Genetic Bottlenecks Driven by Population Disconnection

Abstract: Connectivity among populations plays a crucial role in maintaining genetic variation at a local scale, especially in small populations affected strongly by genetic drift. The negative consequences of population disconnection on allelic richness and gene diversity (heterozygosity) are well recognized and empirically established. It is not well recognized, however, that a sudden drop in local effective population size induced by such disconnection produces a temporary disequilibrium in allelic frequency distributions that is akin to the genetic signature of a demographic bottleneck. To document this effect, we used individual‐based simulations and empirical data on allelic richness and gene diversity in six pairs of isolated versus well‐connected (core) populations of European tree frogs. In our simulations, population disconnection depressed allelic richness more than heterozygosity and thus resulted in a temporary excess in gene diversity relative to mutation drift equilibrium (i.e., signature of a genetic bottleneck). We observed a similar excess in gene diversity in isolated populations of tree frogs. Our results show that population disconnection can create a genetic bottleneck in the absence of demographic collapse.     

原始红松林退化演替后土壤微生物功能多样性的变化

为了全面了解原始红松林退化演替为次生林后土壤生境及土壤微生物功能多样性的变化规律,以小兴安岭典型的原始阔叶红松林、退化演替后先锋阶段的白桦林及亚顶级阶段的硬阔叶林为研究对象,采用Biolog-ECO微平板检测法,分析三者0~ < 10 cm和10~20 cm表层土的土壤微生物功能多样性变化规律.结果表明:各林型土壤微生物的AWCD值（平均颜色变化率）随培养时间的延长而增加,培养初期表现为原始阔叶红松林>硬阔叶林>白桦林;培养末期表现为原始阔叶红松林>白桦林>硬阔叶林,三者的AWCD值在0~ < 10 cm土层分别为1.06、0.86、0.81,10~20 cm土层分别为0.68、0.47、0.45,原始林显著高于次生林（P < 0.05）,说明原始林土壤微生物对单一碳源的代谢活性显著高于次生林;同一林型下土壤微生物的AWCD值均表现为0~ < 10 cm土层显著高于10~20 cm土层（P < 0.05）. Shannon-Wiener多样性指数、Simpson指数、McIntosh指数和Richness丰富度指数也均表现为原始林显著高于次生林（P < 0.05）.原始林土壤微生物对各类碳源的综合利用强度均大于次生林,不同林型下土壤微生物群落的优势碳源类型存在一定的差异,碳水类、氨基酸类、羧酸类和多聚物类碳源是原始林退化演替后土壤微生物群落在碳源利用上发生变化的敏感碳源.      

秦岭中段北坡不同海拔土壤中细菌群落的分布特征及区域差异比较

为深入理解土壤细菌群落沿海拔梯度的分布特征,以秦岭山脉中段的朱雀国家森林公园朱雀山北坡（简称“朱雀北坡”）与太白山自然保护区太白山北坡（简称“太白山北坡”）为研究区域,海拔梯度上每隔400 m设置采样点,通过高通量测序研究土壤细菌群落的海拔变化规律及其关键影响因素.结果表明:研究区域内,随海拔升高,土壤pH趋于降低（太白山北坡不明显）,w（TC）、w（TN）、w（TOC）均显著升高,w（TP）也趋于升高（朱雀北坡不明显）.两个区域土壤细菌中相对丰度最高的均为变形菌门和酸杆菌门,朱雀北坡随海拔梯度变化显著的细菌主要包括变形菌门、硝化螺旋菌门、浮霉状菌门、酸杆菌门、放线菌门,其中,硝化螺旋菌门相对丰度与海拔呈正相关,放线菌门相对丰度与海拔呈负相关;太白山北坡随海拔梯度变化显著的细菌主要包括放线菌门、疣微菌门、浮霉状菌门、绿弯菌门,其中,放线菌门相对丰度与海拔呈负相关,其余三者相对丰度与海拔呈正相关.两个区域土壤细菌多样性指数（如Shannon-Wiener指数、Chao1指数、observed-species指数、PD_whole_tree指数等）沿海拔梯度均无明显变化规律,但太白山北坡数值整体上高于朱雀北坡.典范对应分析（canonical correlation analysis,CCA）结果显示,影响朱雀北坡和太白山北坡土壤细菌群落结构的主要因素均为pH和w（TOC）.研究显示,不同海拔梯度也是导致秦岭中段北坡土壤细菌群落差异的重要因素.      

