Was globin evolution very rapid in its early stages?: A dubious case against the rate-constancy hypothesis

Summary Goodman et al's (1975) claim of accelerated evolution in the early stages of globin evolution is based on an erroneous assignment of the time of divergence of vertebrate myoglobin and hemoglobin. When this is corrected, there is no basis for their claim. The data are much more consistent with the nearly constant rate expected on the neutral mutation-random drift hypothesis than with the uneven rates expected if most amino acid changes were caused by substitution of favorable mutants through Darwinian selection. In addition, the majority of the codons determined by their maximum parsimony method have turned out to be wrong when compared to the actual nucleotide sequences of rabbit and human hemoglobins determined by direct sequencing.Contribution No. 1314 from the National Institute of Genetics, Mishima, 411 Japan.     

Nitrogen fixation in hardwood forests of the northeastern United States

Summary Nitrogen-fixing activity in hardwood forests of the northeastern United States occurred in wood litter, greater than 2 cm in diameter. Activity in large dead wood was independent of species, in the case of deciduous wood litter, but was restricted to partially decayed wood with a high moisture content. Maximum rates of activity were observed in the summer months, minimum rates in the winter. Evidence from six stands of varying ages showed that fixation in large wood litter occurred in only 25% of the samples assayed.Fixation was highest in the youngest, 4 years, and oldest, over 200 years, stands; being about 2 kg/ha/yr. The quantity of nitrogen fixed appears to be related to the biomass of dead wood. Large amounts of wood litter in the youngest stands were from slash left after cutting. As the supply of slash is exhausted by decay, nitrogen fixation decreases, with a low around year 20. Fixation then gradually increases as natural thinning adds wood to the litter compartment.Apparently, the amount of nitrogen fixed in dead wood the first 20 years following clearcutting can only replace a modest fraction of the amount lost as a result of the cutting and product removal. Finally, the results indicate that nitrogen fixation in wood litter does not equal nitrogen fixation in a northern hardwood forest calculated using a mass balance approach, suggesting that additional nitrogen inputs exist.     

Regulating Ecosystem Services of forests in ten Italian Metropolitan Cities: Air quality improvement by PM10 and O3 removal

Urban and periurban forests, which are integrated within the concept of Green Infrastructure, provide important Ecosystem Services, including air purification. In this study, we quantified the Ecosystem Service of particulate matter (PM₁₀) and Ozone (O₃) removal from urban and periurban forests in ten metropolitan cities in Italy, and its total monetary value. In order to gain a better understanding of how Ecosystem Services can be regulated on a wider scale, the vegetation ecosystem types were grouped into Physiognomic-Structural Categories of Vegetation according to morphofunctional criteria. The pollution removal was mapped using a remote sensing and GIS approach, by applying a deposition model and a stomatal flux model. We estimated, for the ten metropolitan cities, an overall pollution abatement of 7150 Mg of PM₁₀ and 30,014 Mg of O₃ in the year 2003, which was an extremely hot year. Our findings indicate that structural characteristics (i.e. Leaf Area Index) and functional diversity, linked to stomatal conductance, exert a marked influence on the provision of the regulating Ecosystem Services, whose total monetary value was estimated to be equal to 47 and 297 million USD for PM₁₀ and O₃ removal, respectively. This study represent the first national-scale assessment of the Ecosystem Services of air pollution removal in Europe, thus providing information that may be useful to stakeholders to manage Green Infrastructure more efficiently.     

