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.     

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.     

Methane emissions reduce the radiative cooling effect of a subtropical estuarine mangrove wetland by half

The role of coastal mangrove wetlands in sequestering atmospheric carbon dioxide (CO₂) and mitigating climate change has received increasing attention in recent years. While recent studies have shown that methane (CH₄) emissions can potentially offset the carbon burial rates in low‐salinity coastal wetlands, there is hitherto a paucity of direct and year‐round measurements of ecosystem‐scale CH₄ flux (F_CH4) from mangrove ecosystems. In this study, we examined the temporal variations and biophysical drivers of ecosystem‐scale F_CH4 in a subtropical estuarine mangrove wetland based on 3 years of eddy covariance measurements. Our results showed that daily mangrove F_CH4 reached a peak of over 0.1 g CH₄‐C m^?2 day^?1 during the summertime owing to a combination of high temperature and low salinity, while the wintertime F_CH4 was negligible. In this mangrove, the mean annual CH₄ emission was 11.7 ± 0.4 g CH₄‐C m^–2 year^?1 while the annual net ecosystem CO₂ exchange ranged between ?891 and ?690 g CO₂‐C m^?2 year^?1, indicating a net cooling effect on climate over decadal to centurial timescales. Meanwhile, we showed that mangrove F_CH4 could offset the negative radiative forcing caused by CO₂ uptake by 52% and 24% over a time horizon of 20 and 100 years, respectively, based on the corresponding sustained‐flux global warming potentials. Moreover, we found that 87% and 69% of the total variance of daily F_CH4 could be explained by the random forest machine learning algorithm and traditional linear regression model, respectively, with soil temperature and salinity being the most dominant controls. This study was the first of its kind to characterize ecosystem‐scale F_CH4 in a mangrove wetland with long‐term eddy covariance measurements. Our findings implied that future environmental changes such as climate warming and increasing river discharge might increase CH₄ emissions and hence reduce the net radiative cooling effect of estuarine mangrove forests.     

1980—2018年祁连山南坡土地利用变化及其驱动力

祁连山是我国第一阶梯和第二阶梯的分界线,生态环境脆弱,对过渡地带土地利用变化及其驱动力研究具有重要的生态意义。本研究以祁连山南坡为研究区,基于1980—2018年遥感影像数据,运用空间自相关分析法、ArcGIS空间分析方法和主成分分析法分析了土地利用的时空变化特征及其驱动力。结果表明: 1980—2018年,草地是研究区土地利用类型的主体,建设用地所占比重最小,水域、草地表现为下降趋势,未利用土地、建设用地和耕地均呈现出增长态势,林地变化较小。不同地类单一土地利用动态度从大到小依次为:建设用地＞水域＞耕地＞未利用土地＞林地＞草地,综合土地利用动态度为0.9%。不同土地利用类型空间分布表现出空间集聚性特征。耕地增加的区域和林地、草地减少的区域主要分布在门源县城所处大通河谷地西北侧,天峻县东北部大通河上游地区存在工矿建设用地占用草地的现象。土地利用变化驱动力主要为人口数量、科技、城市化、经济发展水平和政策。本研究结果可为政府合理规划和利用土地资源提供依据,对祁连山南坡生态环境保护和社会经济可持续发展具有重大意义。     

坡向和坡位对四川夹金山灌丛群落结构与物种多样性特征的影响

研究不同坡向、坡位夹金山灌丛群落结构和物种多样性特征。结果表明: 在 24 个样地中,共有维管植物 186 种,隶属于 50 科 127 属。其中,灌木层有 32 种,隶属于 14 科 22 属,阴坡下坡位物种数最多;草本层有 154 种,隶属于 43 科 109 属,阴坡物种数最少。灌木层的平均高度表现为阳坡>半阳坡>阴坡,平均密度则相反;草本层平均高度表现为阴坡>半阳坡>阳坡,平均密度无显著变化。坡位仅对阳坡草本层平均高度有显著影响,灌木层物种多样性在阴坡较高,草本层物种多样性在阳坡下坡位和阴坡中坡位较高。坡向对灌木层和草本层 Shannon多样性指数、Simpson优势度指数、物种丰富度指数、Pielou均匀度指数影响显著(除草本层 Simpson 指数),坡位对灌木层和草本层物种多样性指数均无显著影响,坡向和坡位的交互作用对草本层物种多样性的影响大于灌木层。冗余分析(RDA)表明,物种多样性不仅与坡向正弦值、坡向余弦值相关,也与群落结构特征相关性较大。