Analysis of synonymous codon usage bias in Chlamydia

Chlamydiae are obligate intracellular bacterial pathogens that cause ocular and sexuallytransmitted diseases,and are associated with cardiovascular diseases.The analysis of codon usage mayimprove our understanding of the evolution and pathogenesis of Chlamydia and allow reengineering of targetgenes to improve their expression for gene therapy.Here,we analyzed the codon usage of C.muridarum,C.trachomatis(here indicating biovar trachoma and LGV),C.pneumoniae,and C.psittaci using the codonusage database and the CUSP(Create a codon usage table)program of EMBOSS(The European MolecularBiology Open Software Suite).The results show that the four genomes have similar codon usage patterns,with a strong bias towards the codons with A and T at the third codon position.Compared with Homosapiens,the four chlamydial species show discordant seven or eight preferred codons.The ENC(effectivenumber of codons used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia is constrained bythe G+C content,while translational selection and gene length exert relatively weaker influences.Moreover,mutational pressure appears to be the major determinant of the codon usage variation among the chlamydialgenes.In addition,we compared the codon preferences of C.trachomatis with those of E.coli,yeast,adenovirus and Homo sapiens.There are 23 codons showing distinct usage differences between C.trachomatisand E.coli,24 between C.trachomatis and adenovirus,21 between C.trachomatis and Homo sapiens,butonly six codons between C.trachomatis and yeast.Therefore,the yeast system may be more suitable for theexpression of chlamydial genes.Finally,we compared the codon preferences of C.trachomatis with those ofsix eukaryotes,eight prokaryotes and 23 viruses.There is a strong positive correlation between the differ-ences in coding GC content and the variations in codon bias(r=0.905,P<0,001).We conclude that thevariation of codon bias between C.trachomatis and other organisms is much less influenced by phylogeneticlineage and primarily determined by the extent of disparities in GC content.     

Life history and habitat preference in the Darling hardyhead,Craterocephalus amniculus (Teleostei,Atherinidae) in the northern Murray‐Darling Basin,Australia

The Darling hardyhead, Craterocephalus amniculus (Atherinidae), is a threatened fish species inhabiting upstream reaches of a number of northern Murray‐Darling Basin catchments. Little is known of its life history. Our goal was to determine patterns of seasonal size structure, interannual and spatial variation in diet, and habitat selection in this species across multiple sites and years in the upper Macintyre River, northern New South Wales. Preserved specimens from a separate study were used to obtain information on diet and size structure. Size structures suggested a single annual spawning season in late September or early October. Diets varied significantly, both between years at the downstream site and among the three sites although the underlying cause of this was untested. Dietary diversity increased with distance downstream. At the two upstream sites, aquatic invertebrates made up most of the diet while over half the gut contents at the downstream site was unidentified detritus. Preference was shown for pool habitats with a sand or cobble substrate, increased channel depth and width and distance from the bank, and reduced flow velocity. Overhanging exotic riparian vegetation and in‐stream woody debris were non‐preferred. This species may be vulnerable to further population decline in light of its restricted habitat preferences and narrow spawning season. However, comparable data from nearby catchments will be necessary to ascertain the species’ conservation status across its broader distribution.     

ednaoccupancy: An r package for multiscale occupancy modelling of environmental DNA data

In this article, we describe ednaoccupancy , an r package for fitting Bayesian, multiscale occupancy models. These models are appropriate for occupancy surveys that include three nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). ednaoccupancy allows users to specify and fit multiscale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model‐selection criteria. We illustrate these features by analysing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.     

Preliminary study on current perceptions and usage of training equipment by horse enthusiasts in Canada

Training practices may impose restrictions on the equine behavioral repertoire through the use of training equipment. Presently, the prevalence of the use of training equipment in Canada is unknown. Through an online survey for horse enthusiasts (n = 654), this study evaluated the prevalence and predominant uses of whips, spurs, and head-control equipment by enthusiasts with direct contact with horses compared to perceptions held by enthusiasts with no direct horse contact using chi-squared analyses. Respondents primarily reported using whips and spurs to augment rider or trainer cues and reported using head-control equipment mainly for lunging purposes. The perceived frequency of spurs and head-control equipment use during riding or training by nonactive horse enthusiasts was significantly greater than reported usage by riders and trainers (p < .05). The results potentially indicate a lack of understanding and miscommunication of training equipment use by riders and trainers. The frequent reporting of training equipment for the purpose of augmenting rider cues may imply misinterpretation of the correct application of learning theory. These preliminary results warrant further investigation of equipment use within the horse industry.     

