Evidence for declines in populations of grassland-associated birds in marginal upland areas of Britain

Capsule We report large declines among summer populations between 1968–80 and 2000.

Aim To assess changes in the status of breeding populations of birds in pastoral uplands.

Methods Volunteer observers revisited 13 areas of marginal upland in Britain where Common Birds Census data were collected during 1968–80. This allowed the status of 35 bird species to be examined over about 20 years and to make a comparison between grassland-based and woodland-based species.

Results For 12 species the decline in abundance was significant, particularly among passerines, such as Skylark Alauda arvensis, Wheatear Oenanthe oenanthe, Whinchat Saxicola rubetra, Yellow Wagtail Motacilla flava and Yellowhammer Emberiza citrinella, each of which declined by over 80%. Redshank Tringa totanus, Yellow Wagtail, Dipper Cinclus cinclus, Whinchat, Wheatear, Ring Ouzel Turdus torquatus and Yellowhammer were found on less than half the number of plots on which they were originally recorded. Most declining species were associated with grassland for nesting and foraging, compared to those species that increased (Wood Pigeon Columba palumbus, Pied Wagtail Motacilla alba, Carrion Crow Corvus corone, Jackdaw C. monedula and Goldfinch Carduelis carduelis) that were less specialized in their habitat requirements. Woodland or woodland edge species showed no significant change in status, suggesting that population declines among grassland species were not due to lower observer effort between recording periods.

Conclusion Long-term changes to grassland ecosystems in marginal upland areas of Britain may have influenced the status of bird populations.     

A review of available methods and description of a new method for eliminating ectoparasites from bird nests

Bird nests offer an ideal situation to manipulate ectoparasites and study how they impact hosts. Several methods are available to eliminate parasites from nests and each has its own suite of advantages and disadvantages. For example, recent toxicity research has revealed that some commonly used insecticides may not be suitable for use in experiments with nestlings. This highlights the need for investigators to control for the effects of methods used to eliminate nest parasites within experimental designs. Methods that can be used across treatment groups are also often needed to study the effects of variation in parasite intensity. To aid investigators in deciding which method(s) to use, we provide a comprehensive review of available methods for eliminating nest ectoparasites and also describe a new heat gun method. We tested the effectiveness of the heat‐gun method with nests of Barn Swallows (Hirundo rustica) to which 100 nest mites were added and then quantified the number of surviving mites and other naturally occurring arthropods. We found that fully heated nests had significantly fewer mites and other arthropods than partially heated or control nests. Use of the heat gun had no negative effects on nestling growth or mortality rates. In studies of avian nest ectoparasites, investigators need to consider methods that can be used across treatment groups to ensure that unaccounted for toxicity effects are not influencing results and leading to underestimation of the often subtle effects of ectoparasites on birds.     

Consensus for experimental design in electromyography (CEDE) project: Single motor unit matrix

The analysis of single motor unit (SMU) activity provides the foundation from which information about the neural strategies underlying the control of muscle force can be identified, due to the one-to-one association between the action potentials generated by an alpha motor neuron and those received by the innervated muscle fibers. Such a powerful assessment has been conventionally performed with invasive electrodes (i.e., intramuscular electromyography (EMG)), however, recent advances in signal processing techniques have enabled the identification of single motor unit (SMU) activity in high-density surface electromyography (HDsEMG) recordings. This matrix, developed by the Consensus for Experimental Design in Electromyography (CEDE) project, provides recommendations for the recording and analysis of SMU activity with both invasive (needle and fine-wire EMG) and non-invasive (HDsEMG) SMU identification methods, summarizing their advantages and disadvantages when used during different testing conditions. Recommendations for the analysis and reporting of discharge rate and peripheral (i.e., muscle fiber conduction velocity) SMU properties are also provided. The results of the Delphi process to reach consensus are contained in an appendix. This matrix is intended to help researchers to collect, report, and interpret SMU data in the context of both research and clinical applications.     

Dynamic Diversification from a Putative Common Ancestor of Scorpion Toxins Affecting Sodium, Potassium, and Chloride Channels