Pseudoreplication in Tropical Forests and the Resulting Effects on Biodiversity Conservation

Tropical forest ecosystems are threatened by habitat conversion and other anthropogenic actions. Timber production forests can augment the conservation value of primary forest reserves, but studies of logging effects often yield contradictory findings and thus inhibit efforts to develop clear conservation strategies. We hypothesized that much of this variability reflects a common methodological flaw, simple pseudoreplication, that confounds logging effects with preexisting spatial variation. We reviewed recent studies of the effects of logging on biodiversity in tropical forests (n = 77) and found that 68% were definitively pseudoreplicated while only 7% were definitively free of pseudoreplication. The remaining proportion could not be clearly categorized. In addition, we collected compositional data on 7 taxa in 24 primary forest research plots and systematically analyzed subsets of these plots to calculate the probability that a pseudoreplicated comparison would incorrectly identify a treatment effect. Rates of false inference (i.e., the spurious detection of a treatment effect) were >0.5 for 2 taxa, 0.3–0.5 for 2 taxa, and <0.3 for 3 taxa. Our findings demonstrate that tropical conservation strategies are being informed by a body of literature that is rife with unwarranted inferences. Addressing pseudoreplication is essential for accurately assessing biodiversity in logged forests, identifying the relative merits of specific management practices and landscape configurations, and effectively balancing conservation with timber production in tropical forests. Pseudoreplicación en Bosques Tropicales y Efectos Resultantes Sobre la Conservación de Biodiversidad     

Effects of site-selection bias on estimates of biodiversity change

Estimates of biodiversity change are essential for the management and conservation of ecosystems. Accurate estimates rely on selecting representative sites, but monitoring often focuses on sites of special interest. How such site-selection biases influence estimates of biodiversity change is largely unknown. Site-selection bias potentially occurs across four major sources of biodiversity data, decreasing in likelihood from citizen science, museums, national park monitoring, and academic research. We defined site-selection bias as a preference for sites that are either densely populated (i.e., abundance bias) or species rich (i.e., richness bias). We simulated biodiversity change in a virtual landscape and tracked the observed biodiversity at a sampled site. The site was selected either randomly or with a site-selection bias. We used a simple spatially resolved, individual-based model to predict the movement or dispersal of individuals in and out of the chosen sampling site. Site-selection bias exaggerated estimates of biodiversity loss in sites selected with a bias by on average 300–400% compared with randomly selected sites. Based on our simulations, site-selection bias resulted in positive trends being estimated as negative trends: richness increase was estimated as 0.1 in randomly selected sites, whereas sites selected with a bias showed a richness change of −0.1 to −0.2 on average. Thus, site-selection bias may falsely indicate decreases in biodiversity. We varied sampling design and characteristics of the species and found that site-selection biases were strongest in short time series, for small grains, organisms with low dispersal ability, large regional species pools, and strong spatial aggregation. Based on these findings, to minimize site-selection bias, we recommend use of systematic site-selection schemes; maximizing sampling area; calculating biodiversity measures cumulatively across plots; and use of biodiversity measures that are less sensitive to rare species, such as the effective number of species. Awareness of the potential impact of site-selection bias is needed for biodiversity monitoring, the design of new studies on biodiversity change, and the interpretation of existing data.     

