Long-term monitoring data meet freshwater species distribution models: Lessons from an LTER-site

Long-term monitoring datasets provide a solid framework for ecological research. Such a dataset from the German long-term ecological research (LTER) site Rhine-Main-Observatory was used to set up a species distribution model (SDM) for the Kinzig catchment. The extensive knowledge on the monitoring data provided by the LTER-site framework allowed to calibrate a robust model for 175 taxa of stream macroinvertebrates and to project their distributions on the Kinzig River stream network using bioclimatic, topographical, hydrological, land use and geological predictors. On average, model performance was good, with a TSS of 0.83 (±0.09 SD) and a ROC of 0.95 (±0.03 SD). The model delivered valuable insights on three sources of bias that plague SDMs in general: (a) level of taxonomic identification of the modeled organisms, (b) the spatial arrangement of sampling sites, and (c) the sampling intensity at each sampling site. Taxonomic resolution did not affect SDM performance. The distribution of high predicted probabilities of occurrence in the stream network coincided with those segments in the stream network most densely and frequently sampled, indicating both a spatial and temporal sampling bias. Species richness curves confirmed the temporal sampling bias. Next to spatial bias, sampling frequency also plays an important role in data collection, affecting further analysis and modeling procedures. Results indicate an underrepresentation of low order streams, an important aspect that should be addressed by both monitoring schemes and modeling approaches.     

A case-case study of mobile phone use and acoustic neuroma risk in Japan

Results of case–control studies of mobile phone use and acoustic neuroma have been inconsistent. We conducted a case–case study of mobile phone use and acoustic neuroma using a self‐administered postal questionnaire. A total of 1589 cases identified in 22 hospitals throughout Japan were invited to participate, and 787 cases (51%) actually participated. Associations between laterality of mobile phone use prior to the reference dates (1 and 5 years before diagnosis) and tumor location were analyzed. The overall risk ratio was 1.08 (95% confidence interval (CI), 0.93–1.28) for regular mobile phone use until 1 year before diagnosis and 1.14 (95% CI, 0.96–1.40) for regular mobile phone use until 5 years before diagnosis. A significantly increased risk was identified for mobile phone use for >20 min/day on average, with risk ratios of 2.74 at 1 year before diagnosis, and 3.08 at 5 years before diagnosis. Cases with ipsilateral combination of tumor location and more frequently used ear were found to have tumors with smaller diameters, suggesting an effect of detection bias. Furthermore, analysis of the distribution of left and right tumors suggested an effect of tumor‐side‐related recall bias for recall of mobile phone use at 5 years before diagnosis. The increased risk identified for mobile phone users with average call duration >20 min/day should be interpreted with caution, taking into account the possibilities of detection and recall biases. However, we could not conclude that the increased risk was entirely explicable by these biases, leaving open the possibility that mobile phone use increased the risk of acoustic neuroma. Bioelectromagnetics 32:85–93, 2011. © 2010 Wiley‐Liss, Inc.     

The Role of Context-Dependent Mutations in Generating Compositional and Codon Usage Bias in Grass Chloroplast DNA

Abstract The influence of local base composition on mutations in chloroplast DNA (cpDNA) is studied in detail and the resulting, empirically derived, mutation dynamics are used to analyze both base composition and codon usage bias. A 4 × 4 substitution matrix is generated for each of the 16 possible flanking base combinations (contexts) using 17,253 noncoding sites, 1309 of which are variable, from an alignment of three complete grass chloroplast genome sequences. It is shown that substitution bias at these sites is correlated with flanking base composition and that the A+T content of these flanking sites as well as the number of flanking pyrimidines on the same strand appears to have general influences on substitution properties. The context-dependent equilibrium base frequencies predicted from these matrices are then applied to two analyses. The first examines whether or not context dependency of mutations is sufficient to generate average compositional differences between noncoding cpDNA and silent sites of coding sequences. It is found that these two classes of sites exist, on average, in very different contexts and that the observed mutation dynamics are expected to generate significant differences in overall composition bias that are similar to the differences observed in cpDNA. Context dependency, however, cannot account for all of the observed differences: although silent sites in coding regions appear to be at the equilibrium predicted, noncoding cpDNA has a significantly lower A+T content than expected from its own substitution dynamics, possibly due to the influence of indels. The second study examines the codon usage of low-expression chloroplast genes. When context is accounted for, codon usage is very similar to what is predicted by the substitution dynamics of noncoding cpDNA. However, certain codon groups show significant deviation when followed by a purine in a manner suggesting some form of weak selection other than translation efficiency. Overall, the findings indicate that a full understanding of mutational dynamics is critical to understanding the role selection plays in generating composition bias and sequence structure.     