Scorpions have survived successfully over millions of years without detectable changes in their morphology. Instead, they have developed an efficient alomonal machinery and a stinging device supporting their needs for prey and defense. They produce a large variety of polypeptidic toxins that bind and modulate ion channel conductance in excitable tissues. The binding site, mode of action, and chemical properties of many toxins have been studied extensively, but little is known about their genomic organization and diversity. Genes representing each of the major classes of Buthidae scorpion toxins, namely, ``long' toxins, affecting sodium channels (alpha, depressant, and excitatory), and ``short' toxins, affecting potassium and chloride channels, were isolated from a single scorpion segment and analyzed. Each toxin type was found to be encoded by a gene family. Regardless of toxin length, 3-D structure, and site of action, all genes contain A+T-rich introns that split, at a conserved location, an amino acid codon of the signal sequence. The introns vary in length and sequence but display identical boundaries, agree with the GT/AG splice junctions, and contain T-runs downstream of a putative branch point, 5′-TAAT-3′. Despite little sequence similarity among all toxin classes, the conserved gene organization, intron features, and common cysteine-stabilized α-helical (CSH) core connecting an α-helix to a three-stranded β-sheet suggest, that they all evolved from an ancestral common progenitor. Furthermore, the vast diversity found among genomic copies, cDNAs, and their protein products for each toxin suggests an extensive evolutionary process of the scorpion ``pharmaceutical factory,' whose success is due, most likely, to the inherent permissiveness of the toxin exterior to structural alterations. Received: 16 March 1998 / Accepted: 30 July 1998     

Functional relevance of synonymous alleles reflected in allele rareness in the population

We provide theoretical evidence supporting the non-neutrality of synonymous alleles by investigating the rareness of synonymous alleles in the population. We find a significantly greater number of synonymous rare alleles than conventional neutral alleles derived from noncoding regions. A permutation experiment shows that the rareness of synonymous alleles is not a byproduct of random statistical noise. We then compare the frequencies of synonymous rare alleles and common alleles in various functional contexts in which synonymous alleles are known to be involved. Subsequently, we perform logistic regression analysis to elucidate the effect size of each independent factor contributing to the rareness of synonymous alleles. Additionally, we show that changes in optimality caused by synonymous mutations resulting in rare SNPs in the population tend to be biased toward optimality loss. We think that our study will contribute to the development of novel strategies for identifying functional synonymous mutations.     

Universal Protein Families and the Functional Content of the Last Universal Common Ancestor

The phylogenetic distribution of Methanococcus jannaschii proteins can provide, for the first time, an estimate of the genome content of the last common ancestor of the three domains of life. Relying on annotation and comparison with reference to the species distribution of sequence similarities results in 324 proteins forming the universal family set. This set is very well characterized and relatively small and nonredundant, containing 301 biochemical functions, of which 246 are unique. This universal function set contains mostly genes coding for energy metabolism or information processing. It appears that the Last Universal Common Ancestor was an organism with metabolic networks and genetic machinery similar to those of extant unicellular organisms.     

Recognising bias in Common Era temperature reconstructions

A steep decline in the quality and quantity of available climate proxy records before medieval times challenges any comparison of reconstructed temperature and hydroclimate trends and extremes between the first and second half of the Common Era. Understanding of the physical causes, ecological responses and societal consequences of past climatic changes, however, demands highly-resolved, spatially-explicit, seasonally-defined and absolutely-dated archives over the entire period in question. Continuous efforts to improve existing proxy records and reconstruction methods and to develop new ones, as well as clear communication of all uncertainties (within and beyond academia) must be central tasks for the paleoclimate community.     

Genetic differences between the Chinese and European races of common carp

Summary Common carp of the Chinese and European races and their cross were tested in different environments. The test groups were either stocked together into the same pond, or each group was stocked separately. Mean growth, taken as a measure of the quality of the environment, varied widely between treatments. Genotype-environment interactions were estimated by the regression of growth of different genetic groups on this measure of environment. Proportional growth differences between the European and European X Chinese crossbreds, were several times higher in manured ponds than in ponds with artificial feed. The Chinese fish showed the fastest relative growth in poor conditions, with manure as the major nutrient input, while the European fish showed the fastest relative growth under improved conditions and irrespective of its source of food. The Chinese X European crossbred is heterotic over a range of intermediate conditions with manure as the principal nutrient.     

Identification of Differential Aberrations in Multiple‐Sample Array CGH Studies

Summary Most existing methods for identifying aberrant regions with array CGH data are confined to a single target sample. Focusing on the comparison of multiple samples from two different groups, we develop a new penalized regression approach with a fused adaptive lasso penalty to accommodate the spatial dependence of the clones. The nonrandom aberrant genomic segments are determined by assessing the significance of the differences between neighboring clones and neighboring segments. The algorithm proposed in this article is a first attempt to simultaneously detect the common aberrant regions within each group, and the regions where the two groups differ in copy number changes. The simulation study suggests that the proposed procedure outperforms the commonly used single‐sample aberration detection methods for segmentation in terms of both false positives and false negatives. To further assess the value of the proposed method, we analyze a data set from a study that identified the aberrant genomic regions associated with grade subgroups of breast cancer tumors.