Changes in functional structure of soil bacterial communities due to fungicide and insecticide applications in canola

The fungicide vinclozolin and insecticide λ-cyhalothrin are widely used to control canola (Brassica spp.) diseases and insect pests, respectively, in Canada. We investigated non-target effects of these pesticides, applied at recommended rates, on soil microbial biomass, functional bacterial diversity and functional community structure of soil bacteria (by evaluating patterns of C substrate utilization) in canola rhizosphere and bulk soil at three locations in Alberta from 2002 to 2004. Experimental treatments were (a) untreated control, (b) vinclozolin fungicide foliar application, (c) λ-cyhalothrin insecticide foliar application, and (d) vinclozolin and λ-cyhalothrin applications. No significant pesticide effects on soil microbial biomass or functional bacterial diversity were observed, but the functional structures of soil bacteria were altered. In 1 of 12 cases, the control treatment had a different soil bacterial community structure from the 3 pesticide treatments. The fungicide treatment had different bacterial community structures from the control or insecticide treatments in 3 of 12 cases, the insecticide treatment had different community structures from the control or fungicide treatments in 4 of 12 cases, and the combined fungicide and insecticide treatment had different community structures from the other treatments in 3 of 12 cases. Therefore, evaluating soil bacterial functional structures revealed pesticide effects that were not detected when bacterial diversity or microbial biomass were measured in canola rhizosphere or bulk soil.     

Effect of lime application on microbial community in acidic tea orchard soils in comparison with those in wasteland and forest soils

Lime application is a conventional technology to control acidification in tea orchard soils. We investigated the e ect of lime application on soil microbial community diversity in the soils of three tea orchards, wasteland and forest. The BIOLOG data showed that both the average well color development of all carbon sources and the functional diversity index increased with the liming rate in the tea orchards and the forest, but decreased in the wasteland. The phospholipid fatty acid (PLFA) analysis showed that the structural diversity index of soil microbial community increased with the liming rate in all the tea orchards, the wasteland and the forest. Lime application also increased the soil-bacterial PLFA content in all the soils. Soil fungal and actinomycete PLFAs in the tea orchards showed an increasing trend from 0 to 3.2 g CaCO3/kg application and then a decreasing trend from 3.2 to 6.4 g CaCO3/kg application. The principal component analysis of BIOLOG and PLFA data suggested that lime application had a significant e ect on soil microbial community structure, and land use had a greater e ect on soil microbial community structure compared to lime application.     

分子生物技术在环境工程微生物领域中的应用

目前分子生物技术发展日新月异,已渗透到各相关学科。本文综述了分子生物技术的基本原理与方法,及其在环境工程微生物领域的应用。讨论了分子生物技术在环境工程微生物的检测应用及在污泥、生物膜、底泥和土壤等微生物种群的多样性分析方面,以及环境工程菌的挑选和培养等方面的研究成果及其巨大研究前景,对该技术在环境工程领域的应用与发展提出了一些见解。     

The relationship between diversity profiles,evenness and species richness based on partial ordering

Problems with the notion of evenness, such as ambiguity, proliferation of indices, choice of indices, etc. can be overcome by a more fundamental, mathematical approach. We show that the Lorenz curve is an adequate representation of evenness. The corresponding Lorenz order induces a partial order in the set of equivalent abundance vectors. Also diversity can adequately be studied through a partial order and represented by a curve derived from the classical Lorenz curve. This curve is known as the intrinsic diversity profile (or k-dominance curve) and was introduced by Patil and Taillie (1979) and Lambshead et al. (1981).     

长江上游向家坝库区鸟类多样性研究及生境价值评估

2011年利用样线法对长江上游向家坝库区夏、秋季鸟类进行了实地考察,共记录110种鸟类,隶属15目39科。通过5个调查点、2个对照点不同生境鸟类的多样性研究发现：（1）夏、秋季库区不同生境鸟类的Shannon Wiener 指数较低,几乎均未超过1.5,鸟类物种多样性相对贫乏;（2）库区各生境鸟类Pielou指数均超过了0.75,说明库区环境虽以人工植被为主,但并不单调;（3）阶地疏林灌丛、竹林与常绿落叶阔叶混交林的鸟类相似性差异最小〖JP2〗,而二者与芦苇、荩草丛滩地的差异最大,库区鸟类在不同生境中的分布存在着显著不同。在上述研究的基础上,从物种多样性和河流景观保护的角度,对库区鸟类的不同生境类型进行多要素综合分析,结果显示: 山地森林生境的物种多样性相对丰富,生态价值最高,而河滩和阶地疏林灌丛、竹林生境具备一定的景观特色,也有相当的生态价值