Testing the precision and sensitivity of density estimates obtained with a camera‐trap method revealed limitations and opportunities

The use of camera traps in ecology helps affordably address questions about the distribution and density of cryptic and mobile species. The random encounter model (REM) is a camera‐trap method that has been developed to estimate population densities using unmarked individuals. However, few studies have evaluated its reliability in the field, especially considering that this method relies on parameters obtained from collared animals (i.e., average speed, in km/h), which can be difficult to acquire at low cost and effort. Our objectives were to (1) assess the reliability of this camera‐trap method and (2) evaluate the influence of parameters coming from different populations on density estimates. We estimated a reference density of black bears (Ursus americanus) in Forillon National Park (Québec, Canada) using a spatial capture–recapture estimator based on hair‐snag stations. We calculated average speed using telemetry data acquired from four different bear populations located outside our study area and estimated densities using the REM. The reference density, determined with a Bayesian spatial capture–recapture model, was 2.87 individuals/10km² [95% CI: 2.41–3.45], which was slightly lower (although not significatively different) than the different densities estimated using REM (ranging from 4.06–5.38 bears/10km² depending on the average speed value used). Average speed values obtained from different populations had minor impacts on REM estimates when the difference in average speed between populations was low. Bias in speed values for slow‐moving species had more influence on REM density estimates than for fast‐moving species. We pointed out that a potential overestimation of density occurs when average speed is underestimated, that is, using GPS telemetry locations with large fix‐rate intervals. Our study suggests that REM could be an affordable alternative to conventional spatial capture–recapture, but highlights the need for further research to control for potential bias associated with speed values determined using GPS telemetry data.     

Goodness of Fit of Discriminant Functions from the Vector Space of Fixed Variates

Alternative proofs of some of KSHIRSAGAR's (1971) results on testing discriminant functions or canonical variables in the vector space of fixed variates are given. These results are derived in terms of the original variates unlike KSHIRSAGAR (1971) who derives the results by using random orthogonal transformations and triangular decompositions of the original matrix variates.     

Adjusting for Nonignorable Missingness When Estimating Generalized Additive Models

Generalized additive models (GAMs) have been widely used for flexible modeling of various types of outcomes. When the outcome in a GAM is subject to missing, practical analyses often assume that missingness is missing at random (MAR). This assumption can be of suspicion when the missingness is not by design. Evaluating the potential effects of alternative nonignorable missing data mechanism on the MAR inference from a GAM can be important but often challenging due to the complicatedness of alternative nonignorable models. We apply the index approach to local sensitivity (Troxel, Ma, and Heitjan 2004 (2004). Statistica Sinica 14 , 1221–1237) to evaluate the potential changes of the GAM estimates in the neighborhood of the MAR model. The approach avoids fitting any complicated nonignorable GAM. Only MAR estimates are required to calculate the resulting sensitivity index and adjust the GAM estimates to account for nonignorable missingness. Thus the proposed approach is considerably simpler to conduct, as compared with the alternative methods. The simulation study shows that the index provides valid assessment of the local sensitivity of the GAM estimates to nonignorable missingness. We then illustrate the method using a rheumatoid arthritis clinical trial data set.     

Association of suboptimal health status with intestinal microbiota in Chinese youths

Suboptimal health status (SHS), a physical state between health and disease, is a subclinical and reversible stage of chronic disease. Previous studies have shown alterations in the intestinal microbiota in patients with some chronic diseases. This study aimed to investigate the association between SHS and intestinal microbiota in a case‐control study with 50 SHS individuals and 50 matched healthy controls. Intestinal microbiota was analysed by MiSeq 250PE. Alpha diversity of intestinal microbiota in SHS individuals was higher compared with that of healthy controls (Simpson index, W = 2238, P = .048). Beta diversity was different between SHS and healthy controls (P = .018). At the phylum level, the relative abundance of Verrucomicrobia was higher in the SHS group than that in the controls (W = 2201, P = .049). Compared with that of the control group, nine genera were significantly higher and five genera were lower in abundance in the SHS group (all P < .05). The intestinal microbiota, analysed by a random forest model, was able to distinguish individuals with SHS from the controls, with an area under the curve of 0.79 (95% confidence interval: 0.77‐0.81). We demonstrated that the alteration of intestinal microbiota occurs with SHS, an early stage of disease, which might shed light on the importance of intestinal microbiota in the primary prevention of noncommunicable chronic diseases.