.89 m above the zero point of the section. A fourth potential stratotype section, the Wangcun South section (Hunan, South China), which contains the P. atavus, P. punctuosus, and L. laevigata zones, is discussed briefly.     

Multilocus sequence typing for global surveillance of meningococcal disease

The global surveillance of bacterial pathogens is particularly important for bacteria with diverse and dynamic populations that cause periodic epidemics or pandemics. The isolate characterization methods employed for surveillance should: (1) generate unambiguous data; (2) be readily implemented in a variety of scenarios and be reproducible among laboratories; (3) be scalable and preferably available in a high throughput format; and (4) be cost effective. Multilocus sequence typing (MLST) was designed to meet these criteria and has been implemented effectively for a wide range of microorganisms. The 'Impact of meningococcal epidemiology and population biology on public health in Europe (EU-MenNet)' project had amongst its objectives: (1) to disseminate meningococcal MLST and sequence-based typing throughout Europe by establishing a centre for training and data generation, and (2) to produce a comprehensive Europe-wide picture of meningococcal disease epidemiology for the first time. Data produced from the project have shown the distribution of a relatively small number of STs, clonal complexes and PorA types that account for a large proportion of the disease-associated isolates in Europe. The project demonstrates how molecular typing can be combined with epidemiological data via the Internet for global disease surveillance.     

Multi-locus sequence typing: a tool for global epidemiology

The characterization of pathogenic isolates plays a pivotal role in the epidemiology of infectious diseases, generating the information necessary for identifying, tracking, and intervening against disease outbreaks. In 1998 multi-locus sequence typing (MLST) was proposed as a nucleotide sequence-based approach that could be applied to many bacterial pathogens. It combined developments in high-throughput sequencing and bioinformatics with established population genetics techniques to provide a portable, reproducible, and scalable typing system that reflected the population and evolutionary biology of bacterial pathogens. MLST schemes have been developed for a variety of procaryotic and eucaryotic pathogens and the data generated have contributed to both epidemiological surveillance and fundamental studies of pathogen biology.