The Accelerated Failure Time Model Under Biased Sampling

Summary Chen (2009, Biometrics) studies the semi‐parametric accelerated failure time model for data that are size biased. Chen considers only the uncensored case and uses hazard‐based estimation methods originally developed for censored observations. However, for uncensored data, a simple linear regression on the log scale is more natural and provides better estimators.     

Codon bias of the gene for chloroplast glycerol-3-phosphate acyltransferase in Camellia sinensis (L.) O. Kuntze

The analysis on codon usage bias of GPAT gene of Camellia sinensis (L.) O. Kuntze may provide a basis for understanding the evolution relationship of C. sinensis and for selecting appropriate host expression systems to improve the expression of target genes. In the present study, the coding sequence of CsGPAT was analyzed with CodonW, CHIPS and CUSP programs, and compared with the genome of C. sinensis and GPAT genes of other 9 plant species. Our results showed that the cluster tree based on CDs could reveal the evolutional relations among the 10 plant species, whereas the cluster tree based on relative synonymous codon usage (RSCU) could not. There were 31 codons showing distinct usage differences between CsGPAT and genome of Escherichia coli, 21 between CsGPAT and yeast, but 13 between CsGPAT and Arabidopsis thaliana. But there were slightly fewer differences in codon usage between CsGPAT and A. thaliana. Therefore, the A. thaliana expression system may be more suitable for the expression of CsGPAT. These results may improve our understanding of the codon usage bias and functional studies of CsGPAT.     

New insights into the interplay between codon bias determinants in plants

Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.     

The fossil record of ichthyosaurs,completeness metrics and sampling biases

Ichthyosaurs were highly successful marine reptiles with an abundant and well‐studied fossil record. However, their occurrences through geological time and space are sporadic, and it is important to understand whether times of apparent species richness and rarity are real or the result of sampling bias. Here, we explore the skeletal completeness of 351 dated and identified ichthyosaur specimens, belonging to all 102 species, the first time that such a study has been carried out on vertebrates from the marine realm. No correlations were found between time series of different skeletal metrics and ichthyosaur diversity. There is a significant geographical variation in completeness, with the well‐studied northern hemisphere producing fossils of much higher quality than the southern hemisphere. Medium‐sized ichthyosaurs are significantly more complete than small or large taxa: the incompleteness of small specimens was expected, but it was a surprise that larger specimens were also relatively incomplete. Completeness varies greatly between facies, with fine‐grained, siliciclastic sediments preserving the most complete specimens. These findings may explain why the ichthyosaur diversity record is low at times, corresponding to facies of poor preservation potential, such as in the Early Cretaceous. Unexpectedly, we find a strong negative correlation between skeletal completeness and sea level, meaning the most complete specimens occurred at times of global low sea level, and vice versa. Completeness metrics, however, do not replicate the sampling signal and have limited use as a global‐scale sampling proxy.     

The Use of Adaptive Blocks in the Design of Clinical Trials

This paper introduces a class of data-dependent allocation rules for use in sequential clinical trials designed to choose the better of two competing treatments, or to decide that they are of equal efficacy. These readily understood and easily implemented rules are shown to reduce, substantially the number of tests with the poorer treatment for a broad category of experimental situations. Allocation rules of this type are applied both to trials with an instantaneous binomial response and to delayed response trials where interest centers on exponentially distributed survival time. In each case, a comparison of this design with alternative designs given in the literature shows that the proposed design is superior with respect to ease of application and is comparable to the alternatives regarding inferior treatment number and average sample number. In addition, the proposed rules mitigate many of the difficulties generally associated with adaptive assignment rules, such as selection and systematic bias.     

Codon usage bias: causative factors,quantification methods and genome‐wide patterns: with emphasis on insect genomes

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole‐genome sequencing of numerous species, both prokaryotes and eukaryotes, genome‐wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole‐genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome‐sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome‐sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.     

Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures

Pollen DNA metabarcoding—marker‐based genetic identification of potentially mixed‐species pollen samples—has applications across a variety of fields. While basic species‐level pollen identification using standard DNA barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities to mixes (qualitative matching) and (b) generates sequence reads proportionally to their relative abundance in a sample (quantitative matching) is unclear, as these have not been assessed relative to known standards. We tested the quantitative and qualitative robustness of metabarcoding in constructed pollen mixtures varying in species richness (1–9 species), taxonomic relatedness (within genera to across class) and rarity (5%–100% of grains), using Illumina MiSeq with the markers rbcL and ITS2. Qualitatively, species composition determinations were largely correct, but false positives and negatives occurred. False negatives were typically driven by lack of a barcode gap or rarity in a sample. Species richness and taxonomic relatedness, however, did not strongly impact correct determinations. False positives were likely driven by contamination, chimeric sequences and/or misidentification by the bioinformatics pipeline. Quantitatively, the proportion of reads for each species was only weakly correlated with its relative abundance, in contrast to suggestions from some other studies. Quantitative mismatches are not correctable by consistent scaling factors, but instead are context‐dependent on the other species present in a sample. Together, our results show that metabarcoding is largely robust for determining pollen presence/absence but that sequence reads should not be used to infer relative abundance of pollen grains.     

A bound for publication bias based on the fraction of unpublished studies

Publication bias in meta-analysis is usually modeled in terms of an accept/reject selection procedure in which the selected studies are the "published" studies and the rejected studies are the "unpublished" studies. One possible selection mechanism is to suppose that only studies that report an estimated treatment effect exceeding (or falling short of) some threshold are accepted. We show that, with appropriate choice of thresholds, this attains the maximum bias among all selection mechanisms in which the probability of selection increases with study size. It is impossible to estimate the selection mechanism from the observed studies alone: this result leads to a "worst-case" sensitivity analysis for publication bias, which is remarkably easy to implement in practice. The method is illustrated using data on the effectiveness of prophylactic corticosteroids.     

The more things changed,the more they stayed the same: Trends in conservation focus 2010–2019

The conservation literature provides an important resource for conservation practice and reflects key areas of current research interest, but not necessarily those of highest priority, in the field of conservation science. In one of the most comprehensive studies of its kind, this paper evaluates 4388 articles from three leading conservation journals with different impact factors (Biological Conservation, Conservation Letters, and Oryx) for the period 2010–2019. The analysis shows that previously identified trends still hold true in many instances, including a continuing taxonomic bias towards vertebrates and particularly in favour of mammals. Geographical biases also persist, favouring Europe and North America with respect to where research is undertaken, who writes about it, and how it is funded, although publication of research conducted in Africa is increasing. It is difficult to evaluate changes in author gender outside the decade studied as this topic has not been widely considered in previous studies, but parity in authorship has not yet been achieved in any of the journals examined. To overcome the biases identified, researchers, editors, and funding organisations collectively still need to do more to redirect conservation efforts where they are most urgently needed and encourage more women and more researchers from lower income countries to participate in research by helping to remove the barriers that currently limit them.     

Under‐representation of avian studies in landscape genetics

Landscape genetics is a rapidly growing discipline that examines how heterogeneous landscapes and other environmental factors influence population genetic variation. We conducted a systematic review of the landscape genetic literature which demonstrates that birds are severely under‐represented relative to their species diversity and general publication prevalence. Most avian studies were on species that have relatively low dispersal ability, and we suggest that this reflects an assumed high vagility of birds that precludes spatial genetic variation relatable to landscape heterogeneity. However, spatial genetic variation exists in several bird species with very high dispersal ability, but this has not been considered in the context of landscape features. Genetic patterns may also relate to landscape due to breeding habitat selection and territorial behaviour, despite the fact that species may be able to move throughout different landscape elements with minimal movement costs. Habitat loss and fragmentation are continuing globally and are strongly related to declines in bird populations. Landscape genetic studies provide a means to understand, predict and mitigate the effects of anthropogenic landscape change on birds. This review promotes the need for landscape genetic studies of birds, such that a greater understanding of the drivers of their genetic structuring can be developed and generalizations can be made from landscape genetic studies that apply more broadly across taxa.     

Assessment of non-response bias in a survey of residential magnetic field exposure in Taiwan

We assessed potential non-response bias in obtaining information on residential extremely low-frequency power frequency magnetic field (MF) in Taiwan. All households occupied by children aged less than 7 years in two study districts, one in an urban town and the other in a rural town, were visited and solicited for on-site measurements in late 2003. The initial response rate was only 32% (33/104, urban) and 60% (61/101, rural). In the same season 1 year later, we performed a second survey of those who declined to be measured at the initial survey and successfully measured another 77 residences (50 and 27 for urban and rural districts, respectively). The two districts were selected mainly because the local public health officers were quite willing to assist the initial survey and to inform residents of the second survey. Except for meteorological conditions, the two surveys came up with very similar findings regarding residential characteristics and power facilities surrounding the houses. The mean residential MF for the urban residences was .121 and .140 micro-Tesla (microT) (P = .620) for the two surveys. The corresponding figures for the rural residences were .119 and .115 microT (P = .802). Although limited in its scope, this study tends to indicate that measurement studies of residential MF are less likely to suffer from serious selection bias if sampling is confined within a small district where people have similar socioeconomic characteristics.     

