Selected codon usage bias in members of the class Mollicutes

Mollicutes are parasitic microorganisms mainly characterized by small cell sizes, reduced genomes and great A and T mutational bias. We analyzed the codon usage patterns of the completely sequenced genomes of bacteria that belong to this class. We found that for many organisms not only mutational bias but also selection has a major effect on codon usage. Through a comparative perspective and based on three widely used criteria we were able to classify Mollicutes according to the effect of selection on codon usage. We found conserved optimal codons in many species and study the tRNA gene pool in each genome. Previous results are reinforced by the fact that, when selection is operative, the putative optimal codons found match the respective cognate tRNA. Finally, we trace selection effect backwards to the common ancestor of the class and estimate the phylogenetic inertia associated with this character. We discuss the possible scenarios that explain the observed evolutionary patterns.     

Anti-mitotic and anti-genotoxic effects of Plantago lanceolata aqueous extract on Allium cepa root tip meristem cells

Plantago is the most important genus of Plantaginaceae family and is used in traditional medicine around the world for different purposes. Plantago coronopus L., Plantago major L., Plantago media L. and Plantago lanceolata L. are most commonly used species of Plantago in traditional medicine in Turkey. The main goal of this study was to investigate the eventual anti-mitotic and anti-genotoxic effects of P. lanceolata L. leaf aqueous extracts (15 g/L and 30 g/L) on Allium cepa L. root tip meristem cells which were treated with 0.7% hydrogen peroxide. For this purpose, two different experiments were performed under the same conditions. In the first experiment, Allium cepa onion bulbs were treated with 0.7% H₂O₂ for 1 h. After the H₂O₂ treatment, the onion bulbs were treated with two different concentrations (15 g/L and 30 g/L) of P. lanceolata extracts for 24 h. In the second experiment, A. cepa onion bulbs were treated with two different extract concentrations (15 g/L and 30 g/L) for 24 h and then with 0.7% H₂O₂ for 1 h. The test concentrations were determined according to doses which are recommended in alternative medicinal usage by people. As positive and negative control 0.7% H₂O₂ and tap water was used, respectively. As a result, it was determined that aqueous extracts reduced mitotic index and chromosome aberrations in treatment groups in comparison with controls. These results showed that P. lanceolata aqueous extracts have anti-mitotic and anti-genotoxic effects.     

地表火干扰时间序列上樟子松林竞争强度的变化

林火是樟子松林重要的干扰因子,通过空间代替时间对地表火干扰时间序列上的天然樟子松林进行全林木定位调查,以单木竞争模型分析林分不同组分的竞争强度,通过Kriging法估计了火后林下更新幼树的密度。结果表明,存活林木各组分的竞争强度均显著地降低;地表火干扰12 a后存活林木各组分的竞争强度均比火后1 a存活林木相应各组分的竞争强度显著地降低;另外,火后更新幼树也更多地趋于地表火干扰形成的林隙中。因此,地表火干扰时间序列上林木竞争强度显著的持续降低,火后存活个体将有更充足的可利用资源和环境,林火成为樟子松林发育演替的重要驱动力。     

The use of ecological integrity indicators within the natural capital index framework: The ecological and economic value of the remnant natural capital of México

In this paper, the ecological integrity hierarchy framework (EIHF) and the natural capital index framework (NCI) are integrated as decision-making tools for evaluating the natural capital of Mexico. Two hierarchy-levels of ecological integrity indicators are used to estimate the quality and quantity of the natural capital, the amount of ecological degradation and ecological sustainability. After human transformation, the extent still considered as “natural” in the country is ∼67%; while the amount of human transformed areas is ∼33%, which gives a total estimate of NCI = 0.334; i.e., only ∼33.4% of the national capital remains available, while ∼33% is ecologically degraded. Furthermore, the critical natural capital; i.e., the legacy for future generations that remains in the country is only ∼12%. The total estimated value of the current natural capital in Mexico is ∼$457.1 billion/yr, which is ∼435 times greater than the national GDP ($1.051 billion in 2010). The cost of maintaining the degradation of the natural capital is ∼$144.6 billion/yr (∼138 times greater than national GDP in 2010). The potential value of the natural capital after restoration would be ∼$602 billion/yr. Valuing the natural capital can be helpful for strategic environmental evaluations and useful for spatial decision support systems that evaluate natural capital as a decision-making tool.     

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K‐Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short‐fuse hypothesis.     

Invasive plants negatively impact native,but not exotic,animals

Despite our growing understanding of the impacts of invasive plants on ecosystem structure and function, important gaps remain, including whether native and exotic species respond differently to plant invasion. This would elucidate basic ecological interactions and inform management. We performed a meta‐analytic review of the effects of invasive plants on native and exotic resident animals. We found that invasive plants reduced the abundance of native, but not exotic, animals. This varied by animal phyla, with invasive plants reducing the abundance of native annelids and chordates, but not mollusks or arthropods. We found dissimilar impacts among “wet” and “dry” ecosystems, but not among animal trophic levels. Additionally, the impact of invasive plants increased over time, but this did not vary with animal nativity. Our review found that no studies considered resident nativity differences, and most did not identify animals to species. We call for more rigorous studies of invaded community impacts across taxa, and most importantly, explicit consideration of resident biogeographic origin. We provide an important first insight into how native and exotic species respond differently to invasion, the consequences of which may facilitate cascading trophic disruptions further exacerbating global change consequences to ecosystem structure and function.     

