The relationship between functional and taxonomic homogenization

Aim Species introductions and extinctions have reorganized the earth's biota, often leaving formerly spatially distinct assemblages more similar in species composition, a process termed biotic homogenization. The study of biotic homogenization has been almost entirely focused on the change in taxonomic similarity between assemblages through time. Here, we provide a trait‐based method for calculating functional similarity through time and compare these trends in functional attributes with those trends generated from a taxonomic perspective. Location Data were produced through computer simulation and gathered from North American Breeding Bird Survey (BBS) data and published accounts of North American birds for 10 locations across the east and west coast of the United States. Methods We simulated change in assemblages with different trait types (binary and continuous), levels of trait overlap, number of traits and species richness to determine the relationship between change in taxonomic similarity (ΔTS) and change in functional similarity (ΔFS). We also assess the relationship between ΔTS and ΔFS for bird assemblages across 10 locales in the USA between 1968 and 2008. We used simple linear regression to determine the slope and correlation between ΔTS and ΔFS and used multiple regression to assess the influence of trait overlap, number of traits, species richness and the ratio of traits to species on the relationship between ΔTS and ΔFS. Results Simulations reveal that trait redundancy governs the relationship between ΔTS and ΔFS. A decrease in trait overlap increases the slope of the regression between ΔTS and ΔFS and an increase in the ratio of traits to species in the regional pool increases the correlation. The relationship between ΔTS and ΔFS for breeding birds is comparable to simulations with low trait redundancy. Main conclusions We show that often losing or gaining species from an assemblage tells us very little about the loss or gain of function, and that this scenario most often occurs when the two assemblages have high trait redundancy. It remains to be seen how prevalent this scenario is within empirical examples; however, the implications for the continued delivery of ecosystem functions in the face of species introductions and extinctions are large.     

The dilemma of negative analysis of variance estimators of intraclass correlation

Summary At least two common practices exist when a negative variance component estimate is obtained, either setting it to zero or not reporting the estimate. The consequences of these practices are investigated in the context of the intraclass correlation estimation in terms of bias, variance and mean squared error (MSE). For the one-way analysis of variance random effects model and its extension to the common correlation model, we compare five estimators: analysis of variance (ANOVA), concentrated ANOVA, truncated ANOVA and two maximum likelihood-like (ML) estimators. For the balanced case, the exact bias and MSE are calculated via numerical integration of the exact sample distributions, while a Monte Carlo simulation study is conducted for the unbalanced case. The results indicate that the ANOVA estimator performs well except for designs with family size n = 2. The two ML estimators are generally poor, and the concentrated and truncated ANOVA estimators have some advantages over the ANOVA in terms of MSE. However, the large biases may make the concentrated and truncated ANOVA estimators objectionable when intraclass correlation () is small. Bias should be a concern when a pooled estimate is obtained from the literature since <0.05 in many genetic studies.     

Bias of maximum likelihood estimator of intraclass correlation

Summary A bias correction was derived for the maximum likelihood estimator (MLE) of the intraclass correlation. The bias consisted of two parts: a correction from MLE to the analysis of variance estimator (ANOVA) and the bias of ANOVA. The total possible bias was always negative and depended upon both the degree of correlation and the design size and balance. The first part of the bias was an exact algebraic expression from MLE to ANOVA, and the corrected estimator by this part was ANOVA. It was also shown that the first correction term was equivalent to Fisher's reciprocal bias correction on hisZ scores. The total possible bias of MLE was large for small and moderate samples. Relative biases were larger for small parametric values and vice versa. To ensure a relative bias less than 10% assuming an intraclass correlation of 0.025, which is not unusual in most of the animal genetic studies, the total number of observations (N) should be not less than 500. From a design point of view, minimum bias occurred atn = 2, the minimum family size possible, underN fixed.     

Comparison of recent estimators of interclass correlation from familial data

The asymptotic and finite-sample properties of several recent estimators of interclass correlation are compared to more traditional estimators in the case of a variable number of siblings per family. It is shown that Karlin's family-weighted pairwise estimator (Karlin, Cameron, and Williams, 1981, Proceedings of the National Academy of Science 78, 2664-2668) is virtually equivalent to the ensemble estimator (Rosner, Donner, and Hennekens, 1977, Applied Statistics 26, 179-187), thus suggesting an estimator of the former's asymptotic variance. Further, an estimator proposed by Srivastava (1984, Biometrika 71, 177-185) is shown to be identical to the modified sib-mean estimator (Konishi, 1982, Annals of the Institute of Statistical Mathematics 34, 505-515) when the sib-sib correlation is estimated by the method of unweighted group means. Although the estimator due to Srivastava has smaller asymptotic variance than the other two, the gain in efficiency is slight, for familial data, both asymptotically and in finite samples.     

Interval estimation for a difference between intraclass kappa statistics

Model-based inference procedures for the kappa statistic have developed rapidly over the last decade. However, no method has yet been developed for constructing a confidence interval about a difference between independent kappa statistics that is valid in samples of small to moderate size. In this article, we propose and evaluate two such methods based on an idea proposed by Newcombe (1998, Statistics in Medicine, 17, 873-890) for constructing a confidence interval for a difference between independent proportions. The methods are shown to provide very satisfactory results in sample sizes as small as 25 subjects per group. Sample size requirements that achieve a prespecified expected width for a confidence interval about a difference of kappa statistic are also presented.     