The effect of repeated testing on judgement biases in sheep

Testing judgement biases of animals may provide insight into their affective states; however important questions about methodologies need to be answered. This experiment investigated the effect of repeated testing using unreinforced, ambiguous cues on the response of sheep to a go/no-go judgement bias test. Fifteen sheep were trained to differentiate between two locations, reinforced respectively with feed (positive) or with the presentation of a dog (negative). The responses to nine ambiguous locations, positioned between the positively and negatively reinforced locations, were tested repeatedly over 3 weeks. Sheep exhibited a symmetrical gradation in response to ambiguous locations between the positive and negative reinforcers. There was a significant decline (P = 0.001) in the total number of approaches to the ambiguous positions over time (weeks). This effect of time suggests that sheep learnt that the ambiguous locations were unrewarded. This result supplies evidence of a limitation identified in current judgement bias methodology, due to repeated testing, which has the potential to provide misleading results.     

Frequent non-reciprocal exchange in microsatellite-containing-DNA-regions of vertebrates

Microsatellites are DNA-fragments containing short repetitive motifs with 2–10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during the replication phase, termed slippage, although recombination is also observed. The aim of this study is to demonstrate evidence that non-reciprocal recombination processes changing the total genomic structure are common in microsatellites and flanking regions. We sequenced DNA fragments from birds in which microsatellites are located, and analyzed the structure of the microsatellites and their flanking regions. Additionally, other data and those from literature of three microsatellite regions of primates coding for the Ataxin-2, the Huntingtin and the TATA-box binding protein were analyzed. The structures of seven avian and three primate microsatellites support the hypothesis that non-reciprocal recombination is a common process that may also contribute considerably to the variation at microsatellite loci. We conclude that results of population genetic studies that are analyzed statistically with methods based on stepwise mutation models should be interpreted with caution if no detailed information on the allelic variation of microsatellites is available.     

Attentional bias in the radial and vertical dimensions of space

Under visual guidance, healthy subjects usually misbisect radial lines farther than, and vertical lines above the true center. It was suggested that radial and vertical misbisection depended on the presence of an attentional bias toward far/upper space. The aim of the present study was to investigate whether such attentional bias depends on a single mechanism or on separate mechanisms. Ninety participants were asked to bisect lines radially and vertically oriented. The results confirmed the presence of a consistent bisection bias farther than (radial lines), and above (vertical lines) the true center. Furthermore, there was a significant correlation between radial and vertical bisection errors. These findings suggest that a single neural mechanism is involved in producing the attentional bias toward far/upper space.     

Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences

We sequenced and analyzed the subtelomeric regions of 1356 macronuclear "nanochromosomes" of the spirotrichous ciliate Oxytricha trifallax. We show that the telomeres in this species have a length of 20 nt, with minor deviations; there is no correlation between telomere lengths at the two ends of the molecule. A search for open reading frames revealed that the 3' and 5' untranslated regions are short, with a median length of approximately 130 nt, and that surprisingly there are no detectable differences between sequences upstream and downstream of genes. Our results confirm a previously reported purine bias in the first approximately 80 nucleotides of the subtelomeric regions, but with this larger data set we curiously detected a 10 bp periodicity in the bias; we relate this finding to the possible regulatory and structural functions these regions must serve. Palindromic sequences in opposing subtelomeric regions, although present in most sequences, are not statistically significant.     

Distance-scaled Force Biased Monte Carlo Simulation for Solutions containing a Strongly Interacting Solute

The force-biased extension of the Metropolis Monte Carlo method [1] improves convergence by sampling moves preferentially along the directions of force (and torque) [2]. For solvated systems it is particularly effective [3] when coupled with the preferential sampling scheme [4] that attempts to move solvents near the solute more frequently. However, in recent force-biased simulations of aqueous ionic solutions [5] some of the water molecules in the vicinity of the solute remained essentially stationary. Only significant reduction in the stepsize produced some accepted moves.