不同海拔梯度高寒草地地下生物量与环境因子的关系

以新疆天山南坡的巴音布鲁克高寒草地为对象, 研究了不同海拔梯度高寒草地地下生物量的变化及其与环境因子的关系.结果表明: 随着海拔的升高, 高寒草原、高寒草原化草甸和高寒草甸的地下生物量逐渐增大, 二者呈极显著正相关( P<0.01 ).地下生物量从表层至底层逐渐递减,呈“T”形分布.高寒草原、高寒草原化草甸和高寒草甸0～10 cm土层的地下生物量分别占总地下生物量的68.1%、84.1%和86.7%.地下生物量与大气温度呈极显著负相关, 与相对湿度和土壤含水量呈极显著正相关(P<0.01 ), 而与有机质、速效氮和pH等无显著相关.     

Predicting species distributions from herbarium collections: does climate bias in collection sampling influence model outcomes?

Aim Species distribution models and geographical information system (GIS) technologies are becoming increasingly important tools in conservation planning and decision‐making. Often the rich data bases of museums and herbaria serve as the primary data for predicting species distributions. Yet key assumptions about the primary data often are untested, and violation of such assumptions may have consequences for model predictions. For example, users of primary data assume that sampling has been random with respect to geography and environmental gradients. Here we evaluate the assumption that plant voucher specimens adequately sample the climatic gradient and test whether violation of this assumption influences model predictions. Location Bolivia and Ecuador. Methods Using 323,711 georeferenced herbarium collections and nine climatic variables, we predicted the distribution of 76 plant species using maximum entropy models (MAXENT) with training points that sampled the climate environments randomly and training points that reflected the climate bias in the herbarium collections. To estimate the distribution of species, MAXENT finds the distribution of maximum entropy (i.e. closest to uniform) subject to the constraint that the expected value for each environmental variable under the estimated distribution matches its empirical average. The experimental design included species that differed in geographical range and elevation; all species were modelled with 20 and 100 training points. We examined the influence of the number of training points and climate bias in training points, elevation and range size on model performance using analysis of variance models. Results We found that significant parts of the climatic gradient were poorly represented in herbarium collections for both countries. For the most part, existing climatic bias in collections did not greatly affect distribution predictions when compared with an unbiased data set. Although the effects of climate bias on prediction accuracy were found to be greater where geographical ranges were characterized by high spatial variation in the degree of climate bias (i.e. ranges where the bias of the various climates sampled by collections deviated considerably from the mean bias), the greatest influence on model performance was the number of presence points used to train the model. Main conclusions These results demonstrate that predictions of species distributions can be quite good despite existing climatic biases in primary data found in natural history collections, if a sufficiently large number of training points is available. Because of consistent overprediction of models, these results also confirm the importance of validating models with independent data or expert opinion. Failure to include independent model validation, especially in cases where training points are limited, may potentially lead to grave errors in conservation decision‐making and planning.     

Stomatal response to air humidity and its relation to stomatal density in a wide range of warm climate species

The gas exchange of 19 widely different warm climate species was observed at different leaf to air vapour pressure deficits (VPD). In all species stomata tended to close as VPD increased resulting in a decrease in net photosynthesis. The absolute reduction in leaf conductance per unit increase in VPD was greatest in those species which had a large leaf conductance at low VPDs. This would be expected even if stomata of all species were equally sensitive. However the percentage reduction in net photosynthesis (used as a measure of the relative sensitivity of stomata of the different species) was also closely related to the maximal conductance at low VPD. Similarily the relative sensitivity of stomata to changes in VPD was closely related to the weighted stomatal density or crowding index.The hypothesis is presented that stomatal closure at different VPDs is related to peristomatal evaporation coupled with a high resistance between the epidermis and the mesophyll and low resistance between the stomatal apparatus and the epidermal cells. This hypothesis is consistent with the greater relative sensitivity of stomata on leaves with a high crowding index.The results and the hypothesis are discussed in the light of selection, for optimal productivity under differing conditions of relative humidity and soil water availablility, by observation of stomatal density and distribution on the two sides of the leaf.Visiting scientist, plant physiologist and research assitant of the Cassava Program     

芜湖市三种生境夏季鸟类多样性分析

1引言鸟类群落结构在一定程度上是鸟类之间相互关系的综合反映.一些鸟类对城市生态环境的变化反应非常敏感,因而对城市生态平衡和环境质量的变化能起到指示剂的作用[8].目前我国正处在城市化加速发展的时期,许多中等城市正在向大城市发展,城市生态建设面临巨大的压力和挑战.鸟类多样性是城市生物多样性的重要组成部分,对维持城市生态平衡具有重要的意义[13],而城市鸟类多样性研究能为城市的生态建设提供重要的参考依据.国内对城市鸟类群落的研究主要集中在北京、武汉、杭州等少数大城市,而对中小城市的研究不多[5,16～19].王宗英等[11]曾对…