植物功能性状与外来植物入侵

揭示影响外来植物入侵性的功能性状及其生态机制是入侵植物生态学的核心任务之一。本文综述了植物功能性状与外来植物入侵性的研究进展, 通过分析植物功能性状对外来植物入侵的贡献以及外来植物的不同入侵阶段对其功能性状的需求, 探讨植物功能性状与外来植物入侵的相关性及其入侵机理。迄今研究较多的影响外来植物入侵性的功能性状主要包括形态性状、生长性状、生理性状、繁殖性状、种子性状、克隆性状、表型可塑性和遗传变异等。这些功能性状对外来植物入侵的贡献随着入侵阶段的不同而变化。在传播到达阶段, 种子性状对入侵具有重要影响; 在定居建群阶段, 与植物抗逆性和适应性相关的生理性状和繁殖性状发挥主要作用; 在扩散入侵阶段, 克隆性状和影响植物竞争能力的生理性状对植物成功入侵具有重要贡献。由于植物入侵性是其功能性状和环境因素互作的结果, 且功能性状的作用随环境因素和入侵阶段不同而异, 因此, 结合外来植物入侵阶段, 并考虑功能性状与环境因子的互作, 是入侵生物学中植物功能性状研究的发展趋势。     

The relationship between early embryo development and tumourigenesis

With the recent substantial progress in developmental biology and cancer biology, the similarities between early embryo development and tumourigenesis, as well as the important interaction between tumours and embryos become better appreciated. In this paper, we review in detail the embryonic origin of tumour, and the similarities between early embryo development and tumourigenesis with respect to cell invasive behaviours, epigenetic regulation, gene expression, protein profiling and other important biological behaviours. Given an improved understanding of the relationship between early embryo development and tumourigenesis, now we have better and broader resources to attack cancer from the perspective of developmental biology and develop next generation of prognostic and therapeutic approaches for this devastating disease.     

The relationship between force and focal complex development

To adhere and migrate, cells must be capable of applying cytoskeletal force to the extracellular matrix (ECM) through integrin receptors. However, it is unclear if connections between integrins and the ECM are immediately capable of transducing cytoskeletal contraction into migration force, or whether engagement of force transmission requires maturation of the adhesion. Here, we show that initial integrin-ECM adhesions become capable of exerting migration force with the recruitment of vinculin, a marker for focal complexes, which are precursors of focal adhesions. We are able to induce the development of focal complexes by the application of mechanical force to fibronectin receptors from inside or outside the cell, and we are able to extend focal complex formation to vitronectin receptors by the removal of c-Src. These results indicate that cells use mechanical force as a signal to strengthen initial integrin-ECM adhesions into focal complexes and regulate the amount of migration force applied to individual adhesions at localized regions of the advancing lamella.     

Quantifying test-retest reliability using the intraclass correlation coefficient and the SEM

Reliability, the consistency of a test or measurement, is frequently quantified in the movement sciences literature. A common metric is the intraclass correlation coefficient (ICC). In addition, the SEM, which can be calculated from the ICC, is also frequently reported in reliability studies. However, there are several versions of the ICC, and confusion exists in the movement sciences regarding which ICC to use. Further, the utility of the SEM is not fully appreciated. In this review, the basics of classic reliability theory are addressed in the context of choosing and interpreting an ICC. The primary distinction between ICC equations is argued to be one concerning the inclusion (equations 2,1 and 2,k) or exclusion (equations 3,1 and 3,k) of systematic error in the denominator of the ICC equation. Inferential tests of mean differences, which are performed in the process of deriving the necessary variance components for the calculation of ICC values, are useful to determine if systematic error is present. If so, the measurement schedule should be modified (removing trials where learning and/or fatigue effects are present) to remove systematic error, and ICC equations that only consider random error may be safely used. The use of ICC values is discussed in the context of estimating the effects of measurement error on sample size, statistical power, and correlation attenuation. Finally, calculation and application of the SEM are discussed. It is shown how the SEM and its variants can be used to construct confidence intervals for individual scores and to determine the minimal difference needed to be exhibited for one to be confident that a true change in performance of an individual has occurred.     

The relationship between human cytomegalovirus infection and atherosclerosis development

Transport characteristics of essential trace elements as zinc, copper, selenium and iron have been studied in maternal–fetal direction in normal pregnancies, using in vitro perfusion of human placental lobules. Solutions of trace elements corresponding to twice the physiological concentrations were injected (100 l bolus) into the maternal arterial perfusate. Serial perfusate samples were collected every 30 sec from venous outflows for a study period of 5 min. Concentrations of these trace elements and their transport kinetics were determined. Transport fractions (TF) of zinc, copper, selenium and iron averaged 0.21, 0.49, 0.55 and 0.10% of maternal load respectively. Other parameters such as area under the curve, clearance, elimination constant, absorption and elimination rates showed some significant differences between the various elements. Copper and selenium appear to be transported passively in maternal–fetal direction, while for iron and zinc, role of active transport for transfer across the human placental membrane cannot be discounted. We speculate that alterations in copper: zinc TR50 (transport rate for 50% efflux) and TF ratios could serve as useful indicators for assessing placental transport status of these essential elements in complicated pregnancy states.     