Uncertainties of Domestic Road Freight Statistics: Insights for Regional Material Flow Studies

Freight statistics are at the core of many studies in the field of industrial ecology because they depict the physical interdependencies of territories and allow links to be made worldwide between production and consumption. Recent studies have focused increasingly on subnational scales, often relying on domestic freight data. In this perspective, this article analyses the uncertainties of the French domestic road freight survey, road being by far the most common mode of transport in the country. Based on a statistical analysis of the survey, we propose a model to estimate the uncertainty of any given domestic road transport flow. We also assess uncertainty reduction when averaging the flows over several years, and obtain for instance a 30% reduction for a three‐year average. We then study the impact of the uncertainties on regional material flow studies such as the economy‐wide material flow analysis of the Bourgogne region. Overall the case studies advocate for a systematic assessment of freight uncertainties, as neither the disaggregation level nor the quantities traded are good enough predictors. This justifies the need for an easy‐to‐implement estimation model. Finally, basic comparison with the German and Swedish surveys tends to indicate that the main conclusions presented in this article are likely to be valid in other European countries.     

Wrong,but useful: regional species distribution models may not be improved by range‐wide data under biased sampling

Species distribution modeling (SDM) is an essential method in ecology and conservation. SDMs are often calibrated within one country's borders, typically along a limited environmental gradient with biased and incomplete data, making the quality of these models questionable. In this study, we evaluated how adequate are national presence‐only data for calibrating regional SDMs. We trained SDMs for Egyptian bat species at two different scales: only within Egypt and at a species‐specific global extent. We used two modeling algorithms: Maxent and elastic net, both under the point‐process modeling framework. For each modeling algorithm, we measured the congruence of the predictions of global and regional models for Egypt, assuming that the lower the congruence, the lower the appropriateness of the Egyptian dataset to describe the species' niche. We inspected the effect of incorporating predictions from global models as additional predictor (“prior”) to regional models, and quantified the improvement in terms of AUC and the congruence between regional models run with and without priors. Moreover, we analyzed predictive performance improvements after correction for sampling bias at both scales. On average, predictions from global and regional models in Egypt only weakly concur. Collectively, the use of priors did not lead to much improvement: similar AUC and high congruence between regional models calibrated with and without priors. Correction for sampling bias led to higher model performance, whatever prior used, making the use of priors less pronounced. Under biased and incomplete sampling, the use of global bats data did not improve regional model performance. Without enough bias‐free regional data, we cannot objectively identify the actual improvement of regional models after incorporating information from the global niche. However, we still believe in great potential for global model predictions to guide future surveys and improve regional sampling in data‐poor regions.     

FIRST ESTIMATES OF VAQUITA ABUNDANCE

The abundance of the only population of vaquitas, Gulf of California harbor porpoise ( Phocoena sinus ), is estimated from four surveys conducted in Mexico between 1986 and 1993, using a variety of methods. A line-transect approach was applied, using some parameters estimated from a related species, the harbor porpoise ( Phocoena phocoena ). Vaquita abundance is estimated as 503 (CV = 0.63) from 1986–1988 boat surveys, 885 (CV = 0.50) from 1988–1989 aerial surveys, 572 (CV = 1.43) from a 1991 aerial survey, and 224 (CV = 0.39) from a 1993 ship survey. A weighted log-linear regression indicates a rate of population change (decline) of −17.7% per year (95% CI =−43.2% to +19.3%) between 1986 and 1993. All of these estimates of vaquita abundance indicate that the species is at a critically low level.     

Decline of the invasive submersed macrophyte Myriophyllum spicatum (Haloragaceae) associated with herbivory by larvae of Acentria ephemerella (Lepidoptera)

Myriophyllum spicatum, an exotic submersed macrophyte causing serious lake management problems throughout much of North America, decreased markedly in biomass in Cayuga Lake, NY, USA, since the beginning of the 1990s. Over the same period, however, the total biomass of all species of submersed macrophytes did not decline, and native macrophytes gained in abundance. The aquatic moth larva, Acentria ephemerella, was first observed on milfoil plants in Cayuga Lake in 1991. However, due to its cryptic habit the larva may have been present prior to that year. When the density of these grazers is high, herbivory by Acentria causes severe damage to the apical meristem of M. spicatum. This moth larva and another milfoil herbivore, Euhrychiopsis lecontei are widespread in 26 lakes surveyed in New York State; they are present in 25 and 24 lakes, respectively. Estimates of Acentria larval densities in summer in Cayuga Lake are 27 to 100 m^-2, and a quantitative survey of larvae hibernating in milfoil stems revealed mean densities of 500 m^-2 in late fall in Seneca Lake. In laboratory experiments, Acentria larvae feed on a wide variety of macrophytes commonly found in New York State. Although Acentria is not a specialist feeder, its life cycle is closely tied to M. spicatum through the moth's use of apical tips and stems for summer and winter refuges; thus deleterious damage to other macrophytes is low. This revised version was published online in July 2006 with corrections to the Cover Date.