A comparison of confidence interval methods for the intraclass correlation coefficient

Different methods of obtaining confidence intervals for the intraclass correlation coefficient rho in the unbalanced one-way random-effects model are investigated, focusing on applications to family studies. Methods based on simple modifications of formulas for the case of equal group sizes are found to provide adequate coverage at small to moderate values of rho. A method based on the large-sample standard error of the sample intraclass correlation, as derived by Smith (1956, Annals of Human Genetics 21, 363-373), is shown to provide consistently good coverage at all values of rho. A method proposed by Thomas and Hultquist (1978, Annals of Statistics 6, 582-587) also provides consistently good coverage, but generates mean interval widths substantially greater than those generated by Smith's method at values of rho likely to arise in practice.     

The relationship between leaf canopy development and yield of barley

A study was carried out into the relationship between sowing date, canopy development and yield of four barley genotypes sown in autumn and spring. Yield was considered as the product of PAR absorbed by the crop canopy up till anthesis, the dry matter: radiation quotient, the ratio of grains m²at maturity to the weight of the crop at anthesis and the mean grain weight. Equations were derived to predict the time course of the proportion of PAR absorbed in relation to date of sowing using thermal time as predictor. In crops that were not short of water and were fully vernalised, genotypic differences were detected in plant population density, date of anthesis, and the four yield components identified above. All attributes except plant population density were affected by shortage of water but genotypes differed in their response.     

西藏草地植物功能性状与多项生态系统服务关系

针对植被功能性状与生态系统服务功能之间的相互关系,构建了西藏草地株高和可食性两种功能性状的9项指标,并基于土壤和植物采样,分析了9项植物功能性状指标和5项生态系统服务指标间的相关性,探讨了4种机制(Mass ratio,Selection,Niche complementarity及Insurance)在西藏草地的适用性。结果表明,9项功能性状指标中,株高Rao和可食种与所有种株高CWM比分别与土壤有机碳、土壤全氮和土壤含水率3项生态系统服务指标呈显著负相关及显著正相关。说明群落植被对光能竞争的互补性及可食性状植株在群落中的光能资源相对竞争力,与土壤固碳、肥力供给及水源涵养有显著相关关系。而群落可食种、优势种、优势种与次优势种对光能资源竞争力水平,可食植株多样性、可食植株在群落中的优势度及其光能资源竞争力均值,对草地生态系统服务无显著影响。西藏草地植物功能性状对多项生态系统服务的影响机制从光能资源竞争角度更符合Niche complementarity和Insurance理论,而从可食功能性状角度更符合Mass ratio和Selection理论。     

The correlation between oxidative stress and leaf senescence during plant development

In plants, besides being the final step leading to the death of the whole organism, senescence has a developmental function involving the coordinated degradation of macromolecules and the mobilization of nutrients out of senescing tissues into developing parts of the plant. Free radicals are thought to play an essential role in senescence, especially those derived from oxygen. Since these molecules are extremely toxic, the levels of the different reactive oxygen species have to be tightly regulated. However, at low concentrations, hydrogen peroxide may also serve as a signalling molecule. Therefore, a coordinated regulation of the free radical scavenging system, which comprises enzymatic components such as catalase, superoxide dismutase and ascorbate peroxidase, and non-enzymatic molecules such as ascorbate and glutathione is essential. The increased radical levels displayed during senescence are not only caused by the elevated production of radicals but also by a loss in antioxidant capacity.     

Confidence interval estimation of the intraclass correlation coefficient for binary outcome data

We obtain closed-form asymptotic variance formulae for three point estimators of the intraclass correlation coefficient that may be applied to binary outcome data arising in clusters of variable size. Our results include as special cases those that have previously appeared in the literature (Fleiss and Cuzick, 1979, Applied Psychological Measurement 3, 537-542; Bloch and Kraemer, 1989, Biometrics 45, 269-287; Altaye, Donner, and Klar, 2001, Biometrics 57, 584-588). Simulation results indicate that confidence intervals based on the estimator proposed by Fleiss and Cuzick provide coverage levels close to nominal over a wide range of parameter combinations. Two examples are presented.     

The relationship between nebkha formation and development and desert environmental changes

Because of the absence of natural records with high resolution, the study of environmental changes in arid and semi-arid desert regions, an important component of the global system, lags behind studies in other regions. In this paper, we summarize the literature on the evolution, forms, and profile features of nebkhas (coppice dunes), and discuss the environmental implications of their formation and development. Based on this review, we argue that future research should focus on the quantitative conversion of environmental proxies revealed by nebkha evolution into the corresponding environmental factors: quantitative definition of the stages of nebkha evolution, enhancing the precision of age-dating, strengthening of cross-disciplinary research, and the comparison of nebkha results with other natural records to provide stronger, more reliable conclusions.